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

Rates of Neandertal introgression in genic versus intergenic regions of the human genome


1Anthropology, University of Michigan, 2Ecology and Evolutionary Biology, University of Michigan, 3Mathematics, University of Michigan

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The Neandertal genome project recently estimated that 1-4% of the genetic material found in non-African populations is the result of the introgression of Neandertal genes. When populations that were previously isolated admix, incompatibility at the genic level can often result in distinctive patterns of introgression. It can be predicted that intergenic regions will be more likely to introgress into a population than protein coding changes when two populations or species have lowered hybrid viability or fertility. As coding changes are more likely to be associated with inviability and infertility due to epistatic interactions between gene products, these regions are less likely to be exchanged between diverging populations. Coding regions, therefore, should show an earlier divergence time than intergenic regions. To test this hypothesis, we looked at Neandertal introgression in five genic and five intergenic regions from six geographically distinct modern human populations (Han Chinese, Gujarati Indian, Italian, Puerto Rican, Japanese, and CEPH Europeans). We chose regions with similar recombination rates that did not show strong departures from neutrality. Using maximum likelihood estimation, we calculated the time to the most recent common ancestor (TMRCA) for each of the 10 regions separately based on human-Neanderthal-chimp sequence alignments. Our results highlight the patterns of introgression for intergenic and coding regions in different human populations while expanding our understanding of Neandertal population dynamics and raising new questions about human-Neandertal admixture.

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