Wednesday, October 5, 2016

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.

Tuesday, October 4, 2016

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.


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, flatter noses and facial features 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.

Friday, August 19, 2016

How things are looking so far

As David's recently pointed out, it does seem as though the old fateful triangle still remains:

Most West Eurasian populations still look like they're mostly, on a basal level, divvied up between a Basal Eurasian rich component (rather similar to the old "ENF" cluster), Ancient North Eurasian-related ancestry and Western European Hunter-Gatherer/Villabruna-cluster-related ancestry.

It seems that, in this set-up, the main distinction between groups such as Neolithic Iranians (alongside Caucasus Hunter-Gatherers) & Neolithic Levantines is that one is "Basal-rich + ANE"  and the other is "Basal-rich + Villabruna":

The first PCA where the triangle is clearly visible is directly based on David's new Basal-rich K=7 ADMIXTURE run but it's data is still in line with what we see in a PCA directly based on autosomal SNPs like the one below:

Here, you can see relatively the same population structure. The more north a population pulls correlates with how much ANE-related ancestry they have, the more east a population pulls correlates with how much "Basal-rich" type ancestry they have and, finally, the more west a population pulls correlates with how much Villabruna-related ancestry they have.

So it seems David's indeed come up with a decent model here. What we really need now is to figure out exactly what "Basal Eurasian" is and to understand some of the earlier pre-history of West Asia to a point where we can grasp how the substantial Ancient North Eurasian-related and Villabruna-related ancestry, found in its Neolithic and Epipaleolithic inhabitants, got there. [note]


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

2. The Demographic Development of the First Farmers in Anatolia, Kılınç et al.


1. The "Basal-rich" cluster itself is likely to be a mixture between something related to European Hunter-Gatherers like those of the "Villabruna/WHG" cluster and Basal Eurasian ancestry. Even the new Lazaridis pre-print implies as much via this figure when demonstrating what makes up the Natufian samples.

Some new Neolithic Anatolians

Well, thanks to a new study, we now have some new Neolithic Anatolian samples. This time they're from South-Central Anatolia and date to between 8300 and 5800 BCE.

Seems the Boncuklu samples (~8300-7500 BCE) are nearly identical to the Barcın (Northwestern) Neolithic Anatolians in terms of WHG/Villabruna-related ancestry and "ENF-like/Basal-rich"-related ancestry whilst the Tepcek samples (~7500-5800 BCE) are less Villabruna-shifted and thus pull a bit more toward Neolithic Levantines and Natufians. You can see this in David's PCA (Principal Component Analysis based on autosomal SNPs) below:

The more left a population pulls; the greater the affinity for Villabruna-type Hunter-Gatherers whilst the more right the pull indicates how ENF-like/Basal-rich they are. Finally, the more north a population pulls indicates how "ANE" shifted they are. Neolithic Anatolians, Neolithic Levantines and Natufians pull the absolute least toward the north as they seem to lack ANE-related admixture.


1. The Demographic Development of the First Farmers in Anatolia, Kılınç et al.


1. The mtDNA diversity among these samples is rather interesting to me as someone from the Horn of Africa, to be honest. N1a1a1, N1b, K1a, K1a12a, U3: these are quite close to or directly overlap with the mtDNA Haplogroups you can find among Somalis and other Horn African populations. 

Sunday, July 31, 2016

East Asians are part Ancient North Eurasian?

This was one helluva bomb the new Lazaridis et al. paper managed to drop at the end of their supplemental where they claimed East Asians are a mixture between MA-1-related peoples and a truly "Eastern Non-African" population:

To be fair, the ANE-related admixture doesn't seem substantial (10-15% ANE + 85-90% ENA/South Eurasian-like) when dealing with East Asians like the Japanese and Han Chinese who still seem mostly Eastern Non-African derived:

Once again we have formal stat based methods like qpAdm picking up on gene-flow which wasn't really caught by ADMIXTURE, to my knowledge. 

Now, it is intriguing to point out that, at least at the higher Ks of some runs, the Japanese & Han did show some Nganasan-like ancestry:

However, the Nganasan-like admixture seems minuscule in the Japanese, Korean and Northern Han Chinese samples and doesn't even show up in the non "Northern" Han Chinese sample-set. Nganasans are a Siberian population whom you'd expect to show some notable ANE-related ancestry but the amounts of ancestry the Japanese, Korean and Northern Han samples are showing from a population like them aren't enough to explain the levels of ANE-related ancestry we see with this study's qpAdm models.

So, ADMIXTURE, in this case, really didn't pick up on something qpAdm did, as far as I can see. David Wesolowski's own K=8 at most had the Japanese at about ~1-3% Ancient North Eurasian and those are negligible/noise levels.

ADMIXTURE might've mildly caught wind of this ANE-related admixture but it's results are definitely not consistent with what these new qpAdm runs are implying.

But I suppose the argument one can make is that how East Asian populations usually form their own cluster at the very early Ks is the problem with ADMIXTURE. It's being heavily skewed by how drifted East Asians are from West Eurasians.

That same substantive genetic drift helps form the genetic structure in the above PCA. The Y-axis marks the divide between African populations (with very little to no Eurasian admixture) and Out-of-Africa populations whilst the X-axis marks the divide between Eastern Non-Africans and West Eurasians (East Asians pulling farther away from West Eurasians than Papuans do in this case).

So, it is possible, I suppose, that all prior ADMIXTURE analyses were being fooled by this substantive and perhaps somewhat recently cemented drift (last 10,000-20,000 or so years?) which analyses like qpAdm are more resistant to. But, what's even more intriguing is that tree-mixes from David Wesolowski support this new paper's claims & data:

Nevertheless, I'm remaining somewhat skeptical about this until we have ancient DNA from around East Asia that might refute or reaffirm these new findings. We might discover something more interesting than these populations simply being part ANE-related. 

What I find especially odd is that even Southeast Asians show such admixture at levels comparable to those of the Japanese, Han and Koreans whom they're somewhat distinct from in terms of their genetic history. ~14% for the Thai and ~12% for Cambodians? Why is everyone so uniformly Ancient North Eurasian here (between 10-15%)? This somewhat brings the whole Mota debacle to mind, actually. [note]

Everyone (other than Siberians, Mongolians & Central Asians whom we've known for a while now have some Ancient North Eurasian-related ancestry) is turning up as 10-15% "ANE" and that's honestly a bit suspicious and is why I'm skeptical about this new data.


2.  Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al. 


1. I think this is honestly a quirk of the qpAdm model they used. Basically modeling these populations as "Onge + ANE"; it could be that all we're seeing is that these populations have an understandable shift away from Onge-like Eastern Non-Africans that may not necessarily be characterized by Ancient North Eurasian-related admixture. However, it does say something that the same pattern presented itself (when dealing with the Han) via tree-mixes. At any rate, we should wait on some East Asian ancient DNA.

Tuesday, July 19, 2016

Natufians were dark-skinned?

The creator of the PuntDNAL ancestry project (Abdullahi Warsame) managed to convert one of the Natufian samples' raw data (I1072) into a .txt file [note] and it seems, as per his findings, that the sample is GG for the SLC24A5 gene's rs1426654 SNP.

I've somewhat gone over this before but that would mean he lacks the derived A allele for the SNP which is important in modern West Eurasians' de-pigmentation. It's responsible for 1/3 of the skin pigmentation difference between Europeans and mostly non-Eurasian admixed African populations.

Lacking it as well the derived alleles for SLC45A2's rs1891982 SNP is why the reconstruction of La Braña-1 above has him being rather pigmented/dark-skinned. Western European Hunter-Gatherers like him had the alleles required for light-eyes but not for light-skin:

Neolithic farmers from Western Anatolia are responsible for bringing the derived alleles required from SLC24A5 and Eastern European Hunter-Gatherers seemingly carried the derived alleles required from SLC45A2 (the farmers carried this particular derived allele at very low frequencies). So, Bronze Age pastoralists from the steppe and Neolithic Farmers from West Asia ultimately brought de-pigmentation/light-skin to much of Peninsular Europe.

Anyway, if this Natufian is really GG for that SNP (he's most likely ancestral for SLC45A2's rs1891982 SNP as well), and none of this is caused by DNA damage and is quite legit, then it seems like this particular Natufian was an individual lacking in modern West Eurasians' de-pigmentation. No idea if the other samples are the same but they might be and it'd be pretty intriguing if they are.

General spread of the Natufian culture

What's even more interesting is that the Neolithic Levantines whose data I've managed to sift through (4 samples) are AA for SLC24A5's rs1426654 SNP, making them more similar to Western Neolithic Anatolians and Early European Farmers in this respect.

If this Natufian's result is truly legitimate and the other samples and numerous future Natufian samples prove to be just like him in this respect; it seems like something from outside the Levant brought the derived allele to the region as Caucasus Hunter-Gatherers carried it, Neolithic Iranians seemingly carried it and Western Neolithic Anatolians did as well. For Neolithic and not Epipaleolithic Levantines to carry it could mean an outside population brought it in perhaps from somewhere more north or east. But we'll see what future data on Natufians reveals.

Reference List: 

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

2. The genetic history of Ice Age Europe, Fu et al.

3. Eight thousand years of natural selection in Europe, Mathieson et al.


I originally made a mistake in not noting that the early farmers (Neolithic Anatolians and Early European Farmers) did seemingly carry the derived allele in SLC45A2's rs1891982 SNP. They did seem to carry the derived (C) allele for this gene but at what look to be somewhat low frequencies (see here). I used to be under the incorrect impression that they didn't carry it. Apologies...