March 31, 2016

Denisovan ancestry in Oceanians (and some in South Asians)

Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.03.037

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

Sriram Sankararaman et al.

Some present-day humans derive up to ∼5% [ 1 ] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [ 2 ]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [ 3 ]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

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5 comments:

terryt said...

Extremely interesting paper.

"This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years".

That is completely normal for mammalian species.

"We document more Denisovan ancestry in South Asia than is expected based on existing models of history"

Which, to me, indicates the 'existing models of history' are wrong.

eurologist said...

I find it disconcerting that the age estimates based on linkage disequilibrium are off by a factor of two or more. How can we then believe previous admixture age estimate based on this method?

Why are the admixture percentages found here so low (e.g., 1% Neanderthal in W Europeans, <1% Denisovans in Oceanians?

I find Fig. 3 intriguing - especially the "desert" regions.

terryt said...

Here's an interesting paper. The 'northern route' has opened for both mt-DNA M and for mt-DNA N (already done in this last case):

http://biorxiv.org/content/biorxiv/early/2016/04/06/047456.full.pdf

Basant said...

Yes, very interesting, especially since we were debating denisovan ancestry in South Asians a few posts ago.

AndyC said...

It is definitely strange that they estimate 1,121+/-16 generations and then interpret that as 50,000 to 60,000 years ago.

Obviously they cannot explain their results, so the only confident claim that they can make is that there is less LD on Denisovan alleles than Neandertal, so the admixture with Denisovans is more recent.