Friday, January 20, 2017

Human Genetic Diversity ≠ Discrete or Pure Races

One thing I've noticed is that a lot of much more "lay" people who glance over at population genetics tend to mistake Human genetic diversity, which is real, as validation of discrete races based on racialist models from the 18th-to-20th centuries or even current models ("Black", "White", "Brown" etc.).


They observe something like the above PCA (principal component analysis) based on 166,000 autosomal SNPs and they assume that because populations cluster apart; this means the discrete  races they believe in exist... That you can, for instance, divide most of the Homo Sapiens Sapiens (HSS) population like this:


This is, quite simply, not true. Simply because a massive portion of the HSS population is not entirely or overwhelmingly descended from one "discrete race" that then formed into another discrete race that then formed into another and another until their ethnic group came into existence.



Instead, the actual truth about several Human populations today is much more in-line with what you see above. In order to properly explain this I'll need to throwback to something I went into in an older post of mine where I pointed out the two main mechanisms by which Anatomically Modern Humans (HSS) diverge through:

Genetic Drift
&
Admixture

  • Genetic Drift: Population A & Population B are more or less "identical" and each have 1,000 people in them but they are geographically separated for 10,000 years... Population A doesn't experience any odd population losses and just continues to prosper from the original 1,000 roster but Population B loses 800 people due to an Earthquake very early on and the descendants of Population B find themselves being descended, 10,000 years into the future, from only those 200 folks who survived the Earthquake; losing a lot of their population's prior genetic diversity and diverging from Population A as a result of this alongside later mutations and selection, and so on. (more on genetic drift here and here)
  • Admixture: Population B's 1,000 remained intact in terms of numbers but they, even within a short time-frame, discovered a far away Population C with ancestry distinct from Population A & B and then intermixed with them to form a new mixed population that is now divergent from Population A due to being a mixture between Population B & C.

The thing about the old racialist model where we were all usually divided into four mega-races known as Mongoloids, Negroids, Caucasoids and Australoids- :


Natural History gallery of the Horniman Museum, London

-is that, even though the anthropologists who originally devised this worldview weren't familiar with the Human genome, it is very based around Genetic Drift and divides Humans up almost like they are "proto-subspecies" of sorts ("biological races" are the level right below subspecies, usually). 

For example, there was a Caucasoid race and then, via some intermediaries, "Aethiopids" and "Nordids" developed and Somalis and Danes developed from these two sub-races respectively. There might, at times, be some acknowledgement of admixture playing a part (Aethiopids are sometimes acknowledged to be slightly "Negroid" influenced, for instance. Or Maasais are noted to be an "Aethiopid+Negroid" mixture of some sort) but the model is still very dependent on the idea that Human phenotypic and thus genomic diversity was mainly shaped by natural selection and this is partly where it falls short.


By this logic, you would have to explain the differences between West Eurasians, as they are in that regional PCA above, as being mostly caused due to the formation of sub-races. I.e. There was a single ancestral West Eurasian population (Caucasoid race) and Northern Europeans formed as a sub-race of this population because their ancestors were separated from the ancestors of "Arabs" for tens of thousands of years and then natural selection & mutations, and therefore genetic drift, took place and that's mainly why we see genetic diversity here.

However, that's simply not the case. 


Instead, none of these West Eurasian populations are separate/discrete races from one another. They in fact share very recent ancestry from, for now, what look to be three or so core pre-historic populations. Villabruna-related West Eurasian Hunter-Gatherers (VHGs a.k.a "WHGs"), Ancient North Eurasian-related peoples (ANEs) and the theoretical "Basal Eurasians". 

They are, in large part, the product of admixture and not simply genetic drift where there was a Population X and then Populations Y and Z descend from it, were separate for a long time, then developed different mutations that altered the genotypes and phenotypes of a few of them, and then went through natural selection and genetic drift to select for those traits and become distinct entities. 

What makes them cluster apart is actually, to some great extent, the genetic drift between the highly divergent pre-historic populations they descend from. For instance, the ancestors of ANEs and VHGs, even though these two groups are closer to each other than they are to Eastern Non-Africans (ENAs), diverged apparently over 35,000 years ago [note]; and Basal Eurasians, whatever they might turn out to be in the end, are more divergent from ANEs and VHGS than they are from ENAs. 


It is ultimately the distinctions in how much ancestry these modern West Eurasians trace back to these pre-historic populations that differentiates them and makes them cluster apart. For example, Finns will pull more toward VHGs than Saudis will as they carry much more ancestry related to such pre-historics than Saudis do whilst Saudis will pull much more toward Basal Eurasian-rich pre-historic West Asians (i.e. Natufians and Neolithic Levantines) as they carry much more of ancestry related to such pre-historics than Finns do. [note]



West Eurasians are thus differentiated very much by admixture rather than merely just genetic drift. [note] So, in their case, various old racialist models fall flat. There was no single ancestral population that sub-races developed from and then yet more sub-races developed from and then the modern groups are just descendants of those separate sub-races... Instead, West Eurasians are interrelated, and most likely also look similar, because they are the result of very recent inter-mixture between these distinct pre-historic groups. [note]




And the thing is, this is similar for several ethnic and regional groups across the world. As a matter of fact, several (or often the majority) of the "native" ethnic groups in all of the following Old-World regions share upwards of 10-20% of their ancestry from arguably within the last 5,000-30,000 or so years via the likes of Basal Eurasian, VHG and ANE related ancestries:

Regions of interest colored in red
Essentially none of those populations can be considered truly "discrete races" from one another despite their differing phenotypes (i.e. Tamils compared to Somalis or ethnic Russians compared to Mauritanians) and distinct plotting points in global PCAs, because they did not develop the way species and subspecies usually develop which is mainly via substantive genetic drift over a long period of time. 

These particular populations mainly differ, again, because of the ancestries they don't share and the levels of ancestries they do share (i.e. East African cluster-related ancestry in Somalis not being present in Tamils and "ASI" ancestry not being present in Somalis and then differing levels of pre-historic West Asian-related ancestry in both groups). They do not differ because they're all downstream developments from an Ancestral-HSS population that mainly differentiated via mutations and subsequent drift.

Basically, you cannot assume that two populations cluster apart or are genetically distinct (by Human standards) simply because they are discrete and pure entities the way the Caucasoid, Negroid, Mongoloid and Australoid model, or any sort of racialist mindset, tends to imply. [note]

"The peoples of Africa"
Nevertheless, I suppose one could argue that certain populations are genuinely "discrete" in that they have not shared certain ancestries in well over 35,000 years. For instance, this can be said about West-Central Africans when compared to East Asians but here things do get a bit dicey as well since, while you can assume they're discrete from one another, they themselves are probably not, to some great extent, "pure" or mostly pure entities. 

By that I mean... They too are probably, in some part, the result of admixture rather than mostly or entirely being linear developments from a singular ancestral population which is how the old racialist model might paint things. 

For example, the quite diverse mtDNA profiles (simply based on their non-M&N lineages) of groups like Omotic speaking Southwestern Ethiopians, Niger-Congo speaking West-Central Africans and Nilo-Saharan speaking Southern Sudanese people tend to imply that they are probably the result of admixture between distinct pre-historic populations within Africa itself. [note]

Some of these ancestral populations were possibly even as distinct from each other as the San are from modern West-Central Africans (time divergence appears greater than the time-divergence between West-Central Africans and the Han-Chinese, and genetic drift (based on Fst) is comparable to the drift between the Han-Chinese and the English).




Groups that would count as "Negroids" within Africa should also not be seen as some sort of genetic monolith. They're not... And even the old racialist model didn't truly imply as much. There's often a West-Central African cluster ("Niger-Congo" above) and an East African-cluster ("Nilo-Saharan" above) in ADMIXTURE runs, for instance. The Fst between these two clusters, as an example, is a little over 1/2 the Fst between the East Asian and European clusters above.

Also, based on Haplotypic data, the time divergence between some of these "African" ancestries (i.e. the African elements in Somalis and the African elements in Yorubas) implies they possibly haven't shared ancestry in over 30,000-40,000 years or so which is comparable to the, so far, supposed time-divergence between ENAs and the ancestors of European Hunter-Gatherers. [note]




These African populations are also often, but not always, mixtures between these distinct modern clusters (as can be seen above) which are quite likely, in my humble opinion, not "pure" clusters either. We may just find that, like West Eurasian clusters from before we had ancient DNA flooding in, they are mixtures between distinct pre-historic African groups. In fact, I'd say this is quite likely given the mtDNA and sometimes Y-DNA profiles of these ethnic and regional groups. They even show slight signs of such mixture at the lower Ks of certain ADMIXTURE runs... [note]

So whilst some of these African populations, that mostly or entirely lack West Eurasian admixture, can be seen as separate from Out-of-Africa groups like ENAs in a manner that can somewhat be drawn onto a "tree"; they too look to be, like West Eurasians, not "pure" entities that linearly developed from one ancestral race that merely developed into discrete sub-races in order to form their current genetic diversity. Admixture played an important role here too, for certain. (also see note 2 below the reference list)

"The Races of Asia"

Things also look grim for the old "Mongoloid race" in that large subsections of it (Native Americans & Siberians) are not even entirely Eastern Non-African in origins. Native Americans are mostly a mixture between Ancient North Eurasian-related people and Han-like people and roughly the same is true for many non-European Siberian populations (Kets, Nganasans et al.) whilst old-school racialism failed to notice that East Asians and "Australoids" were closer to each other than they were to West Eurasian or African populations. [note]

Some like to re-envision these old racial classifications and now, to them, the only true Mongoloids are those in East Asia (the Han, Japanese, Koreans etc.) and, for example, the mixture that formed modern West Eurasians fits with the discrete and pure "Caucasoid race" idea but this is merely someone trying too hard to make these old racial classifications stick when they know the population genetics doesn't truly fit with them as they were traditionally envisioned. 


"American peoples"

And the traditional Mongoloid classification did include Native Americans as a subgroup of it. In fact, one vaguely humorous side note about the term Mongoloid is that its namesake, the Mongols, are not even of purely Eastern Non-African or particularly Han-like descent. See here

At any rate, it seems quite possible to me that a pre-historic population in East Asia is responsible for the traits we traditionally associate with East Asians (i.e. one whom important derived EDAR alleles formed among) and being partly or mostly descended from this population is probably responsible for certain phenotypic traits we see among East Asians like the Han or the Japanese (epicanthic folds et al.)... But even then, East Asians, as a whole, are likely not "pure" or "discrete" entities either, and this is definitely the case for some of them.




The Japanese, as one example, carry Jomon Hunter-Gatherer type ancestry which comes from a population that seems closest to modern East Asians but is still distinct from pretty much all of them (It also looked physically distinct from them as well. See here.) so admixture certainly played a part in the formation of the modern Japanese. And, while I'm still skeptical about the validity of this, various East Asian populations might also be part Ancient North Eurasian-related which again points to admixture playing a role in developing their modern genomic profile rather than them being linear developments from one single ancestral Mongoloid race. [note]


"The Human Races"

Now, one of the main reasons I'd say the old racialist approach fails is because, in a sense, they attempted to divide Humans based on phenotype-hinging taxonomy. There was no knowledge of DNA when these "races" were divised and they were divised, usually, but not always, as these mostly pure and discrete races and sub-races based around, for the most part, the outwardly visible phenotypic traits of various populations (i.e. their craniofacial traits).

Somalis, Oromos, Habeshas and the like were craniofacially most similar to each other and thus formed an "Aethiopid" sub-race of the Caucasoid race as they were supposedly more craniofacially similar to West Asians, North Africans, various South Asians and Europeans than to other Africans and it went on and on from there. [note]

Plot based on craniofacial data from a 10 year old non-racialist peer-reviewed craniofacial study

Some of the main problems with doing this would be:

  • Admixture: The incredibly important role admixture played in forming the modern gene pools of several HSS populations is recurrently down-played or ignored depending on the group being studied or whose work you're reading. I.e. Danes can merely be an off-shoot of Nordids rather than, basally, a mixture between ANEs, VHGs and the, for now, theoretical Basal Eurasians. A certain "craniofacial type" (accompanied by some other phenotypic traits) that occurs on average within a population is ofttimes assumed to be the mark of a "discrete" and, ofttimes, "pure" race of its own. [note]
  • Hinge entirely on phenotypic traits: People often overestimate how much genomic divergence and relations correlate with physical differences. Differences in pigmentation (skin, hair and eye color), hair-type and craniofacial traits among Modern Humans are mainly controlled by seemingly only some hundreds of SNPs among ~10 million SNPs in our entire genomes. Hence why, until genomics set-in for a while, nobody noticed the Andamanese were genetically closer to East Asians than to Africans and West Eurasians. Two populations that are substantially drifted and/or haven't shared ancestry in seemingly over 20,000-40,000 years (Aris and Yorubas, for instance) can look quite similar whilst two that look very distinct can be closer than many would expect (the Han and the Andamanese). [note]

Current racialism is even less scientific and much more arbitrary as it often heavily fixates on one trait: skin pigmentation (though other outward phenotypic traits are definitely taken into account).

In this case Australian Aborigines, Papuans and Yorubas, in many people's eyes, count as part of the same "race" ("Black") because they look vaguely similar and are dark-skinned, and people with pale-skin from Europe are usually seen as "White". And then various South Asians and West Asians are often darker than Europeans (especially Northern Europeans) so they're "Brown" and it goes on and on from there.

This form of racial classification is often pretty arbitrary, to be quite frank. For one, a person's membership in a racial group can seriously depend on who's classifying them or the culture of the place they're in...

In the United States, people of part "Black" and "White" ancestry are often considered "Black" whilst this is not may not be the case in South Africa or certain Caribbean countries where specific terms exist for such people (see here and here). Where I grew up (the UAE) you will see Arabs, Iranians and the like being considered "White" when they certainly wouldn't be seen as such if they went to various parts of Europe or, at times, even the US. 

These currently popular racial groups are simply not well defined, especially from a scientific viewpoint. The Early Modern form of racialism, while obsolete, was much more thought out and wasn't totally wrong on everything [note]. But current racial groupings, at times, merely look like any sort of phenotypic, cultural, ethnic or genetic group suddenly counts as a "race". 




This is why, in my humble opinion, you get notions like "the Jewish race" when Jews (particularly Western and certain Mizrahi Jews) are basically just an ethno-religious group (emphasis on the ethno) and of course not some sort of discrete race when compared to West Asians or Europeans or North Africans and various others.

This is also why various "Latinos/Hispanics" in the US such as ones of Mexican origins, despite commonly (not always) being of mixed origins (Native American, European and sometimes African), are often labeled as their own race category because they form a distinct cultural and sometimes physical group even though they're obviously not actually a "separate race" from "White" Americans (sharing in ancestry from Europe and even in the ANE-related ancestry in their Native American roots), for example. 

This sort of treads on the very notion of what races were originally supposed to mean within a Human context as they were very much centered around a taxonomy inspired notion that we, as Homo Sapiens Sapiens, could be divided into into proto-subspecies based on phenotypic traits (with craniofacial measurements at the forefront) rather than being a continuum of mixtures that oddly count as their own discrete and pure races in the minds of many.

At the end of the day this form of racialism falls flat on its face for similar reasons as the older form, along with its way of dividing everyone based on phenotypic traits being even more shallow (hence why Australian Aborigines and Yorubas can both count as "Black" in the minds of some, mainly based on their similarity in pigmentation and their somewhat superficial facial similarities).



But, there's one thing to keep in mind here... I'm not telling you that Human genetic diversity does not exist and that we're all 100% the same. As the title says: "Human Genetic Diversity Discrete or Pure Races". Homo Sapiens Sapiens genetic diversity, however high or low overall, does exist as the very title of this post basically espouses but what this post means to point out is that the racial groupings and population-structures you most likely believe in, whether based on old and new conventions, do not well and truly correlate with population genetics. [note]

Nevertheless, one is free to create their own divisions based on population genetics, in my humble opinion. I.e. I tend to group "West Eurasians" together as they're closer to each other than to most outside groups, then the same is true for Eastern Non-Africans, West-Central Africans, Horn Africans, and so on.

Then within these groups you can near endlessly create other regional sub-groups that do, genetically, seem closer to each other than to the rest of their macro-grouping like Southern Europeans, Arabians and the like as subdivisions within "West Eurasians" [note] but the main thing to grasp is that these often aren't pure or even always discrete entities that you can draw onto a tree structure like this:

Hence, to a great extent, why both old and new racialism aren't in line with the actual science. Old racialism comes closer than new racialism but they both fall short in the end. Actual Human genetic diversity is a good degree more complex.

References:






Notes:

1. Link

2. Link

3. Link

4. Link

Special thanks go to the author of Vaêdhya and an administrator at Anthrogenica who goes by the pseudonym "DMXX" as well as a long-time friend in this field who goes by pseudonyms such as "Lazara Masho" (23andme) & "Lank" (Antrogenica) online for reading through this post for any inaccuracies and handing out some advice on how to improve it.

Thursday, January 19, 2017

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,

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.


References:

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


References:

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).


References:

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. 


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