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

  • 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] (also check note 6 in the notes section below)
  • 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 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.



1. Link

2. Link

3. Link

4. Link

5. Please do read all of the "[notes]" including the four above as they're crucial for fully grasping this post. If you haven't read them; you have not actually read this post.

6. I also strongly recommend going through a comment section tangent below between myself and a user by the name of Onur. Some key things are elaborated upon there.

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,