The 81st Annual Meeting of the American Association of Physical Anthropologists (2012)

Assessing the pattern of Neandertal ancestry in living human populations


Department of Anthropology, University of Wisconsin-Madison

Friday 3:15-3:30, Parlors Add to calendar

People living outside Africa today derive 2 to 4% of their ancestry from Neandertal populations. This initial estimate was based on whole-genome sequencing of a small number of individuals, and the pattern of Neandertal ancestry has yet to be characterized. Here I employ the sequencing data from the 1000 Genomes Project to identify Neandertal-derived haplotypes in living human populations. Initial sequence-level comparison allowed development of a genome-wide sample of SNP haplotypes informative of Neandertal ancestry. Humans within a population differ little in the amount of Neandertal ancestry, but the fraction does vary significantly among samples from different regions. Most Neandertal genes today are rare, existing only in one or two copies in the 1000 Genomes sample. However, a few have become majority haplotypes, 50% or higher. Europeans, South Asians, and East Asian populations differ substantially in which Neandertal-derived haplotypes are presently common, so that a haplotype present in one of these regions is very likely to be absent in samples from other regions. This heterogeneity of present-day Neandertal ancestry provides information about the Late Pleistocene dispersals of humans. In particular, today's populations outside Africa differentiated under strong genetic drift. A relatively small proportion of Neandertal-derived haplotypes contain candidates for selection in later human populations, based on their current pattern of extended haplotype heterozygosity and fraction of derived SNP alleles. Additionally, I report on the application of these methods to investigate and visualize Neandertal ancestry at the whole-genome level from commercial SNP genotype data.

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