On average, we found 23 Mb of introgressed sequence per individual (Fig. 1F), with East Asian individuals inheriting 21% more Neandertal sequence than Europeans. Within subpopulations, we found small but statistically significant variation in the amount of introgressed sequence among Europeans (Kruskal-Wallis rank sum test; p-value = 4.2 × 10−12), but not among East Asians (p-value = 0.43).and:
Consistent with recent inferences (5, 9), observed patterns of introgression were incom-patible with a one pulse model (Fig. 3B), suggesting that gene flow be-tween Neandertals and humans occurred multiple times. Although we varied many parameters of each model (10) (fig. S14), only the ratio of ancestral effective population size between East Asians and Europeans (NeASN/NeEUR) and the relative amount of introgression between the sec-ond and first pulse (m2/m1) had appreciable effects on model fit (Fig. 3B). We estimate that NeASN/NeEUR is 1.29 (95% CI of 1.15-1.57), and that East Asians received an additional 20.2% (95% CI of 13.4%-27.1%) more Neandertal sequence in the second pulse (10).
Science DOI: 10.1126/science.1245938
Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Benjamin Vernot, Joshua M. Akey
Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.