Statistical Inference of Archaic Introgression In Central African Pygmies

PingHsun Hsieh 1, Jeffrey Wall2, Joseph Lachance3, Sarah Tishkoff3, Ryan Gutenkunst1, Michael Hammer1
1University of Arizona, Tucson, AZ, USA, 2University of California, San Francisco, CA, USA, 3University of Pennsylvania, Philadelphia, PA, USA

Recent evidence from ancient DNA studies suggests that genetic material introgressed from archaic forms of Homo, such as Neanderthals and Denisovans, into the ancestors of contemporary non-African populations. These findings also imply that hybridization may have given rise to some of adaptive novelties in anatomically modern human (AMH) populations as they expanded from Africa into various ecological niches in Eurasia. Within Africa, fossil evidence suggests that AMH and a variety of archaic forms coexisted for much of the last 200,000 years. Here we present preliminary results leveraging high quality whole-genome data (>60X coverage) for three contemporary sub-Saharan African populations (Biaka, Baka, and Yoruba) from Central and West Africa to test for archaic admixture. With the current lack of African ancient DNA, especially in Central Africa due to its rainforest environment, our statistical inference approach provides an alternative means to understand the complex evolutionary dynamics among groups of the genus Homo.

To identify candidate introgressive loci, we scan the genomes of 16 individuals and calculate S*, a summary statistic that was specifically designed by one of us (JDW) to detect archaic admixture. The significance of each candidate is assessed through extensive whole-genome level simulations using demographic parameters estimated by ∂a∂i to obtain a parametric distribution of S* values under the null hypothesis of no archaic introgression. As a complementary approach, top candidates are also examined by an approximate-likelihood computation method. The admixture time for each individual introgressive variant is inferred by estimating the decay of the genetic length of the diverged haplotype as a function of its underlying recombination rate. A neutrality test that controls for demography is performed for each candidate to test the hypothesis that introgressive variants rose to high frequency due to positive directional selection. The present study represents one of the most comprehensive genomic surveys to date for evidence of archaic introgression to anatomically modern humans in Africa.