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Manned Poster Session (P-1000- P-1395)

Based on Symposium numbers 1 - 13
P-1276 The Relative Contributions of Selection for Speed and Accuracy of Translation to Codon Bias in Bacteria
1NCBI,NIH, USA, 2McMaster Univ, Canada
P-1190 A unified framework for inferring population genetic structure and gene-environment associations
Eric Frichot, Sean Schoville, Guillaume Bouchard, Olivier Francois*
University Joseph Fourier, France
P-1246 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
P-1077 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
P-1350 Thermodynamic constraints on protein evolution: sequences, structures and models
Johan Grahnen
University of Wyoming, USA
P-1277 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
P-1114 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
P-1247 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
P-1000 Bioinformatics Resources for Enabling Discoveries from Genomes to Phenotypes (MEGA, TimeTree, and FlyExpress)
Sudhir Kumar
Center for Evolutionary Medicine & Informatics, Arizona State University, USA
P-1058 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
P-1278 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
P-1191 Population structure and demographic pre-history of the Solomon Islands
Ana Duggan*, Mark Stoneking
Max Planck Institute for Evolutionary Anthropology, Germany
P-1248 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
P-1001 Molecular biology and evolution of a candidate immune receptor in Drosophila
Erin Keebaugh*, Todd Schlenke
Emory University, USA
P-1059 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
P-1279 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
P-1136 Mining Genomes for Microinversions: Rare Genomic Characters for Phylogenomics
Gary Stuart*, Arun Seetharam
Indiana State University, USA
P-1351 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
P-1137 Analysis of ancient transposon families using molecular dating and a population genetics paradigm
Elizabeth Hellen*, John Brookfield
University of Nottingham, UK
P-1078 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
P-1192 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
P-1168 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
P-1002 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
P-1115 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
P-1041 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
P-1352 Biased gene conversion in codon substitution models
Laurent Guéguen*, Laurent Duret
LBBE - UMR CNRS 5558, France
P-1353 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
P-1354 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
P-1280 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
P-1281 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
P-1355 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
P-1116 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
P-1282 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
P-1193 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
P-1079 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
P-1080 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
P-1169 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
P-1249 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
P-1117 Phylogenomics on African lake cichlids: the evolution of transcriptomes during explosive speciation
Zuzana Musilova*, Walter Salzburger
University of Basel, Switzerland
Liron Levin, Ilia Zhidkov, Yotam Gurman, Dan Mishmar*
Ben Gurion University of the Negev, Israel
P-1170 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
P-1082 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
P-1083 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
P-1194 Demographic Inference Using Skyline Plots on Approximate Bayesian Computation
Miguel Navascués*1, Concetta Burgarella2
1UMR CBGP - INRA, France, 2UMR AGAP - INRA, France
P-1195 Analysis of inter and intra-species NGS data with a phylogenetic approach.
Nicola De Maio*, Carolin Kosiol
Institute of Population Genetics VetMedUni, Austria
P-1283 Transposable element evolution in Wolbachia bacterial endosymbionts
Nicolas Cerveau, Didier Bouchon, Richard Cordaux*
CNRS/Université de Poitiers, France
P-1356 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
P-1196 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
P-1284 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
P-1042 Cell Tropism Influences RNA Virus Nucleotide Substitution Rates
Allison Hicks*, Siobain Duffy
Rutgers University, USA
P-1250 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
P-1060 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
P-1285 High rates of retrogene formation in the giant nuclear genomes of dinoflagellates.
Renny Lee*, Claudio Slamovits
Dalhousie University, Canada
P-1084 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
P-1186 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
P-1286 The evolution of CRISPR-Cas in Mycobacterium tuberculosis
Daniela Brites*, Mireia Coscolla, Sebastien Gagneux
Swiss Tropical and Public Health Institut, Switzerland
P-1287 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
P-1288 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
P-1197 Parallel differentiation in Australian and North American populations of Drosophila simulans
Alisa Sedghifar*, David Begun
University of California, Davis, USA
P-1061 Does convergent morphology implies convergent development? Towards a comparative transcriptomics of tooth development.
Marie Sémon*, Vincent Laudet, Sophie Pantalacci
IGFL, ENS de Lyon, France
P-1021 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
P-1357 The Likelihood Landscape for Phylogenetic Models
Barbara Wilhelm*, Peter F. Arndt
Max Planck Institute for Molecular Genetics, Germany
P-1289 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
P-1290 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
P-1291 A site-dependent evolutionary model for CRISPR spacer arrays
Anne Kupczok*, Jonathan P. Bollback
IST Austria, Austria
P-1062 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
P-1171 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
P-1251 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
P-1138 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
P-1292 Modelling the Growth and Transmission of Infectious Disease: Linking epidemiology and population genetics
Bethany Dearlove*, Daniel Wilson
University of Oxford, UK
P-1198 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
P-1199 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
P-1085 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
P-1358 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
P-1200 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
P-1139 Distribution of Plastid Gene Signals among Chromalveolates without Plastids
Christian Woehle*, William Martin, Sven B. Gould
Molecular Evolution, Heinrich-Heine-University, Germany
P-1252 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
P-1086 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
P-1293 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
P-1359 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
P-1063 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
P-1360 Toward Computationally Feasible Evolutionary Inference with Biologically Plausible Models
Cory L. Strope*, Jeffrey L. Thorne
Bioinformatics Research Center, North Carolina State University, USA
P-1294 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
P-1295 Analysis of genetic composition of recombined regions in bacteria through whole genome comparisons
Sebastien Leclercq*, Daniel Falush
Max Plank Institute for Evolutionary Anthropology, Germany
P-1022 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
P-1087 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
P-1201 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
P-1187 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
P-1296 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
P-1118 Ensembl Quality Database
Michal Kabza*, Izabela Makalowska
Adam Mickiewicz University, Poland
P-1297 Comparative genomics of louse primary endosymbiotic bacteria
Bret Boyd*, Julie Allen, David Reed, Valerie de Crecy-Lagard, Lauren McIntyre
University of Florida, USA
P-1003 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
P-1202 Population genomic inference for recently bottlenecked selfing species.
Yaniv Brandvain*1, Stephen Wright2, Graham Coop1
1University of California - Davis, USA, 2University of Toronto, Canada
P-1253 The Drosophila miranda neo-Y transcriptome: De novo assembly and expression analysis of neo-sex linked genes
Vera Kaiser*, Doris Bachtrog
UC Berkeley, USA
P-1004 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
P-1361 Goodness of fit tests and outlier identification in phylogenetics
Steffen Klaere
Department of Statistics, University of Auckland, New Zealand
P-1140 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
P-1362 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
P-1119 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
P-1023 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
P-1043 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
P-1298 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
P-1141 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
P-1088 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
P-1203 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
P-1142 Evolution of microRNA in primates
Jennifer McCreight*, Willie Swanson
University of Washington, USA
P-1204 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
P-1064 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
P-1120 Moving beyond ribosomal genes: Metagenomics for microbial eukaryotes
Holly Bik*, Aaron Darling, Guillaume Jospin, Jonathan Eisen
University of California, Davis, USA
P-1024 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
P-1205 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
P-1143 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
P-1089 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
P-1206 Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data
Jacob Crawford*, Brian Lazzaro
Cornell University, USA
P-1005 Phylogeography: a new statistical approach for measuring dispersal ranges and competitive exclusion.
Louis Ranjard*, Stephane Guindon, David Welch
University of Auckland, New Zealand
P-1207 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
P-1090 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
P-1208 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
P-1144 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
P-1091 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
P-1121 Evolution of microsatellite DNA in human and chimpanzee genomes
Naoko Takezaki
Kagawa University, Japan
P-1145 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
P-1299 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
P-1300 Tit for tat - genome analysis of the bacterial endosymbionts of reed beetles (Donaciinae)
Gregor Kölsch
Zoological Instutute, University of Hamburg, Germany
P-1254 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
P-1301 Evolution of the cichlid fishes gut microbiota
Laura Baldo*, Walter Salzburger
University of Basel, Switzerland
P-1209 Identification of elite variety tag SNPs (ETASs) - a new approach unraveling loci underlying crop improvement
Jun Lv*, Wen Wang
Kumming Institute of Zoology, China
P-1210 Genomics of adaptation in Arabidopsis lyrata
Tiina Mattila*, Tuomas Toivainen, Outi Savolainen
University of Oulu, Finland
P-1255 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
P-1146 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
P-1065 Sequencing and analysis of the European amphioxus (Branchiostoma lanceolatum) transcriptome
Silvan Oulion*, Stéphanie Bertrand, Mohamed Belgacem, Yann Le Pétillon, Hector Escriva
CNRS, France
P-1302 A phylogenomic analysis of replication in the Archaea
Kasie Raymann*, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo
Institut Pasteur, France
P-1044 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
P-1066 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
P-1188 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
P-1211 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
P-1045 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
P-1303 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
P-1172 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
P-1212 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
P-1304 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
P-1256 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
P-1006 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
P-1092 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
P-1257 X/Autosome  diversity in Bonobos as compared to Humans
Ines Hellmann*1, Kay Pruefer1,2, Bonobo Genome Consortium1
1MFPL, Austria, 2MPI-EVAN, Germany
P-1305 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
P-1306 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
P-1173 Performance Degradation in Molecular Divergence Time Estimation with the Increase in Calibrations with Large Uncertainty
Kazutaka Takeshita*, Hidemi Watanabe
Hokkaido University, Japan
P-1007 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
P-1147 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
P-1213 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
P-1214 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
P-1093 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
P-1307 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
P-1258 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
P-1094 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
P-1215 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
P-1308 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
P-1309 '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
P-1095 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
P-1008 Characterizing the molecular basis of hybrid seed failure between two wild tomato species
Ana Marcela Florez-Rueda*, Margot Paris, Thomas Städler
ETHZ, Switzerland
P-1259 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
P-1363 PopGenome: An R-library for large-scale population genetic analysis
Bastian Pfeifer*, Ulrich Wittelsbürger, Martin Lercher
Institute for Computer Science Heinrich-Heine-University, Germany
P-1260 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
P-1261 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
P-1009 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
P-1310 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
P-1148 Search for antimicrobial peptide against fungal-infection in Drosophila virilis.
Yosuke Seto*, Koichiro Tamura
Tokyo Metropolitan University, Japan
P-1174 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
P-1311 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
P-1149 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
P-1010 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
P-1096 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
P-1150 Theileria genome architecture: unique structure and divergence between species
Richard Perry*, Paul Sharp
University of Edinburgh, UK
P-1175 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
P-1067 Elucidating the genetic landscape of cellular morphogenesis in an obligate fungal symbiont
Henrik H. De Fine Licht*, Anders Tunlid
Lund University, Sweden
P-1068 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
P-1151 Genome-wide patterns of codon usage bias in sequenced flatworms
Heidi Aisala*, Tiina M. Mattila, Jaakko Lumme
Department of Biology, University of Oulu, Finland
P-1097 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
P-1122 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
P-1216 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
P-1312 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
P-1313 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
P-1011 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
P-1025 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
P-1262 Gene conversion and evolution of sex chromosomes: an NGS approach.
Chiara Batini*, Daniel Zadik, Pille Hallast, Gurdeep Lall, Mark Jobling
University of Leicester, UK
P-1314 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
P-1152 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
P-1123 Decreasing speciation or incomplete sampling?
Disa Hansson*, Sebastian Höhna
Dept. of Mathematics, Stockholm University, Sweden
P-1263 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
P-1124 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
P-1264 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
P-1364 The 'State' of RNA Model Selection
James Allen*, Simon Whelan
University of Manchester, UK
P-1098 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
P-1099 Drift may dominate the evolution of fidelity in unicellular eukaryotes with large genomes
Matthew Ackerman*, Samuel Miller, Micheal Lynch
Indiana University, USA
P-1315 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
P-1100 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
P-1125 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
P-1026 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
P-1265 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
P-1316 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
P-1069 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
P-1317 Uncovering the Molecular Evolution of Plasmid ‘Species’
Edel Hyland*, Andrew Murray
Harvard Univeristy, USA
P-1027 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
P-1126 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
P-1127 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
P-1217 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
P-1318 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
P-1012 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
P-1128 Probabilistic parsimonious reconciliation between genes and species trees
Leonardo de Oliveira Martins*, David Posada
University of Vigo, Spain
P-1319 Genome-wide insights into the evolution of regulatory elements in diverse yeast strains
Caitlin Connelly*, Joshua Akey
University of Washington, USA
P-1028 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
P-1129 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
P-1176 Testing the status of infra generic taxonomic ranks in Triatomini (Hemiptera: Reduviidae)
Silvia Justi*, Claudia Russo
Universidade Federal do Rio de Janeiro, Brazil
P-1218 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
P-1320 The Chimera Hypothesis for the Thermotogae Phylum
Kristen Swithers*, J. Peter Gogarten
University of Connecticut, USA
P-1321 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
P-1101 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
P-1013 Improving metabolic flux predictions using gene expression data
Abdelmoneim Desouki*, Gabriel Gelius-Dietrich, Martin Lercher
Heinrich-Heine-University, Germany
P-1365 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
P-1130 Developing Maximum Likelihood and Bayesian Supertrees
Wasiu Akanni*1, Peter Foster2, Mark Wilkinson2, Davide Pisani1
1NUI, Ireland, 2NHM, UK
P-1102 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
P-1366 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
P-1322 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
P-1014 Genomic structures and gene evolution on mammalian X chromosomes
Yukako Katsura*, Yoko Satta
The Graduate University for Advanced Studies(SOKENDAI), Japan
P-1266 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
P-1367 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
P-1323 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
P-1219 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
P-1324 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
P-1220 Next-generation sequencing and SNP genotyping of poplars reveal chloroplast capture and admixture
Stacey Lee Thompson
Umeå University, Sweden
P-1267 Gene conversion and evolution of sex chromosomes: an NGS approach.
Chiara Batini, Daniel Zadik*, Pille Hallast, Gurdeep Lall, Mark Jobling
uni of leicester, UK
P-1325 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
P-1326 Phylogenetic analysis and alignment of NGS sequence data
Tandy Warnow*, Nam-phuong Nguyen, Siavash Mirarab
University of Texas at Austin, USA
P-1070 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
P-1327 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
P-1268 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
P-1131 Investigating deep nodes in Polyporales
Elisabet Sjökvist*1, Bernard Pfeil1, Ellen Larsson1, Karl-Henrik Larsson2
1University of Gothenburg, Sweden, 2University of Oslo, Norway
P-1132 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
P-1153 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
P-1328 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
P-1103 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
P-1368 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
P-1369 Evolutionary impact of transcription factor binding
Clemens Lakner*, Eric A. Stone, Jeffrey L. Thorne
North Carolina State University, USA
P-1154 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
P-1329 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
P-1269 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
P-1029 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
P-1046 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
P-1030 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
P-1221 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
P-1222 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
P-1047 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
P-1104 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
P-1330 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
P-1223 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
P-1155 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
P-1189 What numerical taxonomy has to say regarding phylogenetics
Alex Griffing, Benjamin Lynch, Eric Stone*
North Carolina State University, USA
P-1105 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
P-1048 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
P-1156 Divergent resolution of duplicate genes among three Paramecium species following whole-genome duplication
Casey L. McGrath*, Thomas G. Doak, Michael Lynch
Indiana University, USA
P-1071 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
P-1157 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
P-1072 Ancestral peptidergic signaling systems of bilaterian animals
Olivier Mirabeau*, Jean-Stéphane Joly
CNRS, France
P-1106 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
P-1224 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
P-1015 The Effects of Purifying Selection on Genealogies
Lauren Nicolaisen*, Michael Desai
Department of Physics and Department of Organismic and Evolutionary Biology, Harvard University, USA
P-1225 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
P-1226 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
P-1370 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
P-1049 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
P-1158 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
P-1227 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
P-1331 On the origin of leprosy: a genomics perspective
Luz-Andrea Pfister*, Anne C. Stone
Arizona State University, USA
P-1371 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
P-1372 Evolution of clonal populations approaching a fitness peak.
Isabel Gordo*1, Paulo Campos2
1Instituto Gulbenkian de Ciência, Portugal, 2Universidade Federal Rural de Pernambuco, Brazil
P-1031 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
P-1332 Genome-wide mutation spectrum and rate of Bacillus subtilis
Way Sung*, Emily Williams, Michael Lynch
Indiana Univeristy, USA
P-1228 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
P-1159 Investigating the Impacts Recombination has on Origin Estimates
Crystal Hepp*, Michael Rosenberg
Arizona State University, USA
P-1229 Estimating genome-wide fine-scale recombination rates in Drosophila melanogaster
Andrew H. Chan*, Paul A. Jenkins, Yun S. Song
University of California, Berkeley, USA
P-1270 Dynamics of Y chromosome evolution in Drosophila affinis
Robert Unckless*, Andrew Clark
Cornell University, USA
P-1271 Duplicate gene evolution on the Y-chromosome: insights from ampliconic genes of Sulawesi macaques.
Ana-Hermina Ghenu*, Ben Evans
McMaster University, Canada
P-1272 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
P-1230 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
P-1273 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
P-1050 Phylodynamics of influenza viruses before, during and after the 2009 swine flu pandemic
Gytis Dudas
University of Edinburgh, UK
P-1231 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
P-1232 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
P-1333 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
P-1032 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
P-1033 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
P-1334 Adaptive Regulatory Substitutions Affect Several Fitness Components of the Bacteriophage ϕX174
Celeste Brown*, Amber Stancik
University of Idaho, USA
P-1034 An improved library preparation method for ancient DNA
Marie-Theres Gansauge*, Svante Pääbo, Matthias Meyer
Max Planck Institute for Evolutionary Anthropology, Germany
P-1335 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
P-1336 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
P-1337 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
P-1338 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
P-1233 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
P-1035 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
P-1160 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
P-1234 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
P-1177 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
P-1036 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
P-1235 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
P-1051 Human evolution and HIV: A deep-time perspective on pathogenesis
M. Cyrus Maher*, Ryan Hernandez
University of California, San Francisco, USA
P-1339 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
P-1052 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
P-1373 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
P-1236 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
Sandra Meid*1, Bernhard Misof1, Christoph Mayer1, Barbara Holland0,2
1ZFMK, zmb, Germany, 2UTAS, Australia
P-1016 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
P-1340 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
P-1178 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
P-1375 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
P-1073 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
P-1074 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
P-1341 RNA-level unscrambling of systematically fragmented genes
Gertraud Burger*1, Georgette Kiethega1, Yifei Yan1, Marcel Turcotte0
1Universite de Montreal, Canada, 2University of Ottawa, Canada
P-1017 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
P-1161 Exceptional sex: the evolution of meiosis when it breaks the rules
John Logsdon
University of Iowa, USA
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
P-1107 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
P-1053 Evolution of dUTPase from Chlorellaviruses and host Chlorella
Hideaki Moriyama
University of Nebraska-Lincoln, USA
P-1037 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
P-1237 ­­­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
P-1162 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
P-1342 Cloning, characterization and expression of an insecticidal crystal protein gene from Bacillus thuringiensis isolates of Andaman and Nicobar Islands
P-1038 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
P-1163 Phenotypic Evolution Driven by New Gene Origination
Manyuan Long
The University of Chicago, USA
P-1179 Phylogenetic reconstruction of malaria vectors in Thailand using multilocus DNA sequences
Uraiwan Arunyawat*, Prin Phunngam, Theeraphap Chareonviriyaphap
Kasetsart University, Thailand
P-1238 Inferences of wolf population genetics using next-generation sequencing data
Violeta Munoz-Fuentes*, Carles Vila
Estacion Biologica de Donana-CSIC, Spain
P-1343 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
P-1039 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
P-1239 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
P-1344 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
P-1180 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
P-1164 Tracing the green algal origin of embryophytes using a comparative mitochondrial genomics approach
Monique Turmel*, Christian Otis, Claude Lemieux
Universite Laval, Canada
P-1108 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
P-1376 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
P-1240 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
P-1075 Transcriptional profiling of the choanoflagellate Salpingoeca rosetta during simple multicellular development
Tera Levin*, Nicole King
University of California, Berkeley, USA
P-1377 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
P-1076 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
P-1181 Molecular phylogenetics of Passerine birds: Sibley and Ahlquist’s Tapestry reloaded
Alexandre Pedro Selvatti*, Claudia Russo
Universidade Federal do Rio de Janeiro, Brazil
P-1345 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
P-1241 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
P-1054 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
P-1182 Bioinformatic Challenges in the 1KITE Project
Alexander Donath
Zoologisches Forschungsmuseum Alexander Koenig, Germany
P-1346 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
P-1133 Deep relationships of Rhizaria revealed by phylogenomics
Roberto Sierra*, Jan Pawlowski
University of Geneva, Switzerland
P-1109 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
P-1134 Reticulated origin of domesticated tetraploid wheat
Peter Civan
Centro de Ciencias do Mar, Universidade do Algarve, Portugal
P-1378 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
P-1165 Successive gain of insulator proteins in arthropod evolution
Peter Heger, Thomas Wiehe*
Universitaet zu Koeln, Germany
P-1166 Searching - and finding - bilaterian specific proteins
Andrea Kraemer-Eis, Peter Heger, Thomas Wiehe*
Universitaet zu Koeln, Germany
P-1018 The horizontal gene transfer events in the genus Aspergillus
Yi-Pei Ho, Chih-Hang Chen*, Yeong-Shin Lin
National Chiao Tung University, Taiwan
P-1135 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
P-1019 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
P-1110 Role of MT3 gene in metalophyte plant, S. vulgaris
Eva NEVRTALOVA*, Roman HOBZA, Jiri BALOUN, Vojtech HUDZIECZEK, Radim Cegan
Institute of Biophysics, Czech Republic
P-1242 Sex specific gene expression and haplodiploidy purging in an ant
Kalevi Trontti*, Heikki Helanterä, Christopher Wheat
Department of Biosciences, Finland
P-1243 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
P-1379 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
P-1040 Maximizing the information of DNA extracts obtained from skeletalremains
Christian Sell*, Susanne Kreutzer, Melanie Strobel
Johannes Gutenberg University Mainz, Germany
P-1380 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
P-1111 Selection against loss-of-function alleles in Drosophila melanogaster populations
Aleksandra I. Akhmadullina*, Georgii A. Bazykin, Aleksey S. Kondrashov
Moscow State University, Russia
P-1347 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
P-1167 Clustering Gene Trees Into Topological Classes
Kevin Gori*, Christophe Dessimoz
European Bioinformatics Institute, UK
P-1112 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
P-1183 Gene transpositions in the primate genomes
Mira Han
P-1113 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
P-1348 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
P-1244 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
P-1184 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
P-1055 Detecting HIV-1 co-receptor usage from sequence variation and V3 structural information
Felix Feyertag*, John Archer, David L Robertson
University of Manchester, UK
P-1056 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
P-1057 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
P-1349 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
P-1020 Revisit the origin of mitochondria using universal mitochondrial proteins.
Ding He
Uppsala University, Sweden
P-1245 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
P-1185 Comparative Genomics and Transcriptomics of Parasitic Nematodes
James Cotton*, Adam Reid, Isheng Tsai, Nancy Holroyd, Matthew Berriman
Wellcome Trust Sanger Institute, UK
P-1275 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