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So many assumptions about Africa


I have been staring and this figure and rereading Ancient West African foragers in the context of African population history. The Shum Laka sample from this paper, dating to four to eight thousand years ago, have drawn my attention, and I’m just looking at them a lot.

It seems ridiculous I’ve been using Nigerians as my “African reference” for decades. Most African populations, including Pygmies and Khoisan, have Eurasian admixture from the last 10,000 years. And what about deeper back-to-Africa ancestry? That seems likely and is hinted at in the above paper.

Modern human lineages have a deep history in Africa and the Near East. I think we’re going to have a transformation of our understanding of what happened in these regions in the near future.

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8 thoughts on “So many assumptions about Africa

  1. I appreciated Lipson et al. 2020 because it is one of a few studies to present a possible model for deep population substructure in Africa and the existence of various basal and “neo” African clades that contributed, to varying degrees, to modern populations (including Nigerians) within and outside the continent. That was the main takeaway for me at least.

  2. People have been using YRI and Mbuti as outgroups for within-sapiens analyses like F-stats for years now. It’s clear that even Mbuti aren’t absolutely ideal given their Bantu admixture (+ East African pastorialist apparently?).

    So, if money + will were no obstacle, what’s the best population we could sequence a bunch of to use as a within-sapiens outgroup, modern or ancient (among the ancient samples we know of)? Is modern Ju|’hoan North better — are we sure they don’t have Eurasian admixture? As many South_Africa_2000BP from Skoglund 2017 as we can find?

  3. @KM

    We can still use Ju|’hoan North and South as outgroups but we have to account for their very minor East African (imbedded Eurasian) and Bantu ancestry. According to Pickrell et al. 2014, Ju|’hoan North can be modeled as 96% South_Africa_2000BP or ancient Khoisan and 4% East African (1% Eurasian) with no Bantu admixture; Ju|’hoan North are very similar as they are 93% ancient Khoisan, 6% East African (1.5% Eurasian), and 1% Bantu.

    http://4.bp.blogspot.com/-sqVhykH78wM/VZeKkuK7HKI/AAAAAAAAC-w/MhsyM23Jzc4/s1600/Khoi%2BKhoi.png

  4. @ Gihanga.Rwanda,

    Correct me if I’m wrong, but I thought the ancient (well, comparably ancient) DNA samples from Southern Africa are of a Ju|’hoan-like group without any evidence of the recent influx of Cushitic ancestry. Couldn’t you use this as an outgroup?

  5. @ Karl

    You are right about South_Africa_2000BP lacking any Cushitic ancestry but if I am not mistaken he’s the only ancient southern African hunter gatherer sample we have at the moment. Hopefully he won’t be lonely for to long.

  6. @Gihanga Rwanda

    IIRC there are 4 ancient South African samples: 2 from Ballito Bay on the east coast (KwaZulu-Natal) and 2 from the sites of St Helena and Faraoskop in Western Cape province. All are about the same age and genetically similar in broad strokes.

    There was a mitochondrial DNA sample from the Green Sahara, are we ever going to get autosomal from that I wonder?

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