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Title Index
  Molecular and Genomic Evolution: Personal Retrospects and Prospects
Wen-Hsiung Li
University of Chicago, USA
:  S7 - Evolutionary genomics: A new synthesis of evolutionary biology (In honor of W-H Li's 70th birthday)  -  15:00-16:30
1000 Insect Transcriptomes - the 1KITE project takes the next step in insect phylogenomics
Karen Meusemann*1, Ralph S. Peters2, Karl M. Kjer3, Xin Zhou4, Bernhard Misof1
1Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für molekulare Biodiversitätsforschung (zmb), Germany, 2Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Germany, 3Rutgers University, Department of Ecology, Evolution and Natural Resources, USA, 4Beijing Genomics Institute (BGI), China
:  S8 - The animal tree of life and its applications  -  17:00-18:30
1001 queens: spatial and temporal variation of kin structure in super-colonial ants
Eva Schultner*1, Jari Saramäki2, Heikki Helanterä1
1University of Helsinki, Finland, 2Aalto University, Finland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
140 million years of multigene family evolution: Origin and recombination history of the avian MHC class IIB
Reto Burri*1,2, Marta Promerová3, Luca Fumagalli2
1Department of Ecology & Genetics, Uppsala University, Sweden, 2Department of Ecology & Evolution, University of Lausanne, Switzerland, 3Institute of Vertebrate Biology, AS CR, Czech Republic
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
2012 sees the 50th birthday of the molecular clock, but has it reached maturity?
Rachel C M Warnock*, Philip C J Donoghue
University of Bristol, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A baculovirus gene inducing hyperactive behavior in caterpillars
Stineke van Houte*, Vera Ros, Monique van Oers
Laboratory of Virology, Wageningen University, The Netherlands
:  S3 - Evolution of host-virus interactions  -  11:30-13:00
A Bayesian Phylogenetic Mixture Model to Detect the Differential Selection Patterns of HIV Sequence According to Host Genetic Background
Sahar Parto*, Nicolas Lartillot
University of Montreal, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A bias toward inflation of the Drosophila melanogaster genome is countered by strong selection
Daniel R. Schrider*1,2, David Houle3, Michael Lynch1, Matthew W. Hahn1,2
1Department of Biology, Indiana University, USA, 2School of Informatics and Computing, Indiana University, USA, 3Department of Biological Science, Florida State University, USA
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  16:30-18:00
A coherent theory of ultraconserved non-coding element evolution
Philipp Bucher1,2
1EPFL, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A combined analysis of Eutherian relationships: microRNAs and Phylogenomics.
James Tarver*1,2, Philip Donoghue1, Kevin Peterson2
1University of Bristol, UK, 2Dartmouth College, USA
:  S8 - The animal tree of life and its applications  -  15:00-16:30
A comparative analysis of orthologs and paralogs in Animals: from sequence to structure.
Romain Studer*, Christine Orengo
University College London, UK
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  14:30-16:00
A comparative evolutionary model for the study of meiotic mechanisms
Joshua Bayes*1,2, Clara Wang1, Abby Dernburg1,2
1Howard Hughes Medical Institute, USA, 2Univ. of California, Berkeley, USA
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  14:30-16:00
A comparison of brain transcriptomes in domesticated and wild animals
Frank W. Albert*1,2, Mehmet Somel3, Miguel Carneiro4, Ayinuer Aximu1, Michel Halbwax1, Olaf Thalmann5, Jose A. Blanco-Aguiar4,7, Irina Plyusnina6, Lyudmila Trut6, Rafael Villafuerte7, Nuno Ferrand4, Sylvia Kaiser8, Per Jensen9, Svante Pääbo1
1Max Planck Institute for Evolutionary Anthropology, Germany, 2Princeton University, USA, 3University of California Berkeley, USA, 4University of Porto, Portugal, 5University of Turku, Finland, 6Siberian Branch of the Russian Academy of Sciences, Russia, 7Instituto de Investigación en Recursos Cinegéticos, Spain, 8University of Münster, Germany, 9Linköping University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A comprehensive census of horizontal gene transfers from prokaryotes to unikonts
Pere Puigbo*, Sergei Mekhedov, Yuri I. Wolf, Eugene V. Koonin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A computational approach to detect population structure and signatures of local adaptation from high-throughput re-sequencing data
Matteo Fumagalli*1, Thorfinn Korneliussen2, Tyler Linderoth1, Anders Albrechtsen2, Rasmus Nielsen1,2
1University of California, USA, 2University of Copenhagen, Denmark
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A divide and concatenate strategy for the phylogenetic reconstruction of large orthologous datasets
Jia-Ming Chang*1,2, Matthieu Muffato2, Paolo Di Tommaso1, Jean-Francois Taly1, Javier Herrero2, Cedric Notredame0
1Centre for Genomic Regulation (CRG) and UPF, Spain, 2European Bioinformatics Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A Family Affair: Resolving the taxonomic position of the Old World Leaf-Nosed Bats, the hipposiderids
Nicole Foley*, Sebastien Puechmaille, Emma Teeling
University College Dublin, Ireland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A formal definition for syntenic blocks
Cristina G. Ghiurcuta*, Bernard Moret
EPFL, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A genetic study of skin pigmentation variation in India
Mircea Iliescu*1, Chandana Basu Mallick2,3, Niraj Rai4, Anshuman Mishra4, Gyaneshwer Chaubey2, Rakesh Tamang4, Märt Möls3, Rie Goto1, Georgi Hudjashov2,3, Srilakshmi Raj1, Ramasamy Pitchappan5, CG Nicholas Mascie-Taylor1, Lalji Singh4,6, Marta Mirazon-Lahr7, Mait Metspalu2,3, Kumarasamy Thangaraj4, Toomas Kivisild1,3
1Division of Biological Anthropology, University of Cambridge, UK, 2Evolutionary Biology Group, Estonian Biocentre, Estonia, 3Institute of Molecular and Cell Biology, University of Tartu, Estonia, 4Centre for Cellular and Molecular Biology, India, 5Chettinad Academy of Research and Education, Chettinad Health City, India, 6Banaras Hindu University, India, 7Leverhulme Centre for Human Evolutionary Studies, Division of Biological Anthropology, University of Cambridge, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A GENOME-WIDE ANALYSIS OF Common Fragile Sites: WHAT FEATURES DETERMINE CHROMOSOMAL instability IN A MAMMALIAN GENOME?
Arkarachai Fungtammasan, Erin Walsh, Francesca Chiaromonte, Kristin Eckert, Kateryna Makova*
Penn State University, USA
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  14:30-16:00
A genomewide map of Neandertal ancestry in modern humans
Sriram Sankararaman*1,2, Nick Patterson2, Swapan Mallick1,2, Svante Paabo3, David Reich1,2
1Harvard Medical School, USA, 2Broad Institute of Harvard and MIT, USA, 3Max Planck Institute for Evolutionary Anthropology, Germany
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  11:30-13:00
A genomic study of the contribution of DNA methylation to regulatory evolution in primates
Julien Roux*, Yoav Gilad
University of Chicago, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A global view of mutation patterns across eukaryotes.
Jean-François GOÛT*, Michael LYNCH
Lynch Lab, Indiana University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A Hidden Markov Model for inferring natural selection and other demographic parameters from allele frequency data
Anand Bhaskar*1, Yun Song1,2, Matthias Steinruecken2
1Computer Science Division, University of California, Berkeley, USA, 2Department of Statistics, University of California, Berkeley, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons
Hidenori Nishihara*1, Anne Teissier2, Naoki Kobayashi1, Kensuke Tashiro1, Akiko Nakanishi1, Takeshi Sasaki3, Masaki Iwakiri1, Kazuki Izawa1, Kuo Yan4, Victor Tarabykin4, Kenta Sumiyama5, Mika Hirakawa6, Alessandra Pierani2, Norihiro Okada1
1Tokyo Institute of Technology, Japan, 2Université Paris Diderot, France, 3Tokyo University of Agriculture, Japan, 4Max Planck Institute for Experimental Medicine, Germany, 5National Institute of Genetics, Japan, 6JT Biohistory Research Hall, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A mathematical approach to study the effects of the distribution of selection coefficients associate with allele replacements at different sites  on the overall rate of evolution
Alice Ledda*1, Fyodor Kondrashov2,3
1INSERM, France, 2CRG, Spain, 3ICREA, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A model for the evolution of a uniquely mammalian T cell receptor
Robert Miller*, Zuly Parra
Center for Evolutionary Immunology, University of New Mexico, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A multi-locus perspective of the Late Pleistocene demography of bison and horses in the Klondike, Yukon Territory, Canada
Beth Shapiro*1,3, Mathias Stiller1,3, Matthew Wooller5, Robert Wayne4, Duane Froese2
1Penn State University, USA, 2University of Alberta, Canada, 3University of California Santa Cruz, USA, 4University of California Los Angeles, USA, 5University of Alaska Fairbanks, USA
:  S2 - Paleogenomics: from fossils to genomes  -  11:30-13:00
A multiplex platform for continuous culture and experimental evolution in yeast
Aaron Miller*, Mei Huang, Annie Young, Bryony Lynch, Maitreya Dunham
University of Washington, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A network of everything? Open issues in lateral gene transfer and network construction
Robert Beiko
Faculty of Computer Science, Dalhousie University, Canada
:  S9 - The network of life: algorithmic and modelling challenges  -  15:00-16:30
A new composite method to detect genomic regions under positive selection in 1000genomes data
Marc Pybus1, Manu Uzcudun1, Giovanni Dall’Olio1, Pierre Luisi1, Jaume Bertranpetit*1, Johannes Engelken1,2
1Institute of Evolutionary Biology (CSIC-UPF), Dr. Aiguader 88, Spain, 2Department of Evolutionary Genetics, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A new haplotype test for the detection of selection signatures using data from multiple populations.
Maria Ines Fariello*, Magali SanCristobal, Simon Boitard, Bertrand Servin
INRA, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A new linkage disequilibrium based method for estimating effective population size
Lucie Gattepaille*, Mattias Jakobsson
Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A new Markovian approximation to the coalescent with recombination.
Gerton Lunter
WTCHG, University of Oxford, UK
Monday 25th June 2012:  S16.2 - Computationally efficient approaches for population genetic inference  -  11:30-13:00
A non-cording DNA region is an origin of three primate orphan gene families on the sex chromosome.
Mineyo Iwase*1, Hielim Kim2, Naoyuki Takahata1, Yoko Satta1
1The Graduate University for Advanced Studies (Sokendai), Japan, 2The Pennsylvania State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A novel method for measuring codon usage bias and estimating its statistical significance
Zhang Zhang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A phylogenomic analysis of replication in the Archaea
Kasie Raymann*, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo
Institut Pasteur, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A Replicate Experiment in Nature: Human Cytomegalovirus Evolution in Congenitally Infected Twins
Nicholas Renzette*1, Jeffrey Jensen2, Timothy Kowalik1
1University Of Massachusetts Medical School, USA, 2Ecole Polytechnique Fédérale de Lausanne, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A Screen for QTLs that Influence the Degree of Morphological Variation in Natural Yeast Isolates
Kerry Geiler-Samerotte*, Naomi Ziv, Mark Siegal
New York University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A screen for selection in humans based on archaic genome sequences.
Daniel Falush*, Michael Lachmann
Max Planck Institute for Evolutionary Anthropology, Germany
:  S2 - Paleogenomics: from fossils to genomes  -  11:30-13:00
A Search For Fusions Of Unrelated Genes In The Yeast Genome
Leanne M. Murphy*, Leanne S. Haggerty
National University of Ireland Maynooth, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage- and chromosome-specific divergence.
Tina Hu*1, Michael Eisen2, Kevin Thornton3, Peter Andolfatto1
1Princeton University, USA, 2Howard Hughes Medical Institute and the Lawrence Berkeley Laboratory, University of California Berkeley, USA, 3University of California Irvine, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A Simple Method for Finding Explicit Solutions to the Dynamics of Diffusion Processes with General Diploid Selection
Yun Song1,2, Matthias Steinruecken*1
1UC Berkeley, Department of Statistics, USA, 2UC Berkeley, Computer Science Division, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A site-dependent evolutionary model for CRISPR spacer arrays
Anne Kupczok*, Jonathan P. Bollback
IST Austria, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A social chromosome in the red fire ant
Yannick Wurm*1,2, John Wang4, Oksana Riba-Grognuz2,3, Mingkwan Nipitwattanaphon2, DeWayne Shoemaker5, Laurent Keller2
1Queen Mary, University of London, UK, 2University of Lausanne, Switzerland, 3Swiss Institute of Bioinformatics, Switzerland, 4Academia Sinica, Taiwan, 5USDA-ARS, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A system-level, molecular evolutionary analysis of mammalian phototransduction
Brandon Invergo*, Ludovica Montanucci, Hafid Laayouni, Jaume Bertranpetit
IBE-Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A tale of four phyla: Contrasts between adaptive coding and noncoding changes during metazoan evolution.
David Garfield*1, Courtney Babbitt2, Olivier Fedrigo2, Eileen Furlong1, Gregory Wray2
1European Molecular Biology Laboratory, Germany, 2Duke University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A Transcript Perspective on Evolution
Yann Christinat*, Bernard Moret
EPFL, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A transcriptomics view on speciation - gene expression studies in Ficedula flycatchers
Severin Uebbing*, Axel Künstner, Linnéa Smeds, Hannu Mäkinen, Páll Ólasson, Hans Ellegren
Institute for Ecology and Genetics, Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
A unified framework for inferring population genetic structure and gene-environment associations
Eric Frichot, Sean Schoville, Guillaume Bouchard, Olivier Francois*
University Joseph Fourier, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A whole genome phylogeny of the staphylococci
Apurva Narechania*1, Paul Planet2,1, Sam Boundy3, Rob DeSalle1, Gordon Archer3, Barry Kreiswirth4
1American Museum of Natural History, USA, 2Columbia University, USA, 3Virginia Commonwealth University, USA, 4Public Health Research Institute, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
A Whole-genome Polymorphism Scan in Two Aquilegia (Columbine) Species Identifies Putative Speciation Genes.
Danièle Filiault*1, Elizabeth Cooper2, Nathan Derieg3, Scott Hodges3, Magnus Nordborg1
1Gregor Mendel Institute for Plant Molecular Biology, Austria, 2University of Southern California, USA, 3University of California, Santa Barbara, USA
:  S1 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Aberrant piRNA Production and Global TE Derepression in Drosophila Interspecific Hybrids Suggests that Rapidly Evolving piRNA Proteins Contribute to Genome Defense
Erin Kelleher*, Daniel Barbash
Cornell University, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  09:30-11:00
Abundance of ultramicro inversions within whole genome alignments between closely related species
Yuichiro Hara*, Tadashi Imanishi
National Institute of Advanced Industrial Science and Technology, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Accelerated exon evolution in duplicated regions in hominids
Belen Lorente-Galdos*1,2, Jonathan Bleyhl3, Laura Vives3, Gregory Cooper1, Arcadi Navarro1,4, Evan Eichler3,5, Tomas Marques-Bonet1
1IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Spain, 2National Institute for Bioinformatics (INB), Spain, 3Department of Genome Sciences, University of Washington School of Medicine, USA, 4Institucio Catalana de Recerca i Estudis Avançats (ICREA), Spain, 5Howard Hughes Medical Institute, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Accelerated Recruitment of New Brain Development Genes into the Human Genome
Yong Zhang*1,2, Patrick Landback1, Maria Vibranovski1, Manyuan Long1
1Department of Ecology and Evolution, University of Chicago, USA, 2Institute of Zoology, Chinese Academy of Sciences, China
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Accurate tracing of a transcriptome changes in the course of hybrid speciation
Till Czypionka*1, Jie Cheng1, Alexander E. Pozhitkov1,2, Arne W. Nolte1
1Max-Planck-Institute for Evolutionary Biology, Germany, 2Department of Periodontics, University of Washington, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptation and evolution of the olfactory subgenome in mammals
Graham Hughes*, Des Higgins, Emma Teeling
University College Dublin, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptation in the genic control regions of murids
Daniel Halligan*1, Athanasios Kousathanas1, Bettina Harr2, Thomas Keane3, David Adams3, Peter Keightley1
1University of Edinburgh, UK, 2Max-Planck-Institute for Evolutionary Biology, Germany, 3Wellcome Trust Saner Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Adaptation of intracellular parasitic bacteria to acidic vacuoles
Pedro M. B. M. Coelho*1, Mafalda Silva2, Miguel C. Seabra2, José B. Pereira-Leal1
1Instituto Gulbenkian de Ciência, Portugal, 2Centro de Estudos de Doenças Crónicas, Faculdade de Ciências Médicas da Universidade Nova de Lisboa, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Adaptation to urban environments in Arabidopsis thaliana
Angela Hancock*1,2, Felice Sperone2, Joy Bergelson2
1University of Vienna, Austria, 2University of Chicago, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptive cis-regulatory evolution of age-related differentially expressed genes in the human brain
Michael McGowen*1, Kirstin Sterner2, Jennifer Baker3, Chet Sherwood3, Christopher Kuzawa4, Harry Chugani1, Leonard Lipovich1, Lawrence Grossman1, Derek Wildman1
1Wayne State University School of Medicine, USA, 2University of Oregon, USA, 3The George Washington University, USA, 4Northwestern University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptive evolution and positive selection in rhodopsin: the dN/dS debate
D. David Yu*1, Belinda S.-W. Chang1,2
1Dept. of Cell & Systems Biology, University of Toronto, Canada, 2Dept. of Ecology & Evolutionary Biology, University of Toronto, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Adaptive evolution of loci covarying with the human African Pygmy Phenotype
Isabel Mendizabal*1, Urko M. Marigorta1, Oscar Lao0,2, David Comas1
1Institut de Biologia Evolutiva (CSIC-UPF), Spain, 2Department of Forensic Molecular Biology, Erasmus University Medical Center, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptive evolution of Mediterranean pines
Delphine Grivet1, Zaida Lorenzo*1, José Climent1, Mario Zabal-Aguirre1, Sara Torre4, David B. Neale2,3, Giovanni G. Vendramin4, Santiago C. González Martínez1
1INIA-CIFOR, Spain, 2Department of Plant Sciences,University of California, Davis, USA, 3Center for Population Biology, University of California, Davis, USA, 4Plant Genetics Institute, Division of Florence, National Research Council, Sesto Fiorentino, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptive evolution of Pseudomonas aeruginosa revealed by archetypal analysis of gene expression data
Juliane Thoegersen*, Lars Jelsbak, Soeren Molin
Technical University of Denmark, Denmark
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Adaptive evolution of the Matrix Extracellular Phosphoglycoprotein in mammals
João Paulo Machado*1,2, Warren Johnson3, Stephen O'Brien3, Vítor Vasconcelos1,4, Agostinho Antunes1,3
1CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal, 2Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal, 3Laboratory of Genomic Diversity, National Cancer Institute, USA, 4Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Adaptive Regulatory Substitutions Affect Several Fitness Components of the Bacteriophage ϕX174
Celeste Brown*, Amber Stancik
University of Idaho, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Admixed human genomes reveal complex demographic patterns from early modern humans to the contemporary era
Simon Gravel*1, Jeffrey M Kidd2, Jake K Byrnes1, Andres Moreno Estrada1, Fouad Zakharia1, Shaila Musharoff1, Francisco M De La Vega1, Carlos D Bustamante1
1Stanford University, USA, 2University of Michigan, USA
:  S10 - Population genetic inference from next-generation sequencing data  -  15:00-16:30
Admixture inference using a sequentially Markov coalescent
Joshua Schraiber*, Eric Durand, Montgomery Slatkin
UC Berkeley, USA
:  S2 - Paleogenomics: from fossils to genomes  -  11:30-13:00
Advanced probabilistic models to study gain and loss dynamics of gene families among microbial species
Tal Pupko*, Ofir Cohen
Tel-Aviv University, Israel
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  11:30-13:00
Age and structural characteristics as determinants of protein evolutionary rate
Macarena Toll-Riera*1, David Bostick2, M.Mar Albà1,3, Joshua B. Plotkin2
1Evolutionary Genomics Group, Fundació Institut Municipal d’Investigació Mèdica (FIMIM)- Universitat Pompeu Fabra (UPF), Spain, 2Department of Biology, University of Pennsylvania, USA, 3Catalan Institution for Research and Advanced Studies (ICREA), Spain
:  S1 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Age-related LincRNAs in human brain
Zhisong He*1, Haiyang Hu1, Philipp Khaitovich1,2
1CAS-MPG Partner Institute for Computational Biology, China, 2Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Aging and the loss of immune repertoire genetic diversity
Philip Johnson*1, Andrew Yates2, Jorg Goronzy3, Rustom Antia1
1Emory University, USA, 2Albert Einstein College of Medicine, USA, 3Stanford School of Medicine, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Agrisims: Simulating crop domestication using individual based modeling
James Kitchen*1, Dorian Fuller2, Terry Brown3, Robin Allaby1
1School of Life Sciences, University of Warwick, UK, 2Institute of Archaeology, University College London, UK, 3Manchester Interdisciplinary Biocentre, University of Manchester, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Alignment error and its impact on the sitewise detection of positive selection
Gregory Jordan*, Nick Goldman
EMBL European Bioinformatics Institute, UK
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  14:00-15:30
Alignment-free Comparison of Microbial Genomes
Bernhard Haubold*1, Mirjana Domazet-Loso2, Peter Pfaffelhuber1
1Max-Planck-Institute for Evolutionary Biology, Germany, 2University of Zagreb, Croatia, 3University of Freiburg, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Alternation of ploidal phases and genome-wide molecular evolution
Peter Szovenyi*1,4, Jonathan Shaw2, Gregory Wray2, Andreas Wagner1,6
1Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland, 2Biology Department, Duke University, USA, 3Swiss Institute of Bioinformatics, Switzerland, 4Institute for Systematic Botany, University of Zurich, Switzerland, 5MTA-ELTE-MTM Ecology Research Group, Hungary, 6The Santa Fe Institute, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Amino acid polymorphism at Drosophila methuselah-like genes is associated with lifespan differences.
Micael Reis*, Ana Araújo, Bruno Aguiar, Helder Rocha, Cristina Vieira, Jorge Vieira
IBMC, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Amino acid substitution regime is dependent upon the protein interaction mode with the GroEL chaperone
Judith Ilhan*, Giddy Landan, Tal Dagan
Institute for Molecular Evolution, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
An evolutionary analysis of miRNA binding sites suggests an important role for genetic drift
Alfred Simkin*1, Fen-Biao Gao1, Jeffrey Jensen2,1
1University of Massachusetts Medical School, USA, 2Ecole polytechnique federale de Lausanne, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
An evolutionary history of the selectin gene cluster in humans
Rachele Cagliani*1, Matteo Fumagalli1, Marco Fracassetti1, Diego Forni1, Uberto Pozzoli1, G. Pietro Comi2, Federico Marini1, Nereo Bresolin1,2, Mario Clerici3, Manuela Sironi1
1Scientific Institute IRCCS E. Medea, Italy, 2Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Italy, 3Chair of Immunology, Department of Biomedical Sciences and Technologies LITA Segrate, University of Milan, Italy, 4Fondazione Don C. Gnocchi, IRCCS, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
An improved library preparation method for ancient DNA
Marie-Theres Gansauge*, Svante Pääbo, Matthias Meyer
Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
An initial survey of the protein-protein interaction network of the plant pathogen Phytophthora infestans and its dynamics during infection
Michael F Seidl*, Adrian Schneider, Berend Snel
University Utrecht, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
An overlooked function for Vaults - Lessons from phylogeny
Asfa Alli Shaik*1, Chengcheng Liu2, Christopher Hogue1,2
1Department of Biological Sciences, National University of Singapore, Singapore, 2Center for Singapore-MIT Alliance, National University of Singapore, Singapore, 3Mechanobiology Institute of Singapore. National University of Singapore, Singapore
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
An Understanding of Alternative Splicing is Essential in Understanding Gene Evolution
Toby Hunt*, Jonathan M Mudge, Adam Frankish, Jennifer Harrow
Wellcome Trust Sanger Institute, UK
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  16:00-17:30
Analyses and computer simulations of hotspot distributions in human genome
Dorota Mackiewicz*1, Paulo Murilo Castro de Oliveira2, Suzana Moss de Oliveira2, Stanisław Cebrat1
1Faculty of Biotechnology, University of Wroclaw, Poland, 2Instituto de Física, Universidade Federal Fluminense, Brazil
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Analysis of ancient transposon families using molecular dating and a population genetics paradigm
Elizabeth Hellen*, John Brookfield
University of Nottingham, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Analysis of genetic composition of recombined regions in bacteria through whole genome comparisons
Sebastien Leclercq*, Daniel Falush
Max Plank Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Analysis of inter and intra-species NGS data with a phylogenetic approach.
Nicola De Maio*, Carolin Kosiol
Institute of Population Genetics VetMedUni, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Analysis of sites of polymorphic deletions in noncoding regions of D.melanogaster genome reveals pervasive epistatic selection
Albert Khajrullin*1, Evgeny Leushkin1,3, Georgii Bazykin1,3, Alexey Kondrashov1,2
1Moscow State University, Russia, 2University of Michigan, USA, 3Institute for Information Transmission Problems of the Russian Academy of Sciences, Russia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory
Daniel Zivkovic*, Pablo Duchen, Wolfgang Stephan
Biocenter, LMU Munich, Germany
Monday 25th June 2012:  S16.2 - Computationally efficient approaches for population genetic inference  -  11:30-13:00
Analyzing recombination and phylogeography in bacteria at once: the case of a recently emerged clone of Staphylococcus aureus.
Santiago Castillo*1, Pekka Marttinen4, Jukka Corander2, Matt Holden3, Mona Aldeljawi1, Edward Feil1
1University of Bath, UK, 2University of Helsinki, Finland, 3The Wellcome Trust Sanger Institute, UK, 4Aalto University, Finland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Ancestral peptidergic signaling systems of bilaterian animals
Olivier Mirabeau*, Jean-Stéphane Joly
CNRS, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Ancient DNA and the history of domestic cattle
Dan Bradley*, Matthew Teasdale, Frauke Stock
Trinity College, Ireland
:  S2 - Paleogenomics: from fossils to genomes  -  09:30-11:00
Ancient DNA from museum skins reveals the progression retroviral endogenization 
María Ávila-Arcos2, Simon Ho3, Yasuko Ishida5, Nikolas Nikolaidis4, Kyriakos Tsangaras1, Karin Hönig1, Rebeca Medina4, Morten Rasmussen2, Sarah Fordyce2, Sébastien Calvignac-Spencer6, Eske Willserslev2, M. Thomas Gilbert2, Kristofer Helgen7, Alfred Roca5, Alex Greenwood*1
1Leibniz Institute for Zoo and Wildlife Research, Germany, 2Centre for GeoGenetics, Natural History Museum of Denmark, Denmark, 3University of Sydney, Australia, 4California State University, USA, 5University of Illinois at Urbana-Champaign, USA, 6Robert-Koch-Institut, Germany, 7Smithsonian Institution, USA
:  S2 - Paleogenomics: from fossils to genomes  -  11:30-13:00
And another paradigm bites the dust: rooted global phylogeny
Ajith Harish*, Anders Tunlid, Charles Kurland
Lund University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Antigenic flux of the influenza virus population
Trevor Bedford*1, Marc Suchard2, Philippe Lemey3, Colin Russell4, Derek Smith4, Andrew Rambaut1
1University of Edinburgh, UK, 2University of California, USA, 3Katholieke Universiteit Leuven, Belgium, 4Cambridge University, UK
:  S3 - Evolution of host-virus interactions  -  11:30-13:00
Approximate Bayesian Computation Sheds Light on the Complex Demographic History of Orangutans (genus: Pongo)
Alexander Nater*, Maja Greminger, Natasha Arora, Carel van Schaik, Michael Krützen
Anthropological Institute and Museum, University of Zurich, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Approximate genealogical models for large-scale population genomic inference
Yun Song*, Joshua Paul, Matthias Steinrücken, Kelley Harris, Sara Sheehan
University of California, Berkeley, USA
Monday 25th June 2012:  S16.2 - Computationally efficient approaches for population genetic inference  -  11:30-13:00
'Archaeoepigenetics: Evidence of epigenetic response to drought stress and viral infection in archaeological plant material'
Oliver Smith*, Sarah Palmer, Robin Allaby
The University of Warwick, UK
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  16:00-17:30
Archaeogenomic evidence of local adaptation in crops
Robin Allaby*, Sarah Palmer, Oliver Smith
University of Warwick, UK
:  S2 - Paleogenomics: from fossils to genomes  -  09:30-11:00
Are changes in lifestyle associated with bursts of HGT in proteobacteria?
Thomas Laubach*, Martin J. Lercher
Heinrich-Heine-University Duesseldorf, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Are there severe limits to the power of selection?
Brian Charlesworth
University of Edinburgh, UK
:  S5 - Adaptive vs. non-adaptive evolution  -  11:30-13:00
Aspergillus genes found in Zea Mays shotgun reads
Chun-Lin Wang*1,2, Yi-Pei Ho1, Chien-Chi Chen2, Shih-Hau Chiu2, Li-Min Sung2, Tsu-pei Chiu2, Yeong-Shin Lin1
1Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Taiwan, 2Bioresource Collection and Research Center, Food Industry Research and Development Institute, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Assembly, annotation and SNP detection in Douglas-fir using cDNA libraries of control and drought stressed trees
Thomas Müller*1, Ingo Ensminger2,3, Karl Schmid1
1University of Hohenheim, Germany, 2University of Toronto Mississauga, Canada, 3Forest Research Institute of Baden-Wuerttemberg, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Assessing and Visualising Genetic Diversity at the Population Level
Jessica W. Leigh*, David Bryant
University Of Otago, New Zealand
:  S9 - The network of life: algorithmic and modelling challenges  -  15:00-16:30
Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data
Jacob Crawford*, Brian Lazzaro
Cornell University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Assessing the evolutionary history of Theobroma cacao from resequenced genomes
Omar Cornejo*1, Keithanne Mockaitis2, Muh-Ching Yee1, Stefan Royaert3, Donald Livingstone III3, Ram Podicheti2, David Kuhn3, Carlos Bustamante1, Juan Carlos Motamayor3
1Stanford University, USA, 2Indiana University Center for Genomics and Bioinformatics, USA, 3USDA ARS SHRS, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Assessing the impacts of mating system and natural selection on genome-wide patterns of nucleotide diversity in wild tomatoes
Margot Paris*, Ana Marcela Florez-Rueda, Thomas Städler
ETH Zurich, Institute of Integrative Biology, Plant Ecological Genetics, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Assessing the molecular evolution of the invasive bivalve Corbicula fluminea in Portugal
Cidália Gomes*1,2, Vítor Vasconcelos1,3, Lúcia Guilhermino1,2, Agostinho Antunes1,3
1CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal, 2ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Departamento de Estudos de Populações, Laboratório de Ecotoxicologia, Portugal, 3FCUP - Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Assessing the Relative Effects of Demography versus Selection on the Human X Chromosome Using Next-Generation Sequencing
Shaila Musharoff*1, Jeffrey M. Kidd2,1, Brenna M. Henn1, M.C. Yee1, Howard M. Cann4, Ghia Euskirchen1, Michael Snyder1, Carlos D. Bustamante1, Sohini Ramachandran3
1Stanford University, USA, 2University of Michigan, USA, 3Brown University, USA, 4Fondation Jean Dausset – Centre d'Étude du Polymorphisme Humain, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Asymmetric evolution of Bmp16 and its sister genes Bmp2 and Bmp4
Nathalie Feiner*1, Gerrit Begemann1, Axel Meyer1, Shigehiro Kuraku1,2
1University of Konstanz, Germany, 2Center for Developmental Biology RIKEN, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Bacterial interactome dynamics: evolutionary and co-evolutionary trends in gene family acquisitions
Ofir Cohen*, Tal Pupko
Tel Aviv University, Israel
Monday 25th June 2012:  S12 - Microbial genome evolution  -  11:30-13:00
Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency
Wenfeng Qian*, Jianzhi Zhang
University of Michigan, USA
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
Bayesian inference of the demographic history of Niger-Congo speaking populations
Isabel Alves*1,2, Lounès Chikhi2,3, Laurent Excoffier1,4
1CMPG, Institute of Ecology and Evolution, Switzerland, 2Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, Portugal, 3CNRS, Université Paul Sabatier, ENFA, France, 4Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Bayesian phylogenomics under mutation-selection codon substitution models
Nicolas Rodrigue*1,2, Daniel Stubbs3, Jacques Richer3, Nicolas Lartillot4
1Agriculture and Agri-Food Canada, Canada, 2University of Ottawa, Canada, 3Calcul Québec, Canada, 4Université de Montréal, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Bgee, a database for the study of gene expression evolution
Frederic Bastian1,2, Julien Roux1,2, Anne Niknejad1,2, Aurelie Comte1,2, Sebastien Moretti1,2, Gilles Parmentier1,2, Marc Robinson-Rechavi*1,2
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Biased gene conversion in codon substitution models
Laurent Guéguen*, Laurent Duret
LBBE - UMR CNRS 5558, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Bioinformatic Analysis and Experimental Validation of Fusion Gene in Human, Rhesus Monkey, and Crab-Eating Monkey
Jae-Won Huh*1, Sang-Je Park1,2, Young-Hyun Kim1,3, Kyu-Tae Chang1,3, Sang-Rae Lee1
1National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Republic of Korea, 2Department of Biological Sciences, College of Natural Sciences, Pusan National University, Republic of Korea, 3University of Science & Technology, National Primate Research Center, KRIBB, Republic of Korea
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Bioinformatic Challenges in the 1KITE Project
Alexander Donath
Zoologisches Forschungsmuseum Alexander Koenig, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Bioinformatics Resources for Enabling Discoveries from Genomes to Phenotypes (MEGA, TimeTree, and FlyExpress)
Sudhir Kumar
Center for Evolutionary Medicine & Informatics, Arizona State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Biological meaning of pseudogenization in human evolution
Yoko Satta
The Graduate University for Advanced Studies (Sokendai), Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Birth and functional evolution of mammalian microRNA genes
julien meunier*1, frédéric lemoine1, magali soumillon1, angelica lietchi1, manuela weier1, katerina guschanski1, haiyang hu1, philipp khaitovitch2, henrik kaessmann2
1University of Lausanne, Switzerland, 2Chinese Academy of Sciences, China
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Birth, death, and replacement of karyopherins in Drosophila
Emily Hsieh*, Nitin Phadnis, Harmit S. Malik
Fred Hutchinson Cancer Research Center, Seattle, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Birth-and-Death Evolution of Multigene Families: An Overview and Update
Alejandro Rooney
U.S. Department of Agriculture, USA
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  14:00-15:30
Bi-stability in proteins as a potential evolutionary response to adaptive conflicts
Tobias Sikosek*1, Hue Sun Chan2, Erich Bornberg-Bauer1
1Institute for Evolution and Biodiversity, University of Muenster, Germany, 2Departments of Biochemistry, Molecular Genetics, and Physics, University of Toronto, Canada
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  14:30-16:00
Brain region specific allelic imbalance for a SNP in the prairie vole oxytocin receptor gene
Lanikea King*1,2, Kiyoshi Inoue1,2, Larry Young1,2
1Center for Translation Neuroscience, USA, 2Behavioral Neuroscience and Psychiatric Disorders, USA
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  16:30-18:00
Brain-specific epigenetic adaptations in humans
Jessica L. Crisci*1, Hennady P. Shulla1, Denis Reshetov2, Iris Cheung1, Rahul Bharadwaj1, Hsin Jung Chou1, Isaac Houston1, Cyril J. Peter1, Wei-Dong Yao3, Richard H. Meyers4, Jiang-fan Chen4, Todd Preuss5, Evgeney Rogaev1,2, Jeffrey D. Jensen1,6, Zhiping Weng1, Schahram Akbarian1
1University of Massachusetts Medical School, USA, 2Vavilov Institute of General Genetics, Russia, 3New England Primate Center, USA, 4Boston University, USA, 5Yerkes National Primate Research Center/Emory University, USA, 6Ecole Polytechnique Fédérale de Lausanne, Switzerland
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  14:00-15:30
Building Structure-based Classification from Multiple Sequence Alignment with the T-RMSD method
Cedrik Magis*1,2, Cedric Notredame1,2
1Center for Genomic Regulation (CRG), Spain, 2Universitat Pompeu Fabra (UPF), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Can the evolutionary dynamics of structural disorder contribute to biological divergence and neostructuralization?
Madolyn MacDonald2, Juan Felipe Ortiz Quinonez1, Patrick Masterson1, Jessica Siltberg-Liberles*1
1University of Wyoming, USA, 2Rochester Institute of Technology, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Can we understand bacterial evolution from MLST data?
Ferran Palero1,2, Fernando Gonzalez-Candelas*1,2
1University of Valencia, Spain, 2CSISP, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Capuchin monkey transcriptome provides insight into primate brain evolution
Amy M. Boddy*1, Mary Ann Raghanti2, Chet Sherwood3, Kimberley A. Phillips4, Stephen H. Montgomery5,6, Nicholas I. Mundy6, Lawrence I. Grossman1, Derek E. Wildman1,7
1Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, USA, 2Department of Anthropology, Kent State University, USA, 3Department of Anthropology, The George Washington University, USA, 4Department of Psychology, Trinity University, USA, 5Department of Genetics, Ecology & Evolution, University College London, UK, 6Department of Zoology, University of Cambridge, UK, 7Department of Obstetrics and Gynecology, Wayne State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Cell Tropism Influences RNA Virus Nucleotide Substitution Rates
Allison Hicks*, Siobain Duffy
Rutgers University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Challenges and prospects for molecular phylogenetics on disparate branches of the eukaryotic Tree of Life
Eduardo Eizirik*, Laura Utz, Taiz Simão, Tatiane Trigo, Alexsandra Schneider
PUCRS, Brazil
:  S6 - Gene/genome data and the limits to  -  17:00-18:30
Changes in gene expression following segmental duplication in mammals
Katerina Guschanski*, Julien Meunier, Henrik Kaessmann
University of Lausanne, Switzerland
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  14:30-16:00
Characterisation of the skin immunones in the most archaic frogs in the world, Leiopelma archeyi and L. hochstetteri
Mette Lillie*1, Phillip Bishop2, Dianne Gleeson3, Katherine Belov1
1Faculty of Veterinary Science, University of Sydney, Australia, 2Department of Zoology, University of Otago, New Zealand, 3Ecological Genetics Laboratory, Landcare Research, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Characterization of Great Ape genetic diversity by whole genome sequencing.
Peter Sudmant*1,3, Javier Prado2,3, Tomas Marques-Bonet2,3, Evan Eichler1,3
1University of Washington Genome Sciences, USA, 2Institut de Bioligia Evolutiva, Spain, 3Great Ape Sequencing Consortium, USA
:  S10 - Population genetic inference from next-generation sequencing data  -  15:00-16:30
Characterization of the olfactory transcriptome in the European eel Anguilla anguilla
Allison Churcher*1, Weiming Li2, Scot Libants2, Alessandro Coppe3, Lorenzo Zane3, Adelino Canário1, Mar Huertas1
1Centre of Marine Science, University of Algarve, Portugal, 2Michigan State University, USA, 3University of Padova, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Characterizing adaptively relevant alleles in wild mice (Mus musculus L.)
Natascha Hasenkamp*, Diethard Tautz
Max Planck Institute for Evolutionary Biology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Characterizing Gene Expression Variation Across Seven Diverse Human Populations
Alicia Martin*1, Helio Costa1, Jeffrey Kidd2, Brenna Henn1, Muh-Ching Yee1, Stephen Montgomery1, Howard Cann3, Michael Snyder1, Carlos Bustamante1
1Stanford University School of Medicine, Department of Genetics, USA, 2University of Michigan School of Medicine, Department of Human Genetics, USA, 3Foundation Jean Dausset, Centre d'Etude du Polymorphisme Humain, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Characterizing recent evolutionary changes on the human lineage using the high-coverage Denisovan genome
Fernando Racimo*, Martin Kircher, Janet Kelso, Svante Pääbo
Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Characterizing regulatory mechanisms underlying gene expression variation and adaptation
Athma Pai*1, Roger Pique-Regi1, Jacob Degner1, Carolyn Cain1, Noah Lewellen2, Katelyn Michelini2, Jonathan Pritchard1,2, Yoav Gilad1
1University of Chicago, USA, 2Howard Hughes Medical Institute, USA
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  14:00-15:30
Characterizing the effect of multiple sequence alignment on downstream analyses
Simon Whelan*, Ben Blackburne
University of Manchester, UK
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  14:00-15:30
Characterizing the molecular basis of hybrid seed failure between two wild tomato species
Ana Marcela Florez-Rueda*, Margot Paris, Thomas Städler
ETHZ, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Characterizing the X-autosome difference in regulation of testes-specific genes in Drosophila melanogaster
Emily Landeen*, Colin Meiklejohn, Daven Presgraves
University of Rochester, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Charting the footprint of natural selection through the genome of Drosophila melanogaster
Antonio Barbadilla*, David Castellano, Maite Barrón, Miquel Ràmia, Sònia Casillas
Institut de Biotecnologia i de Biomedicina - IBB / Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Chemosensory protein gene family evolution in ants
Jonna Kulmuni*1,2, Yannick Wurm3, Pekka Pamilo4
1University of Oulu, Finland, 2Biocenter Oulu, Finland, 3Queen Mary, University of London, UK, 4University of Helsinki, Finland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
CHROMEVALOA: A MOLECULAR DATABASE OF CHROMATIN-ASSOCIATED PROTEINS USEFUL FOR THE EVALUATION OKADAIC ACID GENOTOXICITY IN BIVALVE MOLLUSCS
Victoria Suarez-Ulloa1, Vanessa Aguiar-Pulido2, Rodrigo Gonzalez-Romero1, Ciro Rivera-Casas1, Juan Fernandez-Tajes1, Juan Ausio3, Josefina Mendez1, Julian Dorado2, Jose M. Eirin-Lopez*1
1CHROMEVOL-XENOMAR Group, Department of Cellular and Molecular Biology, University of A Coruna, Spain, 2RNASA-IMEDIR Group, Department of Information and Communication Technologies, University of A Coruna, Spain, 3Department of Biochemistry and Microbiology, University of Victoria, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Chromosome-scale selective sweeps in Caenorhabditis elegans
Joshua Shapiro*1, Erik Andersen1, Justin Gerke1, Marie-Anne Félix Fèlix2, Leonid Kruglyak1,3
1Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA, 2Institute of Biology of the Ecole Normale Superieure, France, 3Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey, USA. 4 Department of Molecular Biology, Princeton University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
CICHLIDomics: uncovering the genetic and developmental basis of diversification in East African cichlid fishes
Walter Salzburger
University of Basel, Switzerland
:  S4 - Genomic basis of Evo-Devo  -  09:30-11:00
Climate adaptation of flowering time in the Mediterranean model species Medicago truncatula
Concetta Burgarella*1, Nathalie Chantret1, J. Marie Prosperi1, Stephane De Mita2, Peter Tiffin3, Joelle Ronfort1
1INRA, France, 2INRA, France, 3Univ. of Minnesota, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Climatic conditions during the Last Glacial Maximum affect the current genetic diversity of the European wild boar (Sus scrofa)
Sibelle Vilaca*1, Laura Iacolina2, Daniela Biosa2, Frank Zachos2, Marco Apollonio2, Massimo Scandura2, Giorgio Bertorelle1
1Università di Ferrara, Italy, 2Università di Sassari, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Cloning, characterization and expression of an insecticidal crystal protein gene from Bacillus thuringiensis isolates of Andaman and Nicobar Islands
H.M.MAHADEVA SWAMY*1, RAMASAMY ASOAKN1, GEETHA G. THIMMEGOWDA1, RIAZ MAHMOOD2, NAGESHA S N1, DILIP KUMAR ARORA3
1INDIAN INSTITUTE OF HORTICULTURAL RESEARCH (IIHR), India, 2KUVEMPU UNIVERSITY, India, 3NATIONAL BUREAU OF AGRICULTURALLY IMPORTANT MICROORGANISMS, India
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Clustal Omega for fast and accurate alignment of many protein multiple sequences
Des Higgins
University College Dublin, Ireland
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  16:00-17:30
Clustering Gene Trees Into Topological Classes
Kevin Gori*, Christophe Dessimoz
European Bioinformatics Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Coalescent analysis of archaic hominin data
Swapan Mallick*, David Reich
Harvard Medical School, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood
Yufeng Wu
University of Connecticut, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Codon usage in large modular proteins in bacteria
John Cullum*1, Heba Al-Hashmi1, Mohamed Lisfi1, Jurica Zucko3, Daslav Hranueli3, Paul Long2
1University of Kaiserslautern, Germany, 2King’s College, UK, 3University of Zagreb, Croatia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Coevolution between C2H2 zinc fingers and retroelements in vertebrates
James Thomas, Sean Schneider*
University of Washington, USA
:  S3 - Evolution of host-virus interactions  -  11:30-13:00
Color vision variation of trichromacy by L/M hybrid genes in wild populations of New World howler monkeys
Yuka Matsushita*1, Hiroki Oota1,2, Barbara Welker3, Mary Pavelka4, Shoji Kawamura1
1The Uniersity of Tokyo, Japan, 2Kitasato University, Japan, 3State University of New York at Geneseo, USA, 4University of Calgary, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Combinatorial properties of coalescent trees and relatives
Filippo Disanto, Thomas Wiehe*
Universitaet zu Koeln, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Combining genomic sequencing and gene expression studies to identify the genetic basis of colour pattern diversity in Heliconius butterflies.
Nicola Nadeau*1, Carolina Pardo-Diaz1, Grace Wu1, Richard Wallbank1, Kanchon Dasmahapatra2, Simon Martin1, Simon Baxter1, Chris Jiggins1
1Department of Zoology, University of Cambridge, UK, 2University College London, UK
:  S4 - Genomic basis of Evo-Devo  -  11:30-13:00
Combining protein structure and sequence variation to identify functionally important sites and sites under positive or negative selection
Austin Meyer, Claus Wilke*
The University of Texas at Austin, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Communities in Dense Networks
Sune Lehmann*1,4, James P Bagrow2,4, Yong-Yeol Ahn3,4
1Technical University of Denmark, Denmark, 2Northwestern University, USA, 3Indiana University Bloomington, USA, 4Northeastern University, USA
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  14:00-15:30
Comparative Analysis of Gene Content Evolution in Phytoplasmas and Mycoplasmas
Ling-Ling Chen1, Wan-Chia Chung1, Chan-Pin Lin0,2, Chih-Horng Kuo*1
1Institute of Plant and Microbial Biology, Academia Sinica, Taiwan, 2Department of Plant Pathology and Microbiology, National Taiwan University, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Comparative genome analysis of Microsporidia reveals gain and expansion of gene families
Sirintra Nakjang*1, Eva Heinz1, Tom A. Williams1, Christophe J. Noël1, Daniel C. Swan1, Alina V. Goldberg1, Simon R. Harris1, Thomas Weinmaier2, Stephanie Markert3, Tal Dagan4, Thomas Schweder3, Thomas Rattei2, Neil Hall5, Robert P. Hirt1, T. Martin Embley1
1Newcastle University, UK, 2University of Vienna, Austria, 3Ernst-Moritz-Arndt-Universitaet Greifswald, Germany, 4Heinrich Heine University Düsseldorf, Germany, 5University of Liverpool, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Comparative Genomics and Transcriptomics of Parasitic Nematodes
James Cotton*, Adam Reid, Isheng Tsai, Nancy Holroyd, Matthew Berriman
Wellcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Comparative genomics of louse primary endosymbiotic bacteria
Bret Boyd*, Julie Allen, David Reed, Valerie de Crecy-Lagard, Lauren McIntyre
University of Florida, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Comparative genomics of Saccharomyces cerevisiae isolates sheds light on the role of neutrality and selection in the emergence of adaptations
Christina Toft*1, Clara Ibañez2, Amparo Querol2, Eladio Barrio1
1University of Valencia, Spain, 2Consejo Superior de Investigaciones Científicas, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Comparative Genomics Reveals Birth and Death of Fragile Regions in Mammalian Evolution
Pavel Pevzner
University of California at San Diego, USA
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  14:30-16:00
Comparative proteomic characterization of protein disorder distribution across Eukaryota
Catherine Mooney*, Denis C. Shields, Therese A. Holton
UCD, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Comparative transcriptome analysis of increased encephalization in mormyrid  fishes
Olivier Fedrigo*1, William J. Nielsen1, Bruce A. Carlson2
1Duke University, USA, 2Washington University in St. Louis, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Comparative Transcriptomics for Eye Diversification of Cephalopod: Evolution of Camera eye and Pinhole eye
Atsushi Ogura
Ochanomizu University, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Comparative transcriptomics without the aid of reference genomes.
Peter Harrison*1, Marie Pointer1,2, Judith Mank1
1University College London, UK, 2University of Oxford, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Comprehensive population genetic modelling unravels the invasion history of four Pristionchus pacificus lineages on La Réunion Island
Angela McGaughran*, Katy Morgan, Ralf Sommer
Max Planck Institute for Developmental Biology, Department for Evoutionary Biology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Computational Prediction and Experimental Validation of Hydrogenosomal Proteins Coded in the Nuclear Genome of Trichomonas vaginalis
David Burstein*1, Sven Gould2, Verena Zimorski2, Thorsten Kloesges2, Fuat Kiosse2, Peter Major2, William Martin2, Tal Pupko1, Tal Dagan2
1Tel Aviv University, Israel, 2Heinrich-Heine University, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Computing Phenotypes from Nucleotide Sequences: Disentangling the Role of Duplication of Network Components in the Navigability of Fitness Landscapes
Jayson Gutierrez Betancur*1,2, Steven Maere1,2
1VIB Department of Plant Systems Biology, Technologiepark 927, B-9052, Belgium, 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052, Belgium
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Computing the joint distribution of tree shapes and tree distances for multiple tree inference with tree metric based models
Yujin Chung*1, Cécile Ané1,2
1Department of Statistics, University of Wisconsin - Madison, USA, 2Department of Botany, University of Wisconsin - Madison, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Conservation and Adaptation in Blindness Genes: A Phylomedicine Approach to Understanding the Evolution of Sensory Perception in Mammals
Emma Teeling*1, Michael Bekeart2, Alisha Goodbla1
1University College Dublin, Ireland, 2University of Stirling, UK
:  S8 - The animal tree of life and its applications  -  17:00-18:30
Conservation and function of noncoding RNAs in primate evolution
Courtney Babbitt*, Lisa Pfefferle, Olivier Fedrigo, Gregory Wray
Duke University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria
Bhanupratap Chouhan*1,2, Alexander Denesyuk1, Jyrki Heino3, Mark S. Johnson1, Konstantin Denessiouk2
1Department of Biosciences, Åbo Akademi University, Finland, 2Turku Center for Biotechnology (University of Turku and Åbo Akademi University), Finland, 3Department of Biochemistry and Food Chemistry, University of Turku, Finland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Context-dependent evolution of protein domains and their repeats
Dan Reshef*1, Liran Carmel2, Ora Schueler-Furman1
1Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Israel, 2Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Israel
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis
Pauline Goubet1, Hélène Bergès2, Arnaud Bellec1, Elisa Prat1, Nicolas Helmstetter1, Sophie Mangenot1, Sophie Gallina1, Anne-Catherine Holl1, Isabelle Fobis-Loisy1, Xavier Vekemans1, Vincent Castric*1
1Laboratoire de génétique et évolution des populations végétales (CNRS-Université Lille1), France, 2Centre National des Ressources Génomiques Végétales (INRA), France, 3Genoscope (CEA), France, 4Laboratoire reproduction et développement des plantes (CNRS-INRA-ENS), France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Contrasted patterns of selective pressures in three recent paralogous gene pairs in the Medicago genus (L.)
Joan Ho-Huu1,2, Joëlle Ronfort1, Stéphane De Mita3,5, Thomas Bataillon4, Jean-Marie Prosperi1, Nathalie Chantret*1
1INRA, France, 2CNRS/Université Lyon1, France, 3IRD, France, 4BiRC, Denmark, 5INRA, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Contribution of epigenetic modification to subfunctionalization after whole genome duplication
Lidija Berke*, Gabino F. Sanchez-Perez, Berend Snel
Utrecht University, The Netherlands
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  16:00-17:30
Convergence of life-history traits and mutations roads in experimentally evolving populations of Saccharomyces cerevisiae
Aymé SPOR1, Daniel KVITEK2, Tibault NIDELET1, Christine DILLMANN1, Aurélie BOURGAIS1, Dominique De VIENNE1, Gavin SHERLOCK2, Delphine SICARD*1
1Université Paris Sud, France, 2Stanford University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Convergent evolution of concerted evolution in a master sex determiner
Eyal Privman*1, Sanne Nygaard2, Alexandra von Siebenthal1, Laurent Keller1, Yannick Wurm1,3
1University of Lausanne, Switzerland, 2University of Copenhagen, Denmark, 3Queen Mary, University of London, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Coordinated histone modifications and small RNAs in gene and genome copy number variations
Misook Ha
Samsung Advanced Institute of Technology, Republic of Korea
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  14:00-15:30
Coprolites as a source of information on the genome and diet of the cave hyena
Jean-Marc Elalouf
CEA Saclay, France
:  S2 - Paleogenomics: from fossils to genomes  -  09:30-11:00
Copy Number Variation in the Porcine Genome
Yogesh Paudel*, Hendrik-Jan Megens, Ole Madsen, Mirte Bosse, Laurent Frantz, Richard Croojimans, Martien A.M. Groenen
Animal Breeding and Genomics Centre, Wageningen University, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Coral reef fishes: the origins of biodiversity hotspots and biogeographic patterns
Peter Cowman*1,2, David Bellwood1,2
1School of Marine and Tropical Biology, James Cook University, Australia, 2Australian Research Council Centre of Excellence for Coral Reef Studies, Australia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Correcting principal components of spatial population genetic variation under isolation by distance models
Eric Frichot*1, Sean Schoville1, Guillaume Bouchard0,2, Olivier François1
1Université Joseph Fourier, CNRS, TIMC-IMAG UMR 5525, France, 2Xerox Research Center Europe, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Cryptic genetic variation underlying stress resistance in evolved lines of Caenorhabditis remanei
Kristin Sikkink*, Catherine Ituarte, Rose Reynolds, Patrick Phillips, William Cresko
University of Oregon, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
DACTAL: Divide-and-conquer trees (almost) without alignments.
Tandy Warnow*1, Serita Nelesen3, Kevin Liu2, Li-San Wang4, C. Randal Linder1
1University of Texas at Austin, USA, 2Rice University, USA, 3Calvin College, USA, 4University of Pennsylvania, USA
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  14:00-15:30
Dawg 2.0: New methods for sequence simulation.
Reed Cartwright1,2
1Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, USA, 2Genomics, Evolution, and Bioinformatics, School of Life Sciences, Arizona State University, USA
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  09:30 - 11:00
De novo analysis of the marine bivalve Macoma balthica transcriptome with the 454 technology
Vanessa Becquet*1, Audrey Rohfritch2, Eric Pante1, Pascale Garcia1
1Laboratoire LIENSs UMR 7266 CNRS-Université de La Rochelle, France, 2CBPG, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
Qi Zhou*1,2, Wen Wang2, Doris Bachtrog1
1University of California, Berkeley, USA, 2Kunming Institute of Zoology, Chinese Academy of Sciences, China
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Deciphering the porcine imprintome
Ole Madsen*1, Djawad Radjabzadeh1, Hendrik-Jan Megens1, Mirte Bosse1, Laurent Frantz1, Yogesh Paudel1, Richard Crooijmans1, Laurie Rund2, Lawrence Schook2, Martien Groenen1
1Wageningen University, The Netherlands, 2University of Illinois, USA
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  14:00-15:30
Decoding the genomic and transcriptional changes underlying the transition to multicellularity in experimentally-evolved Saccharomyces cerevisiae.
Johnathon D. Fankhauser*, William C. Ratcliff, R. Ford Denison, Michael Travisano
University of Minnesota, USA
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
Decreasing speciation or incomplete sampling?
Disa Hansson*, Sebastian Höhna
Dept. of Mathematics, Stockholm University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Deep relationships of Rhizaria revealed by phylogenomics
Roberto Sierra*, Jan Pawlowski
University of Geneva, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Demographic inference and scans for selection in 28 sequenced gorillas
Jeffrey Kidd*1, Joanna Kelley2, Laurie Stevison3, August Woerner4, Laurel Johnstone4, Michael Hammer4, Jeff Wall3, Carlos Bustamante2, Great Apes Genome Diversity Consortium5
1University of Michigan, USA, 2Stanford University, USA, 3University of California, San Francisco, USA, 4University of Arizona, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Demographic inference from the site frequency spectrum with ascertainment bias
Laurent Excoffier1
1University of Berne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
:  S10 - Population genetic inference from next-generation sequencing data  -  17:00-18:30
Demographic Inference Using Skyline Plots on Approximate Bayesian Computation
Miguel Navascués*1, Concetta Burgarella2
1UMR CBGP - INRA, France, 2UMR AGAP - INRA, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Demographic inference using the transition matrix of allelic types from diploid genomic sequences
Yong Wang*, Kirk Lohmueller, Rasmus Nielsen
Department of Integrative Biology, University of California, Berkeley, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Demographic processes or mitochondrial selective sweep in shaping patterns of genetic diversity in a Neotropical treefrog endemic from the Brazilian Atlantic forest
Tuliana Oliveira Brunes*1,2, João Paulo Soares de Cortes2, João Alexandrino3, Célio Fernando Baptista Haddad2, Fernando Sequeira1
1CIBIO-UP/PT, Portugal, 2UNESP, Brazil, 3UNIFESP, Brazil
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Demography and natural selection in chimpanzee populations inferred from full exome sequencing
Christina Hvilsom2,3, Jinjie Duan1, Thomas Bataillon1, Yingrui Li4, Thomas Mailund1, Kasper Munch1, Yu Qian1, Asger Hobolth1, Jun Wang4, Hans R. Siegismund2, Mikkel H. Schierup*1
1Aarhus University, Denmark, 2University of Copenhagen, Denmark, 3Copenhagen Zoo, Denmark, 4BGI, China
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Depth-related changes in coral zooxanthellae
Nikolaos Schizas*1, Matthew Lucas1, Matthew Smith1,2, Ernesto Weil1
1University of Puerto Rico, USA, 2University of Wisconsin - Milwaukee, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Detecting and characterizing selection at loci subject to recurrent mutation.
Ryan Haasl*, Bret Payseur
University of Wisconsin - Madison, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Detecting and correcting alignment overcompression
Daniel Money*, Mark Holder
University of Kansas, USA
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  14:00-15:30
Detecting change in speciation and extinction rates with phylogenetic trees
Sacha Laurent*1,2, Marc Robinson-Réchavi1,2, Nicolas Salamin1,2
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Detecting HIV-1 co-receptor usage from sequence variation and V3 structural information
Felix Feyertag*, John Archer, David L Robertson
University of Manchester, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Detecting selective sweeps from pooled next generation sequencing samples
Simon Boitard*1, Christian Schlötterer2, Viola Nolte2, Ramvinay Pandey2, Andreas Futschik1
1INRA, Laboratoire de G\énétique Cellulaire, France, 2Institut für Populationsgenetik, Vetmeduni Vienna, Austria, 3Institute of Statistics and Decision Support Systems, University of Vienna, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Detection of dual coding regions in mRNAs using ribosomal profiling data.
Audrey M. Michel*1, Kingshuk Roy Choudhury1, Andrew E. Firth2, Nicolas T. Ingolia3, John F. Atkins1, Pavel V. Baranov1
1University College Cork, Ireland, 2University of Cambridge, UK, 3Carnegie Institution for Science, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Detection of Mycobacterium tuberculosis outbreaks using whole-genome sequencing
Timothy M. Walker1, Camilla L.C. Ip*2, Jason T. Evans3, Philip Monk4, Peter M. Hawkey3, Julian Parkhill5, Ruth Harrell3, A. Sarah Walker1, Derrick W. Crook1, Tim E. A. Peto1, Rory Bowden2, E. Grace Smith3
1Nuffield Department of Medicine, UK, 2Department of Statistics, UK, 3Health Protection Agency, UK, 4Health Protection Agency, UK, 5Wellcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Detection of recombination events in bacterial genomes from large population samples
Jukka Corander
University of Helsinki, Finland
Monday 25th June 2012:  S12 - Microbial genome evolution  -  09:30 - 11:00
Detection of traces of selection with numerous SNP in small experimental chicken populations undergoing directional selection.
Frédéric Hospital*1, Bertrand Bed’Hom1, Mathieu Gautier2, Licia Silveri1, Nicolas Bruneau1, Jean-Luc Coville1, David Gourichon3, Marie-Hélène Pinard-van der Laan1
1INRA, France, 2CBGP, France, 3INRA, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Detection of WGDs by modeling duplication dynamics
Kevin Vanneste*1,2, Yves Van de Peer1,2, Steven Maere1,2
1VIB, Belgium, 2UGent, Belgium
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Determination of the mechanisms of regulatory divergence across a large collection of Saccharomyces cerevisiae strains
Brian Metzger*, Patricia Wittkopp
University of Michigan, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Determining the evolutionary history of gene families
Ryan Ames*1, Daniel Money2, Vikramsinh Ghatge1, Simon Whelan1, Simon Lovell1
1University of Manchester, UK, 2University of Kansas, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Determining the power and robustness of the branch-site test of positive selection under conditions of strong divergence
Walid Gharib*1,2, Marc Robinson-Rechavi1,2
1University of Lausanne, Switzerland, 2SIB Swiss institute of bioinformatics, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Developing Maximum Likelihood and Bayesian Supertrees
Wasiu Akanni*1, Peter Foster2, Mark Wilkinson2, Davide Pisani1
1NUI, Ireland, 2NHM, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Developmental constraints on transcriptome evolution vary for different molecular features
Barbara Piasecka*1,2, Pawel Lichocki3, Marc Robinson-Rechavi1,2
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland, 3Ecole Polytechnique Federale de Lausanne, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Devils and disease: Tracing spread and impacts of Devil Facial Tumour Disease on Tasmanian devil populations
Anna Brüniche-Olsen*1, Elizabeth Murchison3, Jeremy Austin2, Chris Burridge1, Menna Jones1
1University of Tasmania, Australia, 2University of Adelaide, Australia, 3The Wellcome Trust Sanger Institute, UK
:  S1 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Diagnosing phylogenetic conflict among genes and proteins: evidence for the origin of plastids and the early diversification of plants.
Blaise Li*1, Peter Foster3, Martin Embley2, Cymon Cox1
1Centro de Ciencias do Mar (CCMAR), Portugal, 2Newcastle University, UK, 3Natural History Museum, UK
:  S6 - Gene/genome data and the limits to  -  17:00-18:30
Did Quaternary glacial cycles drive walrus diversity? A paleogenomic approach.
Tara Fulton*1,2, Grant Zazula3, Michael Cousar1, Beth Shapiro1,2
1The Pennsylvania State University, USA, 2University of California Santa Cruz, USA, 3Government of Yukon, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes
Takeshi Hase1,2, Yoshihito Niimura*1
1Medical Research Institute, Tokyo Medical and Dental University, Japan, 2The Systems Biology Institute, Japan
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  16:00-17:30
Difference in Gene expression between dry and wet thalli of lichen Usnea bismolliuscula
Mieko Kono*1, Yoshihito Ohmura2, Yoko Satta1
1Department of Evolutionary Studies of Biosystems, the Graduate University for Advanced Studies [SOKENDAI], Japan, 2Department of Botany, National Museum of Nature and Science, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Different selective forces on cis and trans acting factors shape gene expression evolution in yeasts
Bernhard Schaefke*1,2, J.J. Emerson3, Tzi-Yuan Wang4,2, Wen-Hsiung Li2,5
1Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taiwan, 2Biodiversity Research Center, Academia Sinica, Taiwan, 3Center for Theoretical Evolutionary Genomics, University of California, Berkeley, USA, 4Genomics Research Center, Academia Sinica, Taiwan, 5Department of Ecology and Evolution, University of Chicago, USA
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  16:00-17:30
Discovery and population genomics of Drosophila viruses: No evidence for an arms-race
Darren Obbard*, Claire Webster
University of Edinburgh, UK
:  S3 - Evolution of host-virus interactions  -  9:30-11:00
Disentangling the phylogenetic signal carried by alignment gaps and guide trees
Salvador Capella-Gutíerrez, Toni Gabaldón*
Centre for Genomic Regulation (CRG), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Dispersal processes underlying the recent pandemic caused by the plant pathogenic fungus Mycosphaerella fijiensis
Jean Carlier*1, Stéphanie Robert1, Adrien Rieux1, Fabien Halkett2, Marie-Françoise Zapater1, Luc De Lapeyre de bellaire1, François Bonnot1, Catherine Abadie1, Virginie Ravigné1
1CIRAD, UMR BGPI, France, 2INRA, UMR 1136, France, 3CIRAD, UPR 26, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Dissecting the Divergence of Dogs from Their Wild Ancestors: Complete Genome Sequences of 5 Close Relatives to Modern Dog Breeds
Adam Freedman*1, Rena Schweizer1, Pedro Silva2, Marco Galaverni3, Zhenxin Fan4, Eunjung Han1, Diego Ortega-Del Vecchyo1, Ilan Gronau5, Belen Lorente-Galdos6, Can Alkan7, Kevin Squire1, Robert Chin1, Adam Boyko5, Zugen Chen1, Heidi Parker8, Christina Chung9, Clarence Lee9, Adam Siepel5, Tomas Marques-Bonet6, Carlos Bustamante10, Elaine Ostrander8, Timothy Harkins9, Stanley Nelson1, Robert Wayne1, John Novembre1
1University of California, Los Angeles, USA, 2Universidade do Porto, Portugal, 3University of Bologna, Italy, 4Sichuan University, China, 5Cornell University, USA, 6Institut de Biologia Evolutiva, Spain, 7University of Washington, USA, 8National Institutes of Health/NHGRI, USA, 9Life Technologies, USA, 10Stanford School of Medicine, USA
:  S10 - Population genetic inference from next-generation sequencing data  -  17:00-18:30
Distribution of Plastid Gene Signals among Chromalveolates without Plastids
Christian Woehle*, William Martin, Sven B. Gould
Molecular Evolution, Heinrich-Heine-University, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Divergence of bacterial gut symbionts between two floricolous flies, Colocasiomyia alocasiae and C. xenalocasiae
Jia-Syuan Chen1, Chau-Ti Ting*1,2, Shu Fang3, Shun-Chern Tsaur4
1Institute of Zoology, National Taiwan University, Taiwan, 2Department of Life Science & Institute of Ecology and Evolutionary Biology, National Taiwan University, Taiwan, 3Biodiversity Research Center, Academia Sinica, Taiwan, 4Department of Life Sciences & Institute of Genome Sciences, National Yang-Ming University, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Divergent gene expression patterns produce highly similar aggressive phenotypes in male and female cichlid fish (Julidochromis)
Suzy Renn
Reed College, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Divergent mitochondrial haplotypes convey clearadjustments in metabolic phenotypes.
Pierre Blier*1, Nicolas Pichaud1,2, Robert M Tanguay1,3, J William O Ballard1,2
1Université du Québec, Canada, 2University of New South Wales, Australia, 3Université laval, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Divergent resolution of duplicate genes among three Paramecium species following whole-genome duplication
Casey L. McGrath*, Thomas G. Doak, Michael Lynch
Indiana University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Diversity of endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia
Amanda Y. Chong*1, Sarah Atkinson1, Sally Isberg1,2, Lorna Melville3, Jaime Gongora1
1University of Sydney, Faculty of Veterinary Science, Australia, 2Porosus Pty Ltd, Australia, 3OIC Berrimah Veterinary Laboratories Department of Resources, Australia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Diversity of immune-related genes in the yellow fever mosquito Aedes aegypti as revealed by resequencing of a wild pool
William J Palmer*1, Jewelna Osei-Poku1, Yung Shwen Ho2, Arnab Pain2, Francis Jiggins1
1University of Cambridge, UK, 2King Abdullah University of Science and Technology, Saudi Arabia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
DNA methylation in Biomphalaria glabrata the intermediate host of the human parasite Schistosoma mansoni: role of epigenetics in the coevolution of host / parasite interactions.
Sara Fneich*1,2, Julie Lepesant1,2, Céline Cosseau1,2, Michael Reichelt3, Christoph Grunau1,2
1Université de Perpignan Via Domitia, France, 2CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), France, 3Max-Planck-Institut fuer Chemische Oekologie, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Does convergent morphology implies convergent development? Towards a comparative transcriptomics of tooth development.
Marie Sémon*, Vincent Laudet, Sophie Pantalacci
IGFL, ENS de Lyon, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Dosage sensitive genes in evolution and disease.
Aoife McLysaght
Trinity College, Ireland
:  S7 - Evolutionary genomics: A new synthesis of evolutionary biology (In honor of W-H Li's 70th birthday)  -  15:00-16:30
Drift constrained by selection: the dynamics of small RNA copy number and expression patterns over evolutionary timescales.
Anthony Poole*1, Marc Hoeppner2
1University of Canterbury, New Zealand, 2Uppsala University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Drift may dominate the evolution of fidelity in unicellular eukaryotes with large genomes
Matthew Ackerman*, Samuel Miller, Micheal Lynch
Indiana University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Drug resistance in malaria - Revealing differences in selective pressure on dhps and dhfr mutations in western Kenya based on a new theoretical model
Andrea M. McCollum1, Kristan A. Schneider*2, Ananias A. Escalante3
1Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, USA, 2Department of Mathematics, University of Vienna, Austria, 3Center for Evolutionary Medicine & Informatics, The Biodesign Institute, Arizona State University, USA
:  S1 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Duplicate and conquer: phylogenomics of MADS-box genes meets evo-devo of plants
Guenter Theissen
Friedrich Schiller University, Germany
:  S4 - Genomic basis of Evo-Devo  -  11:30-13:00
Duplicate gene evolution on the Y-chromosome: insights from ampliconic genes of Sulawesi macaques.
Ana-Hermina Ghenu*, Ben Evans
McMaster University, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Duplication dynamics and functional innovation in the Rab family of small GTPases
Yoan Diekmann*, Jose B. Pereira Leal
Instituto Gulbenkian de Ciência, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Duplications in Streamlined Apicomplexan Genomes
Jeremy DeBarry*, Jessica Kissinger
The University of Georgia, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Dynamic transmission, host quality and population structure in a multi-host parasite of bumble bees
Mario X. Ruiz-González*1,2, John Bryden3, Yannick Moret4, Christine Reber-Funk5, Paul Schmid-Hempel5, Mark J. F. Brown1,3
1Department of Zoology, School of Natural Sciences, Trinity College Dublin, Ireland, 2Instituto de Biología Molecular y Celular de Plantas, C.S.I.C. – U.P.V., Spain, 3School of Biological Sciences, Royal Holloway, University of London, UK, 4Université de Bourgogne, UMR CNRS, France, 5ETH Zurich, Institute of Integrative Biology (IBZ), Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Dynamics and adaptive benefits of emergence and modular rearrangements of protein domains
Erich Bornberg-Bauer
Insitute for Evolution and Biodiversity, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
Anna R. Kersting*1, Andrew D Moore1, Sonja Grath1, Alexander A. Myburg2, Erich Bornberg-Bauer1
1Institute of eVolution and Biodiversity, University of Münster, Germany, 2Forest Molecular Genetics Programme, Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  16:00-17:30
Dynamics of intrachromosomal recombination in human Y-chromosome palindrome P6
Pille Hallast*, Georgina Bowden, Patricia Balaresque, Stéphane Ballereau, Mark A Jobling
University of Leicester, Department of Genetics, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Dynamics of Y chromosome evolution in Drosophila affinis
Robert Unckless*, Andrew Clark
Cornell University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Efficient constraint-based metabolic modeling and optimization in R
Gabriel Gelius-Dietrich*, C. Jonathan Fritzemeier, Abdelmoneim Desouki, Martin J. Lercher
Heinrich-Heine-University, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Efficient Cross-Species Capture Hybridization and Next Generation Sequencing of Mitochondrial Genomes from Non-Invasively Sampled Colugo Museum Specimens.
Victor Mason*1,2, Gang Li1, Kristofer Helgen3, William Murphy1,2
1Department of Veterinary Integrative Biosciences, Texas A&M University, USA, 2Interdisciplinary Program of Genetics, Texas A&M University, USA, 3Smithsonian Institution, National Museum of Natural History, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Efficient representation and propagation of posterior alignment uncertainty
Joseph Herman*, Ádám Novák, Rune Lyngsø, Jotun Hein
University of Oxford, UK
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  16:00-17:30
Efficiently and rapidly modeling the non-homogeneity of evolutionary processes
Mathieu Groussin*, Laurent Gueguen, Bastien Boussau, Manolo Gouy
Lyon 1 University - Laboratoire de Biométrie et Biologie Évolutive, France
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  09:30 - 11:00
Elucidating the genetic landscape of cellular morphogenesis in an obligate fungal symbiont
Henrik H. De Fine Licht*, Anders Tunlid
Lund University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Elucidating the history of a rare spruce species endemic to Taiwan using Approximate Bayesian Computation
Sofia Bodare, Michael Stocks*, Martin Lascoux
Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Emergence and global spread of seventh pandemic cholera
Julian Parkhill
The Sanger Institute, UK
Monday 25th June 2012:  S12 - Microbial genome evolution  -  14:30-16:00
Emergence of Mammals by Emergency: Exaptation
Norihiro Okada
Tokyo Inst.Tech,, Japan
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  16:30-18:00
Emergence of multicellular novelty
Chelsea Du Fresne
University of Minnesota- Twin Cities, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Emergence of new cis-regulatory modules in fish and their role in the evolution of innovation after genome duplication
Ingo Braasch*1, Jason Sydes1,2, Angel Amores1, John H. Postlethwait1
1Institute of Neuroscience, University of Oregon, USA, 2Computer and Information Science Department, University of Oregon, USA
:  S4 - Genomic basis of Evo-Devo  -  09:30-11:00
Empirical fitness landscapes and the predictability of evolution
Lilia Perfeito*1,2, Stephan Schiffels1,3, Michael Lässig1
1Institute of Theoretical Physics, University of Cologne Physics, Germany, 2Instituto Gulbenkian de Ciência, Portugal, 3Welcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Ensembl Quality Database
Michal Kabza*, Izabela Makalowska
Adam Mickiewicz University, Poland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Enzyme flux control predicts polymorphism, divergence between species, and fitness in the field
Carrie F. Olson-Manning*, Kasavajhala Prasad, Bao-Hua Song, S. Thomas Mitchell-Olds
Duke University, USA
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  14:30-16:00
Epigenetic inheritance versus mobility in fluctuating environments
Luca Ferretti*1, Michele Cortelezzi2
1CRAG, Spain, 2Universita' di Pisa, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Epistatis and the order of mutations in real and model fitness landscapes
Guillaume Achaz*1, Dan Weinreich2, Yutaka Kobayashi3, Atsushi Yamauchi4, Fumio Tajima0
1Univerité Pierre et Marie Curie, France, 2Brown University, USA, 3Tokyo University, Japan, 4Kyoto University, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Establishment of new mutations in changing environments
Stephan Peischl*1,2, Mark Kirkpatrick2
1University of Bern, Switzerland, 2University of Texas at Austin, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimate of the spontaneous mutation rate by whole genome sequencing of experimental lines in the green alga Chlamydomonas reinhardtii
Rob Ness*, Andrew Morgan, Nick Colegrave, Peter Keightley
University of Edinburgh, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Estimated demographic parameters of modern human migration to the New World by whole mtDNA sequences of non-admixture Mesoamericans
Jun Gojobori*1, Shintaroh Ueda2
1Graduate School for Advanced Studies, Japan, 2The University of Tokyo, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimating a date of mixture of ancestral South Asian populations
Priya Moorjani*1,2, Nick Patterson2, Periasamy Govindaraj3, Danish Saleheen4, John Danesh4, Lalji Singh*3,5, Kumarasamy Thangaraj*3, David Reich*1,2
1Harvard University, USA, 2Broad Institute, USA, 3Centre for Cellular and Molecular Biology, India, 4Dept of Public Health and Care, University of Cambridge, UK, 5Genome Foundation, India
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimating empirical codon mutation models from re‐sequencing data
Carolin Kosiol*, Nicola De Maio
Vetmeduni Vienna, Austria
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  09:30 - 11:00
Estimating gene gain and loss rates in the presence of error in genome assembly and annotation
Matthew Hahn
Indiana University, USA
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  16:00-17:30
Estimating genome-wide fine-scale recombination rates in Drosophila melanogaster
Andrew H. Chan*, Paul A. Jenkins, Yun S. Song
University of California, Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Estimating population mutation parameters from a single shotgun-sequenced diploid Bactrian camel (Camelus bactrianus) genome
Pamela Burger*, Nicola Palmieri
Institute of Populationsgenetics, Vetmeduni Vienna, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Estimating population sizes using the coalescent with recombination
Sara Sheehan*, Kelley Harris, Yun S. Song
UC Berkeley, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimating selection coefficients in structured populations
Iain Mathieson*, Gil McVean
University of Oxford, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimating selection on codon usage in the face of noisy gene expression.
Edward Wallace*1,2, Edo Airoldi2, D. Allan Drummond1
1University of Chicago, USA, 2Harvard University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimating species divergence times with molecular sequence data but without fossils.
Hui-Jie Lee*1, Hirohisa Kishino2, Jeffrey L. Thorne1
1North Carolina State University, USA, 2University of Tokyo, Japan
:  S8 - The animal tree of life and its applications  -  15:00-16:30
Estimating the rate of irreversibility in protein evolution
Onuralp Soylemez*1, Fyodor Kondrashov1,2
1Center for Genomic Regulation, Spain, 2Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Estimating the rate of meiotic gene conversion rate in humans
Amy Williams*1,2, Nick Patterson1,2, Thomas Dyer3, John Blangero3, David Reich1,2
1Harvard Medical School, USA, 2Broad Institute of Harvard and MIT, USA, 3Texas Biomedical Research Institute, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
European Americans who have rare variation in common.
Timothy O'Connor*1, Paul Auer2, Benjamin Logsdon2, Eimear Kenny3, - NHLBI GO Exome Sequencing Project1,4, Josyf Mychaleckyj5, Carlos Bustamante3, Christopher Carlson1,2, Joshua Smith1, Mark Rieder1, Michael Bamshad1, Joshua Akey1
1University of Washington, USA, 2Fred Hutchinson Cancer Research Center, USA, 3Stanford University, USA, 4Broad Institute, USA, 5University of Virginia, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evaluating epistatic models of protein evolution based on comparative genomics data
Daniel Jordan*1,2, Ivan Adzhubey1, Shamil Sunyaev1
1Div of Genet, Dept of Med, Brigham & Women's Hosp and Harvard Med School, USA, 2Program in Biophysics, Harvard University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evaluating the Ortholog Conjecture using the Structure Function Linkage Database
Kimmen Sjolander*1, Patricia Babbitt2
1University of California Berkeley, USA, 2University of California San Francisco, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evidence for birth-and-death evolution of a secondary metabolite biosynthetic gene cluster and its relocation within and between genomes of the filamentous fungus Fusarium
Robert Proctor1, François Van Hove2, Antonia Susca3, Gaetano Stea3, Mark Busman1, Theo van der Lee4, Cees Waalwijk4, Todd Ward*1, Antonio Moretti3
1U.S. Department of Agriculture, USA, 2Université catholique de Louvain, Belgium, 3National Research Council, Italy, 4Plant Research International, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evidence for Network Evolution in an Arabidopsis Interactome Map
Benoit Charloteaux*1,2, Anne-Ruxandra Carvunis2,3, Matija Dreze2,3, Samuel J. Pevzner2,3, Murat Tassan2,5, Mary Galli6, Sabrina Rabello1,7, Gourab Ghoshal1,7, Jean Vandenhaute4, Michel Georges1, Joseph R. Ecker6, Michael E. Cusick2,3, David E. Hill2,3, Frederick P. Roth1,5, Albert-Laszlo Barabasi1,7, Pascal Braun2,3, Marc Vidal2,3
1Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Belgium, 2Center for Cancer Systems Biology, Dana-Farber Cancer Institute, USA, 3Department of Genetics, Harvard Medical School, USA, 4Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, Belgium, 5Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, USA, 6Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, USA, 7Center for Complex Network Research, Northeastern University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evidence for N-Glycan Shielding of Antigenic Sites during Evolution of Human Influenza A Virus Hemagglutinin
Yuki Kobayashi*1,2, Yoshiyuki Suzuki2
1Department of Zoology, UK, 2Nagoya City University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evidence for positive selection on a number of  microRNA regulatory interactions during recent human evolution including regulation of a pigmentation gene
Jingjing Li1, Yu Liu1, Xiaofeng Xin1, TaeHyung Kim1, Eduardo Aguiar Cabeza1, Jie Ren1, Rasmus Nielsen1,2, Jeffrey Wrana1, Zhaolei Zhang*1
1University of Toronto, Canada, 2UC Berkeley, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication
Toni Gabaldón*1, Jaime Huerta-Cepas1, Joaquin Dopazo2, Martijn Huynen3
1Centre for Genomic Regulation (CRG), Spain, 2Centro de Investigación Príncipe Felipe, Spain, 3Centre for Molecular Life Sciences, The Netherlands
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  16:30-18:00
EVIDENCE FOR WIDESPREAD POSITIVE AND PURIFYING SELECTION ACROSS THE EUROPEAN RABBIT (ORYCTOLAGUS CUNICULUS) GENOME
Miguel Carneiro*1,7, Frank Albert5,6, José Melo-Ferreira1, Nicolas Galtier4, Philippe Gayral4, Jose Blanco-Aguiar2, Rafael Villafuerte62, Michael Nachman3, Nuno Ferrand1,7
1CIBIO-UP, Portugal, 2IREC, Spain, 3Department of Ecology and Evolutionary Biology, University of Arizona, USA, 4Institut des Sciences de l'Evolution Université Montpellier 2, France, 5Princeton University, USA, 6Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Germany, 7Departamento de Biologia, Faculdade de Ciências Universidade do Porto, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution and Architecture of the Inner Membrane Complex of the Malaria Parasite
Maya Kono1, Susann Herrmann2, Noeleen Loughran*3, Ana Cabrera2, Klemens Engelberg1, Christine Lehmann1, Dipto Sinha1, Boris Prinz1, Ulrike Ruch1, Volker Heussler1,4, Tobias Spielman1, John Parkinson3, Tim Gilberger1,2
1Bernhard-Nocht-Institute for Tropical Medicine, Germany, 2McMaster Universtiy, Canada, 3Hospital for Sick Children and University of Toronto, Germany, 4University of Bern, Switzerland
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Evolution and Diversification of Small Heat Shock Protein in Plants
Elizabeth Waters*, Bharath Bharadwaj
San Diego State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of antibiotic resistance: The network of trade-offs
Csaba Pal
Biological Research Center, Hungary
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  14:00-15:30
Evolution of Argonaute genes in Drosophila obscura
Samuel Lewis*, Darren Obbard
The University of Edinburgh, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of BCL-2 homologous proteins: a trip to Indels
Abdel AOUACHERIA
CNRS LBMC UMR5239, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of clonal populations approaching a fitness peak.
Isabel Gordo*1, Paulo Campos2
1Instituto Gulbenkian de Ciência, Portugal, 2Universidade Federal Rural de Pernambuco, Brazil
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
EVOLUTION OF COPY NUMBER VARIATION IN THE RHESUS MACAQUE B-DEFENSIN REGION
Barbara Ottolini*, Edward J. Hollox
University of Leicester, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of de novo originated overlapping genes: a molecular tug of war
Niv Sabath*1,2, Andreas Wagner1,2, David Karlin3
1University of Zurich, Switzerland, 2The Swiss Institute of Bioinformatics, Switzerland, 3Oxford University, UK
:  S1 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Evolution of dFOXO binding sites in the Inslulin-like Receptor (InR) gene of Drosophila
Dorcas J. Orengo*, Montserrat Aguadé, Elvira Juan
Dept. Genètica, Univ. Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of dUTPase from Chlorellaviruses and host Chlorella
Hideaki Moriyama
University of Nebraska-Lincoln, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolution of evolvability of the var gene family in malaria
Adam F. Sander1, Thomas Lavstsen1, Thomas S. Rask2, Michael Lisby4, Thomas P. Gilbert3, Ali Salanti1, Sarah L. Fordyce3, Jakob S. Jespersen1, Eske Willerslev3, Richard Carter5, Thor G. Theander1, Anders Gorm Pedersen*2, David E. Arnot1,5
1Centre for Medical Parasitology, University of Copenhagen, Denmark, 2Center for Biological Sequence Analysis, Technical University of Denmark, Denmark, 3Centre for GeoGenetics, University of Copenhagen, Denmark, 4Department of Biology, University of Copenhagen, Denmark, 5Institute of Infection & Immunology Research, University of Edinburgh, UK
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  16:30-18:00
Evolution of gene structure in conifers.
Juliana Sena*1, Isabelle Giguère1, Brian Boyle1, Kermit Ritland2, Jean Bousquet1, John Mackay1
1Institute for Systems and Integrative Biology and Center for Forest Research, Université Laval, Canada, 2Department of Forest Sciences, University of British Columbia, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of microRNA in primates
Jennifer McCreight*, Willie Swanson
University of Washington, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolution of microsatellite DNA in human and chimpanzee genomes
Naoko Takezaki
Kagawa University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
EVOLUTION OF MRNA EXPRESSION AMONG MICE, MEN, FISH AND FLIES
Samuel Loftus, Douglas Crawford*
University of Miami, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of novel traits in the plant metabolic network through gene and genome duplication
Michaël Bekaert4, Corey Hudson1, Patrick Edger2, Emily Puckett2, Chris Pires2,1, Gavin Conant*1,3
1Informatics Institute, University of Missouri, USA, 2Division of Biological Sciences, University of Missouri, USA, 3Division of Animal Sciences, University of Missouri, USA, 4Institute of Aquaculture, University of Stirling, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of olfactory and gustatory receptor repertoires in Drosophila.
Eri Kudo, Mao Nakamura, Atsushi Ogura, Rumi Kondo*
Ochanomizu University, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of orthologous and paralogous genes: expression, function, and fitness effect
Jianzhi Zhang
University of Michigan, USA
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  16:30-18:00
Evolution of physical interactions between the transcription factor protein HoxA11 and the long non-coding RNA molecule Steroid Receptor Activator 1
Kathryn Brayer*, Gunter Wagner
Yale University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolution of Piwi-interacting RNAs in Humans
Sergio Lukic, Kevin Chen*
Rutgers University, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  09:30-11:00
Evolution of prophages in Escherichia and Salmonella
Louis-Marie Bobay*1, Marie Touchon2,3, Eduardo Rocha2,3
1Univ. Pierre et Marie Curie, Cellule Pasteur UPMC, France, 2CNRS, France, 3Institut Pasteur, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
EVOLUTION OF PROTEIN COMPLEXES BETWEEN SPECIES AND THEIR HYBRID
Jean-Baptiste Leducq*, Guillaume Charron, Guillaume Diss, Alexandre Dubé, Christian Landry
PROTEO – Institut de Biologie Intégrative et des Systèmes - Université Laval, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of Regulatory Domains of the Transcrption Factor HoxA-11 in Mammalian Evolution.
Mauris Nnamani*1, Jens Meiler2, Laura Mizoue2, Gunter Wagner1
1Yale Systems Biology Institute, Department of Ecology and Evolutionary Biology, Yale University, USA, 2Center for Structural Biology, Vanderbilt University., USA
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  16:30-18:00
Evolution of the 20-Gb genome of Norway Spruce (Picea abies)
Douglas Scofield*1, The Norway Spruce Genome Project1,2
1Umeå Plant Science Centre, Sweden, 2SciLifeLab, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of the Cas/CRISPR immune locus in Staphylococcus
Jonathan P. Bollback*1, Anne Kupczok1, Flavia G. G. Leite1,2
1IST Austria, Austria, 2Medical University of Vienna, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolution of the cichlid fishes gut microbiota
Laura Baldo*, Walter Salzburger
University of Basel, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolution of the endometrial transcriptome during the origin of pregnancy in mammals
Vincent Lynch*, Gunter Wagner
Yale University, USA
:  S4 - Genomic basis of Evo-Devo  -  09:30-11:00
Evolution of the Kelch domain-containing family of protein phosphatases from plants and alveolate protists
Claudio Slamovits*1, Santiago Mora-García2
1Dalhousie University, Dept. of Biochemistry and Molecular Biology, Canada, 2Instituto de Investigaciones Bioquímicas "Luis F. Leloir", Argentina
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of the Omp85 protein family and implications for outer membrane protein diversity
Eva Heinz*, Trevor Lithgow
Monash University, Australia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of the Rh family genes and the AVPR-OXTR family genes expressing in the kidney
Akinori Suzuki, Hironobu Ikeya, Mari Sugaya, Kaoru Yamashita, Kouhei Endo, Takashi Kitano*
Ibaraki University, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolution of transcription factor binding and gene expression in the genus Drosophila
Mathilde Paris*, Tommy Kaplan, Susan Lott, Jacqueline Villalta, Michael Eisen
University of California Berkeley, France
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  16:00-17:30
Evolutionary analysis and natural selection in betaine homocysteine methyltransferase (BHMT) and BHMT2 genes
Radhika Ganu, Yasuko Ishida, Alfred Roca*, Timothy Garrow, Lawrence Schook
University of Illinois at Urbana-Champaign, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary analysis of innate immune system network in human and mouse marries phenotype and genotype.
Andrew Webb*, Claire Morgan, Thomas Walsh, Mary O’Connell
Dublin City University, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary and functional evidence for positive selection at the human CD5 immune receptor gene
Elena Carnero-Montoro*1, Lizette Bonet2, Johannes Engelken1,3, Mario Martínez-Florensa2, Francisco Lozano2,4, Elena Bosch1
1Institut de Biologia Evolutiva (UPF-CSIC), Spain, 2Institut d’Investigacions Biomèdiques August Pi i Sunyer, Centre Esther Koplowitz, Spain, 3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Germany, 4Servei d’Immunologia, Hospital Clínic, Spain, 5Departament de Biologia Cel·lular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary and functional investigations of genes subject to regulation by genomic imprinting in plant seeds
Peter McKeown*1, Reetu Tuteja1, Martin Braud1, Antoine Fort1, Mary O'Connell2, Mark Donoghue3, Charles Spillane1
1NUI Galway, Ireland, 2Dublin City University, Ireland, 3Cold Spring Harbor Laboratory, USA
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  16:00-17:30
Evolutionary approaches to vaccine design: Influenza A and Chlamydia trachomatis.
Robin Bush
University of California, Irvine, USA
:  S3 - Evolution of host-virus interactions  -  9:30-11:00
Evolutionary causes and consequences of losing key chaperone genes
Tobias Warnecke
Centre for Genomic Regulation, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary consequences of variation in the processing rate of the Arabidopsis thaliana microRNA824
Jinyong Hu1, Filippos Klironomos2, Johannes Berg2, Juliette de Meaux*3
1MPIZ, Germany, 2Institute Theoretical Physics, Germany, 3IEB, Germany
:  S5 - Adaptive vs. non-adaptive evolution  -  09:30-11:00
Evolutionary contrasts of somatic and imprinted X chromosome inactivation
Andrew Clark*, Xu Wang
Cornell University, USA
:  S11 - Sex chromosome evolution illuminated by next-generation sequencing technology  -  17:00-18:30
Evolutionary dynamics of bacteria in a human host environment
Rasmus Lykke Marvig*, Lars Jelsbak, Søren Molin
Technical University of Denmark, Denmark
Monday 25th June 2012:  S12 - Microbial genome evolution  -  14:30-16:00
Evolutionary dynamics of MADS-box transcription factor binding sites in plants
Suzanne de Bruijn*1, Jose M Muino2, Gerco Angenent2, Kerstin Kaufmann1
1Wageningen University, laboratory for molecular biology, The Netherlands, 2Plant Research International, department Bioscience, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary Genomics of Plant Reproductive Isolation
Toni Gossmann*, Karl Schmid
University of Hohenheim, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary Genomics of The Hedgehog Gene Family in Metazoans: Identification of The Desert Hedgehog Gene on Avian Genomes
Joana Pereira*1, Warren E. Johnson2, Stephen J. O’Brien2, Vitor Vasconcelos1,3, Agostinho Antunes1,2
1CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal, 2Laboratory of Genomic Diversity, National Cancer Institute, USA, 3Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary impact of transcription factor binding
Clemens Lakner*, Eric A. Stone, Jeffrey L. Thorne
North Carolina State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolutionary mitogenomics of the phylum Mollusca
Daniela Almeida*1,2, Vítor Vasconcelos1,2, Agostinho Antunes1,2
1CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Portugal, 2FCUP - Faculty of Sciences of University of Porto, Department of Biology, University of Porto, Rua Campo Alegre s/n, 4169-007, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolutionary origin and process, and genetic diversity of goldfish
Tomoyoshi Komiyama, Atsushi Ogura, Kazuho Ikeo, Takashi Gojobori*
National Institute of Genetics, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary pathways of Pseudomonas aeruginosa during long-term infection of CF airways
Trine Markussen*1, Rasmus Lykke Marvig1, Niels Høiby2,3, Helle Krogh Johansen2, Søren Molin1, Lars Jelsbak1
1Department of Systems Biology, Technical University of Denmark, Denmark, 2Department of Clinical Microbiology, University Hospital, Rigshospitalet, Denmark, 3Institute for International Health, Immunology and Microbiology, University of Copenhagen, Denmark
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Evolutionary patterns of regulatory divergence in Drosophila
Joseph Coolon*1, C. Joel McManus2, Kraig Stevenson1, Brenton Graveley3, Patricia Wittkopp1
1University of Michigan, Department of Ecology and Evolutionary Biology, USA, 2Carnegie Mellon University, Department of Biological Sciences, USA, 3University of Connecticut Health Center, Department of Genetics and Developmental Biology, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Evolutionary transitions in fungus-farming ants: A whole-genome sequencing approach
Sanne Nygaard*1, Cai Li2, Morten Schiøtt1, Guojie Zhang1,2, Jun Wang2, Jacobus Boomsma1
1University of Copenhagen, Denmark, 2BGI-Shenzhen, China
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Evolvability and the space of possible metabolisms
Andreas Wagner
University of Zurich, Switzerland
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  14:30-16:00
Evolving on phenotype landscapes
Jose A Cuesta*1, Susanna C Manrubia2
1Universidad Carlos III de Madrid, Spain, 2Centro de Astrobiología (INTA-CSIC), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Examining Putative SNPs Across Parasite Populations:The First Step in an Examination of Migration Across Populations
Christina Jenkins*1,2, Matt Settles1
1University of Idaho, USA, 2Washington State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Exceptional sex: the evolution of meiosis when it breaks the rules
John Logsdon
University of Iowa, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Exome Capture from Saliva Produces High Quality Genomic and Metagenomic Data on South African Genetic Diversity
Brenna Henn*1, Jeff Kidd1,2, Thomas Sharpton3, Meredith Carpenter1, Paul Norman1, Christopher Gignoux3, Marcus Feldman1, Jeff Wall3, Eileen Hoal van Helden4, Carlos Bustamante1
1Stanford University, USA, 2University of Michigan, USA, 3University of California, San Francisco, USA, 4Stellenbosch University, South Africa
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Expanded phylogenetic analysis of the telomere-associated transposable element, HeT-A, in Drosophila.
Jonathan Clark*, Haylie Cox
Weber State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Experimental annotations in 13 model organisms corroborate ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs
Adrian Altenhoff1,2, Romain Studer2,3, Marc Robinson-Rechavi2,3, Christophe Dessimoz*1,4
1ETH Zurich, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland, 3University of Lausanne, Switzerland, 4EMBL-EBI, UK
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  14:30-16:00
Experimental Characterization of Urzymes Supports a Sense/Antisense Origin of Amino Acid Activation by Class I and II Aminoacyl-tRNA Synthetases
Charles Carter*, Li Li, Srinivas Niranj Chandrasekharan, Martha L. Collier
University of North Carolina at Chapel Hill, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Experimental evolution of a viral protease
Thomas Shafee*, Pietro Gatti-Lafranconi, Florian Hollfelder
University of Cambridge, UK
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  16:30-18:00
Exploring genetic interaction as a predictor for non-random association among loci
Ching-Hua Shih*1, Shuwei Li1, Hyun Jung Park2, Luay Nakhleh1,2, Michael Kohn1
1Department of Ecology and Evolutionary Biology, Rice University, USA, 2Department of Computer Science, Rice University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Exploring The Evolution Of Novel Enzyme Functions Within Structurally Defined Protein Superfamilies
Nicholas Furnham*1, Ian Sillitoe2, Gemma Holliday1, Alison Cuff2, Roman Laskowski1, Christine Orengo2, Janet Thornton1
1EMBL-EBI, UK, 2University College London, UK
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  14:30-16:00
Exploring the roles of molecular evolution, expression patterns and function of posterior HoxA and HoxD genes in teleost paired-fin diversity: novel observations from non-model taxa.
Sophie Archambeault*, Karen Crow-Sanchez
San Francisco State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Extensive intron gain in the ancestor of placental mammals
Dusan Kordis
Josef Stefan Institute, Department of Molecular and Biomedical Sciences, Slovenia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Extreme SNP density on the genome of Macoma balthica, a model system for the study of marine hybrid zone dynamics
Eric Pante*1, Audrey Rohfritsch1, Vanessa Becquet1, Nicolas Bierne2, Pascale Garcia1
1Laboratoire LIENSs, UMR7266 CNRS, Université de La Rochelle, France, 2CNRS, Institut des Sciences de l'Evolution, UMR5554, Station Méditérranéenne de l'Environnement Littoral, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Extreme (X)-QTL Mapping Seed and Seedling Traits in Arabidopsis thaliana
Wei Yuan*, Michael Purugganan
New York University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Facultative exons are enriched for adaptively evolving codons, but much of the pattern is driven by alignment errors
Ryan McGee, Matthew Dean*
Molecular and Computational Biology, University of Southern California, USA
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  14:00-15:30
Fast computation of minimum hybridization networks
Celine Scornavacca*1, Benjamin Albrecht4, Alberto Cenci3, Daniel H. Huson2
1CNRS, ISEM, France, 2ZBIT, Tübingen University, Germany, 3IRD, France, 4LMU, Germany
:  S9 - The network of life: algorithmic and modelling challenges  -  17:00-18:30
Faster-X evolution of gene expression in Drosophila
Richard Meisel*1, John Malone2, Andrew Clark1
1Cornell University, USA, 2Florida State University, USA
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  14:00-15:30
Filtering multiple sequence alignments to avoid artifacts in downstream analyses
Eyal Privman*1,2, Osnat Penn3, Haim Ashkenazy3, Tal Pupko3
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland, 3Tel Aviv University, Israel
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  16:00-17:30
Fine-scale mapping complex signatures of positive selection in the human genome
Leslie Emery*, Joshua Akey
University of Washington Department of Genome Sciences, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Fitting structured models of substitutions and indels(invited talk, symposium: "Estimating and simulating models of molecular evolution")
Ian Holmes
University of California, USA
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  11:30-13:00
Formation of reproductive barriers in a hybrid zone of American and Caribbean Drosophila melanogaster
Joyce Kao*, Sergey Nuzhdin
University of Southern California, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Frequency and genomic distribution of genes with sex-biased expression in the dioecious plant Silene latifolia
Niklaus Zemp*1, Gabriel Marais2, Alex Widmer1
1ETH Zurich, Switzerland, 2University of Lyon, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Frequent and biochemically conservative amino-acid changes have the most moderate impact on codon bias.
Richard Cousins*1,2, Dawn Field2, Laurence Hurst1, Edward Feil1
1University of Bath, UK, 2Centre for Ecology and Hydrology, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Frequent subcellular relocalization after gene duplication during the evolution of the Brassicaceae family
Shao-Lun Liu, Angel Pan, Keith Adams*
University of British Columbia, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
From Gene Trees to the Species Tree in the Adaptive Radiation of Cichlid Fishes from Lake Tanganyika, East Africa
Britta S. Meyer*, Walter Salzburger
University of Basel, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
From Genome to Population Dynamics; the Glanville fritillary butterfly (Melitaea cinxia) as a model system
Rainer Lehtonen*1, Panu Somervuo0,1, Lars Paulin0,1, Leena Salmela0,1, Virpi Ahola0,1, Patrik Koskinen0,1, Minna Taipale0,2, Anne Duplouy0,1, Pasi Rastas0,1, Jouni Kvist0,1, Swee Wong0,1, Niko Välimäki0,2, Jussi Nokso-koivisto0,1, Veli Mäkinen0,1, Mikko Frilander0,1, Jussi Taipale0,2, Esko Ukkonen0,1, Liisa Holm0,1, Petri Auvinen0,1, Ilkka Hanski0,1
1University of helsinki, Finland, 2Karolinska Instututet, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
From trajectories to averages: an improved description of the heterogeneity of substitution rates along lineages
Stephane Guindon1,2
1University of Auckland, New Zealand, 2LIRMM, France
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  09:30 - 11:00
Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of Archeasplastida and Chromalveolata. Gene duplication, endosymbiositic gene transfer, and two independent transitions to Calvin cycle function
Daniel Gaston*, Edward Susko, Andrew Roger
Dalhousie University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Functional evidence that a newly evolved Drosophila sperm-specific gene boots sperm competition
Shu-Dan Yeh1, Tiffanie Do1, Carolus Chan1, Adriana Cordova1, Francisco Carranza1, Eugene Yamamoto1, Mashya Abbassi1, Kania Gandasetiawan1, Pablo Librado2, Elisabetta Damia3, Patrizio Dimitri3, Julio Rozas2, Daniel Hartl4, John Roote5, Jose Ranz*1
1University of California, USA, 2Universitat de Barcelona, Spain, 3Sapienza Università di Roma, Italy, 4Harvard University, USA, 5University of Cambridge, UK
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  14:00-15:30
Functional evolution of an anthocyanin pathway enzyme during a flower color transition
Stacey Smith*1,2, Shunqi Wang2,3, Mark Rausher2
1University of Nebraska, USA, 2Duke University, USA, 3Nanchang Univeresity, China
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Functional evolution of nociceptive receptors TRPA1 and TRPV1 in vertebrates
Shigeru Saito*1, Kazumasa Nakatsuka2, Masashi Ohkita2, Kenji Takahashi2, Naomi Fukuta1, Toshio Ohta2, Makoto Tominaga1,3
1Okazaki Institute for Integrative Bioscience (National Institute for Physiological Sciences), Japan, 2Tottori University, Japan, 3The Graduate University for Advanced studies, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Functional implications of a polymorphism in a primate-specific microRNA
Maria Lopez-Valenzuela*1, Oscar Ramírez1, Ignasi Torruella-Loran1, Antonio Rosas2, Samuel García-Vargas2, Marco de la Rasilla3, Carles Lalueza-Fox1, Yolanda Espinosa-Parrilla1
1Institut de Biologia Evolutiva (UPF-CSIC), Spain, 2Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales (CSIC), Spain, 3Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Functional retrogenes - identification and analysis.
Joanna Ciomborowska*, Michal Kabza, Kamil Sambor, Izabela Makalowska
Adam Mickiewicz University, Faculty of Biology, Laboratory of Bioinformatics, Poland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Functional, transcriptional and sequence evolution asymmetry between paralogs and between orthologs in 12 Drosophila genomes
Lev Yampolsky*1, Michael Bouzinier2
1East Tennessee State University, USA, 2InterSystems Corp., USA
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  16:30-18:00
Fundamentals of Molecular Evolution Revisited
Consortium of Wen-Hsiung's Research Phylogeny*, Soojin Yi
Georgia Institute of Technology, USA
:  S7 - Evolutionary genomics: A new synthesis of evolutionary biology (In honor of W-H Li's 70th birthday)  -  15:00-16:30
GC bias in recombining loci of bacteria and archaea: Evidence that biased gene conversion is universal
Christopher Graves*1,2, Dustin Brisson2
1Brown University, USA, 2University of Pennsylvania, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Gene conversion and evolution of sex chromosomes: an NGS approach.
Chiara Batini*, Daniel Zadik, Pille Hallast, Gurdeep Lall, Mark Jobling
University of Leicester, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Gene conversion and evolution of sex chromosomes: an NGS approach.
Chiara Batini, Daniel Zadik*, Pille Hallast, Gurdeep Lall, Mark Jobling
uni of leicester, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Gene conversion as both a boost and drag on diversity in a gene family across genetically divergent populations of the copepod Tigriopus californicus
Christopher Willett
University of North Carolina, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Gene duplicability in the primate protein-protein interaction network
Aoife Doherty*, David Alvarez-Ponce, James McInerney
National University of Ireland, Maynooth, Ireland
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Gene expression analysis in neural tissues of the Chordate, Ciona intestinalis by the use of a customized microarray
Hiromi Matsumae*1, Mayuko Hamada2, Manabu Fujie2, Hiroshi Tanaka1, Yoshihito Niimura1, Takeshi Kawashima2
1Department of Bioinformatics, Tokyo Medical and Dental University, Japan, 2Marine Genomics Unit and Genome Sequencing Center, Okinawa Institute of Science and Technology Graduate University, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Gene expression patterns in two closely related crow taxa from a common garden RNA-seq experiment.
Jelmer Poelstra*1, Nagarjun Vijay1, Vittorio Baglione3, Inge Müller2, Martin Wikelski2, Jochen Wolf1
1Uppsala University, Sweden, 2Max Planck Institute for Ornithology, Germany, 3University of Valladolid , Spain, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Gene expression, copy number variants and selective sweeps in wild mice
Jarosław Bryk*, Diethard Tautz
Max Planck Institute for Evolutionary Biology, Germany
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  16:30-18:00
Gene flow between human populations during the exodus from Africa, and the timeline of recent human evolution
Aylwyn Scally*, Richard Durbin
Wellcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Gene function prediction in plant genomes from large scale phylogenomics analyses
Mathieu Rouard*1, Jean-François Dufayard2, Valentin Guignon1, Mathieu Conte4, Anne-Muriel Arigon3, Vincent Berry3
1Bioversity International, Commodities for Livelihood Programme, France, 2Cirad, Department BIOS, UMR DAP, France, 3MAB, LIRMM, CNRS, Université Montpellier, France, 4SYNGENTA Seeds SAS, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Gene loss promotes functional complexity in bacteria
Yogeshwar Kelkar*, Howard Ochman
Yale University, USA
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  14:00-15:30
Gene numbers are underestimated in bacterial genomes
Klaus Neuhaus*1, Katharina Mir3, Svenja Simon2, Richard Landstorfer1, Steffen Schober3, Martin Bossert3, Daniel Keim2, Siegfried Scherer1
1Chair for Microbial Ecology, Department for Biosciences, Technische Universität München, Germany, 2Department for Informatics, Universität Konstanz, Germany, 3Institute of Communications Engineering, Universität Ulm, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Gene transpositions in the primate genomes
Mira Han
NESCent, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genes important to C4 evolution identified by comparative genomics
Janina Maß*1, Alisandra Denton2, Martin J. Lercher1
1Institute for Computer Science, Heinrich-Heine-University Duesseldorf, Germany, 2Institute for Plant Biochemistry, Heinrich-Heine-University Duesseldorf, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genes, genomes and efficacy in discerning dimensionalities of the tree of life
Khidir Hilu*, Sunny Crawley
Virginia Tech, USA
:  S6 - Gene/genome data and the limits to  -  17:00-18:30
GENETIC ARCHITECTURE AND EVOLUTION OF HUMAN SKIN AND EYE PIGMENTATION: GENOME-WIDE ASSOCIATION STUDY IN THE ADMIXED POPULATION OF CAPE VERDE
Sandra Beleza*1,2, Nick Jonhson1, Sophie Candille1, Isabel Inês Araújo3, António Correia e Silva3, Mark Shriver4, Jorge Rocha5,6, Greg Barsh1,7, Hua Tang1
1Genetics Department, Stanford University, USA, 2Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal, 3Universidade de Cabo Verde (UNI-CV), Cape Verde, 4Department of Anthropology, Penn State University, USA, 5Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Portugal, 6Departamento de Zoologia e Antropologia, Faculdade de Ciências, Universidade do Porto, Portugal, 7HudsonAlpha Institute for Biotecnhology, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic Differentiation and Local Adaptation of an Ecologically Dominant Prairie Grass Andropogon gerardii (Big Bluestem) Occurring Along a Natural Precipitation Gradient in Midwest US Grasslands
Loretta Johnson*1, Miranda Gray1, Paul St Amand2, Eduard Akhunov1, Karen Garrett1, Mary Knapp1, Ted Morgan1, Bai Guihua2, Sara Baer4, Brian Maricle3, Hannah Tetreault1
1Kansas State University, USA, 2United States Department of Agriculture Agricultural Research Service, Hard Winter Wheat Genetics Research Unit,, USA, 3Fort Hays State University, USA, 4Southern Illinois University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic diversity of the dinoflagellates (Alveolata: Dinophyceae) from the ancient lake Baikal
Natalia Annenkova1,2
1Limnological Institute, Siberian Division of Russian Academy of Science, Russia, 2Lund University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genetic evidence of two major prehistoric migrations of modern humans into the Tibetan plateau
Xuebin Qi1, Chaoying Cui2, Yi Peng1,5, Xiaoming Zhang1,5, Zhaohui Yang1,5, Hui Zhang1, Kun Xiang1,5, xiangyu Cao1,5, Yi Wang1,5, Ouzhuluobu .2, Basang .3, Ciwangsangbu .3, Bianba .2, Gonggalanzi .2, Tianyi Wu4, Hua Chen6, Hong Shi1, Bing Su*1
1State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, China, 2School of Medicine, Tibetan University, China, 3People’s Hospital of Dangxiong County, China, 4National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, China, 5Graduate School of Chinese Academy Sciences, China, 6Department of Epidemiology, Harvard School of Public Health, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic response of Daphnia pulicaria to historic pH changes in lakes
Billy Culver*1,2, Philip Morton2, Dagmar Frisch2, Lawrence Weider1,2
1University of Oklahoma, USA, 2University of Oklahoma Biological Station, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic specificity in an insect virus interaction
Lena Wilfert*3,1, Mike Magwire2, Frank Jiggins3
1Institute of Evolutionary Biology, University of Edinburgh, UK, 2Department of Genetics, North Carolina State University, USA, 3Department of Genetics, University of Cambridge, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genetic structure in North African human populations and the gene flow to Southern Europe
Laura R Botigué1, Brenna M Henn2, Simon Gravel2, Jaume Bertranpetit1, Carlos D Bustamante2, David Comas*1
1Institut de Biologia Evolutiva (IBE, CSIC-UPF), Spain, 2Stanford University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic structure of spatially overlapping contact zones of two Iberian amphibians: a comparative approach
Helena Gonçalves1, Jesús Díaz-Rodríguez1,2, Alexandre Silva-Ferreira1,3, Tiago S. Neves1, Miguel Tejedo2, Iñigo Martínez-Solano4, Fernando Sequeira*1
1CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Portugal, 2Departamento de Ecología Evolutiva, Estación Biológica de Doñana-CSIC, Spain, 3Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Portugal, 4Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic variability of Calvin cycle genes in accessions of Arabidopsis thaliana
Madlen Stange*, Sandra Schwarte, Fanny Wegner, Ralph Tiedemann
University of Potsdam, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic variance-control in genome-wide network expression analyses.
Ronald Nelson*1, Xidan Li1, Xia Shen2, Örjan Carlborg1
1Swedish University of Agricultural Sciences, Sweden, 2Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic variants count for gene expression variability in human lymphoblastoid cells
James Cai
Texas A&M University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic variation in Drosophila subobscura: a multilocus analysis along chromosome J
Roser Pratdesaba*, Carmen Segarra, Montserrat Aguadé
Universitat de Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetic variation of Symbiodinium spp. of the coral host Agaricia lamarcki between shallow and mesophotic habitats
Ramon Rivera Vicens
University of Puerto Rico, Puerto Rico
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetics of malaria susceptibility across three African populations: Kenya, Malawi and Gambia.
Chris Spencer
Wellcome Trust Centre for Human Genetics, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genetics of transcriptome-wide responses to ocean acidification in sea urchins
Daniel Runcie*1, David Garfield2, Narimane Dorey3, Sam Dupont3, Gregory Wray1
1Duke University, USA, 2EMBL, Germany, 3University of Gothenburg, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome evolution of cells with two nuclei: double peaks reveal rare sex in the protist group diplomonads
Jan O. Andersson
Department of Cell and Molecular Biology, Uppsala University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment
Minako Izutsu*1,2, Yuzo Sugiyama1, Osamu Nishimura1, Kiyokazu Agata1,2, Naoyuki Fuse1
1Laboratory for Biodiversity, Global COE Program, Japan, 2Laboratory for Molecular Developmental Biology,Kyoto University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome histories reveal adaptive cladogenesis in A. tumefaciens
Florent Lassalle*1,2, Xavier Nesme2, Vincent Daubin1
1Laboratoire de Biométrie et Biologie Evolutive, France, 2Laboratoire d'Ecologie Microbienne, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome Sequence of the Cyanobacterium Scytonema hofmanni PCC 7110: The Largest Prokaryotic Proteome Sequenced to Date.
Robin Koch*1, Karina Stucken1, Rosmarie Rippka2, Nicole Tandeau de Marsac2,3, Muriel Gugger4, Tal Dagan1, William F Martin1
1Institute of Molecular Evolution, Heinrich-Heine University, Germany, 2Unité des Cyanobactéries, Institut Pasteur, CNRS URA 2172, France, 3Aix-Marseille Univ, LCB, CNRS UPR 9043, France, 4Institut Pasteur, Laboratoire Collection des Cyanobactéries, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome sequencing of rifampicin-resistant Mycobacterium tuberculosis reveals compensatory mutations in the RNA polymerase
Iñaki Comas*1,2, Sonia Borrell3,4, Andreas Roetzer8, Graham Rose2, Bijaya Malla3, Midori Kato-Maeda5, James Galagan6,7, Stefan Niemann8, Sebastien Gagneux3,4
1Center for Public Health Research (CSISP), Spain, 2National Institute for Medical Research, UK, 3Swiss Tropical and Public Health Institute, Switzerland, 4University of Basel, Switzerland, 5San Francisco General Hospital- Univeristy of California San Francisco, USA, 6The Broad Insitute of MIT and Harvard University, USA, 7Boston University, USA, 8Research Center Bosrtel, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomes of saprophytic Thraustotheca clavata and parasitic Achlya hypogyna shed light on the pathogenicity of oomycetes
Ian Misner*1, Cedric Bicep3, Eric Bapteste3, Sebastien Halary4, Philippe Lopez3, J Craig Bailey2, Christopher Lane1
1University of Rhode Island, USA, 2University of North Carolina at Wilmington, USA, 3Universite Pierre et Marie Curie, France, 4Universite de Montreal, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-scale analyses of non-bilaterian metazoans clarify opsin evolution and the origin of vision in animals
Roberto Feuda*, Sinead Hamilton, James O. McInerney, Davide Pisani
N.U.I Maynooth, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-scale simultaneous inference of species and gene trees
Bastien Boussau*1,2, Gergely Szollosi1, Laurent Duret1, Manolo Gouy1, Eric Tannier3, Vincent Daubin1
1LBBE, CNRS, Université Lyon 1, France, 2UC Berkeley, USA, 3LBBE, INRIA, Université de Lyon, France
:  S1 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Genome-wide analyses of recombination suggest that Giardia intestinalis assemblages represent different species
Feifei Xu*, Jon Jerlström-Hultqvist, Jan O. Andersson
Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide analysis of cis-regulatory divergence between species in the Arabidopsis genus
Fei He1, Juliette de Meaux*1, Justin Borevitz2
1University of Münster, Germany, 2University of Chicago, USA
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  16:00-17:30
Genome-wide association mapping in Campylobacter: genetic signals of host adaptation.
Samuel Sheppard*1,2, Xavier Didelot2, Daniel Falush3
1Swansea University, UK, 2Oxford University, UK, 3Max Planck Institute for Evolutionary Anthropology, Germany
Monday 25th June 2012:  S12 - Microbial genome evolution  -  14:30-16:00
Genome-wide association mapping of fertility traits in a natural house mouse hybrid zone
Bettina Harr*1, Leslie Turner2
1Max-Planck-Institut fuer Evolutionsbiologie, Germany, 2University of Wisconsin, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomewide association study for melanoma susceptibility
Susanne Horn
German Cancer Research Center, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-wide copy number variation in African Pygmy hunter-gatherers and Bantu-speaking farmers.
Eddie Loh*1, Etienne Patin1, Katie Siddle1, Hélène Quach1, Christine Harmant1, Noémie Becker2, Béatrice Régnault3, Laure Lemée3, Jean-Marie Hombert4, Alain Froment2, Paul Verdu5, Luis Barreiro6, Nathaniel J. Dominy7, George Perry8, Evelyne Heyer2, Lluís Quintana-Murci1
1Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, France, 2Ecoanthropology and Ethnobiology, CNRS/MNHN/Université P7 UMR 5145, France, 3Genotyping Platform, Institut Pasteur, France, 4Département de Dynamique du Langage, CNRS UMR 5596, Université Lumière-Lyon 2, France, 5Department of Biology, Stanford University, USA, 6Université de Montréal, Centre de recherche CHU Sainte-Justine, Canada, 7Anthropology department, Dartmouth College, USA, 8Department of Human Genetics, University of Chicago, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-Wide Data Reveals the History and Structure of Mexican Populations
Christopher Gignoux*1, Andres Moreno2, Fouad Zakharia2, Juan Carlos Fernández López3, Simon Gravel2, Patricia Ortiz-Tello2, Eimear Kenny2, Karla Sandoval2, Martin Sikora2, Alejandra Contreras3, Victoria Robles3, Sandra Romero Hidalgo3, Rodrigo García Herrera3, Alessandra Carnevale3, Hector Rangel-Villalobos4, Victor Acuña-Alonzo5, Samuel Cañizales-Quinteros6, Irma Silva-Zolezzi3, Esteban González Burchard1, Carlos Bustamante2
1UCSF, USA, 2Stanford University, USA, 3National Institute of Genomic Medicine, Mexico, 4Universidad de Guadalajara, Mexico, 5Escuela Nacional de Antropología e Historia, Mexico, 6Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-wide effects of sex-specific hybrid incompatibility on neutral introgression
Marcy Uyenoyama*, Seiji Kumagai, Liuyang Wang
Duke University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-wide evidence for faster-X adaptive protein evolution in mice
Athanasios Kousathanas*1, Dan Halligan1, Rob Ness1, Thomas Keane2, Dave Adams2, Bettina Harr3, Peter Keightley1
1University of Edinburgh, UK, 2Wellcome Trust Sanger Institute, UK, 3Max Planck Institute for Evolutionary Biology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide genetic architecture of morphological traits in yeast
Wei-Chin Ho*, Jianzhi Zhang
University of Michigan, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genome-wide insights into the evolution of regulatory elements in diverse yeast strains
Caitlin Connelly*, Joshua Akey
University of Washington, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide mutation spectrum and rate of Bacillus subtilis
Way Sung*, Emily Williams, Michael Lynch
Indiana Univeristy, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide mutational dynamics in Saccharomyces cerevisiae lead to complex patterns of selection and coadaptation
Mario Fares*2,1, Orla Keane4, Lorenzo Carretero-Paulet1, Gary Jones3
1Consejo Superior de Investigaciones Cientificas, Spain, 2University of Dublin, Trinity College, Ireland, 3National UNiversity of Ireland Maynooth, Ireland, 4Animal & Bioscience Department, Teagasc, Ireland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide patterns of codon usage bias in sequenced flatworms
Heidi Aisala*, Tiina M. Mattila, Jaakko Lumme
Department of Biology, University of Oulu, Finland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide patterns of natural variation reveal ongoing genomic conflict in Drosophila mauritiana
Viola Nolte, Ram Vinay Pandey, Robert Kofler, Christian Schlötterer*
Vetmeduni, Austria
Monday 25th June 2012:  S16.1 - Adaptive Evolution and Selective Sweeps  -  09:30-11:00
Genome-wide quantification of bacterial mutational-biases 
Ruth Hershberg
Technion - Israel Institute of Technology, Israel
Monday 25th June 2012:  S12 - Microbial genome evolution  -  11:30-13:00
Genome-wide survey of homologous recombination and diversifying selection in an extremely sexual bacterial species
Koji Yahara*1, Mikihiko Kawai2, Yoshikazu Furuta1, Noriko Takahashi1, Naofumi Handa1, Takeshi Tsuru1, Kenshiro Oshima1, Masaru Yoshida3, Takeshi Azuma3, Masahira Hattori1, Ikuo Uchiyama2, Ichizo Kobayashi1
1University of Tokyo, Japan, 2National Institute for Basic Biology, Japan, 3Kobe University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genome-wide usage of accurately translated codons tracks a tRNA modification across the Drosophila phylogeny
John Zaborske1, Vanessa Bauer DuMont2, Tao Pan1, Charles Aquadro2, D. Allan Drummond*1
1University of Chicago, USA, 2Cornell University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genomewide variation in natural populations of Neurospora tetrasperma
Padraic Corcoran*1, Fen Chen2, Martin Lascoux1, Peixiang Ni2, Hanna Johanesson1
1Uppsala University, Sweden, 2BGI, Hong Kong
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomic diversity of Staphylococcus aureus in singly-colonized nasal carriers and the implications for detecting recent transmission
Elizabeth Batty*1, Tanya Golubchik1, Ruth Miller2, Helen Farr2, Hanna Larner3, Rowena Fung2, Heather Godwin2, Daniel Wilson2,3, Derrick Crook2, Rory Bowden1,2
1Department of Statistics, University of Oxford, UK, 2NIHR Oxford Biomedical Research Centre, UK, 3Wellcome Trust Centre for Human Genetics, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomic insights into the evolution of the economically important monogenean flatworm Gyrodactylus salaris
Christoph Hahn*, Philip D. Harris, Bastian Fromm, Tor A. Bakke, Lutz Bachmann
Natural History Museum, University of Oslo, Norway
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomic Modification in Bdelloid Rotifers Following Full-Body Desiccation and DNA Repair
Norian Caporale-Berkowitz*1, Bette Hecox-Lea2,3, David Mark Welch1,2
1Brown University, USA, 2Marine Biological Laboratory, USA, 3Northeastern University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genomic response to drastic environmental change
Thomas Cuypers*, Paulien Hogeweg
Utrecht University, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genomic satellite DNA repeats and small RNAs: bioinformatic, molecular and cytological evidence for the expression of Responder rasiRNAs in the Drosophila melanogaster testis.
Amanda Larracuente*, Daven Presgraves
University of Rochester, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  11:30-13:00
Genomic Sequencing of Patella vulgata: a Further Window into Mollusc and Lophotrochozoan Evolution
Nathan Kenny*, Jerome Hui, Sebastian Shimeld
Department of Zoology, University of Oxford, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population
Hsiao-Han Chang*1, Daniel Park1,2, Kevin Galinsky2, Stephen Schaffner2, Daouda Ndiaye3, Omar Ndir3, Soulyemane Mboup3, Roger Wiegand2, Sarah Volkman2,4, Pardis Sabeti1,2, Dyann Wirth2,4, Daniel Neafsey2, Daniel Hartl1
1Department of Organismic and Evolutionary Biology, Harvard University, USA, 2Broad Institute, USA, 3Cheikh Anta Diop University, Senegal, 4Department of Immunology and Infectious Diseases, Harvard School of Public Health, USA
Monday 25th June 2012:  S12 - Microbial genome evolution  -  09:30 - 11:00
Genomic sources of regulatory variation: mutation, polymorphism, and divergence
Patricia Wittkopp*1, Joseph Coolon1, Jonathan Gruber1, Kraig Stevenson1, David Yuan1, Brian Metzger1, Joel McManus2, Brenton Graveley2, Kara Vogel1, Gizem Kalay1
1University of Michigan, USA, 2University of Connecticut, USA
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  14:00-15:30
Genomic structure and evolution of multigene families: "Flowers" on the human genome
Hie Lim Kim*1,4, Mineyo Iwase1, Satoko Kaneko2, Yukako Katsura1, Takeshi Igawa3, Tasuku Nishioka1, Naoyuki Takahata1, Yoko Satta1
1The Graduate University for Advanced Studies (Sokendai), Japan, 2Kyoto University, Japan, 3Hiroshima University, Japan, 4Pennsylvania State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genomic structures and gene evolution on mammalian X chromosomes
Yukako Katsura*, Yoko Satta
The Graduate University for Advanced Studies(SOKENDAI), Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomics and physiology to investigate the lipid metabolism of 9 oleaginous yeasts
Stéphanie Michely*1, Claude Gaillardin2, Jean-Marc Nicaud3, Cécile Neuvéglise1
1INRA, UMR 1319 Micalis, France, 2AgroParisTech, Micalis, France, 3CNRS, Micalis, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genomics of adaptation in Arabidopsis lyrata
Tiina Mattila*, Tuomas Toivainen, Outi Savolainen
University of Oulu, Finland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Genomics of Oil Exposure
Marjorie Oleksiak*, Douglas Crawford
University of Miami, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Genotyping Candidate Loci for Colorectal Cancer: A Pointer to Ancestral Susceptibility.
Stefanie Huhn*1, Melanie Bevier1, Barbara Pardini2, Alessio Naccarati2, Ludmila Vodickova2,3, Jan Novotny4, Pavel Vodicka2,3, Kari Hemminki1,5, Asta Försti1,5
1Department of Molecular Genetic Epidemiology, German Cancer Research Center Heidelberg, Germany, 2Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Czech Republic, 3Institute of Biology and Medical Genetics, 1st Faculty of Medicine, Charles University, Czech Republic, 4Department of Oncology, General Teaching Hospital, U Nemocnice 2, Czech Republic, 5Center of Primary Health Care Research at the Clinical Research Center, Lund University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
'Genus wide sequence informed design of an evolutionary informative bacterial MLST scheme'
Miquette Hall*1, Sandra Reuter2, Thomas Connor2, Nick Thomson2, Alan McNally1
1Nottingham Trent University, UK, 2Wellcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Global characterization of polymorphic inversions in the human genome
Mario Cáceres*1,2, Alexander Martínez-Fundichely2, Cristina Aguado2, David Vicente2, Meritxell Oliva2, David Izquierdo2, Sergi Villatoro2, Marta Puig2, José Ignacio Lucas-Lledó2, Xavier Estivill3, Juan R. González4, Sònia Casillas2
1Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain, 2Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain, 3Center for Genomic Regulation (CRG-UPF), Spain, 4Center for Research in Environmental Epidemiology (CREAL), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Global Diversity of the smallest planktonic green alga (Mamiellophyceae) and their giant prasinoviruses from marine metagenomes
Eve Toulza*, Nigel Grimsley, Gwenael Piganeau
Observatoire Océanologique, UPMC Univ Paris 06, UMR 7232, BIOM, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Goodness of fit tests and outlier identification in phylogenetics
Steffen Klaere
Department of Statistics, University of Auckland, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Goods-thinking versus Tree-thinking
James McInerney
National University of Ireland Maynooth, Ireland
Monday 25th June 2012:  S21 - Paradigm shifting in phylogeny  -  16:30-18:00
Green and red algal phylogenetic signals in nuclear genes shared by eukaryotes bearing secondary plastids of green algal origin: looking beyond endosymbiotic versus lateral gene transfer
Shinichiro Maruyama*, John Archibald
Dalhousie University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Harnessing Non-Local Evolutionary Events for Tree Inference
Liangliang Wang*, Alexandre Bouchard-Côté
University of British Columbia, Canada
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  11:30-13:00
Heterozygote advantage as a natural consequence of adaptation in diploids
Diamantis Sellis*1, Benjamin Callahan2, Dmitri Petrov1, Philipp Messer1
1Department of Biology, Stanford University, USA, 2Department of Applied Physics, Stanford University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Hierarchical modularity and the evolution of genetic interactomes across species
Colm Ryan*1,2, Assen Roguev1, Kristin Patrick1, Jiewei Xu1, Harlizawati Jahari1, Nevan J. Krogan1
1University of California, San Francisco, USA, 2University College Dublin, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
High prevalence of positive selection in rodent gene duplicates evolving both symmetrically and asymmetrically
Cinta Pegueroles*1, M. Mar Albà1,2
1Evolutionary Genomics Group, Fundació Institut Municipal d’Investigació Mèdica (FIMIM)-Universitat Pompeu Fabra (UPF), Spain, 2Catalan Institution for Research and Advanced Studies (ICREA), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
High rates of retrogene formation in the giant nuclear genomes of dinoflagellates.
Renny Lee*, Claudio Slamovits
Dalhousie University, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
High resolution association mapping in an outbred Drosophila melanogaster population using Pool-Sequencing
Héloïse Bastide, Viola Nolte, Martina Visnovska, Ray Tobler, Andrea Betancourt, Christian Schlötterer*
Vetmeduni, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
High variation of mitochondrial gene order in basidiomycetes
Gabriela Aguileta*1, Elsa Petit2, Tatiana Giraud3, Toni Gabaldon1, Michael Hood2
1Centre for Genomic Regulation (CRG), Spain, 2Department of Biology, Amherst College, USA, 3Ecologie, Systematique et Evolution, Universite Paris Sud, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
High-coverage population genomics of diverse African hunter-gatherers
Joseph Lachance*1, Benjamin Vernot2, Clara Elbers1, Bart Ferwerda1, Alain Froment3, Jean-Marie Bodo4, Godfrey Lema5, Thomas Nyambo5, Timothy Rebbeck1, Kun Zhang6, Joshua Akey2, Sarah Tishkoff1
1University of Pennsylvania, USA, 2University of Washington, USA, 3IRD-MNHN, Musée de l'Homme, France, 4Ministère de la Recherche Scientifique et de l’Innovation, Cameroon, 5Muhimbili University College of Health Sciences, Tanzania, 6University of California at San Diego, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
High-throughput sequencing to identify lineage-specific transcriptomes of M. tuberculosis and the contribution of background genetic diversity
Graham Rose*1, Iñaki Comas1, Douglas Young1, Sebastien Gagneux1
1MRC National Institute for Medical Research, UK, 2Swiss Tropical and Public Health Institute, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Hitch-hiking in spatially extended populations
Nick Barton*1, Jerome Kelleher2, Amandine Véber4, Alison Etheridge3
1IST Austria, Austria, 2IEB, University of Edinburgh, UK, 3Oxford University, UK, 4Ecole Polytechnique, France
Monday 25th June 2012:  S16.1 - Adaptive Evolution and Selective Sweeps  -  09:30-11:00
Homology Network Articulation Points Reveal Rosetta Stone Proteins
Leanne Haggerty*, James McInerney
NUI Maynooth, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Horizontal gene transfer and gene conversion as a novel mechanism of intron loss
Nancy Hepburn, Derek Schmidt, Jeff Mower*
University of Nebraska-Lincoln, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Horizontal Gene Transfer (HGT), Homeoalleles, NISEs, and the Formation and Maintenance of Higher Taxonomic Units in Bacteria and Archaea
J. Peter Gogarten*1, Cheryl P. Andam1,2, David Williams1, Erica Lasek-Nesselquist1, Seila Omer1
1University of Connecticut, USA, 2Cornell University, USA
:  S6 - Gene/genome data and the limits to  -  17:00-18:30
Horse domestication: a computer simulation approach
Michela Leonardi*1, Christine Weber1, Norbert Benecke2, Mark G. Thomas3,4, Joachim Burger1
1AG Palaeogenetik, Institute of Anthropology, SBII, Johannes Gutenberg University, Colonel Kleinmann-Weg 2, 55128, Germany, 2German Archaeological Institute, Im Dol 4-6, 14165, Germany, 3Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, UK, 4Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-752 36, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
How do hosts shape their microbial communities?
Matthew Horton*, Natacha Bodenhausen, Joy Bergelson
University of Chicago, USA
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
How ecological factors influence population phylogenomics?
Philippe Gayral*1, Vincent Cahais2, Georgia Tsagkogeorga3, José Melo-Ferreira4, Marion Ballenghien2, Lucy Weinert5, Ylenia Chiari4, Khakid Belkhir2, Vincent Ranwez2, Nicolas Galtier2
1IRBI - Université François Rabelais, France, 2ISEM - Université Montpellier 2, France, 3Queen Mary University, UK, 4CIBIO Universidade do Porto, Portugal, 5Centre for Outbreak Analysis and Modelling, Imperial College, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
How evolvable are polarization machines?
Liedewij Laan*, Andrew Murray
Fas Institute for Systems Biology, Harvard University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
How often does natural selection targets multiple, interacting genes? The prevalence of epistasis in recent human evolution
Natalia Petit*1, Arcadi Navarro1,4
1Institut de Biologia Evolutiva (CSIC-UPF), Spain, 2Departament de Ciències Experimentals i de la Salut (DCEXS).Universitat Pompeu Fabra, Spain, 3National Institute for Bioinformatics (INB), Population Genomics Node, Spain, 4Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
How protein targeting to primary plastids via the endomembrane system could have evolved?
Przemyslaw Gagat*1, Pawel Mackiewicz1, Andrzej Bodyl2
1Department of Genomics, Faculty of Biotechnology, University of Wroclaw, Poland, 2Department of Biodiversity and Evolutionary Taxonomy, University of Wroclaw, Poland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
How stable are protein domains in the course of evolution?
Tina Koestler*1,2, Bui Quang Minh1,2, Arndt von Haeseler1,2, Ingo Ebersberger1,2
1University of Vienna, Austria, 2Center for Integrative Bioinformatics Vienna, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
How the colonization of subantarctic islands shaped mouse populations
Anna Lorenc*1, Ines Hellmann2, Emilie Hardouin1, Diethard Tautz1
1MPI for Evolutionary Biology, Germany, 2MaBS at MFPL, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
How to survive over the winter on northern latitudes? Cold acclimation in two Drosophila species with different distributions - a comparative genomic approach
Maaria Kankare*1, Laura Vesala1, Tiina Salminen1, Asta Laiho2, Anneli Hoikkala1
1University of Jyvaskyla, Finland, 2Finnish Microarray and Sequencing Centre, Finland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Human evolution and HIV: A deep-time perspective on pathogenesis
M. Cyrus Maher*, Ryan Hernandez
University of California, San Francisco, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Human evolutionary processes and genetic variation as revealed by mtDNA simulations
Aida Miró-Herrans*, Connie Mulligan
University of Florida, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Human population genomics in time and space: paleogenomics of populations in Bulgaria
Meredith L. Carpenter*1, Hannes Schroeder2, Nikola Theodossiev3, M. Thomas P. Gilbert2, Carlos D. Bustamante1
1Department of Genetics, Stanford University, USA, 2Centre for Geogenetics, University of Copenhagen, Denmark, 3Department of Archaeology, Sofia University, Bulgaria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Human postmeiotic sex chromosome inactivation and its impact on sex chromosome evolution
Ho-Su Sin*1,2, Eitetsu Koh3, Satoshi Namekawa1,2
1Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, USA, 2Department of Pediatrics, University of Cincinnati College of Medicine, USA, 3Department of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Japan
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  16:00-17:30
HuntMi: a novel machine learning method for miRNA classification
Michal Szczesniak*1, Adam Gudys2, Marek Sikora2, Izabela Makalowska1
1Adam Mickiewicz University, Poland, 2Silesian University of Technology, Poland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Hypothesis of steady-state genetic robustness implies a dynamic balance between gene essentiality turnovers through gene/genome duplications
Xun Gu*1,2, Zhixi Su2, Wei Huang1, katie Gu1
1Iowa State University, USA, 2Fudan University, China
:  S7 - Evolutionary genomics: A new synthesis of evolutionary biology (In honor of W-H Li's 70th birthday)  -  15:00-16:30
Identification and analysis of trans-splicing in human embryonic stem cells by transcriptome sequencing
Chan-Shuo Wu, Chun-Ying Yu, Ching-Yu Chuang, Hung-Chih Kuo, Trees-Juen Chuang*
Academia Sinica, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Identification and characterization of angiosperm single-copy gene families
Riet De Smet*1,2, Keith Adams3, Klaas Vandepoele1,2, Yves Van de Peer1,2
1VIB, Belgium, 2Ghent University, Belgium, 3University of British Columbia, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Identification and characterization of rhesus monkey genes from placenta full-length cDNA libraries: comparative analysis with human genes
Sang-Je Park*1,2, Young-Hyun Kim1,3, Jae-Won Huh1, Sang-Rae Lee1, Kyu-Tae Chang1,3
1National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Republic of Korea, 2Department of Biological Sciences, College of Natural Sciences, Pusan National University, Republic of Korea, 3University of Science & Technology, National Primate Research Center, KRIBB, Republic of Korea
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Identification of elite variety tag SNPs (ETASs) - a new approach unraveling loci underlying crop improvement
Jun Lv*, Wen Wang
Kumming Institute of Zoology, China
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Identification of Pigment QTL in African Cichlids from Lake Malawi
Claire O'Quin*, Alexi Drilea, Kelly O'Quin, Matthew Conte, Thomas Kocher
University of Maryland, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Identification of potential chemosensory gene families in funnel web spiders using NGS
Cristina Frias-Lopez*1, Francisca C. Almeida1, Sara Guirao-Rico2, Miquel Arnedo3, Julio Rozas1
1Universitat de  Barcelona, Departament de Genètica, Spain, 2University of Edinburgh, Institute of Evolutionary Biology, UK, 3Universitat de Barcelona, Departament de Biologia Animal, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Identification of regulatory networks involved sex-specific mRNA expression
Heidi Viitaniemi*1, Anti Vasemägi1, Juha Merilä2, Craig Primmer1, Erica Leder1
1University of Turku, Finland, 2University of Helsinki, Finland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Identification of Soft Sweeps in the Drosophila melanogaster Genome
Nandita Garud*, Philipp Messer, Dmitri Petrov
Stanford University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Identifying functional variation in viral phylogenies
Kevin Rattigan1, Xiaowei Jiang*1,2, David Robertson2, Mario Fares1
1Department of Genetics, Trinity College Dublin, Ireland, 2Faculty of Life Sciences, University of Manchester, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Identifying  long range cis-regulation in the human genome using evolutionary co-segregation
Magali Naville*, Alexandra Louis, Hugues Roest Crollius
ENS, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Identifying species trees from probabilities of clades or splits.
James Degnan*1,2, Elizabeth Allman3, John Rhodes3
1University of Canterbury, New Zealand, 2National Institute of Mathematical and Biological Synthesis, USA, 3University of Alaska Fairbanks, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Ignoring heterozygosity biases phylogenomic estimates of divergence times
Heidi E.L. Lischer*1,2, Laurent Excoffier1,2, Gerald Heckel1,2
1CMPG, Institute of Ecology and Evolution, University of Bern, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Impact of model selection across the Amphibian Tree of Life
Karen Siu Ting*1, Mark Wilkinson2
1National University of Ireland, Ireland, 2The Natural History Museum, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Impact of selection on genes involved in regulatory network: a modelling study.
Frederic Austerlitz*1,2, Bénédicte Rhoné2, Jean-Tristan Brandenburg1,2
1Laboratoire Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS/MNHN/Université Paris 7, France, 2Laboratoire Ecologie, Systématique et Evolution, UMR 8079 CNRS/Université Paris-Sud/AgroParisTech, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Impact of the M. tuberculosis Genetic Background on the Acquisition of Drug Resistance-conferring Mutations 
Sonia Borrell*1, Graham Rose2, Julia Feldmann1, Sebastien Gagneux1
1Swiss Tropical and Public Health Institute. University of Basel., Switzerland, 2MRC National Institute for Medical Research., UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Impacts of life-style on human evolutionary history: A genome-wide comparison of herder and farmer populations in Central Asia
Michael C. Fontaine*1,2, Laure Segurel2,3, Christine Lonjou4, Tatiana Hegay5, Almaz Aldashev6, Evelyne Heyer2, Frederic Austerlitz1,2
1Ecology, Systematics & Evolution. UMR8079 Univ. Paris Sud - CNRS - AgroParisTech, France, 2Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, France, 3Department of Human Genetics, University of Chicago, USA, 4C2BiG (Centre de Bioinformatique/Biostatistique Génomique d’Ile de France), Plateforme Post-génomique P3S, Hôpital Pitié Salpêtrière, France, 5Uzbek Academy of Sciences, Institute of Immunology, Uzbekistan, 6Institute of Molecular Biology and Medicine, National Center of Cardiology and Internal Medicine, Kyrgyzstan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
Robert Meredith1, Jan Janecka2, John Gatesy1, Oliver Ryder3, Colleen Fisher2, Emma Teeling4, Alisha Goodbla4, Eduardo Eizirik5, Taiz Simao5, Tanja Stadler6, Daniel Rabosky7, Rodney Honeycutt8, John Flynn9, Colleen Ingram9, Cynthia Steiner3, Tiffani Williams2, Terence Robinson10, Angela Burk-Herrick1, Michael Westerman11, Nadia Ayoub1, Mark Springer1, William Murphy*2
1University of California, Riverside, USA, 2Texas A&M University, USA, 3San Diego Zoo’s Institute for Conservation Research, USA, 4University College Dublin, Ireland, 5PUCRS, Brazil, 6Eidgenössiche Technische Hochschule Zurich, Switzerland, 7University of California, Berkeley, USA, 8Pepperdine University, USA, 9American Museum of Natural History, USA, 10University of Stellenbosch, South Africa, 11LaTrobe University, Australia
:  S8 - The animal tree of life and its applications  -  15:00-16:30
Improving metabolic flux predictions using gene expression data
Abdelmoneim Desouki*, Gabriel Gelius-Dietrich, Martin Lercher
Heinrich-Heine-University, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Improving the performance of true-Single Molecule Sequencing for ancient DNA
Aurélien Ginolhac*1, Julia Vilstrup1, Jesper Stenderup1, Maanasa Raghavan1, Morten Rasmussen1, Mathias Stiller2, Beth Shapiro2, Grant Zazula3, Duane Froese4, Kathleen E. Steinmann5, John F. Thompson5,6, Khaled A.S. AL-Rasheid7, Tom Gilbert1, Eske Willerslev1, Ludovic Orlando1
1Centre for GeoGenetics; Natural History Museum of Denmark, Denmark, 2Department of Biology; The Pennsylvania State University, USA, 3Department of Tourism and Culture; Yukon Palaeontology Program, Canada, 4Department of Earth and Atmospheric Sciences; University of Alberta, Canada, 5Helicos BioSciences, USA, 6NABsys Inc, USA, 7Zoology Department; College of Science King Saud University, Saudi Arabia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
In pursuit of functional nucleotides: Molecular mechanisms and fine-scale functional testing of noncoding sequences that contribute to pigmentation divergence in Drosophila.
Arielle Cooley*, Lisa Sramkoski, Wesley McLaughlin, Brad Lankowsky, Patricia Wittkopp
University of Michigan, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Indel Reliability in Phylogenetic Inference
Haim Ashkenazy*1, Ofir Cohen1, Dorothée Huchon2, Tal Pupko1
1Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel, 2Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Indels and the evolution of genome architecture: The long and short of it
Erika Kvikstad*, Laurent Duret
University Lyon 1, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inference in the extinction/recolonisation model
Nick Barton2, Alison Etheridge3, Jerome Kelleher*1, Amandine Veber4
1University of Edinburgh, UK, 2IST Austria, Austria, 3University of Oxford, UK, 4Ecole Polytechnique, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inference of co-evolving Drosophila gene family pairs by likelihood-based methods
Pablo Librado*1,3, Filipe G. Vieira2, Julio Rozas1,3
1Departament de Genètica, Universitat de Barcelona, Spain, 2Department of Integrative Biology, University of California Berkeley, USA, 3Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Spain
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  14:00-15:30
Inference of demographic history and natural selection in African Pygmy populations from whole-genome sequencing data
Martin Sikora*1, Etienne Patin2, Helio Costa1, Katherine Siddle2, Brenna M Henn1, Jeffrey M Kidd1,3, Ryosuke Kita1, Carlos D Bustamante1, Lluis Quintana-Murci2
1Department of Genetics, School of Medicine, Stanford Uni, USA, 2Unit of Human Evolutionary Genetics, Institut Pasteur, CNRS URA3012, France, 3Departments of Human Genetics and Computational Medicine and Bioinformatics, University of Michigan Medical School, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inferences of wolf population genetics using next-generation sequencing data
Violeta Munoz-Fuentes*, Carles Vila
Estacion Biologica de Donana-CSIC, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Inferences on dog domestication - genetic analysis of the most ancient dogs utilizing DNA capture arrays
Olaf Thalmann*1,2, Daniel Greenfield2, Matthias Meyer3, Susanna Sawyer3, Pin Cui3, Mietje Germonpré4, Mikhail V. Sablin5, Francesc López-Giraldez9, Daniel LePont1, Brian Worthington10, Jeff P. Blick6, Jeniffer A. Leonard7, Richard E. Green8, Robert K. Wayne2
1University of Turku, Finland, 2University of California, USA, 3Max Planck Institute for Evolutionary Anthropology, Germany, 4Royal Belgian Institute of Natural Sciences, Belgium, 5Zoological Institute RAS, Russia, 6Georgia College & State University, USA, 7Estación Biológica de Doñana- CSIC, Spain, 8University of California, USA, 9Yale University, USA, 10Southeastern Archaeological Research, Inc., USA
:  S2 - Paleogenomics: from fossils to genomes  -  11:30-13:00
Inferring adaptive evolution in the murid genome
Peter Keightley*1, Daniel Halligan1, Rob Ness1, Athanasios Kousathanas1, Bettina Harr2, David Adams3, Thomas Keane3
1University of Edinburgh, UK, 2Max-Planck-Institute for Evolutionary Biology, Germany, 3Wellcome Trust Sanger Institute, UK
:  S10 - Population genetic inference from next-generation sequencing data  -  15:00-16:30
Inferring human population history from multiple genome sequences
Stephan Schiffels*, Richard Durbin
Wellcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inferring natural selection by stratifying a single genome sequence
Naoki Osada
National Institute of Genetics, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inferring the history of speciation from next-generation sequence data in two nightingale species
Libor Mořkovský*1, Jakub Rídl2, Jan Pačes2, Lukáš Choleva3, Marcin Antczak4, Jiří Reif5, Karel Janko3, Petr Ráb3, Radka Reifová1
1Department of Zoology, Faculty of Science, Charles University in Prague, Czech Republic, 2Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Czech Republic, 3Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Czech Republic, 4Department of Behavioural Ecology, Adam Mickiewicz University, Poland, 5Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Czech Republic
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Inferring the network of life via agreement forest based models
Christopher Whidden*, Norbert Zeh, Robert Beiko
Dalhousie University, Canada
:  S9 - The network of life: algorithmic and modelling challenges  -  15:00-16:30
Influence of mating system on genome evolution in Caenorhabditis
Janna Fierst, John Willis, Timothy Ahearne, Rose Reynolds, Kristin Sikkink, William Cresko, Patrick Phillips*
University of Oregon, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Insertion-biased gene conversion for short indels
Evgeny Leushkin*1,3, Alexey Kondrashov1,2, Georgii Bazykin1,3
1M.V. Lomonosov Moscow State University, Russia, 2University of Michigan, USA, 3Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Russia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Integrating Functional and Population Genomics in Drosophila melanogaster
David Castellano*1,2, Antonio Barbadilla1,3
1Universitat Autónoma de Barcelona, Spain, 2Institut de Biotecnologia i Biomedicina, Spain, 3Departament de Genètica i Microbiologia, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Integration of selection signatures and GWAS data identifies novel susceptibility loci for Crohn's disease
Rachele Cagliani1, Diego Forni1, Uberto Pozzoli1, Andrea Cassinotti4, Matteo Fumagalli1, Matteo Giani1, Stefania Riva1, Rosanna Asselta6, Giacomo P Comi5, Nereo Bresolin5, Mario Clerici3,2, Manuela Sironi*1
1Scientific Institute IRCCS E. Medea, Italy, 2Don C. Gnocchi Foundation ONLUS, IRCCS, Italy, 3Department of Biomedical Sciences and Technologies LITA Segrate, University of Milan, Italy, 4L. Sacco University Hospital, Italy, 5Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Italy, 6Department of Biology and Genetics for Medical Science, University of Milan, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inter-and Intra-specific morphological variation and scaling of microtubule derived-organelles
Beatriz F. Gomes*, José B. Pereira-Leal
Instituto Gulbenkian de Ciência, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Inter-domain horizontal gene transfer, a major role in the adaptation of archaea to mesophilic lifestyles?
Purificacion Lopez-Garcia*1, Philippe Deschamps1, Yvan Zivanovic0,2, David Moreira1
1Unite Ecologie, Systematique et Evolution, CNRS & Universite Paris-Sud, France, 2Institut de Genetique et Microbiologie, CNRS & Universite Paris-Sud, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Interdomain transfer of an intein residing within the archaeal-type ATP synthase catalytic subunit.
J. Peter Gogarten*, Shannon M. Soucy, Kristen S. Swithers, Pascal Lapierre, David Williams
University of Connecticut, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Interspecies transmission of viral haemorrhagic septicaemia virus between marine and freshwater fishes.
Anna Amanda Schönherz*1, Niels Lorenzen2, Katja Einer-Jensen2
1Aarhus University, Faculty of Science and Technology, Department of Molecular Biology and Genetics, Denmark, 2Technical University Denmark, National Veterinary Institute, Department of Poultry, Fish and Fur Animals, Denmark
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Introgression of haplotypes with elevated mutation rate drives radiation of obligate asexuality in Daphnia pulex
Abraham Tucker*, Matthew Ackerman, Brian Eads, Michael Lynch
Indiana University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Intron positional conservation: a new paradigm of evolutionary conservation
Michal Chorev, Liran Carmel*
The Hebrew University of Jerusalem, Israel
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Invariants of genome evolution: selection, stochasticity or both?
Eugene Koonin
National Center for Biotechnology Information, NIH, USA
:  S5 - Adaptive vs. non-adaptive evolution  -  09:30-11:00
Inversion and nucleotide polymorphisms in Drosophila subobscura related with thermal adaptation
Olga Dolgova*1, Gemma Calabria2, Marta Pascual2, Joan Balanya2, Mauro Santos1
1Universitat Autònoma de Barcelona, Spain, 2Universitat de Barcelona, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Investigating deep nodes in Polyporales
Elisabet Sjökvist*1, Bernard Pfeil1, Ellen Larsson1, Karl-Henrik Larsson2
1University of Gothenburg, Sweden, 2University of Oslo, Norway
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Investigating determinants of large-scale recombination rate variation using a recombination map of the human-chimpanzee ancestor.
Kasper Munch*1, Thomas Mailund1, Julien Y Dutheil2, Asger Hobolth1, Mikkel H Schierup1
1Bioinformatics Research Center, Aarhus University, Denmark, 2Intitute of Evolutionary Sciences, University of Montpellier 2, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Investigating the expansion of gene families in otherwise reduced microsporidian genomes
Sirintra Nakjang1, Tom Williams1, Andrew Watson*1, Peter Foster2, Eva Heinz1, Robert Hirt1, Martin Embley1
1Newcastle University, UK, 2Natural History Museum, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Investigating the Impacts Recombination has on Origin Estimates
Crystal Hepp*, Michael Rosenberg
Arizona State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Investigating Two Different Mechanisms of Multiple-Host Recognition in the Bacterial Transferrin Receptor
Anastassia Pogoutse*1, Charles Calmettes1, Rong-hua Yu2, Estela Costa2, Anthony Schryvers2, Trevor Moraes1
1University of Toronto, Canada, 2University of Calgary, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Investment in fast growth modulates the evolutionary rates of essential proteins
Sara Vieira-Silva*1,2, Marie Touchon1, Sophie S. Abby1, Eduardo P.C. Rocha1
1Institut Pasteur, France, 2VIB/VUB, Belgium
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
IQ-TREE: An adaptive and efficient maximum-likelihood tree inference package
Bui Quang Minh*, Lam Tung Nguyen, Heiko Schmidt, Arndt von Haeseler
Center for Integrative Bioinformatics, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Is dioecy an evolutionary dead end for plant species? A case study in the genus Silene
Jos Käfer*1, Martina Talianova2, Alex Widmer3, Gabriel Marais1
1Laboratoire de Biométrie et Biologie Évolutive, UMR 5558 CNRS/Université Lyon 1, France, 2Department of Plant Developmental Genetics, Institute of Biophysics, Czech Republic, 3Institute of Integrative Biology, ETH Zurich, Switzerland
:  S1 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
­­­Is RAD-seq suitable for short-scale phylogenetic inference ? An in silico assesment
Marie Cariou*, Laurent Duret, Sylvain Charlat
Laboratoire de Biometrie et Biologie evolutive UMR5558, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Is the Tree of Life still a workable paradigm for evolution and phylogeny ?
Eric Bapteste
CNRS, France
Monday 25th June 2012:  S21 - Paradigm shifting in phylogeny  -  16:30-18:00
Is there really a universal deletion bias?
Steven Laurie*1, Macarena Toll-Riera1, Núria Radó-Trilla1, Mar Albà1,2
1Fundació Institut Municipal d’Investigació Mèdica (FIMIM)-Universitat Pompeu Fabra (UPF), Spain, 2Institució Catalana de Recerca i Estudis Avançats, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Isolation barriers in Spodoptera frugiperda - a genomic approach
Sabine Haenniger*1, Gerhard Schoefl2, Steffi Gebauer-Jung1, Heiko Vogel1, David G. Heckel1, Astrid T. Groot1,3
1MPICE, Dept. of Entomology, Germany, 2Hans Knoell Institute, Dept. of Cell and Molecular Biology, Germany, 3University of Amsterdam, IBED, The Netherlands
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
It's OK to say 'prokaryote': paradigm wars in microbial systematics
W. Ford Doolittle
Dalhousie University, Canada
Monday 25th June 2012:  S21 - Paradigm shifting in phylogeny  -  16:30-18:00
Jaatha, a fast method to infer demographic parameters - not only for wild tomatoes
Lisha Mathew*1, Laura E. Rose2, Dirk Metzler1
1Ludwig-Maximilians-Universität, Germany, 2Heinrich-Heine-Universität, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Kernel Approximate Bayesian Computation
Shigeki Nakagome*, Kenji Fukumizu, Shuhei Mano
The Institute oif Statistical Mathematics, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Large genomic domains resulting from replication-associated mutational asymmetries are conserved since amniota divergence
Chun-Long Chen*1, Antoine Baker2, Benjamin Audit2, Arach Goldar3, Yves d'Aubenton-Carafa1, Guillaume Guilbaud4, Aurélien Rappailles4, Olivier Hyrien4, Alain Arneodo2, Claude Thermes1
1Centre de Génétique Moléculaire, CNRS, France, 2Laboratoire Joliot Curie, ENS Lyon, CNRS, France, 3CEA, iBiTecS, France, 4ENS Paris, UMR CNRS 8541, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Large scale analysis of plasmids relationships through gene sharing networks and composition analyses
Manu Tamminen2, Emanuele Bosi1, Marko Virta2, Renato Fani1, Marco Fondi*1
1University of Florence, Italy, 2Department of Food and Environmental Sciences, Finland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Large variations in the rate of DNA loss among vertebrates
Stephane Boissinot
Queens College, the City University of New York, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Large-Scale Transcriptome Sequencing and Gene Analyses in the Crab-Eating Macaque (Macaca fascicularis) for Biomedical Research
Young-Hyun Kim*1,2, Sang-Je Park1,3, Jae-Won Huh1, Kyu-Tae Chang1,2
1National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Republic of Korea, 2University of Science & Technology, National Primate Research Center, KRIBB, Republic of Korea, 3Department of Biological Sciences, College of Natural Sciences, Pusan National University, Republic of Korea
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Late Glacial Expansions in Europe revealed through the fine-resolution characterisation of mtDNA haplogroup U8
Marta Daniela Costa*1,2, Joana Barbosa Pereira1,2, Pedro Soares2, Luísa Pereira2,3, Martin Brian Richards1,4
1Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, UK, 2IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal, 3Faculdade de Medicina, Universidade do Porto, Portugal, 4School of Applied Sciences, University of Huddersfield, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Late Pleistocene population dynamics in the European collared lemmings (Dicrostonyx torquatus)
Selina Brace1, Eleftheria Palkopoulou*2, Rebecca Miller3, Mietje Germonpré4, Love Dalen2, John Stewart5, Ian Barnes1
1Royal Holloway, University of London, UK, 2Swedish Museum of Natural History, Sweden, 3University of Liege, Belgium, 4Royal Belgian Institute of Natural Sciences, Belgium, 5Bournemouth University, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Late replicating domains have higher divergence and diversity in Drosophila melanogaster
Claudia Weber*1,2, Catherine Pink1, Laurence Hurst1
1University of Bath, UK, 2Uppsala University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Latitudinal clinal variation in a blue-absorbing visual pigment of butterflies
Furong Yuan, Adriana Briscoe*
University of California, Irvine, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Learning from genetic fossils on the human Y chromosome 
Melissa Wilson Sayres*1,2, Kateryna Makova2
1University of California, Berkeley, USA, 2The Pennsylvania State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Levels and patterns of genetic diversity of AI-2 quorum sensing in Escherichia coli
Patricia H. Brito*1, Eduardo P. C. Rocha2, Isabel Gordo1, Karina B. Xavier1,3
1Instituto Gulbenkian de Ciência, Portugal, 2Institut Pasteur, France, 3Instituto de Tecnologia Quimíca e Biológica, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Life at Extremes: Molecular Adaptations of the Protist Halocafeteria to Hypersaline Environments
Tommy Harding*, Alastair G. B. Simpson, Andrew J. Roger
Dalhousie University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Likelihood-based inference of population relationships in a non-model insect using whole genomes
Konrad Lohse*1, Jack Hearn1, Graham Stone1, Nicholas Barton2
1University of Edinburgh, UK, 2IST, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Linking Codon Usage and tRNA Prevalence In The Smallest Photosynthetic Eukaryotes And Their Giant Viruses
Stephanie MICHELY3, Eve TOULZA1,2, Lucie SUBIRANA1,2, Uwe JOHN4, Valérie COGNAT5, Laurence MARECHAL-DROUARD5, Herve MOREAU1,2, Gwenael PIGANEAU*1,2
1CNRS UMR 7232, France, 2UPMC, France, 3INRA, UMR1319 Micalis, France, 4Alfred Wegener Institute for Polar and Marine Research, Germany, 5UPR 2357 CNRS, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Lizards and LINEs: Host Demography and Selection Affect the Fate of non-LTR Retrotransposons in the Anolis Genome
Marc Tollis*1,2, Stephane Boissinot1,2
1Queens College, City University of New York, USA, 2The Graduate Center, City University of New York, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Long IBD in Europeans and recent population history
Peter Ralph*, Graham Coop
UC Davis, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Long term evolutionary adaptation of yeast to a fluctuating environment
Riddhiman Dhar*, Rudolf Sägesser, Christian Weikert, Andreas Wagner
Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Long-term and Short-term Evolutionary Impacts of Transposable Elements on Drosophila
Grace Yuh Chwen Lee*, Charles H. Langley
Center for Population Biology, University of California, Davis, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  11:30-13:00
Long-term balancing selection may be more common than previously believed: several examples from apes
Ellen M. Leffler*1, Ziyue Gao1, Susanne Pfeifer2, Laure Ségurel1, Adam Auton3, Ryan Hernandez4, Joanna L. Kelley7, Jeffrey Kidd7, S. Cord Melton1, Laurie Stevison4, Aarti Venkat1, Oliver Venn3, Ronald Bontrop6, Carlos Bustamante7, Michael Hammer8, Jeffrey Wall4, Peter Donnelly2,3, Gilean McVean2,3, Molly Przeworski1,5
1University of Chicago, USA, 2University of Oxford, UK, 3Wellcome Trust Centre for Human Genetics, UK, 4University of California, San Francisco, USA, 5Howard Hughes Medical Institute, USA, 6Biomedical Primate Research Centre, The Netherlands, 7Stanford University, USA, 8University of Arizona, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Long-term evolution of quantitative traits in finite populations.
Harold P. de Vladar*, Nick Barton
IST Austria, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Long-term presence versus recent admixture: Bayesian and approximate-Bayesian analyses of genetic diversity of human populations in Central Asia
Friso Palstra*, Evelyne Heyer, Frederic Austerlitz
Eco-anthropologie et Ethnobiologie UMR 7206 CNRS, Equipe Genetique des Populations Humaines, Museum National d'Histoire Naturelle, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Looking for evidence of co-evolution between nuclear and mitochondrial genomes in a situation of interspecific hybridization
José Melo-Ferreira*1, Pierre Boursot2, Nicolas Galtier2, Paulo C. Alves1,3
1CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Universidade do Porto, Portugal, 2Universite Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution, France, 3Dpto. de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Looking for hints of new Domains of Life with similarity networks
Philippe Lopez*1, Sébastien Halary3, Eric Bapteste2
1Université Pierre et Marie Curie, France, 2CNRS, France, 3Institut de Recherche en Biologie Végétale, Canada
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  16:00-17:30
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny
Chung-Shien Wu1, Ya-Nan Wang2, Chi-Yao Hsu1, Ching-Ping Lin1, Shu-Miaw Chaw*1
1Biodiversity Research Center, Academia Sinica, Taiwan, 2School of Forestry and Resource Conservation, National Taiwan University, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
MADS microRNAs: A phylogenomic survey of spliced microRNAs regulating plant developmental control genes
Lydia Gramzow*, Dajana Lobbes, Peer Aramillo Irizar, Sophia Walter, Günter Theißen
Friedrich Schiller University, Germany
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Mammalian X Chromosome Inactivation evolved as a dosage compensation mechanism for dosage-sensitive genes on the X chromosome
Eugénie Pessia*1, Takashi Makino2,3, Marc Bailly-Bechet1, Aoife McLysaght3, Gabriel A.B. Marais1,4
1Université Lyon 1, Centre National de la Recherche Scientifique, UMR5558, Laboratoire de Biométrie et Biologie évolutive, France, 2Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Japan, 3Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland, 4Instituto Gulbenkian de Ciência, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Mapping the evolutionary fitness landscape of C4 photosynthesis
David Heckmann*, Martin J. Lercher
Institute for Computer Science, HHU Düsseldorf, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Mapping the human genome’s missing pieces using population admixture
Giulio Genovese*1,2, Steven McCarroll1,3
1Stanley Center, USA, 2Broad Institute, USA, 3Harvard Medical School, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing
Michaël Bekaert*1, Christos Palaiokostas1, Mairi Cowan1, Andrew Davie1, John B. Taggart1, Karim Gharbi2, Brendan J. McAndrew1, David J. Penman1, Hervé Migaud1
1Institute of Aquaculture, University of Stirling, UK, 2The Gene Pool, Ashworth Laboratories, The King’s Buildings, University of Edinburgh, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Masculinization of the X chromosome in the pea aphid, a system with an unusual sex-chromosome inheritance
Julie Jaquiéry*1, Claude Rispe1, Fabrice Legeai1,2, Solenn Stoeckel1, Lucie Mieuzet1, Corinne Da Silva3, Julie Poulain3, Nathalie Prunier-Leterme1, Béatrice Ségurens3, Denis Tagu1, Jean-Christophe Simon1
1INRA, France, 2INRIA, France, 3Genoscope, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Matching minor allele frequency rectifies confounding effects of purifying selection on population differentiation measures
Takahiro Maruki*1, Jesse Taylor2
1Indiana University, USA, 2Arizona State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Maternal siRNAs as regulators of parental genome imbalance and gene expression during seed development in angiosperms
Jie Lu1, Changqing Zhang1, David Baulcombe2, Z. Jeffrey Chen*1
1The University of Texas at Austin, USA, 2University of Cambridge, UK
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  14:00-15:30
Maximizing the information of DNA extracts obtained from skeletalremains
Christian Sell*, Susanne Kreutzer, Melanie Strobel
Johannes Gutenberg University Mainz, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Maximum-likelihood methods for the estimation of population-genetic parameters from high-throughput sequencing data
Micheal Lynch
Indiana University, USA
:  S10 - Population genetic inference from next-generation sequencing data  -  15:00-16:30
McDonald-Kreitman Test under Frequent Adaptation: Problems and Solutions
Philipp Messer*, Dmitri Petrov
Stanford University, USA
Monday 25th June 2012:  S16.1 - Adaptive Evolution and Selective Sweeps  -  09:30-11:00
Mealybugs nested endosymbiosis: going deeply into functional and evolutionary aspects of the ‘matryoshka' system in Planococcus citri.
Sergio López-Madrigal*1,2, Amparo Latorre1,2, Manuel Porcar3, Andrés Moya1,2, Rosario Gil1,2
1Institut Cavanilles de Biodiversitat i Biologia Evolutiva, UVEG, Spain, 2Departament de Genètica, UVEG, Spain, 3Fundació General de la Universitat de València, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Measuring mixtures of microbes: Bayesian phylogenetics for metagenomic data
John O'Brien*1, Xavier Didelot1, Daniel Falush2
1University of Oxford, UK, 2Max Planck Institute, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Measuring the distance between multiple sequence alignments
Benjamin Blackburne*, Simon Whelan
University of Manchester, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Mechanism Underlying Convergence of Albinism in Cave Adapted Animals
Helena Bilandžija*1, Helena Cetkovic1, William R. Jeffery2
1Rudjer Boskovic Institute, Croatia, 2University of Maryland, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Mechanisms and evolutionary patterns of mammalian and avian dosage compensation
Philippe Julien*1,2, David Brawand1,2, Magali Soumillon1,2, Anamaria Necsulea1,2, Angelica Liechti1, Frédéric Schütz1,2, Tasman Daish3, Frank Grützner3, Henrik Kaessmann3
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland, 3University of Adelaide, Australia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Medaka (Oryzias latipes) as a population model for studying functional differences between the alleles of human polymorphisms
Takafumi Katsumura*1,2, Shoji Oda1, Hiroshi Mitani1, Shoji Kawamura1, Hiroki Oota1,2
1University of Tokyo, Japan, 2Kitasato University School of Medicine, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Melanesian Blond Hair is Caused by an Amino Acid Change in TYRP1
Eimear Kenny*1, Nicholas Timpson2, Martin Sikora1, Muh-Ching Yee1, Andres Moreno Estrada1, Celeste Eng3, Scott Huntsmann3, Esteban Gonzalez Burchard3, Mark Stoneking4, Carlos Bustamante1, Sean Myles1
1Stanford University, USA, 2University of Bristol, UK, 3University of California San Francisco, USA, 4Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Metagenomics analysis of the human gut
Peer Bork
EMBL, Germany
Monday 25th June 2012:  S12 - Microbial genome evolution  -  11:30-13:00
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.
Leszek Pryszcz*, Jaime Huerta-Cepas, Toni Gabaldón
CRG-Centre for Genomic Regulation, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Microevolution of Staphylococcus aureus during progression from carriage to disease
Bernadette Young, Rowena Fung, Elizabeth Batty, Rory Bowden, Derrick Crook, Daniel Wilson*
University of Oxford, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
MicroRNA-driven differentiation of the placental transcriptome among human populations
Song Guo*1, David Hughes2,3, Mark Stoneking2, Philipp Khaitovich1,2
1Partner Institute for Computational Biology, Chinese Academy of Sciences, China, 2Max Planck Institute for Evolutionary Anthropology, Germany, 31Department of Anthropology, University of Florida, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Mining Genomes for Microinversions: Rare Genomic Characters for Phylogenomics
Gary Stuart*, Arun Seetharam
Indiana State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Mining human population-genomic data for demographic inference
Mattias Jakobsson
Uppsala University, Sweden
:  S10 - Population genetic inference from next-generation sequencing data  -  17:00-18:30
Mining microsatellites in seabuckthorn (Hippophae rhamnoides L.) transcriptome
Ankit Jain*, Rajesh Ghangal, Saurabh Chaudhary, Ram Singh Purty, Prakash Chand Sharma
University School of Biotechnology, Guru Gobind Singh Indraprastha University, India
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
MiRCandRef a local assembly algorithm for description of microRNAs in non-genome organisms
Bastian Fromm*1, Thomas D. Otto2, Christoph Hahn1, Philip D. Harris1, Lutz Bachmann1
1Natural History Museum, University of Oslo, Norway, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
MITOCHONDRIAL EVOLUTION ON THE SUB-ANTARCTIC KERGUELEN ARCHIPELAGO: POSITIVE SELECTION OR NEUTRAL EVOLUTION?
Emilie Hardouin*, Diethard Tautz
Max Planck Institute for Evolutionary Biology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Mitochondrial genotypes alter the nuclear transcriptional response to varied levels of hypoxia in Drosophila: Mito-Nuclear Epistasis meets Systems Genetics
David Rand*, Patrick Flight, Nick Jourjine, Lei Zhu
Brown University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Model selection in EnsemblCompara GeneTrees
Mateus Patricio*1, Matthieu Muffato2, Javier Herrero Sanchez2, David Posada1
1University of Vigo, Spain, 2EMBL-EBI European Bioinformatics Institute, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Modeling expression evolution with varying mutational effect sizes
Rori Rohlfs*1, Patrick Harrigan3, Rasmus Nielsen1,2
1University of California, Berkeley, USA, 2University of Copenhagen, Denmark, 3University of California, San Francisco, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Modeling the contributions of GC-biased gene conversion and selection to fast-evolving regions of primate genomes
John A. Capra*1, Melissa J. Hubisz2, Dennis Kostka1, Katherine S. Pollard1, Adam Siepel1
1Gladstone Institutes, University of California, San Francisco, USA, 2Cornell University, USA
:  S5 - Adaptive vs. non-adaptive evolution  -  09:30-11:00
Modelling copper transcriptional reaction norm evolution in Saccharomyces cerevisiae
Andrea Hodgins-Davis*1, Aleksandra Adomas2, Daniel Rice3, Jeffrey Townsend1
1Yale University, USA, 2National Institute of Environmental Health Sciences, USA, 3Harvard University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Modelling the Growth and Transmission of Infectious Disease: Linking epidemiology and population genetics
Bethany Dearlove*, Daniel Wilson
University of Oxford, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular analysis of the mechanisms involved in THBS4 differential gene-expression in the human brain
Raquel Rubio-Acero*1, James W. Thomas2, Todd M. Preuss3, Mario Cáceres1,4
1Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain, 2NIH Intramural Sequencing Center, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), USA, 3Division of Neuroscience and Center for Behavioral Neuroscience, Yerkes National Primate Research Center, Emory University, USA, 4Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Molecular And Functional Evolution Of Two Retroposon-Derived Enhancers Controlling Neuron-Specific Expression Of The Same Brain Gene
Marcelo Rubinstein*1,2, Lucía Franchini1, Flavio de Souza1,2, Daniel Lam3, Malcolm Low3
1INGEBI-CONICET, Argentina, 2University of Buenos Aires, Argentina, 3University of Michigan, USA, USA
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  16:30-18:00
Molecular basis of convergent adaptation to hydrogen sulfite extreme habitats in the Poecilia mexicana complex
Markus Pfenninger*1, Hannes Lerp2, Elisabeth Funke1, Patrick Slattery2, Kaan Erkoc2, Martin Plath2
1Biodiversity and Climate Research Centre by Senckenberg Naturforschende Geselleschaft and Goethe University, Germany, 2Evolutionary Ecology Group, Goethe University, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular basis of increased evolvability as a result of multicellularity evolution
Maria Rebolleda-Gomez*1, Johnathon Fankhauser3, William C. Ratcliff1, Michael Travisano1,2
1Ecology, Evolution and Behavior deppartment, University of Minnesota, USA, 2Biotechology Institute, University of Minnesota, USA, 3Plant Sciences, University of Minnesota, USA
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  16:30-18:00
Molecular biology and evolution of a candidate immune receptor in Drosophila
Erin Keebaugh*, Todd Schlenke
Emory University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular evolution and divergence of vertebrate heat shock factors
Kalle Rytkönen
University of Turku, Finland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Molecular evolution and variation in regions of the Drosophila melanogaster genome that lack crossing over.
Jose L. Campos*, Penelope R. Haddrill, Brian Charlesworth
Institute of Evolutionary Biology, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular Evolution of DNA Sequences on Neo-X and Neo-Y Chromosomes in Drosophila albomicans.
Kazuhiro Satomura*, Koichiro Tamura
Tokyo Metropolitan University, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Molecular evolution of Hox genes after whole genome duplication in a basal ray-finned fish, and surprising patterns of Hox expression in various body plan features at later stages of development.
Karen Crow
San Francisco State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular evolution of immune genes in socially diverse bees
Lumi Viljakainen*1, Brielle J. Fischman2, S. Hollis Woodard2, Gene E. Robinson2, Andrew G. Clark3
1University of Oulu, Finland, 2University of Illinois at Urbana-Champaign, USA, 3Cornell University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Molecular Evolution of piRNA pathway genes in Drosophila simulans and D. mauritiana
Jeffrey Vedanayagam*, Daniel Garrigan
University of Rochester, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  11:30-13:00
Molecular evolution of Rhodopsin in Neotropical cichlids: Differences in selective constraint between African and Neotropical dim-light visual pigments.
Shannon Refvik*1, Hernán López-Fernández1,2, Belinda Chang1
1University of Toronto, Canada, 2Royal Ontario Museum, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular evolution of the genes encoding the PRC2 and PhoRC Polycomb complexes in Drosophila.
Juan Manuel Calvo*, Montserrat Aguadé, Montserrat Papaceit, Carmen Segarra
Universitat de Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Molecular evolution of viral epitopes: frequent associations and selection
Helen Piontkivska*, Sinu Paul, Reeba Paul, Patrice Conway, Michael Rose, Joel Serre
Kent State University, USA
:  S3 - Evolution of host-virus interactions  -  9:30-11:00
Molecular evolutionary analysis of human AQP7 and the pseudogenes
Koyuru Inui*, Yoko Satta
The Graduate University for Advanced Studies (Sokendai), Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Molecular genetic analysis of ancient pig remains excavated from the Pong Takhop archaeological site in Saraburi Province, Thailand
Wunrada Surat*1, Mattana Wannajuk1, Pradit Sangthong1, Surapol Natapintu2, Anchanee Kubera1, Mingkwan Mingmuang1
1Faculty of Science, Kasetsart University, Thailand, 2Faculty of Archaeology, Silpakorn University, Thailand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Molecular phylogenetics of Passerine birds: Sibley and Ahlquist’s Tapestry reloaded
Alexandre Pedro Selvatti*, Claudia Russo
Universidade Federal do Rio de Janeiro, Brazil
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Monoallelic gene expression contributes significantly to expression divergence and diversity in primates
Lisa Stubbs2, Katja Nowick*1
1University Leipzig, Bioinformatics Group, IZBI, Paul-Flechsig-Institute for Brain Research, Germany, 2University of Illinois, Institute for Genomic Biology, USA
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  16:00-17:30
Monophyly and placement of the Drosophila inca species subgroup suggests an early South American diversification of the Drosophila repleta lineage.
Andrea Acurio*1, Deodoro Oliveira1, Violeta Rafael2, Alfredo Ruiz1
1Universitat Autònoma de Barcelona, Spain, 2Laboratorio de Genética Evolutiva, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Ecuador
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Moving beyond ribosomal genes: Metagenomics for microbial eukaryotes
Holly Bik*, Aaron Darling, Guillaume Jospin, Jonathan Eisen
University of California, Davis, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
mtDNA genomes of Khoisan populations deciphered under a linguistic and social anthropological perspective
Chiara Barbieri*1, Blesswell Kure4, Tom Güldemann2, Christfried Naumann1, Linda Gerlach1, Falko Berthold1, Hirosi Nakagawa3, Sunungukuo W. Mpoloka5, Mark Stoneking1, Brigitte Pakendorf6
1Max Planck Institute for Evolutionary Anthropology, Germany, 2Humboldt University, Germany, 3Tokyo University of Foreign Studies, Japan, 4Aarhus University, Denmark, 5University of Botswana, Botswana, 6CNRS / Université Lumière Lyon 2, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Muller’s ratchet and hybrid origins of apomixis:  high quality SNP discovery in the Ranunculus auricomus complex
Marco Pellino*, Diego Hojsgard, Thomas Schmutzer, Elvira Hörandl, Timothy Sharbel
IPK institute, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Multiple sequence alignment over-optimization bias impact downstream on population statistics and inferred phylogeny.
Abhijeet Shah*, Dirk Metzler
University of Munich, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Mutations improving chromatic resolution of L/M opsin alleles in atelid New World monkeys
Shoji Kawamura*1, Yoshifumi Matsumoto1, Yuka Matsushita1, Norihiro Ozawa1, Makiko Nakata1, Satoshi Kasagi1, Chihiro Hiramatsu1,2
1University of Tokyo, Japan, 2Kyoto University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
NATURAL SELECTION IN GENOME EVOLUTION
Giorgio Bernardi
Biology Dept., Rome 3 University, Italy
:  S5 - Adaptive vs. non-adaptive evolution  -  11:30-13:00
Natural selection on X-linked vs. autosomal genes in the D. pseudoobscura subgroup
Sophie Marion de Procé*1, Andrea Betancourt2, Nicola Palmieri2, Christian Schloetterer2, Brian Charlesworth1
1University of Edinburgh, UK, 2Veterinärmedizinische Universität, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Near Neutrality: the Mutational-Hazard Theory of Genome Evolution, and the Drift-Barrier Hypothesis
Micheal Lynch
Indiana University, USA
:  S5 - Adaptive vs. non-adaptive evolution  -  11:30-13:00
Neolithic expansion into Europe is visible in complete mitochondrial genomes
Qiaomei Fu*1, Pavao Rudan0,2, Svante Pääbo0,1, Johannes Krause0,3
1Max Planck Institute for Evolutionary Anthropology, Germany, 2Croatian Academy of Sciences and Arts, Croatia, 3Institute for Archaeological Sciences, University of Tübingen, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Nested Phylogenetic Reconstruction: scalable resolution in large phylogenies
Jaime Huerta-Cepas*, Marina Marcet-Houben, Toni Gabaldón
Centre for Genomic Regulation (CRG) and UPF, Spain
:  S6 - Gene/genome data and the limits to  -  17:00-18:30
Network analysis of ocean plankton communities: from viruses to fish larvae
Gipsi Lima-Mendez1,2
1Vrije Universiteit Brussel (VUB), Belgium, 2VIB, Belgium
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  16:00-17:30
Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations.
Hafid Laayouni*1, Pierre Luisi1, David Alvarez-Ponce2, Martin Sikora3, Jaume Bertranpetit1
1Inuversitat Pompeu Fabra, Spain, 2National University of Ireland Maynooth, Ireland, 3Stanford University School of Medicine, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Networks of Polynesian Language Evolution Reveal Frequent Word Borrowing Across the Islands 
Shijulal Nelson-Sathi*1, Simon Greenhill2, Russell D. Gray2, Tal Dagan1, William F. Martin1
1Institute of Molecular Evolution, Germany, 2Department of Psychology, New Zealand
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
New tools for studying gene family evolution show changes in a single yeast species that correlate with the environment
Simon Lovell*, Simon Whelan, Ryan Ames, Daniel Money
University of Manchester, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Next generation sequencing of archaeological strains of Mycobacterium tuberculosis
Terry Brown
University of Manchester, UK
:  S2 - Paleogenomics: from fossils to genomes  -  09:30-11:00
Next-generation insights into a classic evolutionary system and the development of SenecioDB
Owen Osborne*1, Thomas Batstone2, Simon Hiscock2, Dmitry Filatov1
1University of Oxford, UK, 2University of Bristol, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Next-generation sequencing and SNP genotyping of poplars reveal chloroplast capture and admixture
Stacey Lee Thompson
Umeå University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
NIN, a gene necessary for maintaining neurogenic divisions of radial glial cells, evolved adaptively in anthropoid primates
Stephen Montgomery*1,2, Nicholas Mundy1
1University of Cambridge, UK, 2University College London, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Non-neutral evolution of fatty acid desaturase F pseudogenes in Drosophila
Shun-Chern Tsaur1, Kuang-Hsi Chu2, Wei-Chin Ho2, Wan-Ju Shen3, Kevin Wei3, Chau-Ti Ting2,4, Shu Fang*3
1Department of Life Sciences & Institute of Genome Sciences, National Yang-Ming University, Taiwan, 2Institute of Zoology, National Taiwan University, Taiwan, 3Biodiversity Research Center, Academia Sinica, Taiwan, 4Department of Life Science & Institute of Ecology and Evolutionary Biology, National Taiwan University, Taiwan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Non-random mate choice in humans: insights from a genome scan
Romain Laurent*, Bruno Toupance, Raphaëlle Chaix
Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, France
:  S1 - Open Symposium for Early Stage Researchers  -  11:30-13:00
North American Drosophila melanogaster produced by admixture between African and European populations: An Approximate Bayesian Computation approach
Pablo Duchen*, Stefan Laurent, Daniel Zivkovic, Wolfgang Stephan
University of Munich, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Not another alignment program paper: How to improve multiple alignments by selecting the appropiate isoform combination.
José Luis Villanueva-Cañas*2, M Mar Albà1,2
1Catalan Institution for Research and Advanced Studies, Spain, 2volutionary Genomics Group, Fundació Institut Municipal d’Investigació Mèdica (FIMIM)-Universitat Pompeu Fabra (UPF), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Not Genetic Hitchhiking but Positive Selection Plays a Major Role in Influenza A Hemagglutinin Evolution
Li-Ching Hsieh*1,2, Yi-Chiao Fang3, Wen-Hsiung Li4,5, Arthur Chun-Chieh Shih3
1Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan, 2Biotechnology Center, National Chung Hsing University, Taiwan, 3Institute of Information Science, Academia Sinica, Taiwan, 4Biodiversity Research Center, Academia Sinica, Taiwan, 5Department of Ecology and Evolution, University of Chicago, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica reveals lineage-specific gene loss and genome complexity.
Christa Moore*, John Archibald
Dalhousie University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Ocean Drive: A major factor in opsin diversification in vertebrates was the availability of new ocean ecosystems
Roberto Feuda*, Sinéad Hamilton, Davide Pisani, James McInerney
NUI Maynooth, Ireland
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  16:00-17:30
On the move: sex-biased migration during the Neolithic transition
Rita Rasteiro*1,2, Pierre-Antoine Bouttier1,3, Vítor C. Sousa1,4, Lounès Chikhi1,5
1Instituto Gulbenkian de Ciência, Portugal, 2Department of Genetics, University of Leicester, UK, 3Laboratoire Jean Kutzman, Université de Grenoble, France, 4Department of Genetics, Rutgers University, United States Minor Outlying Islands, 5CNRS, Université Paul Sabatier, ENFA, UMR 5174 EDB, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
On the origin of leprosy: a genomics perspective
Luz-Andrea Pfister*, Anne C. Stone
Arizona State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
On the prospect of identifying adaptive loci in recently colonized populations
Yu-Ping Poh*1,2, Vera Domingues2, Hopi Hoekstra2, Jeffery Jensen1,3
1UMass Medical School, USA, 2Harvard University, USA, 3EPFL, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
On the track of horizontally transferred sequences between two closely related species Drosophila melanogaster and Drosophila simulans.
Laurent MODOLO*, Emmanuelle LERAT
UMR CNRS 5558 Université Lyon1, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
On the tree of life size distribution: A generalization of Yule's model of genera size (how many species are in a genus) to include species extinction.
Yosef Maruvka*1,2, Nadav Shnerb3, David Kessler3, Robert Ricklefs4
1Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute, USA, 2Department of Biostatistics, Harvard School of Public Health, USA, 3Department of Physics, Bar-Ilan University, Israel, 4Department of Biology, University of Missouri St. Louis, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
On the use of Gene Ontology annotations to assess functional similarity among orthologs and paralogs
Paul Thomas*1, Valerie Wood2, Christopher Mungall3, Suzanna Lewis3, Judith Blake4
1University of Southern California, USA, 2University of Cambridge, UK, 3Lawrence Berkeley National Laboratory, USA, 4The Jackson Laboratory, USA
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  16:30-18:00
One lane, one population: Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster.
Yuan Zhu*1, Alan Berglans1, Josefa González2, Dmitri Petrov1
1Stanford University, USA, 2Passeig Maritim de la Barceloneta, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
One step mutation matrices: A fresh view on modeling sequence evolution
Arndt von Haeseler*1, Minh Anh Thi Nguyen1, Tanja Gesell1, Steffen Klaere2
1CIBIV-MFPL, Austria, 2Dept Mathematics, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Opsin Phylogenetics Iluminates the Evolution of Colour Vision in Mammals
Bruno Simoes*1, Huabin Zhao2, Shuyi Zhang2, Emma Teeling1
1UCD School of Biology and Environmental Science, University College Dublin, Ireland, 2School of Life Science, East China Normal University, China, China, 3School of Biological and Chemical Sciences, Queen Mary University of London, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Origins and evolution of the Etruscans’ DNA
Silvia Ghirotto*1, Francesca Tassi1, Erica Fumagalli2,1, Vincenza Colonna3,1, Anna Sandionigi4, Martina Lari4, Stefania Vai4, Emmanuele Petiti4, Giorgio Corti5, Ermanno Rizzi5, Gianluca De Bellis5, David Caramelli4, Guido Barbujani1
1Department of Biology and Evolution, University of Ferrara, Italy, 2Department of Biotechnologies and BiosciencesUniversity of Milano-Bicocca, Italy, 3Institute of Genetics e Biophysics "Adriano Buzzati-Traverso", National Research Council, Italy, 4Department of Evolutionary Biology, University of Firenze, Italy, 5Institute for Biomedical Technologies (ITB), National Research Council (CNR), Italy
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Origins and genetic legacy of Northern European Neolithic farmers and hunter-gatherers
Pontus Skoglund*1, Helena Malmström1, Maanasa Raghavan2, Jan Storå3, Per Hall4, Eske Willerslev2, M. Thomas P. Gilbert2, Anders Götherström1, Mattias Jakobsson1
1Uppsala University, Sweden, 2University of Copenhagen, Denmark, 3Stockholm University, Sweden, 4Karolinska Institutet, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Ortho-Gen: The ortholog dataset constructing tool for phylogenetic analysis
Tokumasa Horiike*1, Ryoichi Mimai1, Daisuke Miyata1,2, Yoshio Tateno1,3
1Shizuoka University, Japan, 2Chiba University of Commerce, Japan, 3Pohang University of Science and Technology, Republic of Korea
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Orthology: a simple concept marred in complexity but still holding
Eugene Koonin
National Center for Biotechnolgoy Information, NIH, USA
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  14:30-16:00
p { margin-bottom: 0.21cm; } Methods to detect regional genomic variation in evolutionary history
Daniel Hartleb*, Christian Eßer, Martin J. Lercher
Institute for Computer Science Heinrich-Heine-University Duesseldorf, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
p { margin-bottom: 0.21cm; } Rapid desktop sequencing transforms Staphylococcus aureus and Clostridium difficile outbreak detection and surveillance
David Eyre1,3, Tanya Golubchik*2, Claire Gordon1,3, Rory Bowden2,3, Paolo Piazza4, Elizabeth Batty2, Camilla Ip2, Daniel Wilson1,3, Xavier Didelot1,3, Lily O'Connor1,5, Rochelle Lay5, David Buck4, Angela Kearns6, Angela Shaw7, John Paul8, Mark Wilcox9, Peter Donnelly4, Tim Peto1,3, Sarah Walker1,10, Derrick Crook1,3
11. Nuffield Department of Clinical Medicine, Experimental Medicine Division, UK, 22. Department of Statistics, University of Oxford, UK, 33. NIHR Oxford Biomedical Research Centre, UK, 44. Wellcome Trust Centre for Human Genetics, UK, 55. Oxford University Hospitals NHS Trust, UK, 66. Health Protection Agency Centre for Infections, Staphylococcus Reference Unit, UK, 77. Ashford and St Peter's NHS Foundation Trust, Department of Microbiology, UK, 88. Health Protection Agency, UK, 99. Leeds Teaching Hospitals & Univ of Leeds, Microbiology, UK, 1010. Medical Research Council, Clinical Trials Unit, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Pairwise Evolutionary Distance Estimation Under Alignment Uncertainty
Ge Tan
Department of Computer Science ETH Zuerich, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Paleogenomics: hunting our genetic past.
Eske Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, Denmark
:  S2 - Paleogenomics: from fossils to genomes  -  09:30-11:00
Parallel differentiation in Australian and North American populations of Drosophila simulans
Alisa Sedghifar*, David Begun
University of California, Davis, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Parallel evolution by parallel genetic mechanisms, or is evo-devo different?
Axel Meyer*, Kathryn Elmer
Univ. of Konstanz, Germany
:  S4 - Genomic basis of Evo-Devo  -  11:30-13:00
Parallel evolution in Drosophila species along a latitudinal cline
Heather Machado*1, Alan Bergland1, Paul Schmidt2, Dmitri Petrov1
1Stanford University, USA, 2University of Pennsylvania, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Parallel evolution of Mycobacterium tuberculosis and modern humans
Sebastien Gagneux
Swiss Tropical and Public Health Institute, Switzerland
Monday 25th June 2012:  S12 - Microbial genome evolution  -  09:30 - 11:00
Parallel evolution of rpoB mutants of Escherichia coli during thermal stress adaptation
Alejandra Rodriguez Verdugo*1, Brandon Gaut1, Pamela McDonald1, Rebecca Gaut1, Albert Bennett1, Anthony Long1, Olivier Tenaillon1,2
1University of California Irvine, USA, 2INSERM U722 and Université Paris 7, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Parallel reduction in opsin and hedgehog gene expression in independently derived cave populations of the amphipod Gammarus minus
Ariel Aspiras, Rashmi Prasad, Daniel Fong, David Angelini, David Carlini*
American University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Parallel tagged next-generation sequencing for population genetics and phylogeography: a case study using the New Zealand frog Leiopelma hochstetteri.
Monika Zavodna*, Catherine Grueber, Neil Gemmell
Centre for Reproduction and Genomics, Department of Anatomy, University of Otago, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
PartitionFinder and PartitionFinderProtein - combined selection of partitioning schemes and substitution models for phylogenetic analyses.
Robert Lanfear*1, Brett Calcott1, Simon Ho2, Stephane Guindon3
1Australian National University, Australia, 2Sydney University, Australia, 3University of Auckland, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Pathway analysis of the action of natural selection on coding and non-coding genomic elements
Gabriel Santpere*1, Elena Carnero1, Natalia Petit1, Jordi Rambla1,2, François Serra5, Christina Hvilsom4, Hernan Dopazo5, Arcadi Navarro1,3, Elena Bosch1
1Institute of Evolutionary Biology (UPF-CSIC), Spain, 2National Institute for Bioinformatics, Universitat Pompeu Fabra, Spain, 3Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain, 4Research and Conservation Copenhagen Zoo, Denmark, 5Evolutionary Genomics Lab, Bioinformatics & Genomics Department, Centro de Investigación Principe Felipe, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Pathways to the Amphibian Tree of Life
Mark Wilkinson*1, Karen Siu Ting1
1The Natural History Museum, UK, 2National University of Ireland, Ireland
:  S8 - The animal tree of life and its applications  -  17:00-18:30
Patterns of gene expression divergence and protein evolution in mammals
Maria Warnefors*1, Henrik Kaessmann1
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Patterns of genetic diversity across the European rabbit (Oryctolagus cuniculus) hemoglobin beta (HBB) cluster suggest a recent and incomplete selective sweep at the HBB gene
Rita Campos*1,2, Nuno Ferrand1,2
1CIBIO - Centro de Investigacao em Biodiversidade e Recursos Geneticos, Portugal, 2Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Patterns of genetic diversity and population structure in domestic rabbits: early steps of domestication and the subsequent process of breed formation
Joel Alves*1,2, Miguel Carneiro1,2, Sandra Afonso1, Susana Lopes1, Hervé Garreau3, Samuel Boucher4, Daniel Allain3, Guillaume Queney5, Pedro Esteves1,6, Gerard Bolet3, Nuno Ferrand1,2
1CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal, 2Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal, 3INRA, Institut National de la Recherche Agronomique, France, 4Labovet Conseil, France, 5ANTAGENE, Wildlife Genetics Laboratory, France, 6CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Patterns of KLK2 and KLK3 diversity in Cercopithecoidea
Patrícia Marques*1,2, Rui Bernardino3, Teresa Fernandes3, Víctor Quesada2, Susana Seixas1, Belen Hurle4
1Institute of Molecular Pathology and Immunology of the University of Porto, Portugal, 2Department of Biochemistry and Molecular Biology, University of Oviedo, Spain, 3Lisbon Zoo Veterinary Hospital, Portugal, 4Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Patterns of shared polymorphism in humans and apes
João C Teixeira*, Juan R Meneu, Genís Parra, Aida M Andrés
Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Patterns of strong selective sweeps in Northern Swedish Arabidopsis thaliana
Christian Huber*1, Quan Long2, Magnus Nordborg2, Ines Hellmann1
1Max F. Perutz Laboratories, Austria, 2Gregor Mendel Institute of Molecular Plant Biology GmbH, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Performance Degradation in Molecular Divergence Time Estimation with the Increase in Calibrations with Large Uncertainty
Kazutaka Takeshita*, Hidemi Watanabe
Hokkaido University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Personal and population genomics of human regulatory variation
Benjamin Vernot*, Andrew Stergachis, John Stamatoyannopoulos, Joshua Akey
Department of Genome Sciences, University of Washington, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Pervasive epistatic interactions between nearby sites in coding and non-coding sequences of D. melanogaster
Vladimir Seplyarskiy*1,2, Alex Kondrashov1,3, Egor Bazykin1,2
1Moscow State University, Russia, 2IPPI, RAS, Russia, 3University of Michigan, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
pH adaptation of archaeal ammonia oxidizers
Cecile Gubry-Rangin*1, Christopher Quince3, Robert Griffiths4, Michael Schloter2, James Prosser1, Graeme Nicol1
1University of Aberdeen, UK, 2Helmholtz Zentrum München, Germany, 3University of Glasgow, UK, 4Centre for Ecology and Hydrology, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phenol metabolisms in yeasts: identification and evolutionary analysis of genes involved in gentisate and 3-oxoapidate pathways in Candida parapsilosis
Leszek Pryszcz*1, Josef Nosek2, Toni Gabaldón1
1Department of Bioinformatics and Genomics, CRG-Centre for Genomic Regulation, Spain, 2Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Slovakia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Phenotypic Evolution Driven by New Gene Origination
Manyuan Long
The University of Chicago, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phenotypic plasticity of body size in Daphnia pulex
France Dufresne
Université du Québec à Rimouski, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Philosophy of paradigms and phylogeny
Maureen O'Malley
University of Sydney, Australia
Monday 25th June 2012:  S21 - Paradigm shifting in phylogeny  -  16:30-18:00
Photoactivation of zebrafish rhodopsin: insights into the molecular evolution of retinal release.
James Morrow*, Belinda Chang
University of Toronto, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Phylodynamics of influenza viruses before, during and after the 2009 swine flu pandemic
Gytis Dudas
University of Edinburgh, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenetic analysis and alignment of NGS sequence data
Tandy Warnow*, Nam-phuong Nguyen, Siavash Mirarab
University of Texas at Austin, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenetic analysis of cave bear specimens from Niedźwiedzia Cave, Sudetes, Poland
Pawel Mackiewicz*1, Mateusz Baca2, Anna Stankovic3, Krzysztof Stefaniak4, Adrian Marciszak4, Michael Hofreiter5, Adam Nadachowski6, Piotr Weglenski3
1Faculty of Biotechnology, University of Wroclaw, Poland, 2Center for Precolumbian Studies, University of Warsaw, Poland, 3Institute of Biochemistry and Biophysics, Polish Academy of Science, Poland, 4Zoological Institute, University of Wroclaw, Poland, 5Department of Biology (Area 2), The University of York, UK, 6Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Poland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenetic and Environmental Influences on the Saliva Microbiome of Pan and Homo
Jing Li*1, Ivan Nasidze1, Dominique Quinque1, Mingkun Li1, Michel Halbwax1, Anne Fischer1,2, Mark Stoneking1
1Max Planck Institute for Evolutionary Anthropology, Germany, 2Microbiology and Biotechnology Department, International Center for Insect Physiology and Ecology, Kenya
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenetic network construction as default method for reticulated evolution
Naruya Saitou
National Institute of Genetics, Japan
:  S9 - The network of life: algorithmic and modelling challenges  -  15:00-16:30
Phylogenetic reconstruction of malaria vectors in Thailand using multilocus DNA sequences
Uraiwan Arunyawat*, Prin Phunngam, Theeraphap Chareonviriyaphap
Kasetsart University, Thailand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenetic signal and noise: predicting the power of a dataset to resolve molecular phylogeny
Jeffrey Townsend*1, Zhuo Su1, Yonas Tekle2
1Yale University, USA, 2Spelman College, USA
:  S6 - Gene/genome data and the limits to  -  15:00-16:30
Phylogenomic analysis of myzostomid transcriptome data supports an annelid origin of myzostomids
Stefanie Hartmann*1, Christoph Bleidorn2
1University of Potsdam, Germany, 2University of Leipzig, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenomic analysis of the diverse evolutionary origins of eukaryotic genes.
Nicolas Rochette*, Manolo Gouy
Laboratoire de Biométrie et Biologie Évolutive; CNRS; Université Lyon 1; Université de Lyon, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenomic Networks
Tal Dagan
Heinrich-Heine University Düsseldorf, Germany
:  S9 - The network of life: algorithmic and modelling challenges  -  17:00-18:30
Phylogenomic networks provide insights into the chimerical origin of eukaryotes
David Alvarez-Ponce*1, Eric Bapteste2, Philippe Lopez2, James McInerney1
1National University of Ireland Maynooth, Ireland, 2Université Pierre et Marie Curie, France
:  S9 - The network of life: algorithmic and modelling challenges  -  15:00-16:30
Phylogenomics on African lake cichlids: the evolution of transcriptomes during explosive speciation
Zuzana Musilova*, Walter Salzburger
University of Basel, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogenomics, and microRNAs congruently resolve the ecdysozoan phylogeny
Davide Pisani*1, Omar Rota-Stabelli2, Lahcen Campbell1
1The National University of Ireland Maynooth, Ireland, 2IASMA Research and Innovation Centre, Fondazione Edmund Mach, Italy
:  S8 - The animal tree of life and its applications  -  17:00-18:30
Phylogeny and Nomenclature of Histone Variants
Paul B. Talbert*1, Kami Ahamd2, Geneviève Almouzni3, Juan Ausio4, Frederic Berger5, Prem L. Bhalla6, William M. Bonner7, W. Zacheus Cande8, Brian P. Chadwick9, Simon W. L. Chan10, George A. M. Cross11, Liwang Cui12, Stefan I. Dimitrov13, Detlef Doenecke14, José M. Eirin-López15, Martin A. Gorovsky16, Sandra B. Hake17, Barbara A. Hamkalo18, Sarah Holec5, Steven E. Jacobsen19
1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, USA, 2Department of BCMP, Harvard Medical School, USA, 3CNRS, Institut Curie, Centre de Recherche, France, 4University of Victoria, Canada, 5Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 6Plant Molecular Biology and Biotechnology Group, The University of Melbourne, Australia, 7Laboratory of Molecular Pharmacology, CCR, NCI, NIH,, USA, 8Department of Molecular and Cell Biology, University of California, USA, 9Department of Biological Science, Florida State University, USA, 10Department of Plant Biology, UC Davis / HHMI, USA, 11Laboratory of Molecular Parasitology, The Rockefeller University, USA, 12Department of Entomology, Pennsylvania State University, USA, 13Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation, Institut Albert Bonniot, France, 14Department of Biochemistry, University of Goettingen, Germany, 15Department of Cellular and Molecular Biology, University of A Coruna, Spain, 16Department of Biology, University of Rochester, USA, 17Center for Integrated Protein Science Munich at the Adolf-Butenandt Institute, Department for Molecular Biology, Ludwig-Maximilians-University Munich, Germany, 18Department of Molecular Biology & Biochemistry, University of CA, USA, 19Howard Hughes Medical Institute, Department of Molecular Cellular and Developmental Biology, University of California, Los Angeles,, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Phylogeny of Prokaryotic Cyanobacteria: a tale of two species
Cristiana Moreira*1,2, Vitor Vasconcelos1,2, Agostinho Antunes1,2
1CIMAR/CIIMAR/ Laboratory of Ecotoxicology, Genomics and Evolution, Portugal, 2Faculty of Sciences University of Porto, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylogeny-aware Analysis of Metagenomic Samples
Alexandros Stamatakis*, Simon Berger, Nikos Alachiotis
Heidelberg Institute for Theoretical Studies, Germany
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  11:30-13:00
Phylogeography in habitat generalists and specialists in the granite inselbergs of Namibia.
Sara Tromp, Anne Goldizen, Jenny Seddon*
The University of Queensland, Australia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Phylogeography: a new statistical approach for measuring dispersal ranges and competitive exclusion.
Louis Ranjard*, Stephane Guindon, David Welch
University of Auckland, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Phylomedicine: Evolutionary Diagnosis of Variants in Personal Exomes
Sudhir Kumar
Center for Evolutionary Medicine & Informatics, Arizona State University,, USA
:  S8 - The animal tree of life and its applications  -  17:00-18:30
PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences
Gaurav Bhardwaj*1, Sree Chintapalli1, Yoojin Hong0,2, Zhenhai Zhang0,2, Edward Holmes0,2, Damian van Rossum0,2, Randen Patterson1
1University of California, Davis, USA, 2Pennsylvania State University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement
Wenwen Fang1, Xing Wang1, John Bracht1, Mariusz Nowacki1,2, Laura Landweber*1
1Princeton University, USA, 2University of Bern, Switzerland
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  09:30-11:00
Placental endogenous retroviruses facilitate rapid evolution of core trophoblast regulatory network.
Edward Chuong*1, Mohammad Rumi2, Michael Soares2, Julie Baker1
1Stanford University, USA, 2University of Kansas Medical Center, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Plant population paleogenomics using long-term balanced polymorphisms: detection of old genetic bottlenecks using allelic genealogies at the self-incompatibility locus in Brassicaceae
Xavier Vekemans*, Céline Poux, Pauline Goubet, Sophie Gallina, Vincent Castric
UMR CNRS GEPV, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Polycistronic microRNAs arise by tandem duplication and de novo emergence
Antonio Marco*, Sam Griffiths-Jones
University of Manchester, UK
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  14:00-15:30
Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
Hunter Fraser*1, Sasha Levy1,4, Arun Chavan2, Hiral Shah2, Christian Perez3, Yiqi Zhou1, Mark Siegal4, Himanshu Sinha2
1Stanford University, USA, 2Tata Institute of Fundamental Research, India, 3UCSF, USA, 4New York University, USA
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  14:00-15:30
Polymorphism Pattern of a MITE Locus Downstream of the Domestication Gene Teosinte-Branched1 in Wild and Cultivated Pearl Millet
Yann Dussert*1, Marie-Stanislas Remigereau2, Fontaine Michaël1,3, Alodie Snirc1, Ghayas Lakis1, Solenn Stoeckel4, Thierry Langin5, Aboubakry Sarr1, Thierry Robert1
1Ecologie, Systématique et Evolution, UMR 8079, Univ. Paris Sud, France, 2University of Southern California Molecular & Computational Biology, USA, 3Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ. Paris Diderot, France, 4INRA, UMR 1099, Biology of Organisms and Populations applied to Plant Protection, France, 5INRA, UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Polymorphism, recombination and selection efficiency along the complete genome of Drosophila Melanogaster.
Maite Garazi Barron Aduriz*1,2, David Castellano Esteve1,2, Miquel Ramia Jesus1,2, Antonio Barbadilla Prados1,2
1Universitat Autonoma de Barcelona, UAB, Spain, 2Institut de Biotecnologia i Biomedicina, IBB, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
PopGenome: An R-library for large-scale population genetic analysis
Bastian Pfeifer*, Ulrich Wittelsbürger, Martin Lercher
Institute for Computer Science Heinrich-Heine-University, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population and sex differences in Drosophila brain gene expression
Ana Catalan*, John Parsch
LMU, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Population dynamics of bacteriophage T7 on heterogeneous Escherichia coli substrates
Wolfram Möbius*1, Andrew W. Murray2, David R. Nelson1
1Department of Physics and FAS Center for Systems Biology, Harvard University, USA, 2FAS Center for Systems Biology and Department of Molecular and Cellular Biology, Harvard University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genetic inference from single genomes
Priyanka Sinha*1, Aslihan Dincer2, Daniel Virgil2, Guang Xu2, Yu-Ping Poh2, Jeffrey Jensen1
1ÉCOLE POLYTECHNIQUE FÉDÉRALE DE LAUSANNE, Switzerland, 2Univ of Massachusetts Medical School, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genetic properties of time serial data with examples from ancient population-genomic data
Mattias Jakobsson
Uppsala University, Sweden
:  S2 - Paleogenomics: from fossils to genomes  -  11:30-13:00
Population genetic structure of genome-wide SNP variation in wild Arabidopsis thaliana from the Western Mediterranean region
Adrian C. Brennan*1, Belen Méndez-Vigo2, Abdel Haddioui3, José M. Martínez-Zapater4, F. Xavier Picó1, Carlos Alonso-Blanco2
1Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Spain, 2Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Spain, 3Faculté des Sciences et Techniques, Université Sultan Moulay Slimane, Morocco, 4Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas (CSIC), Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population Genetics of the Sex-Locus in a closed Population of the Honey Bee (Apis mellifera) Marcel Medrano, Dr Michael Lattorff, Pr Dr Robin Moritz
Marcel Medrano*, Michael Lattorff, Robin Moritz
Martin-Luther-Universität Halle-Wittenberg, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Population genomic analysis and de novo genome assembly of the mangrove rivulus, Kryptolebias marmoratus, a self-fertilizing hermaphroditic fish
Joanna L. Kelley*1, Muh-Ching Yee1, Clarence Lee2, Elizabeth Levandowsky2, Minita Shah2, Craig Cummings2, Ryan Earley3, Carlos Bustamante1, Timothy Harkins2
1Stanford University, USA, 2Life Technologies Corporation, USA, 3University of Alabama, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genomic evidence for widespread selection on symbiosis-related genes in the facultatively mutualistic rhizobia Sinorhizobium meliloti and S. medicae
Brendan Epstein*, Michael Sadowsky, Peter Tiffin
University of Minnesota, USA
Monday 25th June 2012:  S12 - Microbial genome evolution  -  09:30 - 11:00
Population genomic inference for recently bottlenecked selfing species.
Yaniv Brandvain*1, Stephen Wright2, Graham Coop1
1University of California - Davis, USA, 2University of Toronto, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genomics of highly polymorphic species Ciona savignyi using high-throughput sequencing
Mariya Baranova*1, Yegor Bazykin1, Alexei Kondrashov1,2
1MSU, Russia, 2University of Michigan, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genomics of Ostreococcus tauri
Blanc-Mathieu Romain*, Derelle Evelyne, Grimsley Nigel, Moreau Hervé, Piganeau Gwenael
Observatoire Océanologique, UPMC Univ Paris 06, UMR 7232, BIOM, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genomics of sub-Saharan Drosophila melanogaster:  African diversity and non-African admixture
John Pool*1, Kristian Stevens2, Charis Cardeno2, Ryuichi Sugino1, Russell Corbett-Detig3, Marc Crepeau2, Pablo Duchen4, James Emerson5, Perot Saelao2, David Begun2, Charles Langley0
1University of Wisconsin - Madison, USA, 2University of California - Davis, USA, 3Harvard University, USA, 4Ludwig Maximilians Universitat, Germany, 5University of California - Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population genomics of threespine stickleback after 30-year evolution experiment
Nadezhda Terekhanova*1, Nicolai Mugue2, Georgii Bazykin1,4, Alexey Kondrashov1,3
1Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Russia, 2Institute of Developmental Biology RAS / VNIRO, Russia, 3Life Sciences Institute, USA, 4A. A. Kharkevich Institute for Information Transmission Problems, Russia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Population mitogenomics of Eurasian mammoths using barcoded microarray capture and high-throughput sequencing
Michael Knapp*1, Matthias Meyer2, Sebastian Lippold2, Martin Kircher2, Beth Shapiro3, Michael Hofreiter4
1University of Otago, New Zealand, 2Max Planck Institute for Evolutionary Anthropology, Germany, 3Pennsylvania State University, USA, 4University of York, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population structure and demographic pre-history of the Solomon Islands
Ana Duggan*, Mark Stoneking
Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Population structure and evidence of selection in the Khoe-San and Coloured populations from southern Africa
Carina Schlebusch*1, Pontus Skoglund1, Per Sjödin1, Lucie Gattepaille1, Sen Li1, Flora Jay2, Dena Hernandez3, Andrew Singleton3, Michael Blum2, Himla Soodyall4,5, Mattias Jakobsson1
1Uppsala University, Sweden, 2Université Joseph Fourier, France, 3National Institute on Aging (NIH), USA, 4University of the Witwatersrand, South Africa, 5National Health Laboratory Service, South Africa
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Populations genetics of the Neolithic transition
Joachim Burger*1, Mark Thomas2,3
1Johannes Gutenberg University, Institute of Anthropology, Germany, 2Research Department of Genetics, Evolution and Environment, University College London, UK, 3Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
:  S2 - Paleogenomics: from fossils to genomes  -  09:30-11:00
Positionally-biased gene loss after whole genome duplication: evidence from human, yeast and plant
Takashi Makino*1,2, Aoife McLysaght1
1Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland, 2Graduate School of Life Sciences, Tohoku University, Japan
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  14:30-16:00
Positive and negative selection in splice sites
Stepan Denisov*1, Georgii Bazykin1,2, Alexander Favorov3,4, Andrey Mironov1,2, Mikhail Gelfand1,2
1A.A. Kharkevich Insitute for Information Transmission Problems, Russia, 2M.V. Lomonosov Moscow State University, Russia, 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, USA, 4N.I. Vavilov Institute of General Genetics, Russia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Positive selection and diversification of the V1R gene family in strepsirrhine primates
Nick Mundy*1, Philipp Kappel1,2, Ute Radespiel2
1University of Cambridge, UK, 2University of Hannover, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Positive selection for gains of N-linked glycosylation sites in hemagglutinin during evolution of H3N2 human influenza A virus
Yoshiyuki Suzuki
Nagoya City University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Positive Selection on Genes involved in Zinc Homeostasis in Modern Humans
Johannes Engelken*1,2, Elena Carnero-Montoro1, Marc Pybus1, Manu Uzcudun1, Giovanni M. Dall’Olio1, Pierre Luisi1, Jaume Bertranpetit1, Mark Stoneking2, Elena Bosch1
1Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Spain, 2Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Germany
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Positively charged residues affect the speed of translation much more than non-optimal codons
Catherine Charneski*, Laurence Hurst
University of Bath, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
PRDM9 binding targets occur within most human recombination hotspots
Nudrat Noor*2, Alexandru Aricescu1, Julian Knight2, Gil McVean1,2, Simon Myers1,2
1Department of Statistics, UK, 2Wellcome Trust Centre for Human Genetics, UK, 3Division of Structural Biology, Wellcome Trust Centre for Human Genetics, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Predicting and Testing Human-specific Developmental Enhancers
John Capra*, Genevieve Erwin, Katherine Pollard
Gladstone Institutes, University of California, San Francisco, USA
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  14:30-16:00
PRELIMINARY SEQUENCING AND COMPARATIVE ANALYSIS OF CARNIVORE Y CHROMOSOMES
GANG LI*1, Alison Pearks-Wilkerson1, Tess Crider1, Terje Raudsepp1, Victor Mason1, Brian Davis1, Bhanu Chowdhary1, Malcolm Ferguson-Smith2, Patricia O’Brien2, Tina Graves3, Derek Albracht3, Wesley Warren3, William Murphy1
1Department of Veterinary Integrative Biosciences, Texas A&M University, USA, 2Cambridge Resource Centre for Comparative Genomics, UK, 3Washington University Genome Sequencing Center, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Preservation of the Y transcriptome in a 10 million-year-old plant sex chromosome system 
Roberta Bergero*, Deborah Charlesworth
Inst. Evolutionary Biology, University of Edinburgh, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Prevalence and Genetic Diversity of Microsporidia intracellular parasites across fire ant species in South America
Gebreyes Kassu
University of Florida, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Private haplotypes as detectors for population-specific selection
Agnès Sjöstrand*1,2, Per Sjödin2,3, Mattias Jakobsson2
1MNHN, France, 2EBC, Uppsala University, Sweden, 3SLU, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Probabilistic parsimonious reconciliation between genes and species trees
Leonardo de Oliveira Martins*, David Posada
University of Vigo, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Profiling diverse levels of natural selection across regions of coding gene sequences
Ning Li*1, Zhang Zhang2, Jeffrey Townsend1
1Yale University, USA, 2Beijing Institute of Genomics, China
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Promoter regions of duplicated Schistosoma mansoni genes crucial for infection success undergo rapid epigenetic modifications in varying environments while remaining genetically stable
Cecile Perrin1, Julie MJ Lepesant1, Emmanuel Roger2, David Duval1, Virginie Thuillier1, Jean Francois Alliene1, Guillaume Mitta1, Christoph Grunau1, Celine Cosseau*1
1UMR5244 CNRS UPVD, France, 2CNRS UMR 8204, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Protein-Chaperone Connectivity in Yeast and Protein Ancestry
David Bogumil*1, David Alvarez-Ponce2, Giddy Landan1, James McInerney2, Tal Dagan1
1Institute of Molecular Evolution, Heinrich-Heine University, Germany, 2Department of Biology, National University of Ireland, Ireland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
“Proto-genes” and de novo gene birth
Anne-Ruxandra Carvunis*1,2, Thomas Rolland1, Ilan Wapinski3, Muhammed Yildirim1, Nicolas Simonis1, Benoit Charloteaux1, Cesar Hidalgo4, Michael Calderwood1, Balaji Santhanam1, Gloria Brar5, Jonathan Weissman5, Aviv Regev6, Nicolas Thierry-Mieg2, Michael Cusick1, Marc Vidal1
1Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, USA, 2UJF-Grenoble 1 / CNRS / TIMC-IMAG UMR 5525, Computational and Mathematical Biology Group, France, 3Department of Systems Biology, Harvard Medical School, USA, 4The MIT Media Lab, Massachusetts Institute of Technology, USA, 5Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, USA, 6Broad Institute of MIT and Harvard, USA
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  16:30-18:00
Purifying and positive selection in the Medicago truncatula genome
Timothy Paape*1, Peng Zhao1, Thomas Batiallon2, Nevin Young1, Peter Tiffin1
1University of Minnesota, USA, 2University of Denmark-Aarhus, Denmark
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Quantifying beta diversity over phylogenetic networks
Donovan Parks*, Robert Beiko
Dalhousie University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Quantifying genome-wide fine-scale recombination rates in Saccharomyces cerevisiae from advanced intercross lines
Christopher Illingworth*1, Leopold Parts2, Gianni Liti3, Ville Mustonen1
1Wellcome Trust Sanger Institute, UK, 2University of Toronto, Canada, 3University of Nice Sophia-Antipolis, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Quantifying phylogenetic signal
Mike Steel
University of Canterbury, New Zealand
:  S6 - Gene/genome data and the limits to  -  15:00-16:30
Quantitative analysis of genetic and environmental factors determining variation in cell growth
Naomi Ziv*, Mark Siegal, David Gresham
New York University, USA
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  16:30-18:00
Quantitative trait mapping of trans-regulatory factors associated with opsin gene expression in cichlid fishes
Kelly O'Quin*, Jane Schulte, Zil Patel, Matthew Conte, Karen Carleton
University of Maryland, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Radical Genome Architectures in Oxytricha: Diminution, Unscrambling, and Comparative Genomics in a Single Cell
Xiao Chen1, John Bracht1, Aaron Goldman*1, Egor Dolzhenko1,2, Estienne Swart1, Laura Landweber1
1Princeton University, USA, 2University of South Florida, USA
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  14:30-16:00
Rapid and Dynamic Evolution of Biosynthetic Gene Clusters in Microbial Genomes
Marnix H Medema*1,2, Peter Cimermancic3, Michael A Fischbach3, Rainer Breitling2,4, Eriko Takano1
1Department of Microbial Physiology, University of Groningen, The Netherlands, 2Groningen Bioinformatics Centre, University of Groningen, The Netherlands, 3Department of Bioengineering and Therapeutic Sciences, UCSF, USA, 4Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes
Aline Muyle1, Niklaus Zemp2, Clothilde Deschamps3, Sylvain Mousset1, Alex Widmer2, Gabriel Marais*1
1CNRS / Université Lyon 1, France, 2ETH Zurich, Switzerland, 3Pôle Rhône-Alpes de Bioiformatique, France
:  S11 - Sex chromosome evolution illuminated by next-generation sequencing technology  -  17:00-18:30
Rapid development of novel protein-coding gene markers for population genetics and phylogenetics in crucifers (Brassicaceae) using a next generation sequencing approach
Stefan Zoller*1, Martin C. Fischer2, Rie Inatsugi4, Felix Gugerli3, Rolf Holderegger3, Kentaro Shimizu4, Alex Widmer2
1Genetic Diversity Centre, ETH Zurich, Switzerland, 2Plant Ecological Genetics, ETH Zurich, Switzerland, 3Biodiversity and Conservation Biology, WSL Federal Research Institute, Switzerland, 4Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Rapid diversification of Drosophila telomere capping genes.
Raphaëlle Dubruille*1, Gabriel Marais2, Benjamin Loppin1
1CGphiMC - University of Lyon - CNRS, France, 2LBBE - University of Lyon - CNRS, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Rapid ecological speciation driven by selection on a small set of ‘adaptation' genes
Mark Chapman*, Dmitry Filatov
University of Oxford, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Rapid evolution in lipid and metabolic composition of the human brain
Kasia Bozek*1, Patrick Giavalisco2, Philipp Khaitovich1
1Partner Institute for Computational Biology MPG-CAS, China, 2Max Planck Institute of Molecular Plant Physiology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Rapid fixation of duplications and deletions in experimental Caenorhabditis elegans populations during adaptive recovery.
Vaishali Katju*, James Farslow, Ulfar Bergthorsson
University of New Mexico, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Recent and contrasting evolutionary change in human and chimpanzee bone phenotypes: primate population genetics of type I collagen (COL1A1)
Daryn Stover*2,1, Anne Stone1, Brian Verrelli1
1Arizona State University, USA, 2Simon Fraser University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Recent ecological speciation and local adaptation along an altitudinal gradient on Mount Etna.
Owen Osborne*1, Graham Muir1,3, Jonas Sarasa-Marcuello1, Simon Hiscock2, Dmitry Filatov1
1University of Oxford, UK, 2University of Bristol, UK, 3Heidelberg University, Germany
:  S1 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Recent specialization of the human and mouse X chromosomes for the male germline
Jacob Mueller*1, Helen Skaletsky1, Laura Brown1, Sara Zaghul1, Susie Rock2, Wesley Warren2, Richard Wilson2, David Page1
1Whitehead Institute, USA, 2Washington University Genome Center, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Recombination in the Human Pseudo-Autosomal Region (PAR1)
Anjali Hinch*1, Arti Tandon2, David Reich2, Simon Myers1
1Oxford University, UK, 2Harvard Medical School, USA
:  S11 - Sex chromosome evolution illuminated by next-generation sequencing technology  -  17:00-18:30
Recombinations associated with Gene Transfer Events Reveal a Complex Evolutionary History of Aminoacyl-tRNA Synthetases
Greg Fournier1,2
1MIT, USA, 2NASA Astrobiology Institute, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Reconstructing cell-lineages trees using somatic microsatellite instability
Yosef Maruvka*1,2, Yitzhak Reizel3, Noa Chapal-Ilani3, Ehud Shapiro3
1Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute, USA, 2Department of Biostatistics, Harvard School of Public Health, USA, 3Department of Computer Science and Applied Mathematics, Weizmann Institute of Science,, Israel
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Reconstructing demographic histories from long tracts of DNA sequence identity
Kelley Harris*1, Rasmus Nielsen1,2
1UC Berkeley, USA, 2University of Copenhagen, Denmark
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
Reconstructing functional networks of the last common ancestor
Aaron Goldman*, Laura Landweber
Princeton University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Reconstructing past Native American genetic diversity in Puerto Rico from contemporary populations
Marina Muzzio*1,2, Fouad Zakharia1, Karla Sandoval1, Jake K. Byrnes3, Andres Moreno-Estrada1, Simon Gravel1, Eimear Kenny1, Juan L. Rodriguez-Flores5, Chris R. Gignoux6, Wilfried Guiblet4, Julie Dutil7, The 1000 Genomes Consortium0, Andres Ruiz-Linares8, David Reich9,10, Taras K. Oleksyk4, Juan Carlos Martinez-Cruzado4, Esteban Gonzalez Burchard6, Carlos D. Bustamante1
1Department of Genetics, Stanford University School of Medicine, USA, 2Facultad de Ciencias Naturales, Universidad Nacional de La Plata, Argentina, 3Ancestry. com®, USA, 4Department of Biology, University of Puerto Rico at Mayagüez, Puerto Rico, 5Department of Genetic Medicine, Weill Cornell Medical College, USA, 6Institute for Human Genetics, University of California San Francisco, USA, 7Ponce School of Medicine, Puerto Rico, 8Department of Genetics, Evolution and Environment. University College London, UK, 9Department of Genetics, Harvard Medical School, USA, 10Broad Institute of MIT and Harvard, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Reconstruction of ancestral maltase enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication
Karin Voordeckers1,2, Chris A. Brown1,3, Kevin Vanneste4,5, Elisa van der Zande1,2, Arnout Voet6, Steven Maere*4,5, Kevin J. Verstrepen1,2
1VIB Laboratory for Systems Biology, Belgium, 2CMPG Laboratory for Genetics and Genomics, K.U.Leuven, Belgium, 3Faculty of Arts and Sciences Center for Systems Biology, Harvard University, USA, 4VIB Department of Plant Systems Biology, Belgium, 5Department of Plant Biotechnology and Genetics, Ghent University, Belgium, 6Laboratory for Molecular en Structural Biology, K.U.Leuven, Belgium
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  14:00-15:30
Recreating the Past: Reconstruction of a One-Billion-Year-Old-Enzyme
Joanne Hobbs*1, Charis Shepherd2, David Saul3, Nicholas Demetras1, Svend Haaning1, Colin Monk1, Roy Daniel1, Vickery Arcus1
1University of Waikato, New Zealand, 2Otago Medical School, New Zealand, 3ZyGEM Corporation Ltd., New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
RECURRENT MUTATIONS IN THE HUMAN MITOCHONDRIAL GENOMIC PHYLOGENY - EVIDENCE FOR CONVERGENT EVOLUTION?
Liron Levin, Ilia Zhidkov, Yotam Gurman, Dan Mishmar*
Ben Gurion University of the Negev, Israel
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Recurrent patterns in the evolution of self-compatibility in Arabidopsis (Brassicaceae)
Takashi Tsuchimatsu, Pascal Kaiser, Julien Bachelier, Chow Lih Yew, Kevin Ng Kit Siong, Kentaro Shimizu*
University of Zurich, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Recurrent positive selection at the same amino acids in primates and human populations
Renee George*1, Graham McVicker2, Josh Akey1, Willie Swanson1
1University of Washington, USA, 2University of Chicago, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species 
Suo Qiu1,2, Kai Zeng1, Tanja Slotte4, Stephen Wright3, Deborah Charlesworth*1
1University of Edinburgh, UK, 2Sun Yat-Sen University, China, 3University of Toronto, Canada, 4Uppsala University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Regions of Homozygosity in the Porcine genome: interactions between demography and the recombination landscape
Mirte Bosse*, Ole Madsen, Hendrik-Jan Megens, Richard Crooijmans, Laurent Frantz, Yogesh Paudel, Martien Groenen
Wageningen University, The Netherlands
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of land plants and green algae
David Smith*1, Jimeng Hua2, Robert Lee2, Patrick Keeling1
1University of British Columbia, Canada, 2Dalhousie University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Relaxation of selective constraint in the human genome
Mehmet Somel*, Emilia Huerta-Sanchez, Kirk Lohmueller, Melissa Wilson Sayres, Anna Ferrer-Admetlla, Matteo Fumagalli, Rori Rohlfs, Rasmus Nielsen
UC Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Repeatability in evolution varies with scale, organism, and the nature of selection.
Elizabeth B. Perry*, Kristin Alligood, Brendan J.M. Bohannan
University of Oregon - Institute of Ecology and Evolution, USA
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
Reticulate evolutionary history of eudicot model species
Martin Lercher*, Christian Esser, Daniel Hartleb
Heinrich-Heine-University, Germany
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  16:00-17:30
Reticulated origin of domesticated tetraploid wheat
Peter Civan
Centro de Ciencias do Mar, Universidade do Algarve, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Revaluating duplication gene evolution from the perspective of their phylogenetic origin
Krishna Swamy*1,2, Chien-Hao Su2, Daryi Wang3, Huai-Kuang Tsai1,2
1Bioinformatics Program, Taiwan International Graduate Program,Academia Sinica, Taiwan, 2Institute of Information Science, Academia Sinica, Taiwan, 3Biodiversity Research Center, Academia Sinica, Taiwan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
RevBayes: One program for your whole phylogenetic analysis
Sebastian Höhna*1, Fredrik Ronquist2, John Huelsenbeck3
1Stockholm University, Sweden, 2Swedish Museum of Natural History, Sweden, 3University of California, Berkeley, USA
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  11:30-13:00
Reverse engineering the gap gene network in dipterans.
Anton Crombach*1, Karl Wotton1, Damjan Cicin-Sain1, Maksat Ashyralyyev2, Johannes Jaeger1
1Centre for Genomic Regulation (CRG), Spain, 2Bahçesehir Üniversitesi, Turkey
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Revisit the origin of mitochondria using universal mitochondrial proteins.
Ding He
Uppsala University, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Rewiring of the bacterial core gene regulatory network by homologous recombination may facilitate niche adaptation
Yaara Oren*, Tal Pupko
The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University,, Israel
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
RNA silencing, DNA methylation and its effects on plant genome size, structure and function
Brandon Gaut
University of California, Irvine, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  11:30-13:00
RNA-level unscrambling of systematically fragmented genes
Gertraud Burger*1, Georgette Kiethega1, Yifei Yan1, Marcel Turcotte0
1Universite de Montreal, Canada, 2University of Ottawa, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Roadmap to a Bat's Major Histocompatibility Complex (MHC) Class I Region: Organization & Characterization
Justin Ng*1,2, Katherine Belov2, Lin-Fa Wang1, Michelle Baker1
1CSIRO (Livestock Industries) - Australian Animal Health Laboratory, Australia, 2Faculty of Veterinary Science, University of Sydney, Australia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Robust Codon Usage in Protein Ligand Binding Sites
Tugce Bilgin*1,3, Isil Aksan Kurnaz4, Turkan Haliloglu5, Andreas Wagner1,2
1Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Switzerland, 2The Santa Fe Institute, USA, 3The Swiss Institute of Bioinformatics, Switzerland, 4Department of Genetics and Bioengineering, Yeditepe University, Turkey, 5Polymer Research Center, Bogazici University, Turkey
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Robust estimates of heterozygosity from low coverage sequencing data
Katarzyna Bryc*1, Nick Patterson2, David Reich1,2
1Harvard Medical School, USA, 2Broad Institute, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Robust handling of alignment uncertainty when inferring positive selection
Benjamin Redelings
NEScent, USA
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  16:00-17:30
Robust identification of local adaptation to environmental gradients with an application to Arabidopsis thaliana.
Torsten Günther*1, Christian Lampei1, Oliver Simon1, Karl J. Schmid1, Graham M. Coop2
1University of Hohenheim, Germany, 2University of California, USA
:  S10 - Population genetic inference from next-generation sequencing data  -  17:00-18:30
Robustness to stress in antibiotic resistant Escherichia coli
Ana Sousa*, Sandra Trindade, Isabel Gordo
Instituto Gulbenkian de Ciencia, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Role of low-complexity regions in protein formation and functional diversification
Núria Radó-Trilla*1, Macarena Toll-Riera1, Florian Martys1, M. Mar Albà1,2
1Evolutionary Genomics Group, Fundació Institut Municipal d’Investigació Mèdica (FIMIM)-Universitat Pompeu Fabra (UPF), Spain, 2Catalan Institution for Research and Advanced Studies (ICREA), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Role of MT3 gene in metalophyte plant, S. vulgaris
Eva NEVRTALOVA*, Roman HOBZA, Jiri BALOUN, Vojtech HUDZIECZEK, Radim Cegan
Institute of Biophysics, Czech Republic
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Role of positive selection versus relaxed negative selection in genes showing human-specific evolutionary rate acceleration
Magdalena Gayà-Vidal*1, M. Mar Albà1,2
1Evolutionary Genomics Group IMIM-UPF Research Programme on Biomedical Informatics. Barcelona Biomedical Research Park (PRBB), Spain, 2Catalan Institution for Research and Advanced Studies (ICREA), Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Rooted Phylogenetic Networks From Real Trees
Daniel Huson
University of Tuebingen, Germany
:  S9 - The network of life: algorithmic and modelling challenges  -  17:00-18:30
Salt tolerance in Arabidopsis thaliana: polymorphism and phenotypic response to salt stress
Eva Puerma*, Montserrat Aguadé
Universitat de Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Screening for transposable element-induced adaptations in Drosophila melanogaster using next-gen sequencing data
Anna-Sophie Fiston-Lavier*1, Josefa González2, Dmitri Petrov1
1Dept. of Biology, Stanford University, USA, 2Institute of Evolutionary Biology, (CSIC-UPF), Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Search for antimicrobial peptide against fungal-infection in Drosophila virilis.
Yosuke Seto*, Koichiro Tamura
Tokyo Metropolitan University, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Searching - and finding - bilaterian specific proteins
Andrea Kraemer-Eis, Peter Heger, Thomas Wiehe*
Universitaet zu Koeln, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Searching the genetic basis underlying the evolution of the human brain.
Lucía Franchini
INGEBI-CONICET, Argentina
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  14:30-16:00
Selection against loss-of-function alleles in Drosophila melanogaster populations
Aleksandra I. Akhmadullina*, Georgii A. Bazykin, Aleksey S. Kondrashov
Moscow State University, Russia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Selection on noncoding DNA in the Brassicaceae
Annabelle Haudry*1,2, Adrian Platts3, Stephen I. Wright2, Robert Williamson2, Emilio Vello3, Paul Harrison3, Thomas Bureau3, Alan Moses2, Mathieu Blanchette3
1University of Lyon, France, 2University of Toronto, Canada, 3McGill University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Selection on Wobble Sites in tRNA Anticodons in Vertebrate Mitochondrial Genomes with Codon Usage Reversal
Miguel M Fonseca*1,2, Sara Rocha1,2, David Posada2
1CIBIO-UP, Research Center in Biodiversity and Genetic Resources, Portugal, 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Selective constraint beyond apparent sequence conservation
Olga Vakhrusheva*1,2, Georgii Bazykin1,2, Alexey Kondrashov1,3
1Department of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Russia, 2Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Russia, 3Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Selective processes affecting candidate genes in contrasting adaptive chromosomal inversions
Marta Pascual*, Pedro Simoes, Gemma Calabria, Cinta Pegueroles, Francesc Mestres, Joan Balanya
Universitat de Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster
Sarah Saminadin-Peter, Claus Kemkemer, Pavlos Pavlidis, John Parsch*
University of Munich, Germany
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  14:30-16:00
Sequence conservation and gene-conversion; insights into highly conserved elements in mating-type loci in Saccharomyces cerevisiae
Yutaka Watanabe*, Denise Brooks, Alexander S. Mikheyev
Okinawa Institute Of Science And Technology, Japan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sequence Features That Determine Transcriptional Enhancers
Jeffrey Chuang*1, Deborah Ritter1, Ningtao Shi1, Kourosh Zarringhalam1, Zhiqiang Dong2, Su Guo2
1Boston College, USA, 2University of California, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Sequence similarity networks reveal gene fusion evolution.
Pierre-Alain Jachiet*1, Romain Pogorelcnik1, Eric Bapteste1, Philippe Lopez1
1Université Pierre et Marie Curie, France, 2LIMOS UMR CNRS 6158, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Sequencing and analysis of the European amphioxus (Branchiostoma lanceolatum) transcriptome
Silvan Oulion*, Stéphanie Bertrand, Mohamed Belgacem, Yann Le Pétillon, Hector Escriva
CNRS, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sequencing and analysis of the whole genome of the guppy, a model for natural variation and sex chromosome evolution
Axel Künstner*, Margarete Hoffmann, Christine Dreyer
Max Planck Institute for Developmental Biology, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sequencing of a Darwin's finch genome: evidence against the selective thermal stability hypothesis, and evidence for a neutral explanation for the origin of isochores
Chris Rands*1, Matthew Fujita2,1, Lesheng Kong1, Aaron Darling3, Céline Clabaut2, Richard Emes4, Andreas Heger1, Tim Harkins5, Clotilde Teiling5, Matthew Webster6, Stephen Meader1, Peter Grant7, Rosemary Grant7, Jonathan Eisen3, Arkhat Abzhanov2, Chris Ponting1
1University of Oxford, UK, 2Harvard University, USA, 3University of California, Davis, USA, 4University of Nottingham, UK, 5Roche Applied Science, USA, 6Uppsala University, Sweden, 7Princeton University, USA
:  S5 - Adaptive vs. non-adaptive evolution  -  09:30-11:00
Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster
Robert Kofler, Andrea Betancourt*, Christian Schlötterer
Institute for Population Genetics, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Sergey A. Naumenko and Alexey S. Kondrashov. Rate and breadth of protein evolution are only weakly correlated
Sergey Naumenko*1,2, Alexey Kondrashov2
1IITP RAS, Russia, 2Moscow State University, Russia, 33Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sex can restrict evolvability
Ricardo Azevedo*1, Tiago Paixão1,2
1University of Houston, USA, 2Institute of Science and Technology, Austria
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  14:30-16:00
Sex chromosome differentiation and evolution across multiple natural stickleback populations
Frédéric Chain*1, Philine Feulner2, Mahesh Panchal1, Christophe Eizaguirre3,1, Martin Kalbe1, Andrew Moore2, Erich Bornberg-Bauer2, Thorsten Reusch3, Manfred Milinski1
1Max Planck Institute for Evolutionary Biology, Germany, 2Westfaelische Wilhelms University, Germany, 3IFM-GEOMAR, Institute for Marine Sciences, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sex determination in the brown alga Ectocarpus
Sophia Ahmed1, Rémy Luthringer1, Alexandre Cormier1, Akira Peters2, Marine Robouchon1, John Bothwell4, Denis Roze1, Gabriel Marais3, Cock Mark1, Coelho Susana*1
1Station Biologique de Roscoff, CNRS and UPMC, France, 2Bezhin Rosko, France, 3UMR CNRS 5558 - LBBE, France, 4Queen's University, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sex ratio between Y/A chromosomes, Y-haplotype diversity and frequency spectrum patterns confirms a marked ancient isolation in pigs (Sus scrofa)
Oscar Ramirez1, Ana Ojeda2, Marcel Amills2,3, Greger Larson4, Miguel Pérez-Enciso2,3, Sebastian Ramos-Onsins*3
1Institute of Evolutionary Biology (UPF-CSIC), Spain, 2Departament de Ciència Animal i dels Aliments Facultat de Veterinaria. Universitat Autònoma de Barcelona (UAB), Spain, 3Department of Animal Genetics Centre for Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB Edifici CRAG, Campus UAB, Spain, 4Department of Archaeology, University of Durham, UK, 5Institut Català de Recerca i Estudis Avançats (ICREA), Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Sex specific gene expression and haplodiploidy purging in an ant
Kalevi Trontti*, Heikki Helanterä, Christopher Wheat
Department of Biosciences, Finland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sex, flies and (possibly) conflict: the molecular evolution of Germline Stem Cell genes
Charles “Chip” Aquadro*1,2, Heather A. Flores1,2, Vanessa Bauer DuMont1,2, Jae Choi1,2, Daniel Barbash1,2
1Cornell Center for Comparative and Population Genomics, Cornell University, USA, 2Department of Molecular Biology and Genetics, Cornell University, USA
Posters:  Nei Lecture: Sex, flies and (possibly) conflict: the molecular evolution of Germline Stem Cell genes  -  18:00 - 19:00
Sex-specific embryonic gene expression at different stages of sex chromosome evolution
Susan E. Lott*, Jacqueline E. Villalta, Doris Bachtrog, Michael B. Eisen
University of California, Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Shaping microbial genomes: the source of each gene and the impact of habitat and evolutionary distance on lateral gene transfer
Conor Meehan*, Robert Beiko
Dalhousie University, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Shifting fitness consequence of variation in LCB2 gene expression in yeast
Joshua Rest*1, Christopher Morales1, John Waldron1, Dana Opulente1, Julius Fisher1, Seungjae Moon1,2, Kevin Bullaughey3, Lucas Carey4, Demitri Dedousis1
1Stony Brook University, USA, 2Weill Cornell Graduate School of Medical Science, USA, 3University of Chicago, USA, 4Weizmann Institute of Science, Israel
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Signals of positive selection in North African human populations
Laura R. Botigué*1, Brenna M. Henn2, David Comas1, Carlos D. Bustamante2
1IBE (UPF-CSIC), Spain, 2Department of Genetics, Stanford University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Signatures of divergence and selection in Cardiocondyla obscurior
Lukas Schrader*1, Antonia Klein1, Jürgen Heinze1, Jürgen Gadau2, Jan Oettler1
1University Regensburg, Germany, 2Arizona State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Signatures of genome-wide convergent molecular evolution: initial results.
Joe Parker*1, Georgia Tsagkogeorga1, James A. Cotton3, Elia Stupka2, Stephen J. Rossiter1
1School of Biological and Chemical Sciences, Queen Mary, University of London, UK, 2Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Italy, 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Signatures of nitrogen limitation in the Bison Pool metagenomeSignatures of nitrogen limitation in the Bison Pool metagenome
Claudia Acquisti*, Tabea Hoemann
IEB, WWU Muenster, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
SIGNIFICANT CLUSTERING ON GEOMETRIC MORPHOMETRICS DATA: DEFINING EVOLUTIONARY MODULES IN COMPLEX BIOLOGICAL DATASETS
Jose Sergio Hleap*1,2, Christian Blouin1
1Dalhousie University, Canada, 2Fundación SQUALUS, Colombia
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Signs for balancing selection in S. paradoxus
Na Gao*, Martin J. Lercher
Institute for Computer Science Heinrich-Heine-University Duesseldorf, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Signs of adaptation in interacting genes
Joséphine Daub*1,3, Marc Robinson-Rechavi2,3, Laurent Excoffier1,3
1University of Berne, Switzerland, 2University of Lausanne, Switzerland, 3Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Simulating evolutionary scenarios to test whether they can induce reductive evolution
Berenice Batut*1,2, Mathilde Dumond1, Gabriel Marais2, Guillaume Beslon1, Carole Knibbe1
1INRIA Beagle Team, France, 2BGE Team (LBBE), France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Simulating genome evolution with ALF
Daniel Dalquen*1,2, Maria Anisimova1,2, Gaston Gonnet1,2, Christophe Dessimoz1,2
1ETH Zurich, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Simultaneous protein multiple sequence alignment and tree construction using hidden Markov models.
Kimmen Sjolander
University of California Berkeley, USA
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  16:00-17:30
Simultaneously reconstructing species and gene histories by modelling gene duplication, transfer and loss.
Gergely J Szollosi*1, Bastien Boussau1,2, Eric Tannier1, Vincent Daubin1
1UMR CNRS 5558 LBBE, France, 2UC Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.
Nuno R Faria*1, Marc A Suchard2,3, Daniel G Streicker4, Philippe Lemey1
1Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium, 2Department of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, USA, 3Department of Biostatistics, UCLA School of Public Health, University of California, USA, 4Odum School of Ecology, University of Georgia, USA
:  S3 - Evolution of host-virus interactions  -  11:30-13:00
SINE-derived element as a regional determinant for the hypothalamic specificity of mammalian diencephalic Fgf8 enhancer
Akiko Nakanishi*1, Naoki Kobayashi1, Asuka Hirano-Suzuki2, Hidenori Nishihara1, Takeshi Sasaki1,5, Mika Hirakawa3,6, Kenta Sumiyama4, Tomomi Shimogori2, Norihiro Okada1
1Graduate School of Biotechnology, Tokyo Institute of Technology, Japan, 2RIKEN Brain Science Institute, Japan, 3Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan, 4National Institute of Genetics, Japan, 5Department of Human and Animal-Plant Relationships, Faculty of Agriculture, Tokyo University of Agriculture, Japan, 6Science Communication and Pruduction, JT Biohistory Research Hall, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model
Hannes Schabauer*1,2, Mario Valle3, Christoph Pacher4, Heinz Stockinger2, Alexandros Stamatakis5, Marc Robinson-Rechavi1,2, Ziheng Yang6, Nicolas Salamin1,2
1University of Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Switzerland, 3Swiss National Supercomputing Center, Switzerland, 4AIT Austrian Institute of Technology, Austria, 5Heidelberg Institute for Theoretical Studies, Germany, 6University College London, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Sox duplicate evolution and constraints from molecular properties
Emilien Voldoire*, Frédéric Brunet, Jean-Nicolas Volff, Delphine Galiana-Arnoux
The Institute of Functional Genomics of Lyon, ENS de Lyon, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Speciation within genomic networks: a case study based on lower Congo cichlidsp { margin-bottom: 0.21cm; }a:link {
Julia Schwarzer*1,2, Bernhard Misof1, Ulrich K. Schliewen2
1Zoologisches Forschungsmuseum A. Koenig, Zentrum für molekulare Biodiversitätsforschung, Germany, 2Zoologische Staatssammlung München, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Spot the difference! The genetic basis of an evolutionary novelty in cichlid fishes
M. Emilia Santos*, Walter Salzburger
University of Basel, Switzerland
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Statistical Methods for Detecting Selection Associated with High Altitude in Tibetans and Ethiopians
Rasmus Nielsen
UC Berkeley, USA
Monday 25th June 2012:  S16.1 - Adaptive Evolution and Selective Sweeps  -  09:30-11:00
Stepwise colonization of the Andes by Ruddy Ducks dispersing from North America accompanied by the evolution of novel beta-globin variants
Violeta Munoz-Fuentes*1,4, Maria Cortázar Chinarro4, Maria Lozano3, Kevin McCracken2
1Estacion Biologica de Donana-CSIC, Spain, 2University of Alaska Fairbanks, USA, 3Universidad de Los Andes, Colombia, 4Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Stop codons in bacteria are not selectively equivalent.
Inna Povolotskaya*1, Fyodor Kondrashov1,2, Peter Vlasov1
1Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Spain, 2Institució Catalana de Recerca i Estudis Avançats, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Stress and polyphenism: an RNA-Seq analysis in the butterfly Bicyclus anyana
Christopher Wheat1,2
1University of Helsinki, Finland, 2Stockholm University, Sweden, 3Leiden University, The Netherlands, 4University of California, Irvine, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Strong Purifying Selection at Synonymous Sites in D. melanogaster
David Lawrie*1, Philipp Messer1, Ruth Hershberg2, Dmitri Petrov1
1Stanford University, USA, 2Technion, Israel Institute of Technology, Israel
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Strong signatures of natural selection driving the evolution of MC1R in the Spanish population
Saioa López*1, Arrate Sevilla1, Neskuts Izagirre1, Conrado Martínez-Cárdenas5, Gloria Ribas2, Concepción de la Rúa1, Isabel Smith1, Montserrat Hervella1, Alicia Galdeano1, Mari Luz Cañavate1, Oscar García4, Jesús Gardeazabal3, Santos Alonso1
1Universidad del País Vasco/Euskal Herriko Unibertsitatea, Spain, 2Fundación Hospital Clínico Universitario-INCLIVA, Spain, 3Hospital de Cruces, Spain, 4Área de Laboratorio Ertzaintza. Sección de genética forense, Spain, 5Fundación Hospital Provincial de Castellón, Spain
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Structural evolution in high-grade serous ovarian cancer and its influence on patient outcome and chemotherapy resistance
Roland Schwarz*1,2, Susanna Cooke3, Charlotte Ng1,2, Jill Temple1, James Brenton1,2, Florian Markowetz1,2
1Cancer Research UK Cambridge Research Institute, UK, 2Department of Oncology, University of Cambridge, UK, 3The Wellcome Trust Sanger Institute, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Structural evolution of primate genomes mediated by highly similar duplicated sequences undergoing gene conversion
Jeffrey Fawcett*, Hideki Innan
Graduate University of Advanced Studies, Japan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Structural haplotypes and recent evolution of the human 17q21.31 locus
Linda Boettger*1,2, Robert Handsaker1,2, Michael Zody1,2, Steven McCarroll1,2
1Department of Genetics, Harvard Medical School, USA, 2Program in Medical and Population Genetics, Broad Institute, USA
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  16:30-18:00
Structural variation within and between natural stickleback populations
Philine Feulner*1, Frédéric Chain2, Mahesh Panchal2, Marvin Mundry1, Christophe Eizaguirre3, Martin Kalbe2, Tobias Lenz2, Andrew Moore1, Irene Samonte-Padilla2, Erich Bornberg-Bauer1, Thorsten Reusch3, Manfred Milinski2
1Westfaelische Wilhelms University, Germany, 2Max Planck Institute for Evolutionary Biology, Germany, 3Institute for Marine Sciences, Germany
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  16:30-18:00
Structured variations in intron/exon architecture according to gene intron number in two angiosperm species
Adrienne Ressayre*1,2, Pierre Montalent1,2, Christine Dillmann2, Johann Joets1,2
1INRA, France, 2Université Paris-Sud, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Studying patterns of genetic variation in long non coding RNAs along the Great Ape lineage
Marta Melé*1,2, Roderic Guigó2, Tomàs Marquès1
1IBE, Spain, 2CRG, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Studying Recoding in Bacterial genes
Virag Sharma*1, David Murphy1, Christophe Penno1, John F Atkins1,2, Pavel V Baranov1
1University College Cork, Ireland, 2University of Utah, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Studying the indirect impact of intrachromosomalrearrangements on the genome structure of microbes
Stephan Fischer*1,3, Carole Knibbe1,4, Samuel Bernard2,4, Guillaume Beslon1,3
1Inria Beagle Team, France, 2Inria Dracula Team, France, 3INSA-Lyon, France, 4Université Lyon I, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Successive gain of insulator proteins in arthropod evolution
Peter Heger, Thomas Wiehe*
Universitaet zu Koeln, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Successive masculinization of the avian Z chromosome
Alison Wright*1,2, Hooman Moghadam1, Judith Mank2
1University of Oxford, UK, 2University College London, UK
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
SuiteMSA and improving MSAs
Catherine Anderson, Etsuko Moriyama*
University of Nebraska-Lincoln, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Superessential reactions in metabolic networks and the evolution of drug resistance
Aditya Barve*1,3, João F. Matias Rodrigues2,3, Andreas Wagner1,3
1Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland, 2Institute of Molecular Life Sciences , University of Zurich, Switzerland, 3The Swiss Institute of Bioinformatics, Switzerland, 4The Santa Fe Institute, USA
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  14:00-15:30
Systematic error in seed plant phylogenomics
Bojian Zhong*1,2, Oliver Deusch1, Vadim V Goremykin3, David Penny1, Peter Lockhart1
1Institute of Molecular BioSciences, New Zealand, 2Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand, 3Istituto Agrario San Michele all’Adige Research Center, Italy
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
TAKING A MORE DETAILED LOOK AT MODEL ADEQUACY: RESIDUAL DIAGNOSTICS FOR PHYLOGENETICS
Sandra Meid*1, Bernhard Misof1, Christoph Mayer1, Barbara Holland0,2
1ZFMK, zmb, Germany, 2UTAS, Australia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Targeted sequencing of ancient DNA on a population level scale
Mathias Stiller*1,6, Duane Froese2, Grant Zazula3, Matthew Wooller4, Robert Wayne5, Beth Shapiro1,6
1Department of Ecology and Evolutionary Biology, University of California Santa Cruz, USA, 2Department of Earth and Atmospheric Sciences, University of Alberta, Canada, 3Department of Tourism and Culture, Yukon Palaeontology Program, Canada, 4Water and Environmental Research Center, University of Alaska Fairbanks, USA, 5Department of Ecology and Evolutionary Biology, University of California Los Angeles, USA, 6Department of Biology, The Pennsylvania State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Testing the link between human cognitive evolution and cognitive disorders
Xiling Liu*1, Philipp Khaitovich1,2
1Partner Institute for Computational Biology, Chinese Academy of Sciences, China, 2Max Planck Institute for Evolutionary Anthropology, Germany
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  16:00-17:30
Testing the status of infra generic taxonomic ranks in Triatomini (Hemiptera: Reduviidae)
Silvia Justi*, Claudia Russo
Universidade Federal do Rio de Janeiro, Brazil
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Testing the “suppressed recombination” model of chromosomal evolution during human-chimpanzee speciation.
Marta Farré1, Aurora Ruiz-Herrera*1,2
1Departament de Biologia Cel•lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Spain, 2Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Teximy - a newly identified gene on the Y chromosome of the platyfish is a member of an SGNH hydrolase multigene family mainly expressed in gonads
Marta Tomaszkiewicz*1, Manfred Schartl2, Delphine Galiana-Arnoux1, Jean-Nicolas Volff1
1The Institute of Functional Genomics of Lyon (IGFL), ENS de Lyon, France, 2University of Würzburg, Physiologische Chemie I, Biozentrum, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Adaptive Evolution Database: An Update  Russell Hermansen and David A. LiberlesDepartment of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
Russell Hermansen, David Liberles*
University of Wyoming, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Amborella Genome: An Evolutionary Reference Sequence for Comparative Plant Genomics
Jim Leebens-Mack*1, Josh Der2, Saravanaraj Ayyampalayam1, James Burnett5, Srikar Chamala3, Andre Chanderbali3, James Estill1, Yuannian Jiao2, Kun Liu5, Tianying Lan4, Eric Lyons6, Lynn Tomsho2, Hiabao Tang8, Eric Wafula2, Brandon Walts3, Victor Albert4, Brad Barbazuk3, Hong Ma2, David Sankoff7, Stephan Schuster2, Doug Soltis3, Pam Soltis3, Sue Wessler5, Claude dePamphilis2
1University of Georgia, USA, 2Pennsylvania State University, USA, 3University of Florida, USA, 4University of Buffalo, USA, 5University of California, Riverside, USA, 6University of Arizona, USA, 7University of Ottawa, Canada, 8J. Craig Venter Institute, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The ancient syntenic roots of the human genome
Manuel Irimia*1,2, Juan J. Tena3, Maria S. Alexis1, Ana Fernandez-Miñan3, Ignacio Maeso4, Ozren Bogdanović3, Elisa de la Calle-Mustienes3, Scott W. Roy1, Jose L. Gómez-Skarmeta3, Hunter B. Fraser1
1Stanford University, USA, 2University of Toronto, Canada, 3Centro Andaluz de Biología del Desarrollo (CABD), Spain, 4University of Oxford, UK
:  S4 - Genomic basis of Evo-Devo  -  11:30-13:00
The antigenic evolution of influenza viruses
Derek Smith
University of Cambridge, UK
:  S3 - Evolution of host-virus interactions  -  11:30-13:00
The asymptotic null distribution of certain likelihood ratio test statistics for detecting natural selection in codon sequences
Jean Kai Ling Lim
National University of Singapore, Singapore
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The BH Mixture Model
Liwen Zou*2, Edward Susko1, Chris Field1, Andrew J. Roger1
1Dalhousie University, Canada, 2North Carolina State University, USA
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  11:30-13:00
The Chimera Hypothesis for the Thermotogae Phylum
Kristen Swithers*, J. Peter Gogarten
University of Connecticut, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The complete mitochondrial genome of a third individual from Denisova Cave
Susanna Sawyer*1, Bence Viola1, Marie-Theres Gansauge1, Michael Shunkov2, Anatoly Derevianko2, Svante Pääbo1
1Max Planck Institute for Evolutionary Anthropology, Germany, 2Paleolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Russia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The crucial first step: Computational analysis of ancient DNA reads
Stinus Lindgreen3,1
1University of Copenhagen, Denmark, 2Centre for GeoGenetics, Denmark, 3University of Canterbury, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The demographic and adaptive history of domesticated and wild yeast
Angela Bean*1, Nicholas Renzette1, Oliver Rando1, Jeffrey Jensen1
1University of Massachusetts Medical School, USA, 2EPFL, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The details in the Devils: horizontal transfer of transposable elements in a carnivorous marsupial
Sarah Schaack
Reed College, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The Drosophila buzzatii Genome Project
Yolanda Guillén*1, Nuria Rius1, Alejandra Delprat1, Marta Puig1, Alfredo Ruiz1, Sònia Casillas2, Miquel Ràmia2, Antonio Barbadilla2, Gisela Mir3, Jordi Garcia-Mas3, Ivo Gut4, Jordi Camps4, David Torrens5, Valentí Moncunill5, Andrew G. Clark6, Robert L. Unckless6, Cedric Feschotte7, Aurelie Kapusta7
1Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain, 2Plataforma Bioinformàtica de la UAB, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain, 3Centre for Research in Agricultural Genomics (CRAG), Campus UAB, Edifici CRAG, Spain, 4Parc Científic de Barcelona, Centro Nacional de Análisis Genómico (CNAG), Torre I, Baldiri Reixac 4, Spain, 5Barcelona Supercomputing Center (BSC), Edifici TG (Torre Girona), Jordi Girona 31, Spain, 6Department of Molecular Biology and Genetics, Cornell University, USA, 7Department of Biology, University of Texas at Arlington, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The Drosophila miranda neo-Y transcriptome: De novo assembly and expression analysis of neo-sex linked genes
Vera Kaiser*, Doris Bachtrog
UC Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The effect of recurrent partial sweeps on patterns of neutral diversity
Graham Coop*, Peter Ralph
Dept. of Evolution and Ecology, UC Davis, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The effects of alternative splicing and structural disorderness on exonic evolutionary rates
Feng-Chi Chen*1,2, Chia-Lin Pan1, Hsuan-Yu Lin1
1National Health Research Institutes, Taiwan, 2China Medical University, Taiwan
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The effects of non-protein-coding RNA structure and function on intron evolution
Katarzyna Hooks*, Daniela Delneri, Sam Griffiths-Jones
University of Manchester, Faculty of Life Sciences, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Effects of Purifying Selection on Genealogies
Lauren Nicolaisen*, Michael Desai
Department of Physics and Department of Organismic and Evolutionary Biology, Harvard University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The effects of sweeps on surrounding loci in large populations
Daniel Weissman*, Nicholas Barton
IST Austria, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The enigma of cADPR/NAADP calcium messenger biosynthesis and the limited taxonomic distribution of the ADP-ribosyl cyclases by computational multi-genome survey
Enza Ferrero*, Nicola Lo Buono, Fabio Malavasi
University of Torino, Italy
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The epigenetics and evolution of TE control by piRNA: The role of dose.
Justin Blumenstiel*, Dean Castillo, Chris Harrison, Christine Yoder, Kim Box, Jianwen Fang
University of Kansas, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  11:30-13:00
The evolution of alternative splicing patterns and splicing regulatory mechanisms in vertebrates.
Adem Bilican*1,2, Anamaria Necsulea1,2, Henrik Kaessmann1,2
1University of Lausanne, Switzerland, 2Swiss Institue of Bioinformatics, Switzerland
:  S1 - Open Symposium for Early Stage Researchers  -  11:30-13:00
The evolution of cold tolerance in Drosophila: from phylogenetics to gene expression
Ramiro Morales-Hojas*, Micael Reis, Cristina P. Vieira, Jorge Vieira
IBMC - University of Porto, Portugal
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Evolution of Cold Tolerance in the Endemic New Zealand Stick Insect Fauna using RNA-Seq: Counts, Pathways and Selection
Luke Thomas Dunning*1,2, Alice Dennis2,3, Richard Newcomb1,4, Thomas Buckley1,2
1Auckland University, New Zealand, 2Landcare Research, New Zealand, 3Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand, 4Plant and Food, New Zealand
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The evolution of CRISPR-Cas in Mycobacterium tuberculosis
Daniela Brites*, Mireia Coscolla, Sebastien Gagneux
Swiss Tropical and Public Health Institut, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The evolution of eukaryotes from archaea
Tom Williams*1, Peter Foster2, Cymon Cox3, T. Martin Embley1
1Newcastle University, UK, 2Natural History Museum, UK, 3University of Algarve, Portugal
Monday 25th June 2012:  S21 - Paradigm shifting in phylogeny  -  16:30-18:00
The evolution of GC content in avian genomes
Carina Mugal*1, Peter Arndt2, Hans Ellegren1
1Evolutionary Biology Centre, Uppsala University, Sweden, 2Max Planck Institute for Molecular Genetics, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The evolution of gene expression in numerous cancer lines
Corey M. Hudson*1, Michaël Bekaert0,2, Gavin C. Conant1
1University of Missouri, USA, 2University of Stirling, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The evolution of gene expression underlying sexual development in fungi
Nina Lehr1, Usha Sikhakholli2, Zheng Wang1, Francesc Lopez-Giraldez1, Ning Li1, Frances Trail2, Jeffrey Townsend*1
1Yale University, USA, 2Michigan State University, USA
:  S4 - Genomic basis of Evo-Devo  -  09:30-11:00
The evolution of mammalian tissue transcriptomes
Henrik Kaessmann1,2
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  16:00-17:30
The Evolution of Reproductive Complexity in Male-Pregnant Fishes
Tony Wilson*1, Marie Gauthier1, Kai Stoelting1,2, Camilla Whittington1
1University of Zurich, Switzerland, 2University of Fribourg, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The evolution of sex determination and sexual differentiation in species-flock of cichlid fishes of Lake Tanganyika, East Africa
Astrid Boehne*, Corina Heule, Walter Salzburger
University of Basel, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The evolution of silencing suppression and other ways viruses have to escape from RNA silencing
Santiago F. Elena1,2
1IBMCP (CSIC-UPV), Spain, 2Santa Fe Institute, USA
Monday 25th June 2012:  S15 - RNA silencing and heterochromatin as genome defence: TEs, viruses and selfish elements  -  09:30-11:00
The Evolution of Species Interaction Networks
Miguel A. Fortuna
Estacion Biologica de Doñana (EBD-CSIC), Spain
Tuesday 26th June:  S22 - Evolutionary networks: Proteins, Genomes, Organisms  -  16:00-17:30
The evolutionary consequences of DNA replication onto the mutational profile of yeast genomes
Gilles Fischer*, Nicolas Agier, Fabrice Touzain, Marco Cosentino Lagomarsino, Orso Maria Romano
Université Pierre et Marie Curie, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Evolutionary Consequences of Meiotic Recombination:New Insights from Double Strand Breaks in Mouse
Yves Clement*1, Laurent Duret2, Peter Arndt1
1Max Planck Institute for Molecular Genetics, Germany, 2UMR CNRS 5558 Laboratoire de Biométrie et Biologie Evolutive, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The evolutionary dynamics of Ppp1 catalytic subunits in the Metazoan
Susana Pereira*1, Vítor Vasconcelos1,2, Agostinho Antunes1,2
1CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal, 2Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The evolutionary fate of short linear motifs in paralogous proteins
Alex N. Nguyen Ba*, Alan M. Moses
University of Toronto, Canada
Monday 25th June 2012:  S18 - The complex relationship between orthology, paralogy, and function  -  16:30-18:00
The evolutionary history of the eukaryotic ribosome biogenesis pathway from a yeast perspective.
Ingo Ebersberger*1, Stefan Simm2, Enrico Schleiff2
1CIBIV MFPL, Austria, 2Institute for Molecular Biosciences, Goethe University, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The Evolutionary Significance of Y-linked Regulatory Variation in Drosophila
Timothy Sackton*1, Jun Zhou1, Bernardo Lemos2, Daniel Hartl1
1Harvard University, USA, 2Harvard School of Public Health, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The fate of S-RNase gene duplications in Rosaceae
Bruno Aguiar*1, Jorge Vieira1, Ana Cunha1, Nuno Fonseca2, Cristina Vieira1
1IBMC, Portugal, 2CRACS-INESC, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The Fates of Duplicate Genes at the Subcellular Level
Lydia Bright*, Casey McGrath, Tom Doak, Michael Lynch
Indiana University, USA
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  16:00-17:30
The functional evolution of mammalian Y chromosomes
Diego Cortez*1, Laure Froidevaux1, Angélica Liechti1, Frank Grützner2, Henrik Kaessmann1
1Center for Integrative Genomics, University of Lausanne, Switzerland, 2The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Australia
:  S11 - Sex chromosome evolution illuminated by next-generation sequencing technology  -  17:00-18:30
The genetic basis of the evolution of eye and head morphology in Drosophila
Maarten Hilbrant*1, Saad Arif1, Corinna Hopfen2, Linta Kuncheria1, Nico Posnien1, M. Daniela Nunes1, Christian Schlötterer2, Alistair P. McGregor1
1Oxford Brookes University, UK, 2Veterinärmedizinische Universität Wien, Austria
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The genetic impact of infectious disease on indigenous southern African populations
Katharine Owers
Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The genome of a gut parasite of Daphnia provides evidence for an ancient origin of Microsporidia.
Karen Haag*1, Tobias Schaer1, Dominik Refardt2, Dieter Ebert1
1University of Basel, Switzerland, 2ETH, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The genomic accordion model of large DNA virus evolution
Nels Elde*1,2, Stephanie Child2, Michael Eickbush2, Jacob Kitzman3, Jay Shendure3, Adam Geballe2,3, Harmit Malik2,4
1University of Utah, USA, 2Fred Hutchinson Cancer Research Center, USA, 3University of Washington, USA, 4Howard Hughes Medical Institute, USA
:  S3 - Evolution of host-virus interactions  -  9:30-11:00
The genomic basis of local adaptations in orangutans (Pongo spp.)
Maja P. Greminger*1, Kai N. Stölting2, Alexander Nater1, Maria Anisimova3,4, Giada Ferrari1, Heidi E. L. Lischer8, Remy Bruggmann5,6, Benoit Goossens7, Natasha Arora1, Carel P. van Schaik1, Michael Krützen1
1Anthropological Institute and Museum, University of Zurich, Switzerland, 2Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Switzerland, 3Computational Biochemistry Research Group, Department of Computer Science, Swiss Federal Institute of Technology (ETH), Switzerland, 4Swiss Institute of Bioinformatics (SIB), Switzerland, 5Functional Genomics Center, University of Zurich, Switzerland, 6Department of Biology, University of Bern, Switzerland, 7School of Biosciences, Cardiff University, UK, 8Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity
Luisa Antunes*1, Francesco Imperi2, Jochem Blom3, Laura Villa4, Alessandra Carattoli4, Paolo Visca1
1Department of Biology, University Roma Tre, Italy, 2Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Italy, 3Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Germany, 4Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Italy
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Homology of Feathers and Scales: Using New High-throughput Methods to Address a Classic Question
Jacob Musser*1,2, Gunter Wagner1,3, Richard Prum1,2
1Dept. of Ecology & Evolutionary Biology, Yale University, USA, 2Peabody Museum of Natural History, Yale University, USA, 3Yale Systems Biology Institute, USA
:  S4 - Genomic basis of Evo-Devo  -  09:30-11:00
The horizontal gene transfer events in the genus Aspergillus
Yi-Pei Ho, Chih-Hang Chen*, Yeong-Shin Lin
National Chiao Tung University, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The identification of putative dihydrofolate reductase (DHFR) duplicates and their phylogenetic distribution
Robert Carton*, Gráinne McEntee, Anne Parle-McDermott, Mary O’Connell
Dublin City University, Ireland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The impact of recombination on the X to autosome diversity ratio in Drosophila melanogaster and D. pseudoobscura
Penelope Haddrill*, Jose Campos, Brian Charlesworth
University of Edinburgh, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The impact of selection for female fitness on autosomal and W-linked genes
Marie Pointer*1,2, Hooman Moghadam1, Alison Wright1, Judith Mank2
1University of Oxford, UK, 2University College London, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The influence of natural selection in the antigen presentation pathway
Felix M Schulze*, Genís Parra, Cesare de Fillipo, Aida M Andrés
Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The inhibition of the S-RNase cytoxicity in Rosaceae: the Prunus 'one S-pollen gene' model and the Pyrinae 'non-self recognition by multiple S-pollen factors' model
Bruno Aguiar1, Jorge Vieira1, Nuno Fonseca2, Olivier Raspé3, Cristina Vieira*1
1Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Portugal, 2CRACS-INESC Porto, Portugal, 3National Botanic Garden of Belgium, Belgium
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The joint allele frequency spectrum of multiple populations: A coalescent theory approach
Hua Chen
Department of Epidemiology and Biostatistics, Harvard School of Public Health, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The joint effects of background selection and genetic recombination on local gene genealogies
Kai Zeng*1, Brian Charlesworth2
1University of Sheffield, UK, 2University of Edinburgh, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The known unknowns of complex environments: how reliably can we place metagenomic samples onto reference phylogenetic trees?
Nick Goldman1, Eliza Loza*2
1EMBL-European Bioinformatics Institute, UK, 2Department of Computational & Systems Biology, Rothamsted Research, UK
:  S6 - Gene/genome data and the limits to  -  15:00-16:30
The landscape of recombination rate variation in Western Lowland Gorillas
Laurie S. Stevison*1, Jeffrey M. Kidd4, Joanna L. Kelley2, August E. Woerner3, Laurel Johnstone3, Carlos D. Bustamante2, Michael Hammer3, Jeff Wall1, the Great Apes Genome Diversity Consortium5
1University of California, San Francisco, USA, 2Stanford University, USA, 3University of Arizona, USA, 4University of Michigan Medical School, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The lifestyles of vertically and horizontally transmitted endosymbiotic bacteria affect the balance between selection and drift acting on their genomes.
Meg Woolfit*, Elizabeth McGraw
Monash University, Australia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Likelihood Landscape for Phylogenetic Models
Barbara Wilhelm*, Peter F. Arndt
Max Planck Institute for Molecular Genetics, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Mechanisms and Expression of Copy Number Variation in Drosophila
Manyuan Long
The University of Chicago, USA
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  16:30-18:00
The microbial lag phase is an evolvable trait that underlies specialist and generalist growth strategies.
Aaron New*1,2, Sander Govers1,2, Bram Cerulus1,2, Joao Xavier3, Kevin Verstrepen1,2
1VIB Laboratory of Systems Biology, Belgium, 2CMPG Laboratory of Genetics and Genomics, Belgium, 3Program in Computational Biology, Memorial Sloan Kettering Cancer Center, USA
Monday 25th June 2012:  S17 - Molecular, Genomic, and Phenotypic Evolvability  -  16:30-18:00
The mitochondrion-related organelles of a novel breviate protist: Enigmatic organelles in a microaerophilic lineage of eukaryotes.
Courtney Stairs*1, Matthew Brown1, Mark van der Giezen2, Andrew Roger1
1Dalhousie University, Canada, 2University of Exeter, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The molecular basis of rapid temperature-driven divergence in European grayling (Thymallus thymallus) as revealed by shotgun proteomics
Spiros Papakostas*1, Mei Ning2, Asbjørn Vøllestad3, Craig Primmer1, Erica Leder1, Matthieu Bruneaux1
1University of Turku, Finland, 2Institute for Nutritional Sciences, China, 3University of Oslo, Norway
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The molecular basis of speciation in Drosophila.
Nitin Phadnis*, Harmit Malik
Fred Hutchinson Cancer Research Center, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The Neolithic trace in mitochondrial haplogroup U8
Joana Barbosa Pereira*1,2, Marta Daniela Costa1,2, Pedro Soares2, Luísa Pereira2,3, Martin Brian Richards1,4
1Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, UK, 2Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal, 3Faculdade de Medicina da Universidade do Porto, Portugal, 4School of Applied Sciences, University of Huddersfield, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The origin and evolution of the melanopsin gene family: the OPN4x and OPN4m paralogs
Rui Borges*1,2, Vítor Vasconcelos1,2, Agostinho Antunes1,2
1CIIMAR, Portugal, 2FCUP, Portugal
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The origin and maintenance of a butterfly wing pattern supergene
Annabel Whibley*1, Lise Frezal1, Robert Jones1, Nicola Nadeau2, Chris Jiggins2, Mathieu Joron1
1CNRS/Muséum National d'Histoire Naturelle, France, 2Department of Zoology, University of Cambridge, UK
Monday 25th June 2012:  S20 - Structural evolution of genomes  -  14:30-16:00
The origins and evolution of long non-coding RNAs in tetrapods
Anamaria Necsulea*1,2, Magali Soumillon1,2, Angélica Liechti1,2, Manuela Weier1,2, Henrik Kaessmann1,2
1University of Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The origins of spontaneous mutations and the role of mismatch repair in shaping the genome of the model prokaryote, Escherichia coli
Patricia Foster*, Ellen Popodi, Heewook Lee
Indiana University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The PhyloFacts Phylogenomic Encyclopedia of Gene Families Across the Tree of Life
Jonathan Dobbie*, Cyrus Afrasiabi, Ajithkumar Warrier, Bushra Samad, Kimmen Sjölander
University of California, Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Plant Proteome Folding Project : Structure and Positive Selection in Plant Protein Families
Melissa Pentony*1, Patrick Winters1, Duncan Penfold-Brown1, Kevin Drew1, Apurva Narechania2, Rob DeSalle2, Richard Bonneau1, Michael Purugganan1
1New York University, USA, 2American Museum of Natural History, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The poor man's 1000 genomes project: Recent human population expansion confounds detection of disease alleles in 7,099 complete mitochondrial genomes
Hie Lim Kim*, Stephan C. Schuster
Pennsylvania State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The population structure and genome architecture of Staphylococcus aureus
Richard Everitt*, Bernadette Young, Ruth Miller, Antonina Votintseva, Rory Bowden, Kyle Knox, Derrick Crook, Daniel Wilson
University of Oxford, UK
Monday 25th June 2012:  S12 - Microbial genome evolution  -  14:30-16:00
The porcine colonization of the Americas: A 60k SNP story
William Burgos-Paz*1, Carla Souza1,2, Hendrik-Jan Megens3, Samuel Paiva2, Martien Groenen3, Miguel Pérez-Enciso1,4, AmMap Consortium0
1Center for Research in Agricultural Genomics (CRAG) – Universitat Autònoma de Barcelona (UAB), Spain, 2Embrapa Recursos Genèticos e Biotecnologia – CENARGEN, Brazil, 3Animal Breeding and Genomics Centre, Wageningen University, The Netherlands, 4Institut de Recerca i Estudis Avançats de Catalunya, ICREA, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The probability of gene trees in the presence of hybridization
Yun Yu1, James Degnan2, Luay Nakhleh*1
1Rice University, USA, 2University of Canterbury, New Zealand
:  S9 - The network of life: algorithmic and modelling challenges  -  17:00-18:30
The Promotion of Microbial Sociality by Horizontal Gene Transfer and Gene Dosage
Sorcha Mc Ginty*1,2, Evandro Ferrada3, Andreas Wagner1,2, Daniel Rankin1,2
1Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland, 2The Swiss Institute of Bioinformatics, Switzerland, 3The Santa Fe Institute, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The Protein Diversity Enhanced by Young Chimera in Rice Genome Through DNA-based and RNA-based Recombination
Chuanzhu Fan*1, Manyuan Long2, Rod Wing3
1Wayne State University, USA, 2University of Chicago, USA, 3University of Arizona, USA
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
The Puerto Rican parrot genome project: an international effort supported by the local community
Taras K. Oleksyk*1, Jean-François Pombert2, Daniel Siu3, Anyi Mazo-Vargas1, Brian Ramos1, Wilfried Guiblet1, Yashira Afanador1, Christina T. Ruiz-Rodriguez4, Michael L. Nickerson4, Michael Dean4, David Logue1, Luis Figueroa5, Ricardo Valentin6, Juan L. Rodriguez-Flores7, Steven E. Massey8, Juan Carlos Martinez-Cruzado1
1UPRM, Puerto Rico, 2UBC, Canada, 3Axeq Technologies, USA, 4NCI-Frederick, USA, 5Compania De Parques Nacionales, Puerto Rico, 6DNER, Puerto Rico, 7Cornell University, USA, 8UPRRP, Puerto Rico
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The rate of adaptation of pandemic H1N1 influenza virus.
Jessica Hedge*, Samantha Lycett, Andrew Rambaut
University of Edinburgh, UK
:  S3 - Evolution of host-virus interactions  -  9:30-11:00
The Relative Contributions of Selection for Speed and Accuracy of Translation to Codon Bias in Bacteria
WENQI RAN*1, PAUL HIGGS2
1NCBI,NIH, USA, 2McMaster Univ, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The role of epigenetics in the evolution of sexual attraction in moths
Astrid T. Groot
University of Amsterdam, The Netherlands
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The role of epistasis on the response to selection
Tiago Paixao*, Nick Barton
IST Austria, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The role of prolactin in male pregnancy
Camilla Whittington*, Marie-Emilie Gauthier, Anthony Wilson
University of Zurich, Switzerland
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
The role of selection, biased gene conversion and mutation bias in the evolution of genomic GC content in bacteria
Adam Eyre-Walker*1, Falk Hildebrand1,2
1University of Sussex, UK, 2Vrije Universitet Brussel, Belgium
:  S5 - Adaptive vs. non-adaptive evolution  -  09:30-11:00
The Role, Function, and Conservation of Upstream Open Reading Frames in Human
Yi-Chiao Fang*1, Arthur Chun-Chieh Shih2, Yeong-Shin Lin1
1National Chiao Tung University, Taiwan, 2Academia Sinica, Taiwan
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The sex-specific impact of meiotic recombination on nucleotide composition.
Alexandra Popa*1, Paul Samollow2, Christian Gautier1, Dominique Mouchiroud1
1Laboratoire de Biometrie et Biologie Evolutive, France, 2Department of Veterinary Integrative Biosciences, Faculty of Genetics, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella.
Touchon marie*, Rocha Eduardo
Département Génomes et Génétique, Institut Pasteur, Microbial Evolutionary Genomics, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The 'State' of RNA Model Selection
James Allen*, Simon Whelan
University of Manchester, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The story of wheat domestication and improvement as told by the nutrient content gene NAM-B1
Jenny Hagenblad
Linkoping University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The Ties That Bind:  Gene genealogies within a fixed pedigree
Sohini Ramachandran*1, Leandra King2, Peter Wilton2, John Wakeley2
1Brown University, USA, 2Harvard University, USA
Monday 25th June 2012:  S16.2 - Computationally efficient approaches for population genetic inference  -  11:30-13:00
The Timescale of Mammalian Phylogeny
Mario dos Reis*1, Jun Inoue2,1, Masami Hasegawa3, Robert Asher4, Philip Donoghue5, Ziheng Yang1
1University College London, UK, 2University of Tokyo, Japan, 3Fudan University, China, 4University of Cambridge, UK, 5University of Bristol, UK
:  S8 - The animal tree of life and its applications  -  15:00-16:30
The tree of Life circa 2012: Is there reasonable middle ground between tree-hugging and clearcutting?
Andrew Roger
Dept. of Biochemistry and Molecular Biology, Dalhousie University, Canada
Monday 25th June 2012:  S21 - Paradigm shifting in phylogeny  -  16:30-18:00
The unusual hox clusters of the basal teleost, Pantodon bucholzi, reveal tetralogy as a cryptic subtype of homology.
Kyle Martin*1, Peter Holland1
1University of Oxford, UK, 2University of Oxford, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The use of Heterogeneous Evolutionary models to infer the Placental Mammal Phylogeny.
Claire C. Morgan*1,2, Peter G. Foster3, Andrew E. Webb1,2, Davide Pisani4, James O. McInerney4, Mary J. O'Connell1,2
1Dublin City University, Ireland, 2Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Ireland, 3Natural History Museum, UK, 4Molecular Evolution and Bioinformatics Unit, Ireland
:  S8 - The animal tree of life and its applications  -  15:00-16:30
The use of mitochondrial data to infer the mammalian  phylogeny: a cautionary tale.
Claire C. Morgan*1,2, Christopher J. Creevey3, Paul Kilroy-Glynn4, Mary J. O’ Connell1,2
1Dublin City University, Ireland, 2Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Ireland, 3Teagasc, Ireland, 4Comparative Genomics Unit NIH, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
The WFDC locus: a preferred target of natural selection in humans
Zelia Ferreira*1,2, Susana Seixas2, Aida Andres1, Warren Kretzschmar1, Jim Mullikin4, Pedro Cruz4, Praveen Cherukuri4, Eric Green1,4, NISC Comparative Sequencing Program1,4, Belen Hurle1
1National Human Genome Research Institute (NHGRI), USA, 2Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Portugal, 3Department of Zoology and Anthropology, Faculty of Sciences, University of Porto, Portugal, 4NIH Intramural Sequencing Center (NISC), USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
The worldwide spread of transposable element insertions associated with pesticide exposure and impact on linked polymorphism in Drosophila simulans.
Pierre Gerard*, Francois Wurmser, Romain Fougeyrollas, David Ogereau, Catherine Montchamp-Moreau
Lab Evolution Genome Speciation, CNRS-Universite Paris-Sud, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Theileria genome architecture: unique structure and divergence between species
Richard Perry*, Paul Sharp
University of Edinburgh, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Thermodynamic constraints on protein evolution: sequences, structures and models
Johan Grahnen
University of Wyoming, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Tit for tat - genome analysis of the bacterial endosymbionts of reed beetles (Donaciinae)
Gregor Kölsch
Zoological Instutute, University of Hamburg, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Topological structure of the space of phenotypes: The case of RNA neutral networks
Jacobo Aguirre1, Javier M. Buldú2, Michael Stich1, Susanna C. Manrubia*1
1Centro de Astrobiología (INTA-CSIC), Spain, 2Complex Systems Group, Universidad Rey Juan Carlos, Spain
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Toward Computationally Feasible Evolutionary Inference with Biologically Plausible Models
Cory L. Strope*, Jeffrey L. Thorne
Bioinformatics Research Center, North Carolina State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Toward identifying Bateson-Dobzhansky-Muller incompatibilities in yeast: A simulation study
Chuan Li*1, Zhi Wang2,1, Jianzhi Zhang1
1University of Michigan, USA, 2Sage Bionetworks, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Towards a Timeline in Networks of Lateral Gene Transfer during Prokaryote Evolution
Ovidiu Popa*, Giddy Landan, Tal Dagan
Institute of Molecular Evolution, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Towards population genomics with Approximate Bayesian Computation
Daniel Wegmann
École polytechnique fédérale de Lausanne, Switzerland
Monday 25th June 2012:  S13 - Estimating and simulating models of molecular evolution  -  09:30 - 11:00
Tracing the emergence, transmission and adaptation of pandemic MRSA
Paul R. McAdam*1, Kate E. Templeton2, Giles F. Edwards3, Matthew T. G. Holden4, Edward J. Feil5, David Aanenson6, Mark C. Enright7, Anne Holmes2, E. Kirsty Girvan3, Paul A. Godfrey8, Michael Feldgarden8, Angela M. Kearns9, Andrew Rambaut10, D. Ashley Robinson11, J. Ross Fitzgerald1
1Roslin Institute, University of Edinburgh, UK, 2Microbiology, Royal Infirmary of Edinburgh, UK, 3Scottish MRSA Reference Laboratory, UK, 4Wellcome Trust Sanger Institute, UK, 5University of Bath, UK, 6Imperial College, UK, 7AmpliPhi Biosciences, UK, 8Broad Institute, USA, 9Microbiology Services Division, Health Protection Agency, UK, 10Institute of Evolutionary Biology, University of Edinburgh, UK, 11Department of Microbiology, University of Mississippi Medical Center, USA
Monday 25th June 2012:  S12 - Microbial genome evolution  -  14:30-16:00
Tracing the evolutionary history of the Escherichia coli O104:H4 outbreak strains
Lionel Guy*1, Cecilia Jernberg2, Jenny Arvén Norling1, Britta Björkholm2, Sofie Ivarsson2, Ingela Hendenström2, Lars Engstrand2,3, Siv Andersson1
1Department of Molecular Evolution, Uppsala University, Sweden, 2Department of Preparedness, Swedish Institute for Communicable Disease Control, Sweden, 3Department of Microbiology, Tumour- and Cell Biology, Karolinska Institute, Sweden
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Tracing the green algal origin of embryophytes using a comparative mitochondrial genomics approach
Monique Turmel*, Christian Otis, Claude Lemieux
Universite Laval, Canada
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Tracking protein length changes reveals pseudogenization in action.
Wilson Sung, Brian Golding*
McMaster University, Canada
Monday 25th June 2012:  S12 - Microbial genome evolution  -  11:30-13:00
Tracking the emergence of new virulent lineages of Staphylococcus aureus using whole-genome sequencing.
Ruth Miller1, James Price2, Antonina Votintseva1, Xavier Didelot1, Daniel Wilson1, David Wyllie3,1, Liz Batty1, Tanya Golubchik1, John Paul3, Martin Llewelyn2, Derrick Crook1, Rory Bowden*1
1University of Oxford, UK, 2Royal Sussex County Hopital, UK, 3Health Protection Agency, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Tracking the molecular mechanisms responsible for GC-biased gene conversion in yeast
Yann Lesecque*, Laurent Duret
Laboratoire de Biométrie et Biologie Evolutive, France
:  S1 - Open Symposium for Early Stage Researchers  -  11:30-13:00
Transcriptional profiling of the choanoflagellate Salpingoeca rosetta during simple multicellular development
Tera Levin*, Nicole King
University of California, Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Transcriptional trade-offs across tissues in human evolution
Gregory Wray*, Lisa Pfefferle, Olivier Fedrigo, Courtney Babbitt
Duke University, USA
Tuesday 26th June:  S23 - Evolutionary analysis of gene expression  -  14:00-15:30
Transcriptome profiling studies in spruce trees reveal gene family evolution, high levels of diversity in gene expression and a novel insect resistance mechanism
Jukka-Pekka Verta1,2, Nathalie-Suzett Delvas2, Elie Raherison1,2, Isabelle Giguère1,2, Sébastien Caron1,2, Claude Bomal1,2, Éric Bauce2, Christian Landry1, John MacKay*1,2
1Institute of integrative and systems biology, Laval University, Canada, 2Center for forest research, Laval University, Canada
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species
Susanne U. Franssen*1, Jenny Gu1, Nina Bergmann2, Gidon Winters2, Ulrich C. Klostermeier3, Philip Philip Rosenstiel3, Erich Bornberg-Bauer1, Thorsten B.H. Reusch2
1Institute for Evolution and Biodiversity, University of Münster, Germany, 2Evolutionary Ecology of Marine Fishes, Leibniz-Institute for Marine Sciences, Germany, 3Institute of Clinical Molecular Biology, Christian-Albrechts-University, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Transformations of the site frequency spectrum and application to human populations
Alexander Klassmann, Thomas Wiehe*
Universitaet zu Koeln, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Transgenerational epigenetic inheritance in Drosophila melanogaster
Jaime Grace*, Urban Friberg
Uppsala University, Sweden
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Transition between environmental and genetic sex determination in Daphnia: Evolution of a novel, partially sex-determining chromosome region
Celine Reisser*1, Yan Galimov2, Cathy Haag-Liautard1, Dominique Fasel1, Anne Roulin3, Jarkko Routtu3, Christoph Haag1
1University of Fribourg, Switzerland, 2Institute of Developmental Biology, Russian Academy of Sciences, Russia, 3University of Basel, Switzerland
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Transposable element evolution in Wolbachia bacterial endosymbionts
Nicolas Cerveau, Didier Bouchon, Richard Cordaux*
CNRS/Université de Poitiers, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Transposable element mediated gene regulatory network innovation: the evolution of pacental mammals
Gunter Wagner*, Deena Emera, Vincent Lynch
Yale University, USA
Monday 25th June 2012:  S19 - Molecular and functional evolution of transcriptional enhancers  -  14:30-16:00
Unbiased and Exhaustive Experimental Measurement of Point-mutant Fitness Effects
Dan Bolon
University of Massachusetts Medical School, USA
Monday 25th June 2012:  S16.1 - Adaptive Evolution and Selective Sweeps  -  09:30-11:00
Uncertainty on multiple sequence alignment: an approach using the bootstrap
Jia-Ming Chang*, Salvador Capella, Jean-Francois Taly, Toni Gabaldon, Cedric Notredame
Centre for Genomic Regulation (CRG) and UPF, Spain
Tuesday 26th June:  S25 - Multiple sequence alignment, alignment confidence, and impact on downstream analyses  -  16:00-17:30
Uncovering the molecular basis of the centromere paradox
Benjamin Ross*1,2, Harmit Malik1,2
1University of Washington, USA, 2Fred Hutchinson Cancer Research Center, USA
Tuesday 26th June:  S24 - Origin and long-term evolution of gene families: gene turnover rates, the birth-and-death process and molecular adaptation  -  16:00-17:30
Uncovering the Molecular Evolution of Plasmid ‘Species’
Edel Hyland*, Andrew Murray
Harvard Univeristy, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Uncovering the Tree of Life in the genomic era: separating the wheat from the chaff
Jeremy Brown
Louisiana State University, USA
:  S6 - Gene/genome data and the limits to  -  15:00-16:30
Understanding genetic adaptations to varying dietary selenium intakes in human populations
Louise C White*, Genís Parra, Sergi Castellano
Max Planck Institute for Evolutionary Anthropology, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Understanding the exceptional amplification of the STS gene family involved in resveratrol synthesis in grapevine
Claire Parage1, Raquel Tavares*2, Stéphane Réty4, Raymonde Baltenweck1, Anne Poutaraud1, Dimitri Heintz5, Raphaël Lugan5, Gabriel Marais2, Sébastian Aubourg3, Philippe Hugueney1
1University f Strasbourg / INRA, France, 2University of Lyon1 / CNRS, France, 3INRA, France, 4CNRS, France, 5CNRS, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Understanding the transcriptional gene regulation networks: a quantitative genetics approach
Murat Tugrul*, Tiago Paixao, Gasper Tkacik, Nick Barton
IST-Austria, Austria
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
UNEARTHING THE FOSSIL RECORD OF ENDOGENOUS RETROVIRUSES WITHIN THE PRIMATE LINEAGE
Ravi Subramanian*, John Coffin
Tufts University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Unraveling the life dynamics of Sirevirus LTR Retrotransposons: major players in the organization and evolution of the maize and other angiosperm genomes
Alexandros Bousios*1, Yiannis Kourmpetis2, Pavlos Pavlidis3, Evangelia Minga1, Nikos Darzentas1
1Bioinformatics Analysis Team, Institute of Agrobiotechnology, CERTH, Greece, 2Laboratory of Bioinformatics, Wageningen University, The Netherlands, 3The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Germany
:  S1 - Open Symposium for Early Stage Researchers  -  09:30 - 11:00
Using a High Powered Computing Network to Facilitate Genomics Focused Research at a Medium Sized Research Institute
Daniel White
Landcare Research New Zealand, New Zealand
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Using comparative genomics to disentangle the evolution of the Animal Kingdom
Jordi Paps Montserrat*, Peter W.H. Holland
Department of Zoology, University of Oxford, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Using deterministic functions to derive approximate coalescent distributions
Ethan Jewett*, Noah Rosenberg
Stanford University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Using high density 3D image registration to identify genetic loci associated with facial morphological variations
Shouneng Peng*1, Jingze Tan2, Hang Zhou1, Sile Hu1, Jing Guo1, Li Jin1,2, Kun Tang1
1CAS-MPG Partner Institute for Computational Biology,SIBS,CAS, China, 2School of Life Sciences, Fudan University, China
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Using semi-natural enclosure experiments to study the role of imprinting and epigenetic modifications in the evolution of house mouse populations
Diethard Tautz
Max-Planck Institute for Evolutionary Biology, Germany
Tuesday 26th June:  S26 - Epigenetics and molecular evolution  -  14:00-15:30
Using the doubly-conditioned site frequency spectrum to distinguish between alternative demographic models
Melinda Yang*, Anna Sapfo-Malaspinas, Eric Durand, Montgomery Slatkin
UC Berkeley, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Using Transcription Factor Binding Site Motifs to Predict Enhancer Function for Noncoding Sequences
Dennis Kostka*1,4, Katherine S. Pollard2,3
1Department of Developmental Biology, University of Pittsburgh, USA, 2Gladstone Institute of Cardiovascular Disease, University of California San Francisco, USA, 3Division of Biostatistics and Institute of Human Genetics, University of California San Francisco, USA, 4Department of Computational and Systems Biology, University of Pittsburgh, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Variation in exonic splice related constraints across taxa: why the impact of selection can be more evident when the effective population size is low
Laurence Hurst*, Joanna Parmley, Toby Warnecke, Andreas Schueler
University of Bath, UK
:  S5 - Adaptive vs. non-adaptive evolution  -  09:30-11:00
Vertebrate ultraconserved noncoding elements are ultra-cooperative
Slavica Dimitrieva*1,2, Philipp Bucher1,2
1EPFL, Switzerland, 2Swiss Institute of Bioinformatics, Switzerland
:  S4 - Genomic basis of Evo-Devo  -  11:30-13:00
VLR-encoding loci in lamprey: Illuminating the origin and early evolution of adaptive immunity
Sabyasachi Das*, Masayuki Hirano, Qifeng Han, Jianxu Li, Brantley R. Herrin, Peng Guo, Max D. Cooper
Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, USA
Monday 25th June 2012:  S14 - Open Symposium for Early Stage Researchers  -  11:30-13:00
What is evolutionary time in a non-stationary substitution process?
Von Bing Yap*1, Gavin Huttley2
1National University of Singapore, Singapore, 2Australian National University, Australia
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
What numerical taxonomy has to say regarding phylogenetics
Alex Griffing, Benjamin Lynch, Eric Stone*
North Carolina State University, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Where classic theory meets genomic technology: the distribution of fitness effects in yeast
Claudia Bank*1, Jeffrey D. Jensen1, Daniel N. A. Bolon2
1School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland, 2Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, USA
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
Which way did they go? Detecting directional migration from genetic data
Benjamin Peter*, Montgomery Slatkin
University of California, Berkeley, USA
Tuesday 26th June:  Walter M. Fitch Symposium  -  10:00 - 12:30
Whole transcriptome sequencing to identify candidate genes in the response of the water flea, Daphnia magna, to infection with its parasite, Pasteuria ramosa.
Seanna McTaggart*1, Desiree Allen1, Timothee Cezard2, Carolyn Riddell1, Marian Thomson2, Urmi Trivedi2, Mark Blaxter1,2, Tom Little1
1University of Edinburgh, UK, 2The GenePool, UK, 3Center for Immunity, Infection and Evolution, UK
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Whole-genome sequence versus SNP-array insights into the genetics of phenotypic variation and local adaptation in the model legume Medicago truncatula
Peter Tiffin*1, John Stanton-Geddes1, Jeremy Yoder1, Tim Paape1, Brendan Epstein1, Joann Mudge2, Andrew Farmer2, Arvind Bharti2, Peng Zhou1, Roman Briskine1, Nevin Young1
1University of Minnesota, USA, 2National Center for Genomic Resources, USA
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Whole-genome sequences of 6 pigs species shed light on natural and Human-mediated migration routes across insular South-East Asia.
Laurent Frantz*1, Joshua Schraiber2, Ole Madsen1, Hendrik-Jan Megens1, Mirte Bosse1, Yogesh Paudel1, Richard Crooijmans1, Greger Larson3, Montgomery Slatkin2, Martien Groenen1
1Wageningen University, The Netherlands, 2University of California, Berkeley, USA, 3Durham University, UK
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Why do so many fungal open reading frames contain repeats?
Jan Schmid*1, Matt Wilkins2, Ningxin Zhang1, Rosie Bradshaw1, Murray Cox1, Richard Cannon3, Chris Schardl4
1Massey University, New Zealand, 2Scientific Consulting, New Zealand, 3University of Otago, New Zealand, 4University of Kentucky, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Why have sex? Mutational meltdown in asexual organisms
Philipp H. Schiffer*, Einhard Schierenberg
Institute for Zoology, University of Cologne, Germany
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus
Fei He1, Justin Borevitz2, Juliette de Meaux*1
1IEB, Germany, 2University of Chicago, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
X/Autosome  diversity in Bonobos as compared to Humans
Ines Hellmann*1, Kay Pruefer1,2, Bonobo Genome Consortium1
1MFPL, Austria, 2MPI-EVAN, Germany
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
X-chromosome haplotypes as markers for population history
Pierpaolo Maisano Delser*1, Pille Hallast1, Rita Neumann1, Stéphane Ballereau1,2, Mark Jobling1
1University of Leicester, UK, 2CNRS, France
Posters:  Manned Poster Session (P-1000- P-1395)  -  18:30-19:30
Y-by-background effects on global gene expression in Drosophila melanogaster
Pan-Pan Jiang*, Bernardo Lemos, Lene Martinsen, Daniel Hartl
Harvard University, USA
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00
Yeast evolution: comparative genomics of 10 Lachancea species
Véronique Sarilar*1, Jean-Philippe Meyniel2, Cécile Neuvéglise1
1INRA UMR1319, AgroParisTech, Institut Micalis, Biologie intégrative du métabolisme lipidique microbien, France, 2ISoft, Bioinformatic Team, France
Posters:  Manned Poster Session (P-2000- P-2365)  -  18:00-19:00