Friday, September 30, 2016

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


Thursday, September 29, 2016

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).


Thursday, September 22, 2016

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. 


Sunday, September 18, 2016

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. 



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".

Sunday, September 11, 2016

New additions to the Eastern Non-African family tree

It looks like we finally have some Jomon ancient genomes from Japan. We have five ~3,000 year old samples from around Fukushima who've been genotyped for their autosomal DNA and they're quite intriguing to say the least.

They seem to look like proto-East Asians of some sort. Genetically distinct enough to be separate from Eastern Non-Africans like Papuans but clearly not exactly like East Asians such as the Han Chinese.

However, I think I should give some people a low-down on the Jomon before I go any further. Japan used to be entirely inhabited by Hunter-Gatherers between ~10,000 BCE to roughly ~300 BCE (Jomon period). They were quite an intriguing Hunter-Gatherer culture as they produced a certain degree of sedentism thanks to the rich resources around them allowing for such a life-style.

Another interesting fact about them that's long had people's curiosities piqued is that they didn't seem traditionally East Asian in terms of phenotypic traits like facial morphology, hair & eye type, teeth shape and so on. They, at best, looked like the traditional East Asian looks still in their "proto-stage" of development:

Jomon man reconstruction

They were seemingly quite hairy, lacked epicanthic folds as well as the more thick straight hair you often see among East Asians while having perhaps more wide facial features as well as fuller-lips (see here, for example). They did, however, seem to be de-pigmented in a manner similar to modern East Asians so they weren't dark-skinned like the Villabruna-cluster Hunter-Gatherers of Europe.

However, much like in Europe, Japan was eventually settled by farmers from the outside. In the case of Europe the farmers came from West Asia (specifically Anatolia) but the farmers came from mainland East Asia in Japan's case. They were people carrying the rice-farmer cultural package which formed in China and they seemingly migrated to Japan from mainland East Asia. Their advent brought about the Yayoi period of Japanese history.

Above is a reconstruction of what some Yayoi period farmers looked like. They looked much more traditionally East Asian than the Jomon period Hunter-Gatherers (epicanthic folds, thicker straight hair etc.). It was these people who seemingly brought alleles in genes like EDAR which are responsible for certain East Asian phenotypic traits, traits that were seemingly missing in pre-agricultural Japan. (see here)

Anyway, due to the interesting phenotypic differences at play, some people have wondered if the Jomon Hunter-Gatherers would turn out notably distinct, from a genomic standpoint, from other East Asians and that does indeed seem to be the case based on these samples:

When more "regional PCAs" (principal component analyses) based on autosomal SNPs are produced; they definitely seem notably distinct from virtually all modern East Asians and Southeast Asians with the modern Mainland Japanese, Ainus and Ryukyuans coming off as intermediates of sorts between them and other East Asians like the Han Chinese which clearly implies that they're some sort of mixture between Sanganji Jomon-related people and Han Chinese-related people. [note]

And if you're wondering who the Ainu and Ryukyuan are... The former are considered the indigenous people of Japan (Hokkaido and Northeastern Honshu) and latter are considered the indigenous people of the Ryukyu islands. Both groups seem to have more ancestry from Jomon Period Hunter-Gatherers than Yamato Japanese do. 

At any rate, when thrown into a global PCA- :

- these Jomon samples don't seem too distinct from East Asians like the Han Chinese. But it does say something that virtually all modern East Asians in that global PCA cluster rather tightly together whilst the Sanganji Jomon break off on their own. So they're notably distinct from modern East Asians but still clearly closer to them than to other groups. 

It's intriguing how they pull downward along the Y-axis and a bit more toward West Eurasians than groups like the Han Chinese do (if you're having trouble with the population acronyms click here). This is something Melanesians and Papuans also do in comparison to East Asians like the Han Chinese:

Though those groups also show a strange pull towards African populations (how they pull downward on the above Y-axis) even though they're, in terms of genetic drift (i.e. as noticeable via Fst values) and divergence datings (likely slightly exaggerated by their Denisovan admixture), more distant from African populations with little to no Eurasian ancestry than East Asians are. (see here

At any rate, these Jomon samples seem "East Asian" but not "East Asian" if that makes any sense. They're essentially distinct enough Eastern Non-Africans to be split from Papuans yet they're not exactly like East Asians such as the Han Chinese, though they definitely share a lot of genetic drift with modern East & Southeast Asians in general and are closer to them than they are to populations like Papuans and Melanesians:

This is quite intriguing as it implies much of what makes "East Asians" genetically East Asians (as in differentiated from other Eastern Non-Africans) formed well before the phenotypic traits we traditionally associate with them developed. 

This is of course possible because phenotypic traits like hair-type, facial morphology as well as skin, eye and hair pigmentation (major traits that tend to distinguish modern Humans from each other) seem to be, collectively, controlled by a few hundred SNPs among the 10 million SNPs found in our genomes. It doesn't take radical genetic shifts to create notable phenotypic differences between modern Humans. I.e. less than 10 SNPs are responsible for most of the skin pigmentation difference between Norwegians and Yorubans.



1. Should be interesting when some third-parties get their hands on these genomes. I'll be interested to see qpAdm and ADMIXTURE results using these samples so we can see exactly how much ancestry the average Japanese person owes to Jomon-type people. The PCA implies it's rather significant but the allele sharing and tree-mix imply somewhat otherwise... Modern Japanese people also have a whole lot of Y-DNA D which really peaks in Ainus and has, as a result, long been thought to trace back to Jomon Hunter-Gatherers, for example.

2. I also wonder if these samples show any Ancient North Eurasian-related ancestry (also see here). Though the study did include MA-1/Mal'ta boy and they make no mention of such admixture.