March 20, 2016

Neandertal and Denisovan DNA from Melanesians

Admixture models are out of control these days, with 4 inferred archaic introgressions into three groups of Eurasians (Europeans, East Asians, Melanesians). The model on the left has to be a simplification/incomplete/wrong in some way (Melanesians are not an outgroup to Europeans and East Asians; Europeans have "Basal Eurasian" ancestry via Early European Farmers; Denisovans have some kind of weird archaic ancestry that Neandertals don't, and according to a recent study, the Altai Neandertal also has some kind of weird Proto-Modern Human lineage). In any case, this may not matter much for the problem at hand which is excavating archaic DNA from Melanesian genomes.

But, if you combined all the admixtures inferred in the literature, you'd probably need something like 8 admixtures to  model 5 populations. Time and data will show which of them are real, and reveal news ones (e.g., in Africans, who remain blissfully simple in the absence of archaic African genomes).

Science DOI: 10.1126/science.aad9416

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

Benjamin Vernot et al.

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 new Island Melanesian genomes. In aggregate, we recovered 1.34 Gb and 303 Mb of the Neandertal and Denisovan genome, respectively. We leverage these maps of archaic sequence to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequence, and identify signatures of adaptive introgression.



terryt said...

"you'd probably need something like 8 admixtures to model 5 populations".

I think that is getting somewhere near approaching the reality. Gone is the simple Out of Africa scenario. I found the most interesting part was the statement Neanderthal admixture had occurred multiple times, not just once. I think we already knew that the 2-4% Neanderthal all non-Africans have was not all the same. Now we see the reason.

eurologist said...

I agree this article seems a bit rushed - perhaps because they thought they would be scooped, otherwise. AMHs' history outside of Africa (and even within) is certainly complicated, and is becoming more complicated as we speak. Nevertheless, this paper shows that Neanderthal (and Denisovan) admixture also was anything but simple. Eventually, this will help understanding and clarifying that there were several population movements outside of Africa, and late reversal movements from S and SE Asia towards W & SW Asia, Africa, and Europe.

Also, the genetic time line of European and Asian divergence may need adjustment to earlier than 50 kya because some of their differences are due to more recent and different Neanderthal admixture events (and additional Denisovan admixture in Asians) .

David Jacobson said...

It is relatively easy to look at linkage disequilibrium of common genetic variants in thousand genome data. It does not take much analysis to understand that the patterns of human migration assumed from the results of admixture studies are a gross over simplification. It only takes a few years to walk across the Eurasian land mass. All the history we have any record of shows large amounts of human movement. No doubt it is true that the populations of East Asia, South Asia, Europe, and Africa have been isolated from each other by a band of deserts and the Himalayan mountains. It is also surely the case that genetic evolution of adaptability to different climates has played a role in the history of human migrations. But, in fifty to a hundred thousand years, human beings have had time to move around a lot. There is no way to tell what period of movement the genetic variation of modern human beings reflects. There is no way to tell how general the few analyzed ancient DNA samples really are. The rational expectation is for continual growth in complexity as new knowledge emerges.