African population genetics and "Out of Africa"

[Angela]

See:

Aaron P. Ragsdale and Simon Gravel

"Models of archaic admixture and recent historyfrom two-locus statistics"

https://www.biorxiv.org/content/biorxiv/early/2018/12/07/489401.full.pdf

"We learn about population history and underlying evolutionary biology through patterns of geneticpolymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number ofinformative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium.We show that many commonly used statistics are part of a broad family of two-locus moments whoseexpectation can be computed jointly and rapidly under a wide range of scenarios, including complexmulti-population demographies with continuous migration and admixture events. A full inspection ofthese statistics reveals that widely used models of human history fail to predict simple patterns oflinkage disequilibrium. To jointly capture the information contained in classical and novel statistics,we implemented a tractable likelihood-based inference framework for demographic history. Using thisapproach, we show that human evolutionary models that include archaic admixture in Africa, Asia, andEurope provide a much better description of patterns of genetic diversity across the human genome. Weestimate that individuals in two African populations have 6 − 8% ancestry through admixture from anunidentified archaic population that diverged from the ancestors of modern humans 500 thousand yearsago."

In terms of Africa:

"We inferred an archaic population to have contributed measurably to Eurasian populations. This branch (putatively Eurasian Neanderthal) split from the branch leading to modern humans between ∼ 470 − 650 thousand years ago, and ∼ 1% of lineages in modern CEU and CHB populations were contributed by this archaic population after the out-of-Africa split. This range of divergence dates compares to previous estimates of the time of divergence between Neanderthals and human populations, estimated at ∼650 kya (Pr¨ufer et al., 2014). The “archaic African” branch split from the modern human branch roughly 460 − 540 kya and contributed ∼ 7.5% to modern YRI in the model (Table A2)."

I can't remember. Was it Dienekes who used to expound on this?

Anyway, Razib Khan has a post up on it.
https://www.gnxp.com/WordPress/2018...istory/?utm_source=dlvr.it&utm_medium=twitter

 

[Angela]

Insight podcast on "The genetics of Africa"

https://blog.insito.me/the-insight-show-notes-season-2-episode-9-the-genetics-of-africa-897fc8b9b533

 

[Jovialis]

Very interesting episode.

Particularly the part about Yoruba not necessarily being a good baseline for African populations. That modern West Africans are possibly an uncertain degree of mixture between indigenous eastern Africans, and an indigenous West African population that diverged from the eastern group 200-300 kya. That being aside from the later west Eurasian back migration back into east Africa. Razib Khan mentions that David Reich, and a few other groups presume that the Hadza are the most closely related to ancient Africans that left for Eurasia.

 

[Johane Derite]

From a tweet of Chris Stringer:

"We estimate that individuals in two African populations have 6−8% ancestry through admixture from an unidentified archaic population that diverged from the ancestors of modern humans 500 thousand years ago"

LINK: https://www.biorxiv.org/content/early/2018/12/07/489401

in the comments below a commenter specifies which these two populations are:

"Yoruba (Nigerian) 7.5% admixture and Luhya (Kenyan) 6% admixture - estimated."



TWEET LINK: https://twitter.com/ChrisStringer65...7sxXq_RCsHRebDyz18v0I0ZfF0ULfId5_VczJqWDTeUWs

 

[markod]

Very interesting episode.

Particularly the part about Yoruba not necessarily being a good baseline for African populations. That modern West Africans are possibly an uncertain degree of mixture between indigenous eastern Africans, and an indigenous West African population that diverged from the eastern group 200-300 kya. That being aside from the later west Eurasian back migration back into east Africa. Razib Khan mentions that David Reich, and a few other groups presume that the Hadza are the most closely related to ancient Africans that left for Eurasia.

I think Hellenthal (2014) reported a migration edge from Hadza into Europeans, most pronounced in North-Eastern Europeans like Lithuanians.

This could suggest that Hadza-like populations used to occupy a larger area in the Paleolithic, and that they came into contact with the ancestors of the Villabruna population at one point. African components in WHG are also something that Dienekes predicted years go, much like the now confirmed archaic admixture in West Africans.