I'm not dead

For those wondering... I'm not dead or anything along those lines. I've just been away due to exams (I'm still a university student) and projects as well as other commitments before that. I wish it didn't have to be 2 and a half months of being away but that's how it ultimately turned out.

Nevertheless, I plan to be back real soon with all new posts and more. And by "more" I mean that I plan to go back into old posts and edit them around to be more succinct, straight-forward and, where needed, perhaps also more accurate. 

For example, the page pictured and linked to above used to be quite different over a year ago until I edited it to its current form where I think it's a lot more straight-forward than its prior "cluttered" state (and where it's also more accurate to a certain degree). I'll be doing more of those sorts of "refurbishings" alongside making new posts so do stay tuned.

Thank you,

Sudanese Arab and Nubian mtDNA is mostly non-Eurasian?

I was looking back at some old data like from Hisham Yousif Hassan Mohamed's 2009 thesis and there's something intriguing about Sudanese Arab and Nubian mtDNA:

There aren't too many samples but there's definitely a pattern going on with the Nubians and the Arakien, Gaalien and Meseria (the three groups used to create the "Arab" grouping above); most of their mtDNA is non-M&N. The overwhelming majority of their maternal lineages look to be African rather than West Eurasian.

This is surprising because it's notably different from how things are with Horn African Cushitic and Ethiopian Semitic speakers as well as Bejas who are a northern Sudanese population like Nubians and Sudanese Arabs (Bejas are Cushitic speakers though):

Somalis, Amharas, Oromos, Tigrinyas, Beta Israels and Bejas all have a more balanced mtDNA profile. 40-60, 50-50, 50-50, 60-40, 50-50 and 30-70 are the types of frequency ratios you see in terms of Eurasian (West Eurasian derived) and African (non-M&N) lineages.

Now, the thesis sample sizes arguably aren't large, to be honest, but it's still notable that Sudanese Arabs and Nubians have very low frequencies for M&N lineages even when the sample sizes are comparable to those of the Horn African groups and Bejas. It's also notable that this pattern holds in all of the groups (the Nubians and the three Arab groups).

Despite this, they actually have high frequencies for West Eurasian Y-DNA lineages (i.e. J1):

Fifty to seventy percent or more of their Y-DNA lineages are of clearly Eurasian (West Eurasian derived) origins. [note] A friend once brought up the idea that this implies much of their West Eurasian ancestry since after the Sudanese Neolithic (something Cushitic speakers from the Horn of Africa seemingly descend from) is probably "male mediated" as in what largely happened is that males carrying substantive West Eurasian ancestry intermixed with local Northeast African women and brought lineages like Y-DNA J & I in abundance.

I do wonder if that's seriously the case...

This would be unlike the case in the Horn where there's about 5-30% Y-DNA J (mainly J1) among Cushitic and Ethiopian Semitic speakers alongside 5-35% Y-DNA T as well. [note]

The Horn looks somewhat more "balanced" in terms of Y-DNA & mtDNA lineages. There's a substantial amount of both blatantly West Eurasian and more local African lineages on both a maternal and paternal level but things look quite skewed in the case of Nubians and Sudanese Arabs who look to have very low M&N lineage frequencies mtDNA wise but very high frequencies for lineages descended from F in terms of Y-DNA.

Should be interesting to see more and more mtDNA & Y-DNA data from Nubians and Arabic speaking groups in Sudan to see how much this pattern holds in the future. Getting mtDNA results from different Arab groups is also key as I've only really seen results for three groups at this point.

References:

1. Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan, by Hisham Yousif Hassan Mohamed (thesis)

2. Variation in Y chromosome, mitochondrial DNA and labels of identity on Ethiopia, Plaster et al.

3. mtDNA variation in East Africa unravels the history of afro-asiatic groups, Boattini et al.

4. Forensic and phylogeographic characterisation of mtDNA lineages from Somalia, Mikkelsen et al.

5. The Genome-wide structure of the Jewish people, Behar et al.

Southeast Africans and Chadians from Triska et al. 2015

Some other interesting things to note about this paper's new samples are the Southeast African and Chadian samples.

Some simple observations:

• The Samburu samples look to be highly Horn African-shifted. Their African and West Eurasian ancestry levels seem only a bit lower than those of the Somalis and Oromos. I suppose this implies that they have quite a bit of admixture from East/South Cushitic speakers. Something people have assumed long before genome sequencing, as far as I know... Their mtDNA lineages also implied such admixture, last I checked, so this makes some sense. It's just that the level of this admixture that's a bit surprising.

• The Turkana samples seem less Horn African-shifted than them but also seem to clearly have substantive admixture from Horn African Cushitic speakers who were probably quite genomically similar to modern Somalis. Again, this was somewhat expected and Tishkoff et al. 2009, albeit with less high-resolution data, ultimately indicated that Turkanas had such admixture anyway. Both them and the Samburus, despite being Nilo-Saharan speakers, are clearly mixtures between Nilotic speaking, Bantu speaking and Cushitic speaking Southeast Africans.

• The Daza Chadians are an intriguing case too. Despite being Nilo-Saharan speakers; they're clearly rich in West Eurasian ancestry. They're about as shifted toward West Eurasia & North Africa as Fulanis are (pulling about as eastward as they do in the PCA). The main difference, however, is that the Fulanis clearly seem like more of a mixture between West-Central Africans and Northwestern Africans whilst the Daza look to, mostly, be a mixture between the East African cluster and West Eurasians. [note]

• The Kanembu essentially just look like more West-Central African shifted versions of the Daza, understandably showing less of a pull toward the West Eurasians and North Africans as a result.

What I find most interesting about all of this are the Chadians, quite frankly. What's quite intriguing about their West Eurasian ancestry is that it, based on the ADMIXTURE results above, looks to be mainly derived from Northwestern African-related people (Mozabite-like peoples) as its mainly derived from the light blue cluster. This means they're basically some sort of East African version of the Fulani samples, especially in the Daza samples' case. They seem to lack the more Bedouin and Druze related affinities the Oromo, Somali, Nubian and Sudanese Arab groups are showing.

Although, they also differ from the Fulani samples in that they mostly don't show ancestry from the grey Sardinian peaking cluster. Their West Eurasian elements are wholly swallowed up by the light-blue Mozabite peaking cluster. I don't know what significance that might have but it's worth taking note of.

I really don't know much about Chad's history but I wonder if they used to be Chadic speakers? I'd be interested in seeing what sort of R1b-V88 frequencies these two populations have if anyone's seen Y-DNA data on them... Baqara Arabs (بقرة العرب) like the Messiria tribe seem to have notable R1b-V88 frequencies (see here) which, to me, implies some of their ancestors were Chadic speakers (like the Hausa) before their Arabization.

A Baqara Arab man and child riding cattle

Anyway, I'll leave any further theorizing and observations to future posts that will hopefully be based on new PCAs and perhaps also ADMIXTURE runs where these new samples will be run alongside the various other HSS samples out there.

References:

1. Extensive Admixture and Selective Pressure Across the Sahel Belt, Triska et al.

Comments on the new Horn African and north Sudanese samples

Well, as you can see here, we have 13 new samples from southern Somalia, 10 from Ethiopia of -West-Central Oromo origins and about 17 Sudanese-Arab+Nubian samples from northern Sudan.

Some interesting things to note would be:

• The Somalis seem rather uniform in terms of their "African" & "West Eurasian" ancestry levels once you set aside the 3 outliers who look to have 30-50% West-Central African-related admixture of probably recent origins from Somali Bantus. [note] This is interesting because these same ~10 remaining Somalis display an odd substructure in the PCA where 3 samples, alongside at least two Oromos, pull quite northwards as though they're somehow slightly distinct from the other Horn Africans present in the PCA, even though all of the Somalis, except for those three outliers, seem more or less the same in regards to their admixture levels.

• The West-Central Oromos seem to be about as African & West Eurasian as the Somalis and, if I recall correctly, these types of Oromos tend to vary between being 40-50% West Eurasian from what I remember so the Somalis in question look to be relatively standard in terms of admixture levels for pulling about as eastwards toward West Eurasians as these Oromos. Some of these Oromos are more West Eurasian-shifted than the Somali samples which would make sense as well.

• The Sudanese Arabs and Nubians seem mostly more West Eurasian-shifted than the Somali and Oromo samples which, I suppose, could mean most of them are at Habesha~Agaw levels of African and West Eurasian ancestry while some, or even a decent number, possibly also surpass those admixture levels. They also definitely display signs of notable heterogeneity in terms of admixture levels which correlates well with prior data owed to Dobon et al.

One thing the way some of those Somalis cluster reminds me of is this, actually:

That PCA above, as discussed here, basically shows us that some of Lazaridis et al. 2013-2014's Somalis from Garissa seem slightly "Ethiopian-shifted" in a manner that might imply admixture from people like Borana Oromos, they're also very slightly less West Eurasian (on average) than the Somalis we so far have from Ethiopia and Somalia.

Now, this new study's Somali samples, originally from southern Somalia, are classified as "Sedentarian" which looks to impart that they're sedentary farmers rather than semi-nomadic pastoralists. Perhaps they're of the Rahanweyn clan (though they don't have to be) which has long had sedentary farmers within its clan-structure in the south? Some might notice that I once entertained the notion that some Rahanweyn clan members might have notable Ari-like admixture the way various Ethiopian populations do (see here). [note]

Well, perhaps the reason the majority of these Somalis are clustering so close to the West-Central Oromos is because they carry admixture from Oromo-related/like people and the ~3 who don't cluster that way and pull very upwards actually lack such admixture? 

But then it doesn't explain why all of the samples seem to be roughly the same in terms of West Eurasian and African ancestry levels (they're basically homogeneous in this case). Also, why do at least two West-Central Oromos actually pull north as well? And why do these Somalis seem so close to West-Central Oromos in terms of admixture levels which implies all of them have relatively typical Somali admixture levels? [note]

These issues don't make much sense if some of them are part Oromo (or even Borana Oromo-like) while others aren't.

So I suppose it may not be worth speculating too much with this study's PCA and ADMIXTURE run until we have these samples out in the open. There are also other odd things about these results like the Oromos showing tiny hints of West-Central African-related admixture when the non-outlier Somalis show none and that honestly doesn't make much sense to me so I'll have to just see these samples for myself when the time comes. 

I wouldn't be sure of too much until we can run these samples through other analyses but these are my quick two cents for now. 

References:

1. Extensive Admixture and Selective Pressure Across the Sahel Belt, Triska et al.

New African samples

I'm surprised I hadn't noticed this paper last year when it came out but someone recently linked me to it and it definitely has some exciting new samples that looked to have been genotyped at a high-resolution.

I've emailed the corresponding author about getting the various new samples like the supposedly sedentary-farmer Somalis from southern Somalia, the West-Central Oromos, the Samburus and the Nubians and Sudanese Arabs because it should be real interesting to see how some of these groups turn out once run through various sorts of PCAs and the like.

The author in question has yet to reply and its been a little while (I may have to contact some other authors) but I'm sure the samples will be out in the open soon enough.

This current post is mostly just for spreading the fact that this paper and its samples are out there. I'll speculate on some of what we have on the new samples soon, either via the paper's own results or once the samples are out and about (or both).

References:

1. Extensive Admixture and Selective Pressure Across the Sahel Belt, Triska et al.

The validity of Eastern Non-African as a clade based on genetic-drift

I got curious and asked David over at Eurogenes to try and run something to see how valid "Eastern Non-African" looked in terms of genetic drift shared between groups.

Green = various native populations have significant (>10%) "ENA" ancestry

For instance, would Han-Chinese people share more genetic drift with Onges and Papuans than with Villabruna-Cluster Hunter-gatherers (basically "WHG"), Ancient North Eurasians and Eastern European Hunter-Gatherers? Well, it does seem so:

Han-Chinese people share more drift with Onges and Papuans than they do with MA-1, the Karelia HG or the Villabruna HG which, I suppose, outright shows that they share more ancestry with the former two populations which implies their ancestors diverged from them later than when they diverged from the majority of the ancestry in VHGs, EHGs and ANEs.

One thing that intrigues me about this is how we apparently have very early evidence of "Modern Humans" in Oceania. From what I understand, there's archaeological evidence in places like Australia that imply Homo Sapiens Sapiens began inhabiting the region as early as ~50,000ybp which really makes things a little confusing if those Humans were the ancestors of modern Australian-Aborigines and, to some extent, also Papuans. [1] 

It's confusing because it's unlikely that the "clade" mostly ancestral to VHGs & ANEs differentiated from the "clade" mostly ancestral to ENAs that early, given that we have a Homo Sapien Sapien from that time-frame (Ust-Ishim, ~45,000ybp) whose genetic state predates this divergence:

Ust-Ishim is basal to all Out-of-Africa populations from East Asians to Onges to European & Siberian HGs and seemingly also Papuans and Australian-Aborigines [2]. The only exception so far being the theoretical "Basal Eurasians".

So, if the arrival date was ~50,000-40,000 years ago then ENAs, and whatever Paleolithic Europeans and Siberians are mainly descended from, would not, likely, have too notably diverged yet (or diverged at all) and it's thus incredibly unlikely that notable "ENA" substructure had formed by this point.

Basically, this implies modern Oceanians are either not the descendants of these early migrants at all or are perhaps some sort of mixture between them and later "ENA" migrants, with the latter group comprising much more of their ancestry? 

But I wonder if even the latter situation would cause modern Oceanians to look as "closer" to East Asians as they do. If they're a mixture between something ENA + a highly drifted Human population who may have not even participated in the traditional dispersals out of Africa + Denisovan admixture; they should look arguably much more divergent from other Out-of-Africa populations as a whole but Ust-Ishim looks to be basal to their non-Denisovan ancestry like he is to everyone else and they seem to share in a later ancestral clade with East Asians and the Andamanese that they do not share with Paleolithic Europeans and Siberians.

An abundance of ancient DNA from "Eastern Non-African" regions should make things more illuminating if anything, I guess. 

References:

1. First Footprints: The Epic Story of the First Australians, reviewed by Douglas Bird

2. Massive migration from the steppe is a source for Indo-European languages in Europe, Haak et al.

Recommended reads:

East Eurasians: the ones you don't know about

Is the Eastern Non-African situation more complex?

New additions to the Eastern Non-African family tree

Ancestral North & South Indians and South Asia

A while back, actually almost 8 years ago, Dr. David Reich at Harvard Med and his colleagues came out with a rather intriguing model for South Asian population genetics. They proposed that virtually all South Asians were mostly some sort of mixture between two core populations. Ancestral North Indians and Ancestral South Indians with the model only growing more complex ever since. [1]

South Asia

The basic concept being that one population related to modern-day West Asians and Europeans came in from the Northwest (ANIs) whilst one was seemingly indigenous to South Asia and was, originally, proposed to be somewhat intermediary between West Eurasians and East Asians (ASIs). 

And, as you can see, the model got somewhat more complex as time went by, even without our recent influxes of ancient DNA. "ANI" came to be seen for what it was; a composite. It seems to be mostly made up of Neolithic Iranian-related ancestry with some steppe ancestry owed to Indo-Aryan speaking pastoral nomads whose descendants descended upon Central and South Asia late into the Bronze Age, bringing the Indo-Aryan languages to South Asia. [note]

There they would have encountered farmers of the BMAC culture in Central Asia who were likely quite Neolithic Iranian-like. These Indo-Aryan speakers, likely quite similar to Northeastern Europeans (i.e. Lithuanians), most likely intermixed with farmers in Central Asia and then moved on into Northwestern South Asia (i.e. the Indus Valley) to a pre-modern civilization more or less on the verge of collapsing (The Indus Valley Civilization) and from there; further intermixing with locals seems to have occurred.

IVC on the decline close to when the Indo-Aryan speakers began arriving

In my opinion, based on the population genetics of modern South Asians, the inhabitants of Northwestern South Asia were likely, as is likely the case with the BMAC farmers, quite similar to Neolithic Iranians and were thus a mixture between Basal-rich/"ENF"-like ancestry and Ancient North Eurasian-related ancestry. They probably, at this point in time, also carried ancestry from local Hunter-Gatherers whom they'd encroached upon by migrating over from West Asia and that's where "ASI" comes in.

The local Hunter-Gatherers look to have been Andamanese and Australo-Melanesian-related peoples who today have their most persistent descendants in populations like Paniyas who actually cluster somewhat close to the likes of Papuans on a global PCA (principal component analysis) based on 166,000 autosomal SNPs:

The "ASI" model somewhat changed in that ASI now seems like something Eastern Non-African  (rather than being some intermediate between West Eurasians and East Asians) and is often acknowledged by academics such as Reich to be something related to Andamanese Islanders like the Onge, hence why the Onge are used as a stand-in for "ASI" in this run from the recent Lazaridis et al. paper:

Onges are probably somewhat better stand-ins than Paniyas since they seem to lack West Eurasian admixture entirely when Paniyas, despite looking to be mostly "Eastern Non-African", are definitely partly West Eurasian so something like an ADMIXTURE cluster based on them and some other heavily ASI admixed South Asians won't yield a pristine enough "ASI" stand-in. Though Harappa did a pretty good job as far as I can see.

Granted, even utilizing Onges won't really do as, while they're certainly related to whatever "ASI" is, they're definitely not exactly like it and some notable genetic drift has occurred between the two as far as I can tell. Basically, we need ancient DNA if we're to really make things solid when dealing with ASI. 

Paniya Man

Things also became a little more complicated on the West Eurasian front lately. For example, you might notice that that figure from the Lazaridis paper shows more "Steppe" related ancestry in the various South Asian populations than the Harppa run implies.

This is mostly because, up until now, we've generally seen the Steppe admixture in South Asians as being something Northeastern European-like (i.e. similar to Lithuanians) based on how South Asians often registered such ancestry alongside Gedrosian, Caucasus (or Caucasus-Gedrosia which seems to correlate well with the Neolithic Iranian and Caucasus Hunter-Gatherher-like ancestry in the region), Southwest Asian and Mediterranean. (some bits of these other clusters like "Mediterranean" are probably owed to their steppe ancestors too) [note]

And lo and behold, when we finally got our hands on some Sintashta and Andronovo cultures samples; they indeed looked quite similar to modern Northeastern Europeans. A mixture between Yamnaya-like people, Neolithic Anatolians and Villabruna-Cluster Hunter-Gatherer (WHG) ancestry leaning more on being Yamnaya-like.

This is important because the Sintashta and Andronovo cultures are pretty much accepted by most to be early Indo-Iranian speaking steppe cultures and as being the source for the Indo-Iranian languages in Iran and South Asia (Iranian languages in West Asia, Afghanistan and Pakistan + Indo-Aryan languages in South Asia). [4]

So... Things should seem settled I suppose and the old "Caucasus-Gedrosia + Mediterranean + Southwest Asian + Northeastern European + Ancestral South Indian + others" model should be all done, no? South Asians are probably, in my humble opinion, something Sintashta-Andronovo-like + something Neolithic Iranian-like + ASI + others. 

But, some argue that the model is just somewhat different and roughly agree with the figure above which implies that the steppe ancestry in South Asia is perhaps more Yamnaya-like [note] and thus, thanks to the greater Caucasus Hunter-Gatherer-related ancestry (Caucasus Hunter-Gatherers and Neolithic Iranians are very closely related) in these types of steppe pastoralists; South Asians (as well as others) might be more Steppic than originally imagined via models dependent on Northeastern Europeans and ancients like Sintashtas. 

David Wesolowski over at Eurogenes is one proponent of this alternative view on things. However, I personally don't, for now, make much of this model. I think Yamnaya-like steppe pastoralists prove a better fit at times because of their Caucasus Hunter-Gatherer-related ancestry which works to deflate the Neolithic Iranian-related ancestry in South Asians and over-represent how "steppe" they really are.

Their steppe ancestry levels, in my humble opinion, are perhaps somewhat decently-represented by the data in an old run created by "Kurd" at Anthrogenica where he used Sintashta samples which was then pored over by the author of Vaedhya to show us the following results:

I find the alternative Yamnaya-like admixture model less convincing because, as far as I know, there's really no archaeological proof for Yamnaya-Afanasevo-like pastoralists making deep incursions into Central Asia and Northwestern South Asia and, even if they did, it's strange that they'd remain so heavily steppe after wading through Central Asia (inhabited by farmers such as those of the BMAC culture who were most likely Neolithic Iranian-like for the most part), Afghanistan and then also more northerly areas of Northwestern South Asia given the heavy steppe proportions that arise when they're utilized on South Asians. [note]

For all I know, David could very well be right here but, for the time being, I find the "Sintasha-Andronovo-like + Neolithic Iranian-like + ASI + others" model more convincing than anything else. 

But regardless of which of the two models is true, most South Asians are mostly made up of Neolithic-Iranian-related ancestry, some form of Steppe ancestry and whatever ASI exactly is, alongside negligible, non-existent, or quite notable admixture from the likes of East Asian-related people and Africans depending on the population (i.e. Bengalis and their notable East/Southeast Asian-related ancestry). 

Things will definitely become more clear once ancient DNA starts flooding in from South Asia and I hear that's certainly in the works. 

References:

1. Reconstructing Indian population history, Reich et al. 

2. The genetic structure of the world's first farmers, Lazaridis et al. 2016 

3. The Near-Eastern Roots of the Neolithic in South Asia, Gangal et al.

4. The Horse, the Wheel, and Language. Princeton, NJ: Princeton University Press, by David W. Anthony

Notes:

1. There is interestingly a phenotypic and not just genetic difference between Yamnaya-like people and Sintashta-Andronovo-like people: [-]

2. There is apparently some notable Ancient North Eurasian-related ancestry in South Indian populations like Paniyas despite how they don't at all show more proper "West Eurasian" components to justify the levels of ANE-related ancestry they show. i.e. I've heard but can't confirm that groups like Paniyas may show at most ~20% CHG-related admixture but in fact about ~25% "ANE".

I have no idea why this is (if it's true) or if there seriously was ANE-related ancestry in South Asia that predated even the arrival of Neolithic West Asians but if this admixture is quite legitimate; there's something even more complex than simply being Australo-Melanesian and Andamanese-related in "ASI".