Sunday, May 29, 2016

Mehris are fully Eurasian?

Excerpt from an Abstract:

"Consistent with other studies, we found that North African and Near Eastern populations (including the Yemeni) generally have less Neanderthal ancestry than other western Eurasian populations. However, our ADMIXTURE results indicate that a subset of Yemeni samples from the Mahra governate share a very high level of ancestry (~85%) with a single Near Eastern component. Interestingly, these individuals have Neanderthal ancestry estimates that are greater than estimates from almost all Near Eastern and North African populations and are more consistent with estimates from European and South/Central Asian populations, suggesting that eastern Yemen may be an area of elevated Neanderthal introgression in the Near East. Greater sampling of Near Eastern populations is needed to better understand variation in Neanderthal ancestry and the site(s) where modern humans and Neanderthals interbred."

The subject matter of this study is Neanderthal ancestry, of course, but what's interesting to me is that they've noted a population from the Mahra Governorate of Yemen who, unlike other Arabians like the Yemenites farther westwards, have higher Neanderthal ancestry estimates that are closer to what one might expect from Europeans or South/Central Asians who are mostly of Out-of-Africa/Eurasian origins, lacking the noticeable Post-OoA African influences in various West Asian Arab and North African populations.

A Soqotri girl

In my opinion, they've basically come across the "Mehri people" who, along with the likes of Soqotris like the girl in the picture above, have long interested some folks such as myself because of their phenotypic traits. They essentially look rather "Arabian" in regards to most of their traits but are, interestingly, very pigmented (dark-skinned) in many but not all cases. Arabic is also not their first language, they instead speak the "Modern South Arabian" languages which people should not confuse as being descendants of the "Old South Arabian" languages (i.e. Sabaean) or the likes of Himyaritic.

I've encountered people over the years who've fervently asserted that the pigmentation these peoples display is mostly owed to African admixture whilst using the seemingly, make what you will about his other ideas, very real Cushitic substratum in their languages discovered by Militarev [2] as an indicator that this might be the case. Yet, so far we've only gotten uniparental data on Soqotris which didn't imply that were very African influenced  [3] and now we might just have some Mehri autosomal DNA on our hands which is also not proving consistent with African admixture.

Supposedly a Mehri man

Nevertheless, I've personally just looked upon them as looking like highly pigmented Arabians. Upon looking at their facial features, save for those who have recent outside admixture from Southeast African Bantu speaking people or Yemenite Arabs, I always got the impression that these folks looked quite similar to other Arabians like the Rashaida, they were just more pigmented on average and it seems my instincts may have been correct if these Mahra governorate samples are them.

Why are they this pigmented, then? Well, read this older post (as well as some links it shares) to get some of the dynamics behind pigmentation and you might get what's causing their pigmentation to be the way it is. Though, not all of them are as pigmented as the man or girl above, mind you. The two of them are meant to be "extreme examples" I've chosen for dramatic effect. These folks, nevertheless, have seemingly been isolated from the rest of the Arabian Peninsula for quite a long time (from a genetic perspective) so that likely has something to do with their looks as well.

I reached out to one of the authors of the forthcoming study but the thing is; it's still a forthcoming study/paper (all that's available right now is the abstract) and they've opted out of making the samples available to me or anyone else until the study's been published so we'll have to wait before we can fiddle with these new samples and really learn some mind-blowing stuff.

Reference List:

1. Neanderthal ancestry in Yemeni populations, Vyas et al.

2. Afro-Asiatic Migrations: Linguistic Evidence

3. Out of Arabia—The settlement of Island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity, Černý et al.

Saturday, May 28, 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


"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:


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.