A genomewide map of Neandertal ancestry in modern humans. S. Sankararaman1,2, N. Patterson2, S. Mallick1,2, S. Pääbo3, D. Reich1,2 1) Harvard Medical School, Boston, MA; 2) Broad Institute of MIT and Harvard, Cambridge, MA; 3) Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

   Analysis of the genomes of archaic hominins, such as Neandertals and Denisovans, has revealed that these groups have contributed to the genetic variation of modern human populations. Yet, we know little about how these ancient mixtures have shaped the genetic structure of human populations and even less about their impact on human evolution. To answer these questions, we need a map of archaic ancestry.
    Building such a map is technically challenging because of the antiquity of these gene flow events. We have developed a method based on the statistical framework of Conditional Random Fields (CRFs) that integrates single SNPs as well as haplotypes informative of ancient gene flow to give highly accurate predictions.
    We applied this method to polymorphism data in European and East Asian individuals from the 1000 genomes project, in conjunction with the draft sequence of the Neandertal genome, to obtain the first genome-wide map of Neandertal ancestry. Analysis of this map leads to several novel findings:
  1. We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.
  2. We also identify over 100 Neandertal-derived alleles that are likely to have been the target of selection since introgression. One of these has a frequency of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow.
  3. Several of the Neandertal-derived alleles identified are found among the >6,000 SNPs associated with common diseases listed in the NHGRI catalog. This list of Neandertal-derived variants include a risk variant associated with obesity and a protective variant against breast cancer.
  4. Using the uncorrelated ancestries in Europe and East Asia, we can reconstruct about 600 Mb of the genome of the introgressing Neandertal.
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