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Brwn_trd
12-14-2020, 12:33 AM
Revisiting the Out of Africa event with a novel Deep Learning approach (http://www.biorxiv.org/content/10.1101/2020.12.10.419069v1)

Abstract

Anatomically modern humans evolved around 300 thousand years ago in Africa. Modern humans started to appear in the fossil record outside of Africa about 100 thousand years ago though other hominins existed throughout Eurasia much earlier. Recently, several researchers argued in favour of a single out of Africa event for modern humans based on whole-genome sequences analyses. However, the single out of Africa model is in contrast with some of the findings from fossil records, which supports two out of Africa, and uniparental data, which proposes back to Africa movement. 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.

I wasn't sure where to place this. It's not really Africa specific but touches on some of the modelling that Chad has been doing

RP48
12-14-2020, 12:44 AM
Can someone comment on the main diagram of their calculated “tree”?
I understand most of it. Though not in the figure legend it seems AA is Ancient African. This model is saying that a population that left Africa contributed the majority of current genome of West Africans today if I am following it right. I’m wondering what “happened” to allow that to occur.

pmokeefe
12-14-2020, 01:19 AM
Can someone comment on the main diagram of their calculated “tree”?
I understand most of it. Though not in the figure legend it seems AA is Ancient African. This model is saying that a population that left Africa contributed the majority of current genome of West Africans today if I am following it right. I’m wondering what “happened” to allow that to occur.

There is a new version of the preprint (https://www.biorxiv.org/content/10.1101/2020.12.10.419069v2) in which Figure 1 has changed, if that's the one you are referring to.

REVISION SUMMARY
Update with correct Figure 1

gihanga.rwanda
12-14-2020, 03:53 AM
This is a really interesting study that provides further support for deep population substructure in Africa.

I am posting some excerpts from the study that I found particularly interesting or informative.

1. Could we be underestimating the extent of AMH admixture in Neanderthals, which may explain some of the Neanderthal affinities in Yoruba and other Africans?


We cannot also reject a simpler model of no Neolithic migration55. Even if we assume the Neolithic migration affected Yoruba, the predicted total length of Neanderthal sequence in an average Yoruba genome would be less than 5 Mb compared to the 17 Mb identified by Chen et al55. This discrepancy also cannot be explained by the back to Africa model as introgression happened much later after the separation. This suggests that most of the Neanderthal signal in Yoruba should be explained by some other migration (for example from Human to Neaderthal28).

2. Let’s just name the model “African population substructure or regionalism” or even “Back to Equatorial Africa” and call it a day. The data seems to suggest (overwhelmingly even) that the split between the “Back to Africa” and “Out of Africa” populations (60 kya) took place in Africa, since it’s estimated to have taken place 20 kyr before the admixture event that led to Neanderthal introgression in the OoA population (40 kya), which must have taken place in the Middle East or West Asia more broadly. On the other hand, the same model suggests that the B2A population absorbed “Ancient African”, assumingely in West Africa, in half that time at 48 kya.


We would like to caution that although we are naming the model “Back to Africa”, the OOA 224population did not need to be geographically out of Africa68. Our estimates, particularly the 225effective population size of B2A (N_BC) and the time of Neanderthal introgression (T_NIntro), 7advocate that the split might have happened within Africa itself before the actual out of Africa 227event. In such a case, our results can be explained by the separation of West and East African 228population 80 kya (T_B) and then later the primary separation of OOA and East African population 22967 kya (T_Sep) (assuming mutation rate of 1.25×10-8per bp per generation58,59and generation 230time of 29 years69). In this regard, our model is more akin to Lipson et al. 202036model rather than 231what is suggested by Cole et al. 202035. If we assume model from Lipson et al. to be true, the most 232parsimonious explanation would be that our B2A population represents Basal West African 233population which separated from OOA populations 67 kya (T_Sep). Our AA represents Ghost 234modern36which contributed to modern West African population around 10% which admixed 235around 60 kya from our prediction. On the other hand, if we assume true back to Africa, then most 236likely the OOA event took place less than 80 kya (T_B). This suggests that most of the older fossils 237(>80 kya) found outside Africa2–4are unlikely to have contributed to OOA populations (assuming 238the ancestor of all modern human originated in Africa and never left Africa before OOA event). 239Geographical location where B2A separated from OOA is immensely important for this hypothesis 240but cannot beestimated from our approach. It will be especially fascinating to test this hypothesis 241using ancient genomes from those areas from that time point when they will be available.

piye
12-15-2020, 08:31 AM
Haplogroyp E (or even DE) people.

Is it that people dont see it?

It is the haplogroup most close to so called "Eurasian" populations, yet ubiquitous in Africa (and not due to founder effects)

Ancient DNA remains the limiting factor in these modelling tho