Thursday, February 18, 2016

The earliest Modern Humans to leave Africa mostly died out?

There's a new study out with some very intriguing genetic implications that have been somewhat implied in the past which is that there was (or were) a much earlier dispersal(s) out of Africa by Anatomically Modern Humans (Homo Sapien Sapiens):

"It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought."

But one important detail pointed out by this study that is escaping some people aware of it is the following:

"However, it is clear that the source of the gene flow is a population equally related to present-day Africans and non-Africans (Extended Data Fig. 3). We conclude that the introgressing population diverged from other modern human populations before or shortly after the split between the ancestors of San and other Africans (Fig. 3a), which occurred approximately 200,000 years ago."

What they've found is that the hypothetical Homo Sapien Sapien population responsible for this admixture into those Neanderthals diverged from the ancestors of all Modern Humans (San & Yoruba included) well over 150,000 years ago so these people were not ancestral to modern Out-of-Africa/Eurasian populations to the exclusion of African populations like Yorubas and they probably did mostly die out whilst current Out-of-Africa populations seem like they're descended from later migrations out of Africa.

There have long been theories about Eastern Non-Africans like Australo-Melanesians tracing some of their ancestry to people who may have left Africa before the OoA migration (or migrations) mostly responsible for modern OoA populations, I do wonder if there is any truth to that.

Reference List:

Tuesday, February 9, 2016

Y-DNA & mtDNA data from Eritrea forthcoming

For a while now, a friend has been mentioning a forthcoming uniparental study on Eritrea to me and just recently he got his hands on its abstract (I'm not sharing all of it but just some of it):

"Eritrea is strategically located at the eastern part of the African Sahel belt over what is believed to be the original scene of modern humans’ evolution and dispersal. The country’s peculiarity is also reflected in the presence of nine ethno-linguistic populations that speak Cushitic, Semitic and Eastern Sudanic languages, makes it all interesting in addressing some of the significant questions pertaining to history of human expansion within and beyond the African landscape. Major Y chromosome haplogroups A (24.73%), B (7.52%), E (46.24%) and J (21.51%) were detected in all Eritrean samples. Further high-resolution analysis of the macrohaplogroups resulted in high frequency of A-M13, E-V32 and J-P58 with different proportions found in the populations analyzed to indicate the prehistoric and historic demography of the populations."

I'll hold back on any comments until we get the full-paper but I must say... I'm extremely excited at the idea of comprehensive mtDNA data for ethnic groups like Afars, Sahos and Tigres.

Reference List:

More Benadiris and the story isn't changing

Well, I was contacted a while back by a Benadiri of a different tribe than the two whose samples I had acquired prior then wrote about here and interestingly... :

... the story hasn't changed, so to speak. This Benadiri seems to be 35-40% "African" & 60-65% Eurasian on a fundamental level then in terms of more recent ancestry he seems to be roughly 40-50% Horn African (Somali or Somali-related ancestry), ~20% South to South-Central Asian, perhaps less than 5% Southeast African Bantu with the remaining ancestry clearly being West Asian ancestry of perhaps various origins (Arabian, Iranian etc.).

He is also quite clearly related to the two other people whose samples I have despite not knowing them:

Him and the paternally as well as maternally Shanshiyo fellow

Him and the paternally Bravanese but maternally Shanshiyo fellow

It's not very shocking though... I imagine most "Benadiris" and such are interrelated due to endogamy and the relatively small size of their community.

On another note, his ADMIXTURE results are very interesting because he's paternally of a different group (i.e. Tribe) than either of them with his line claiming Arabian descent and the Shanshiyo fellow's claiming Eastern-Iranian/Central-Asian descent yet they all look extremely similar from an autosomal perspective.

They're all most certainly made up of the same base ancestries and are all interestingly ~20% South Asian, something even a run as simple as 23andme's ancestry composition could pick-up about the paternally Bravanese fellow:

Then as all analyses find; all three of them seem substantially Horn-African (Somali and/or Somali-related) at levels of 30-50% of their ancestry. They're more Horn-African than they are Arabian or Iranian, oddly. Yet all three of them posit that they don't really have any or much recent Somali ancestry, positing that most of their ancestries are clearly "old" (centuries old).

The reason I think this is (why they have little recollection of a lot of Somali ancestry despite being so substantially Somali-related) might be the following upon doing some research a while back on the history of Southern Somalia:

As also mentioned above... "Deftextra" (the paternally and maternally Shanshiyo fellow) is aware of at least 3 other Benadiris on AncestryDNA and they too get pretty much the same results on there that he does. Unfortunately though, he hasn't been able to get them to fork-over their raw data from what I've noticed.

If I had to add any further notes; the Hatimi chap claims one of his cousins got tested for his Y-DNA Haplogroup and is of Y-DNA J1 which intriguingly could coincide with his family's claims of paternally Arabian (Hejazi) descent but since AncestryDNA doesn't give us any uniparental data; we don't know what his own Y-DNA and mtDNA markers are. Well, technically the person who contacted me is the brother of the "Hatimi" whose raw data I have so we lack his brother's Y-DNA and mtDNA data which they obviously share.


1. Here is his Gedmatch kit-number: A902267. I'm sharing this so people won't just be taking my word for his ADMIXTURE results in particular.

2. I believe I made a few mistakes when outlining the history of the South in that post (i.e. the Caliphate detail is incorrect as I was a little too trusting by this one book and a source outside of the literature that I found now was wrong on this detail that has no real evidence to it, as far as I can see) and may edit this post a little in the future but I gave it a re-read and most of it seems on-point. Granted, I'd add that the time-period for when the "Ajuran" arose can vary to being beyond the 1200s (I.e. 1300s-1500s).

3. I might make a new post with some more accurate estimates. For now I'd say these samples I have vary between 35-45% Somali/Horn-African, ~20% South Asian, 5-15% SE African Bantu speaker-related with the rest being West Asian ancestry of either Iranian or "Arab" origins or both.

Recommended reads:

Fruitful Anthrogenica discussion (important points regarding the term "Azanian" can be read via the latest posts in this thread)

Thursday, February 4, 2016

Admixture into and within Sub-Saharan Africa

A new study is out on Africa, and while there unfortunately aren't any new ancient genomes or even many new samples from what I've noticed, it's pretty hulking and while some of it, after having sifted through it, seems a little lackluster; it does have some interesting things to share such as the following:

"To quantify the extent of the genetic difference between groups we used two different metrics. First, we used the classical measure FST [Hudson et al., 1992; Bhatia et al., 2013] which measures the differentiation in allele frequencies between populations. It can be thought of as measuring the proportion of the heterozygosity at SNPs explained by the group labels. The second metric uses the similarity in copying patterns between two groups to estimate the total variation difference (TVD) at the haplotypic level...

...When compared to non-African populations, FST measured at our integrated set of SNPs is relatively low between many groups from West, Central, and East Africa (yellows on the upper right triangle), whereas TVD in the same populations can reveal haplotypic differences as strong as between Europe and Asia (pink and purples in lower left triangle). For example, the Chonyi from Kenya have relatively low FST but high TVD with West African groups, like the Jola (Chonyi-Jola FST = 0.019; Chonyi-Jola TVD = 0.803) suggesting that, whilst allele frequency differences between the two populations are relatively low, when we compare the populations’ ancestry vectors, the haplotypic differences are some the strongest between sub-Saharan groups."

It's interesting that for various African populations, Fst, which measures differences in allele frequencies, is not as useful for measuring divergence as it is for Eurasian / Out-of-Africa populations who've suffered through lower population sizes in early Human pre-history (+ dips like the "Eurasian-bottleneck") which were more conducive to genetic drift. For African populations, like the "Khoisan" for example, they've had larger population sizes throughout a good chunk of Human pre-history and have maintained greater genetic diversity as a result:

For these sorts of populations, it seems that haplotypic differences and Haplogroup divergence dating (like formation dates for E-V95, E-M329 and E-M215) is much more relevant to seeing how divergent they are. I.e. both these methods would imply that the African element in Somalis and Habeshas diverged from the African element in Yorubas roughly ~40,000 years ago.

That's a time-depth comparable to when the shared Homo Sapien Sapien ancestors of Eastern Non-
Africans and the non-Basal Eurasian ancestors of Europeans diverged.

Reference List: