The main conclusion of this new study seems to be that East Asians have normally more Neanderthal admixture than South or West Eurasians. Also the Maasai from East Africa have been shown to have minor Neanderthal admixture, consistent with the also minor Eurasian genetic component they have.
Jeffrey D. Wall et al., Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans. Genetics 2013. Freely accessible at the time of writing this → LINK [doi: 10.1534/genetics.112.148213]
Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.
There is a sentence in page 8 in which the authors claim that:
By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.
However I fail to see it in the D-statistic graphs, which show less than 15% more Neanderthal admixture in Eastern Asians than in Europeans (on average and discounting error margins, which strongly overlap). It may be therefore another case of hair-splitting.
Instead the evidence of weak Neanderthal admixture (via minor Eurasian genetic influence) in the Maasai of East Africa seems more solid: while error margins of Maasai and Luhya do overlap, the main blocs do not.
It is surely convenient to look carefully at all the data, including the supplementary materials, before jumping to any strong conclusions. Among them I found more interesting fig. S1:
|Figure S1: Box plot of the D-statistics for Analyses A and B for the set (Afr, X), where X was any of the non-African populations, CEU or TSI (Europeans, green), CHB or JPT (East Asians, blue), or GIH (South Asian, pink) (PDF, 222 KB).|
As we can see here, the error margins continue overlapping very strongly, but, assuming that we can jump to conclusions based on the norm (thick black line), which is assuming some risks indeed but also the only way to (tentatively) agree with the authors' conclusion of greater Neanderthal admixture among East Asians, then the causes should be:
- Founder effect among East Asians, known to have less overall genetic diversity and suspected to have undergone some extra (mild?) bottleneck at their ancient origins.
- Low-level African (and surely also early OoA residuals from West Asia) admixture among West Eurasians, notably Tuscans (TSI) in these samples but also to some extent all Europeans (incl. CEU). This has the effect of increasing genetic diversity but also of slightly diluting Neanderthal admixture. The control here are Indians (GIH), which show slightly more Neanderthal admixture than Europeans (but are still closer to these than to East Asians also in this aspect).
Indians (who don't seem to have any post-OoA African admixture, unlike Europeans and West Asians, who have it at variable low levels) suggest that factor #2 (dilution) weights only somewhat and therefore that factor #1 (East Asian founder effect) must be considered the main one instead.
But, unless someone can point me where I am wrong, I fail to see neither the alleged 40% excess Neanderthal admixture in Orientals nor why would these results question the single admixture episode (or period) at the origins of migration out of Africa (OoA).
To finish this entry, it must be mentioned that the authors could only detect at most the tiniest fraction of Denisovan admixture among the sampled populations (i.e. nothing relevant and with no regional differences). However they did not research, admittedly, the South China populations suggested to have slight more Denisovan input by Skoglund and Jakobsson 2011.
- On some details of the Neanderthal genome draft (Leherensuge 2010, when I noticed that Chinese, but not Japanese, samples looked like having slightly more admixture)
- Splitting hairs on the Neanderthal affinity, questioning if the slight greater Neanderthal admixture detected by John Hawks among Europeans (the opposite of what is claimed here) was actually meaningful at all.
- East Asians now claimed to be more Neanderthal than Europeans (prelude of this paper in a sense)
- Intriguing North African Neanderthal admixture paper