Ancient Admixture into Africa from the ancestors of non-Africans

Cole, Christopher B.; Zhu, Sha; Mathieson, Iain; Prüfer, Kay; Lunter, Gerton

doi:10.1101/2020.06.01.127555

Cited by 6 publications

(10 citation statements)

References 60 publications

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“…In such a case, our results can be explained by the separation of West and East African population 80 kya (T_B) and then later the primary separation of OOA and East African population 67 kya (T_Sep) (assuming mutation rate of 1.25×10 -8 per bp per generation 58,59 and generation time of 29 years 69 ). In this regard, our model is more akin to Lipson et al 2020 36 model rather than what is suggested by Cole et al 2020 35 . If we assume model from Lipson et al to be true, the most parsimonious explanation would be that our B2A population represents Basal West African population which separated from OOA populations 67 kya (T_Sep).…”

Section: Discussionmentioning

confidence: 60%

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Revisiting the Out of Africa event with a novel Deep Learning approach

Montinaro

Pankratov

Yelmen

et al. 2020

Preprint

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Anatomically modern humans evolved around 300 thousand years ago in Africa1. Modern humans started to appear in the fossil record outside of Africa about 100 thousand years ago though other hominins existed throughout Eurasia much earlier2–4. Recently, several researchers argued in favour of a single out of Africa event for modern humans based on whole-genome sequences analyses5–7. However, the single out of Africa model is in contrast with some of the findings from fossil records, which supports two out of Africa8,9, and uniparental data, which proposes back to Africa movement10,11. Here, we used a novel deep learning approach coupled with Approximate Bayesian Computation and Sequential Monte Carlo to revisit these hypotheses from the whole genome sequence perspective. Our results support the back to Africa model over other alternatives. We estimated that there are two successive splits between Africa and out of African populations happening around 60-80 thousand years ago and separated by 12-13 thousand years. One of the populations resulting from the more recent split has to a large extent replaced the older West African population while the other one has founded the out of Africa populations.

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Section: Discussionmentioning

confidence: 60%

“…This observation might be explained by a back to Africa migration 11 or a more complicated scenario 32 . Some autosomal analyses also suggest that the separation between Africa and OOA populations might not be a single split event [33][34][35][36] .…”

Section: Introductionmentioning

confidence: 99%

Revisiting the Out of Africa event with a novel Deep Learning approach

Montinaro

Pankratov

Yelmen

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Back-migration from Eurasia into Africa post OOA and post-Neanderthal introgression likely introduced not just Eurasian ancestry into Africa ( Henn et al 2012 ; Pagani et al 2012 ; Hodgson et al 2014 ; Pickrell et al 2014 ; Petr et al 2019 ), but also Neanderthal ancestry ( Sánchez-Quinto et al 2012 ). Furthermore, a ∼4,000-year-old ancient Ethiopian genome ( Gallego Llorente et al 2015 ) confirms that back migration was occurring after ∼4000 YBP, but it may have also been occurring as early as the European-East Asian split ( Chen et al 2020 ), or even concurrent with or immediately following the OOA event ( Cole et al. 2020 ).…”

Section: New Insights On the Demography Of Archaic African Populationsmentioning

confidence: 77%

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

Ahlquist

Bañuelos

Funk

et al. 2021

Genome Biology and Evolution

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The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: i) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; ii) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; iii) how these novel methods can detect archaic introgression in modern African populations; and iv) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.

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“…The detection, in the extant population of Saudi Arabia, of the basal African Y-chromosome lineage E-M96*[128] is in support of this back flow. Furthermore, whole genome sequence analyses also favor models involving possible African returns 70-60 kya[129,130]. Interestingly, a similar model, involving back flow to Africa, has been proposed to explain the complex mtDNA phylogeography of hamadryas baboons lineages present in Africa and Arabia [131].…”

Section: Resultsmentioning

confidence: 99%

Section: An Earlier Out Of Africamentioning

confidence: 99%

Following the evolution of Homo sapiens across Africa using a uniparental genetic guide

Cabrera

2022

Preprint

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The origin and evolution of modern humans in Africa has reached a multidisciplinary consensus but the age and regions where it originated and evolved are current topics of discussion. In this study I put forward an integrative model guided by the phylogeny and phylogeography of mitochondrial DNA (and Y-chromosome) haplogroups. I propose an early origin of modern humans in northwest Africa in a temporal window of 257-345 thousand years ago. A first population split in central Africa around 175-288 thousand years ago. A subsequent northward spread with additional population subdivisions during a long statistical interval that culminated in a first successful out of Africa migration around 130 thousand years ago. A population constriction in southwest Asia motivated an early return to Africa between 79 and 107 thousand years ago. This ample Eurasian-ebb to Africa, detected by mitochondrial haplogroup L3 and Y-chromosome haplogroup E preceded other later and geographically more limited Eurasian backflows. The archaeological and fossil finds that could be coetaneous to this molecular journey have been integrated into this interdisciplinary model.

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Ancient Admixture into Africa from the ancestors of non-Africans

Cited by 6 publications

References 60 publications

Revisiting the Out of Africa event with a novel Deep Learning approach

Revisiting the Out of Africa event with a novel Deep Learning approach

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

Following the evolution of Homo sapiens across Africa using a uniparental genetic guide

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