We estimate admixture proportions of 14 % (95% CI: 8 – 20 %) in the European-American sample and 1.5% (95% CI: 0.5 – 2.5 %) in the East Asian sample. In both cases, the relative log-likelihood for a = 0 (i.e., no ancient admixture) is significantly lower than the maximum likelihood (likelihood-ratio test, p < 10-3) , which provides additional evidence (along with the S* results in the previous paragraph) that ancient admixture occurred. The estimates of admixture rates in Europeans are consistent with estimates of Neandertal admixture obtained from analyses of Neandertal DNA (Serre et al. 2004; Noonan et al. 2006), [. . .] Unlike previous studies, we incorporated admixture between archaic and modern humans as an additional demographic parameter to be co-estimated. Interestingly, we could exclude no admixture (i.e., exclude a = 0) in both of the non-African populations studied. [. . .]MBE Advance Access published online on May 6, 2009
We estimate low levels of ancient admixture in East Asia, perhaps with either Asian Homo erectus or H. floresiensis. [. . .] For simulations under our best-fit model, approximately 6% of loci have at least some archaic ancestry (i.e., have at least one sequence that inherited DNA from the archaic Asian population). [. . .]
Our signal of ancient admixture (as measured by S*) is strongest in the West African samples, though the spotty fossil record in sub-Saharan Africa makes it difficult to speculate about potential source populations or the times and locations of admixture. This said, there was thought to be a substantial amount of hominin taxonomic diversity within Africa during the Pleistocene. We note that our simple two-population model does not allow for any population structure within continental groups, and there may be a substantial amount of unsampled population structure within Africa (e.g., between West Africans and pygmies or San, cf. Wall et al. 2008) that serves as a confounding factor. The observation that all (three) populations studied seem to have evidence for ancient admixture suggests that ancient population structure may be a common feature of all contemporary human populations, and this ancient structure may predate the initial expansion of modern humans out of Africa. Future work that estimates the lengths of the putative chunks of sequence inherited from archaic populations may help to estimate the timing of ancient admixture events.
Molecular Biology and Evolution, doi:10.1093/molbev/msp096
Detecting ancient admixture and estimating demographic parameters in multiple human populations
Jeffrey D. Wall, Kirk E. Lohmueller and Vincent Plagnol
We analyze patterns of genetic variation in extant human polymorphism data from the NIEHS SNPs project to estimate human demographic parameters. We update our previous work by considering a larger data set (more genes and more populations), and by explicitly estimating the amount of putative admixture between modern humans and archaic human groups (e.g., Neandertals, Homo erectus, H. floresiensis). We find evidence for this ancient admixture in European, East Asian and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.