The complex origins of our species in Africa

The figure to the right illustrates a model that is put forward in a new paper, Recovering signals of ghost archaic introgression in African populations. This was originally a preprint, Recovering signals of ghost archaic introgression in African populations. So we’ve discussed the implications extensively. Carl Zimmer has covered the story in The New York Times, while Georbe Busby did so in The Conversation.

Broadly, the results are getting at something which plenty of people have been noticing for many years: when it comes to Sub-Saharan Africans, there is something deeply diverged in West Africans vis-a-vis non-West Africans. These results seem to suggest that the divergence between this outgroup lineage and our own is a bit earlier than the modern-Neanderthal/Denisovan split. There are many abstruse statistical inferences and simulations, and it looks like the reviewers made them do a lot of analyses. But the general result is something other groups have seen as well, so I believe it. Additionally, the admixture of this lineage into West Africans seems to have occurred about 50,000 years ago, suspiciously close to the general expansion of modern humans out of Africa (or the most recent expansion).

From the discussion:

The signals of introgression in the West African populations that we have analyzed raise questions regarding the identity of the archaic hominin and its interactions with the modern human populations in Africa. Analysis of the CSFS in the Luhya from Webuye, Kenya (LWK) also reveals signals of archaic introgression, although our interpretation is complicated by recent admixture in the LWK that involves populations related to western Africans and eastern African hunter-gatherers (section S8) (20). Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations. A detailed understanding of archaic introgression and its role in adapting to diverse environmental conditions will require analysis of genomes from extant and ancient genomes across the geographic range of Africa.

This work seems more a question than an answer.

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2 thoughts on “The complex origins of our species in Africa

  1. The admixture does seem to have ocurred slightly before or around the time of the main/most recent OOA migration. And the study does (as also quoted above) seem to find the archaic admixture (that they found in West Africans) also to be in non-Africans/Eurasians (or at least some of it) and that it was likely acquired before the African/non-African split.

    It would be interesting to analyze other groups of East Africans (Nilotes/Nilo-Saharans, Horn Africans, Omotics, Hadzas) as well, along with a greater range of African groups.

    Another excerpt from the study (“YRI”=Nigerian Yoruba from West Africa):

    “Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU (section S9.2).”

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  2. This study suggests that archaic admixture in West Africans took place before the Out-of-Africa event, which implies that Non-Africans also likely have this kind of admixture, or at least some/a component of the admixture. However, the paper also says that it’s possible that this archaic admixture was diluted or lost during the Out-of-Africa bottleneck. As many here already said, we need more genetic research on the deep ancestry in Africa. Besides the range of the suggested archaic admixture (~2-19%), I personally find difficult to understand or to make a sense out of it. Besides, IF all humans, West Africans, and non-Africans have this Ghost DNA why does the study only talk about West Africans? Were Non-Africans tested for this archaic admixture in the same study? Once again when Non-Africans have this kind of archaic genetic input what is so special about West Africans or the Yoruba then? And what about East Africans? However, this archaic Ghost ancestry in West Africans is very likely from Homo heidelbergensis.

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