Ancient admixture into Africa from the ancestors of non-Africans

[Anfänger]

Ancient admixture into Africa from the ancestors of non-Africans

Abstract

Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species' history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species' demographic history around the out-of-Africa event is more complex than previously appreciated.

It is a preprint for now: https://www.biorxiv.org/content/10.1...06.01.127555v1

Good summary by Razib Khan: https://www.gnxp.com

[Angela]

It's a blog post from Razib Khan and one of his really good ones.

It's a reaction to this recent paper:

"Ancient admixture into Africa from the ancestors of non-Africans"

View ORCID ProfileChristopher Bernard Cole, View ORCID ProfileSha Joe Zhu, Iain Mathieson, Kay Prfüer, View ORCID ProfileGerton Lunter
https://www.biorxiv.org/content/10.1...555v1.full.pdf

"Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species' history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species' demographic history around the out-of-Africa event is more complex than previously appreciated."


From Khan:
"Massive “Basal Eurasian” Back-Migration”

POSTED ON JUNE 2, 2020 BY RAZIB KHAN

In 2005 Dienekes Pontikos had a post up, The mitochondrial time depth of humanity:

It is common to distinguish between Africans and non-Africans, with the former being much more genetically diverse than the latter. But, the real “gap” in human origins seems to be between the really old Africans (“Paleoafricans”) and the rest (“Afrasians”).
The Paleoafrican element is entirely confined to Africa, while the Afrasian one is found in both Africa and Eurasia. Indeed, modern humans can be entirely split into two groups: (i) a group of “pure” Afrasians which includes all non-Africans, and (ii) a group of Afrasian-Paleoafricans which includes all non-Caucasoid Africans. Human groups of entirely Paleoafrican origin, unhybridized with the younger Afrasians are no longer in existence.

Today, a preprint with very sophisticated computational methods of data analysis was posted, Ancient admixture into Africa from the ancestors of non-Africans. The figure to the right shows the proportion of deep “Eurasian” admixture into each major Sub-Saharan African population. Basically this preprint very formally breaks down the high likelihood that Dienekes’ model outlined in the mid-aughts was correct."

View ORCID ProfileChristopher Bernard Cole, View ORCID ProfileSha Joe Zhu, Iain Mathieson, Kay Prfüer, View ORCID ProfileGerton Lunter

[Regio X]

Awesome paper.

Angela, there's already a thread about it. Perhaps these two could be merged: https://www.eupedia.com/forum/thread...f-non-Africans

[Angela]

Sorry, Anfanger. I didn't notice you had posted it.

Threads are now merged.

[real expert]

It's a blog post from Razib Khan and one of his really good ones.

It's a reaction to this recent paper:

"Ancient admixture into Africa from the ancestors of non-Africans"



View ORCID ProfileChristopher Bernard Cole, View ORCID ProfileSha Joe Zhu, Iain Mathieson, Kay Prfüer, View ORCID ProfileGerton Lunter
https://www.biorxiv.org/content/10.1...555v1.full.pdf

"Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species' history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species' demographic history around the out-of-Africa event is more complex than previously appreciated."


From Khan:
"Massive “Basal Eurasian” Back-Migration”

POSTED ON JUNE 2, 2020 BY RAZIB KHAN

In 2005 Dienekes Pontikos had a post up, The mitochondrial time depth of humanity:

It is common to distinguish between Africans and non-Africans, with the former being much more genetically diverse than the latter. But, the real “gap” in human origins seems to be between the really old Africans (“Paleoafricans”) and the rest (“Afrasians”).
The Paleoafrican element is entirely confined to Africa, while the Afrasian one is found in both Africa and Eurasia. Indeed, modern humans can be entirely split into two groups: (i) a group of “pure” Afrasians which includes all non-Africans, and (ii) a group of Afrasian-Paleoafricans which includes all non-Caucasoid Africans. Human groups of entirely Paleoafrican origin, unhybridized with the younger Afrasians are no longer in existence.

Today, a preprint with very sophisticated computational methods of data analysis was posted, Ancient admixture into Africa from the ancestors of non-Africans. The figure to the right shows the proportion of deep “Eurasian” admixture into each major Sub-Saharan African population. Basically, this preprint very formally breaks down the high likelihood that Dienekes’ model outlined in the mid-aughts was correct."

View ORCID ProfileChristopher Bernard Cole, View ORCID ProfileSha Joe Zhu, Iain Mathieson, Kay Prfüer, View ORCID ProfileGerton Lunter

In the paper Basal Eurasians are referred to as the ancestors of Eurasians or Non-Africans because nobody knows where the bottleneck occurred, right? Many believe if the Basal Eurasians lived in North or East Africa that would make them "genetically" African instead of "Eurasians". Hence some argue only Eurasians without BE are real Eurasians. They concluded therefore that all Europeans are part African due to their Basal Eurasian admixture. Others go so far to totally deny the existence of Eurasians genetically speaking. The more studies or papers we get more questions than answers I do have.

[Angela]

In the paper Basal Eurasians are referred to as the ancestors of Eurasians or Non-Africans because nobody knows where the bottleneck occurred, right? Many believe if the Basal Eurasians lived in North or East Africa that would make them "genetically" African instead of "Eurasians". Hence some argue only Eurasians without BE are real Eurasians. They concluded therefore that all Europeans are part African due to their Basal Eurasian admixture. Others go so far to totally deny the existence of Eurasians genetically speaking. The more studies or papers we get more questions than answers I do have.

Shall I guess as to "who" the many is? :)

If it's an academic(s), could you please provide the paper(papers)?

[real expert]

Shall I guess as to "who" the many is? :)

If it's an academic(s), could you please provide the paper(papers)?

​

Well, the "many" are amateurs who base their opinion about BE being an archaic African lineage on ANA and the Shum Laka study.

I just want to be discrete and not tell to much since I had an e-mail correspondence with a known professional geneticist a while ago. However, I found out that according to the geneticist the figure in Shum Laka paper was rather misleading. The authors of the Shum Laka study really can't say much about the timing of those deep divergence events based on their data. I was told that this respective lab is working on a study that will hopefully help clarify. So we should stay tuned!

[Jovialis]

​

the "many" are amateurs

I figured as much, because it reads like something a t-roll on a sub-par forum, or blog would declare. Where are they from?

I recommend to stick with academic studies, rather than listen to the musings of dubious characters.

[Riverman]

​

Well, the "many" are amateurs who base their opinion about BE being an archaic African lineage on ANA and the Shum Laka study.

I just want to be discrete and not tell to much since I had an e-mail correspondence with a known professional geneticist a while ago. However, I found out that according to the geneticist the figure in Shum Laka paper was rather misleading. The authors of the Shum Laka study really can't say much about the timing of those deep divergence events based on their data. I was told that this respective lab is working on a study that will hopefully help clarify. So we should stay tuned!

If you look into the supplements of the Shum Laka paper they provide alternative scenarios for the admixture events. They know very well that this case is not closed yet, they can just construct plausible models from the current data.

[real expert]

If you look into the supplements of the Shum Laka paper they provide alternative scenarios for the admixture events. They know very well that this case is not closed yet, they can just construct plausible models from the current data.

I think that in the nearer future we can expect a study from Tishkoff about ancient African genomes. That would help to clarify the Shum Laka paper. Hopefully we get an insight into the African deep ancestry.

The researchers found that African individuals on average had significantly more Neanderthal DNA than previously thought—about 17 megabases (Mb) worth, or 0.3% of their genome. They also found signs that a handful of Neanderthal genes may have been selected for after they entered Africans’ genomes, including genes that boost immune function and protect against ultraviolet radiation.

The results jibe with as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. She told Science she has also found higher-than-expected levels of apparent Neanderthal DNA in Africans.

https://www.sciencemag.org/news/2020/01/africans-carry-surprising-amount-neanderthal-dna