Friday, May 27, 2016

Elhaik's at it and wrong again

Seems Dr. Eran Elhaik, despite being proven wrong in the past, is at it again but this time with a seemingly new game plan. You see, Ashkenazim are now no longer simply Khazarians but are originally  Northeastern Anatolians who spoke a... "Slavo-Irano-Turkic" language. And that language is apparently Yiddish because all of the linguists who are pretty sure it's a Germanic language are quite wrong according to Elhaik and this is because the genetics supposedly supports a nonsensical fringe theory.



First off, linguistics is linguistics and population genetics is population genetics. The two fields can compliment one another for sure but linguistic issues will principally be solved via linguistic study but that doesn't even matter because the genetic data is not actually on Elhaik's side this time either.

I wouldn't let all of this disingenuous "GPS" talk fool you... Simply observe any decent PCA (principal component analysis) based on autosomal DNA and- :




-you'll catch onto the fact that Ashkenazi Jews are nearly identical to Sephardi Jews and cluster extremely close to them (often overlapping with them as well) whilst the other groups they cluster closest to are Sicilians, the Maltese, certain Greeks (i.e. Cretans) and Cypriots. Mostly Mediterranean islander populations and not Northeastern Anatolians or Northern Caucasians

Ashkenazim are basically, from a genetic perspective, a Mediterranean population who seem to be a mixture between Southern Europeans (Italian or Greek related) and Hebrew speaking Levantines (I'd say more of the latter than the former) and they're, at a basal level, of mostly Near Eastern origins (i.e. Anatolian Neolithic & Caucasus Hunter-Gatherer type ancestries) and we have an array of studies and data supporting this but Elhaik still seems hellbent on preaching this type of gobbledygook with a straight face. Whatever floats his boat, I guess. [1] [2] [3] [4] [5]

Reference List:






Suggested reads:




Early pottery and it's history in Northeast Africa

Abstract:

"Where did pottery first appear in the Old World? Statistical modelling of radiocarbon dates suggests that ceramic vessel technology had independent origins in two different hunter-gatherer societies. Regression models were used to estimate average rates of spread and geographic dispersal of the new technology. The models confirm independent origins in East Asia (c. 16000 cal BP) and North Africa (c. 12000 cal BP). The North African tradition may have later influenced the emergence of Near Eastern pottery, which then flowed west into Mediterranean Europe as part of a Western Neolithic, closely associated with the uptake of farming."


What's interesting is that by "North Africa" they actually mean "Northeast Africa" as the map above implies and they make clear here:

"Early Holocene pottery sites are found within a 4000km-long band encompassing the southern Sahara and northern Sahel, with early dates clustering in the Middle Nile valley and the Western Desert of Egypt, in the vicinity of the mountainous regions of southern Algeria and northern Niger, and at Ounjougou, Mali (Close 1995; Nelson et al. 2002; Jesse 2003; Huysecom et al. 2009).....

A number of locations inNorth Africa have sites with pottery dated to the earlyHolocene. Ounjougou, in Mali, has some of the very earliest dates but lies quite distant from the Near East (Huysecom et al. 2009). Pottery that is potentially as early as the Ounjougou material has been found at sites that are geographically closer to the Near East. Bir Kiseiba, in theWestern Desert of Egypt, has the earliest dates coming from site E-79-8, although with large margins of error, and in the central Nile Valley of Sudan, the Saggai site has produced the region’s earliest date for pottery (Close 1995)... We have taken... Saggai in Sudan (e.g. Caneva 1983) as the origin point in Africa. The exact location of the source point in the broader region of origination is unlikely to significantly affect the modelled results.."

I imagine these early potters, given the early datingwould've been pretty similar to modern Dinkas from an autosomal DNA perspective, just discounting the West-Central African-related ("Yoruba-like") elements in them. Some West Asian input is possible, I guess, but I somehow doubt it. Just my opinion on the matter from a genetic stand-point.


Saturday, May 14, 2016

Using Somalis as a proxy: The second attempt

Over a year ago I made a post where I essentially took Somalis and tried to run-down, based on data from Shriner et al. 2014 and Hodgson et al. 2014,  how much "Somali-like" ancestry (labeled as "Cushitic" back then) is seemingly found in populations such as Tigrinyas, Amharas, Beta Israels and Xamir Agaws. [1] [2]

What I'd like to do now is have a second go at that with less "linguistic" terms so as to not completely 1:1 the relationship between linguistics and genetics but still be true to the genetic relationships between the populations at hand:

The above chart is pretty much based on an interesting notion explored in a prior blog post which is that there seems to possibly be a later West Eurasian ancestry carrying gene flow into Agaw speakers that predates the arrival of Proto-Ethiopian-Semitic, the latter of which modern Habeshas such as Tigrinyas likely owe about 10-15% of their ancestry to.

If there really was such an admixture event then it explains why the Xamir Agaw samples (possibly Afars. Check the comment section) and the Beta Israel samples (former Agaw speakers Ethio-Semitized relatively "recently") have about ~10% less of the later West Eurasian elements in the Horn than Habeshas such as various Tigrinya and Amhara samples do and it also explains some discrepancies in mtDNA lineages.




For example mtDNA N lineages such as X, T, H & J which are found in Tigrinyas and Amharas are, so far, not found in Beta Israels. Could these mark what the Southwestern Arabian migrants brought with them? And for one, there are N lineages in Beta Israels, so far, not found in Somalis such as mtDNA U6a1 & W. Could some of these be marks of the theoretical admixture event that may have hit Northern Highlanders before the arrival of Proto-Ethiopian-Semitic? [3]

For one, a recent study even dated the age of U6a1 in the Horn as being about ~4kya with an origin for it being further north in Northeast Africa (it's also found in modern Sudan and peaks in Copts) [4] which really fits with what I outlined in this former blog post as a theoretical point of origin for this admixture in Agaw speakers that is mostly not present in Somalis:


Link to former blog post

If the above was truly the case then what we have is that whatever this admixture event was caused by; it brought with it about ~10% new West Eurasian elements [note] to the Northern Highlands to inhabitants who would have been more or less identical to modern Somalis save for what could have been some admixture from Ari Blacksmith-like peoples who were likely Omotic speakers at a rate of 5-20%.

You can also adopt upper-thresholds from the data above like the Ari Blacksmith-like ancestry being up-to about ~15% as it can be for some Northern Highlander groups such as Beta Israels (I recall their average being a smidgen above that, in fact) and perhaps even the Copt-like West Eurasian elements going up to about ~15% as well just to have an idea of a lower and upper threshold. [note]

But the point here is that this was then added onto by elements from Southwestern Arabia which, about ~3,000 years ago (give or take a century or two)[5] [6], would have most likely housed people much more similar to Yemenite Jews than many modern Yemenite Muslims who, since the Islamization & Arabization of Yemen, have experienced new gene flows such as extra "African" ancestry.

So this would have taken the Agaw speaking group, which over-time would have become an Ethiopian Semitic speaking group due to this influx, and made them more like what modern Ethiopian & Eritrean Tigrinyas look to be:




The truth is much more right in-between the two above thresholds but I hope that can give one a general idea of what we're dealing with here. [note]


Although, there is a possible, but, in my opinion, less likely state of affairs which is that virtually all of the later West Eurasian elements are owed to Southwestern Arabia. Read through here to understand some of the possible rationale for and/or against such a possibility but this, by some slim chance, may in fact be the real state of affairs:

The "upper threshold" levels could be a percentage or two lower for the Somali-like ancestry as Amharas and Beta Israels in particular can be a few percentage points, on average, over ~15% Ari Blacksmith-like (see here) but all in all; I'd say that should give anyone interested a good idea of the ball-park estimates at hand here.

What makes these models intriguingly possible is that, at least all so far sampled, ethnic Somalis tend to seem rather un-admixed with foreign elements within at least the last ~3,000 years, particularly from an autosomal perspective. So they can, to some extent, be used as a slight proxy "basal" population state for many other groups in the Horn.

I.e. Tigrinyas = ancestors practically identical to Somalis ("Somali-like") + Ari Blacksmith-like peoples + peoples likely from Sudan who brought some Copt-like elements with them + admixture from some Yemenite Jew-like peoples OR you entirely do away with the hypothetical Sudan bunch when observing this model.



This is the same reason why even the Maasai, who seemingly have admixture from Southern & possibly also Eastern Cushitic speaking migrants from the Horn, will cluster between Somalis and populations such as relatively un-admixed Nilotic and Niger-Congo speakers as in the PCA above or the one below:





Now, there are perhaps some nuanced distinctions between their likely South Cushitic speaking ancestors and Somalis (something I've taken note of in the past) but for the most part, remarkably, Somalis still seem very close to the Horn-African Cushitic speaker admixture in Maasais which is remarkable because South Cushitic speakers began departing the Horn of Africa quite a long time ago for Southeast Africa.

The point of this post is; trying to outline the related-ness between Somalis and Ethiopian populations such as Tigrinyas whilst trying to give people an idea of roughly just how much non-Somali-like ancestry is in some of these respective groups whilst mapping out the relative effect various gene flow events we've noticed via genetic testing have had on these populations.

Reference List:







Notes:

1. I've refrained from adding Oromos because of their heterogeneity and all the extra work it would take for me to do ball-park estimates for all the subgroups but honestly; the percentages presented here are hardly distinct from the ones I shared last year so use a little bit of your imagination and figure out how Oromos would look in this post for yourself.

2. The "methodology" for how the ball-park estimates in the chart were made were explained quite well in the old post from last year but to put it simply: it's clear that mostly all of the non-Ari Blacksmith-like & later West Eurasian elements in Northern Highlanders, like Beta Israels and Tigrinyas, are shared with Somalis based on data from Hodgson et al. & Shriner et al.'s ADMIXTURE analyses as well as runs from other studies and even what is implied via uniparentals like mtDNA lineages so I took everything that's mostly not found in Somalis (Ari Blacksmith-like elements, later West Eurasian influences discussed here and here) and marked them out as different from the remaining clearly "Somali-like" ancestry.

3. I'm working on conducting analyses on my own nowadays and would like to try out something similar to these exercises with formal stats someday but this should do for now.

4. The PCAs are owed to David Wesolowski who's the author of the Eurogenes genome blog and project.

5. Somalis themselves may very well, as some ADMIXTURE analyses (like the ones from Hodgson et al. and Shriner et al. posit) show, have some Ari Blacksmith-like ancestry so the Somali-like ancestry, I suppose, would go up to some extent in all the charts in this post if Somalis in fact a total "dead-zone" for such ancestry as posited in this old post.

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.

Notes:

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)


Wednesday, February 3, 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: