Race is not just skin color

“The southern Indians resemble the Ethiopians a good deal, and, are black of countenance, and their hair black also, only they are not as snub-nosed or so woolly-haired as the Ethiopians; but the northern Indians are most like the Egyptians in appearance.”

– Arrian

I might almost say that the same animals are to be found in India as in Aethiopia and Egypt, and that the Indian rivers have all the other river animals except the hippopotamus, although Onesicritus says that the hippopotamus is also to be found in India. As for the people of India, those in the south are like the Aethiopians in colour, although they are like the rest in respect to countenance and hair (for on account of the humidity of the air their hair does not curl), whereas those in the north are like the Egyptians.


The plot above is from Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. It’s a 2007 paper. For those of you not versed in genetics, 10 years is like the difference between the First Age and Third Age on Middle Earth. For those of you not versed in Tolkien, 10 years is like the difference between Gupta India and Maratha India? I think?

Basically, the authors looked around the regions of the genome of loci known to be implicated in pigmentation variation in 2007, which mostly started from differences between Europeans and Africans. In the plot above you see pairwise genetic distances visualized in a neighbor-joining tree. The populations are:

SA = Asians, IM = Island Melanesians, WA = West Africans, EU = Europeans, EA = East Asians, and NA = Native Americans

What you see is that pigmentation loci are not phylogenetically very informative. Because of ascertainment bias in discovery Europeans are an out-group on many of the genes. But overall you see that the trees generated by a relationship on pigmentation genes do not conform to what we’d expect, where Africans are an outgroup to non-Africans. This is not surprising, as any given locus is not too phylogenetically informative. Additionally, pigmentation is a trait where selection has likely changed allele frequencies a lot, so it’s not a very good trait to look at to determine evolutionary relationships.

A white actress?

I bring this up because The New York Times and other publications are reporting on a new paper in Science, Loci associated with skin pigmentation identified in African populations, with headlines like Genes for Skin Color Rebut Dated Notions of Race, Researchers Say.

The Science paper is very interesting because it helps to make up for the long-term ascertainment bias in the literature, whereby European differences from other groups helped to discover pigmentation loci of interest. The big topline result is that there’s a lot of extant variation within Africans, and much of it is very old, pre-dating modern humans by hundreds of thousands of years, implying long-term balancing selection to maintain polymorphism.

Here’s a quote from The New York Times piece:

For centuries, skin color has held powerful social meaning — a defining characteristic of race, and a starting point for racism.

“If you ask somebody on the street, ‘What are the main differences between races?,’ they’re going to say skin color,” said Sarah A. Tishkoff, a geneticist at the University of Pennsylvania.

The widespread distribution of these genes and their persistence over millenniums show that the old color lines are essentially meaningless, the scientists said. The research “dispels a biological concept of race,” Dr. Tishkoff said.

I can go along with all the sentences more or less except the last. Skin is the largest organ we have, and it’s pretty salient. West Asian Muslims regularly referred to Indians as “black” (early Islamic Arabs referred to the people of Sindh as “black crows”). They defined themselves as white (though contrasted their own olive complexion with ruddy Europeans). The Chinese referred to themselves as white, and Southeast Asians, such as the inhabitants of the ancient Cambodian kingdom of Funan, as black. Among South Asians, skin color is also very salient. During the period when Pakistan included a western and eastern half the West Pakistanis were known to refer to the Bengalis as blacks, while East Pakistanis who went to study in the West, like my father, were surprised that not all Pakistanis were white like Ayub Khan.

Sharon Muthu, Indian American actress

But racial perception and categorization are not identical with skin color. The ancients knew this intuitively, as the quotes from Arrian and Strabo above suggest. They were aware that South Asians were dark-skinned, but those in the north were lighter than those in the south, and that those in the south resembled Africans in the range of their complexion. But, they also knew that it was not difficult to distinguish a South Asian from an African in most cases, because South Asians have different hair forms and to some extent facial features, from Africans.

I know this myself personally. Living in almost white areas of the United States for most of my childhood I encountered some racism. My skin tone is within the range of African Americans. But when it came to racial slurs I was usually called “sand nigger”, or more sometimes “camel jockey.” Please note that the modifier sand. Even racists understood to distinguish people of similar hues who were clearly physically distinctive.

Conversely, African Americans did not usually recognize me as African American. Living in the Pacific Northwest there aren’t many non-whites. It’s also very rainy. Sometimes when I was wearing my Columbia jacket with hood black men walking from the other direction on the sidewalk would start to nod at me, assuming I was black. But mid-way through the nod as they approached me they recognized that despite my brown color I was not African American and would stop the motion and switch to a manner of distanced politeness as opposed to informal warmth.*

Finally, I also had East Asian friends who were very light-skinned. As light-skinned as any white person of Southern European heritage. That did not prevent racists from calling them “chinks” or (more rarely) “gooks.” These racists were seeing beyond the skin color.

If ancient authors from 2,000 years ago understood that race is more than skin color, and if genuine bigots understand race is more than skin color, I fail to understand why so often the public discourse in the United States acts as if race is just skin color. We know it’s not so.

The reason I’m posting this on Brown Pundits is that the focus on skin color made sense to me growing up in the United States, but as someone of South Asian ancestry I also knew it was not sufficient as a classifier. I knew when I was probably around five. Many South Asians see a huge range in skin color within their immediate families. That is, empirically the fact that there were large effect QTLs segregating within South Asians is obvious to any South Asian who grew up around South Asians.**

My mother is of light brown complexion. My father is of dark brown complexion. My mother’s complexion is fair enough that she is usually assumed to be Latina if she doesn’t speak (her accent is clearly South Asian), and in cases has been misjudged to be Southern European. My father, like his mother, is in contrast on the darker side. Their Bengali friends would joke that they were an interracial relationship.

My father’s father was very light skinned, and his mother was very dark skinned. Some of his siblings were dark, some of them were light, and some of them were between. One of my father’s brothers is basically a doppelganger of my father, except he is lighter skinned.

And yet there was never a question that both my parents were ethnically Bengali. They were both people with deep roots in Comilla in eastern Bengal. Now that I have their genotypes I can tell you that my parents are genetically clearly from the same region of Bengal; they cluster together even compared to other Bangladeshis. In fact, my father is more Indo-Aryan (every so slightly) shifted than my mother. I suspect it is through his mother, whose father was born into a family of recently converted Brahmins. It is clear that skin color is not predicting phylogeny in this case, and I am sure many South Asians intuitively grasp this because of the variation in complexion they see across their families, who are usually from the same sub-ethnic group in any case.***

A multiracial United States is going to be more complex world than the situation before 1965, when America’s racial consciousness was partitioned between black and white (notwithstanding Native Americans, Hispanos and other Latinos in the Southwest, and a residual of Asian Americans). But sometimes I feel the intellectual and cultural elite of this nation is stuck in the paradigm of 1964.

* I have a friend from Kerala in South India who has talked about being mistaken for being Ethiopian.

** I am the only South Asian my daughter has grown up around, and her complexion is far closer to her mother’s than my own. She did have a difficult time distinguishing me from black males in her early years because to her my dark-skin is very salient. When her mother asked her to give reasons why African American males might look different from her father, she immediately clued in on the hair and facial features.

*** Black Americans and Middle Easterners, and a whole host of other groups where pigmentation loci segregation in appreciable frequencies, can all see that differences in skin color do not necessarily denote differences in race, since there is so much intra-familial variation.

The Indo-Aryan question nearing resolution

India Today published my review of the current state of the genetics and genomics of the Indian subcontinent, and what it can tell us about the ethnogenesis of South Asians generally. In the piece I tried to be very circumspect and stick to what we know with a high, if not perfect, degree of certainty. Here I will add some comments where I reduce the threshold of certainty somewhat. That is, I’m going to include here my beliefs where I think I’m right, but in some details wouldn’t be surprised if I was wrong.

First, the title is Aryan wars: Controversy over new study claiming they came from the west 4,000 years ago. Writers don’t get to choose titles, and this is not one I would have chosen. But I am not in a position to care or know what draws clicks. Let’s note that this “controversy” is restricted mostly to India. Outside of India it’s not controversial, but a matter of the science, because people don’t have any political or social investment in the topic. It reminds me of debates about genetics and intelligence in the West, where emotions get overwrought and lies fly wildly with abandon.*

Second, there is a reference in the figures to an “Out of India” (OIT)  model. That is, the Aryans migrated out of India, and implicitly the Indo-European languages derive from South Asia. I don’t think this theory has any support at all. That is, I think it is rather clear that proto-Indo-European probably emerged neither in Europe proper, nor in South Asia, but in the Inner Eurasian spaces between. But for an Indian audience ignoring OIT would seem a peculiar lacunae, so there was a reference added to the figure on that account (I pushed back against this, but do not make ultimate decisions on figures).

But I do think it was plausible up until 2009’s Reconstructing Indian History to suggest that most modern South Asian ancestry dates to the Pleistocene. In this framework the Indo-Europeanization of the subcontinent was primarily a cultural one, where small groups of Central Asians imposed their language on the native population. What the genome-wide work has shown is that South Asians are the product of a large-scale mixing process between a population very distant from West Eurasians (“Ancestral South Indians”, ASI) and a population which was indistinguishable from other West Eurasians (“Ancestral North Indians”, ANI).

Since ANI is indistinguishable from West Eurasians I hold it is clearly a West Eurasian population in provenance. Those who reject this position from a scientific perspective believe that there could have been some sort continuous zone of “ANI-like” habitation from northwestern South Asia up into northern Inner Eurasia (and perhaps toward West Asia as well) dating from the late Pleistocene. I do not that believe this is plausible, and I will tell you that prominent researchers who I have brought up this idea to are somewhat incredulous.**

Third, there are major unresolved issues genetically in relation to the dates and the total number of mixing populations. I am quite confident saying around half of the total South Asian genomic ancestry today derives from populations who were living outside of South Asia on the Holocene-Pleistocene boundary 11,700 years ago. Much of that ancestry probably flourished between the Caucasus and Zagros mountains. The remainder somewhere in the vast swath of territory between the Baltic and Siberia (perhaps further south, toward the Pamirs?).

But I am not confident of the relative balances of contribution to the ANI. It does seem that the northern component, which is derived in part from the southern component, is much more prominent in upper castes and northwestern populations. In contrast the southern component is found throughout the subcontinent.

In Genomic insights into the origin of farming in the Near East there is analysis of South Asia in the supplements. The author concludes that ANI can not be modeled as a single population (Zack Ajmal and I were saying this in 2010). The top hits for the sources of ANI tend to be the genomic sample from the Zagros, in western Iran (before subsequent admixture with Levantine farmers), and a population similar to the Yamna culture of the steppe. The issue seems to be that later steppe populations which harbor a fair amount of “Early European Farmer” ancestry (e.g., LBK in Central Europe) due likely to back migration aren’t good model fits.

Below are two plots, one showing a scatter of South Asian groups with their Iran_N (a sample from ~10,000 years ago) vs. Yamna (from ~5,000 years ago), and another with the ratios.


DO NOT TAKE THE PROPORTIONS LITERALLY.  My intuition is that these models are overestimating the proportion of steppe ancestry, but my confidence in my intuition is low.

There are two groups enriched for Iran_N ancestry:

  1. Lower caste groups, especially from South India.
  2. Populations in southern Pakistan.

The reasons differ. If you have done genetic analysis of the Pakistani populations it seems quite obvious that unlike other groups in South Asia Pakistani groups facing the Arabian sea across from Oman have genuine Near Eastern ancestry. This affinity declines as you go north in Pakistan rather rapidly. Notice though one South Indian group: Jews from Cochin. This population clearly has recent Near Eastern ancestry.

The Kharia are an Austro-Asiatic Munda group. For whatever reason Austro-Asiatic groups seem to consistently have very little steppe ancestry. The Mala are Dalits from South India. The further up you go on the modal Iran_N-Yamna cline you see the populations are either upper caste, or, they are from the far northwest of the subcontinent.

The conclusion I derive from this is that first there was an early migration of West Eurasian populations consisting of Iranian farmers. This group mixed with the ASI element. The Indo-Aryans, which probably correlates with the Yamna-like component, arrived later as an overlay (and nearly half of their ancestry was derived from Iranian farmers). Then many South Asian populations have modifications on this base model of compound ANI + ASI; Munda and Bengali have later East Asian ancestry, while populations on the Arabian sea have Near Eastern ancestry.

Fourth, the story in India Today leans heavily on Y chromosome of R1a1a lineage. It is true we are Lords of the Steppe and destined to drive our enemies before us. But, it is not the primary story. And yet Y chromosomal phylogenies are easy for the public to understand. But they only make sense in light of the above framework. R1a1a is found in South Indian tribal populations. It seems likely that Indo-Aryan paternal lineages were highly invasive across the subcontinent, just as they were in Europe. In many cases they likely extended far beyond domains where Indo-European acculturation occurred.

I’m probably wrong on some of the details. But I suspect the final story will not be so different from this.

Finally, I will mention the cultural element here. There is a fair amount of the discussion of the form “so you are saying the ancestors of Indians are Europeans?” or “does this mean Hinduism is not Indian?”

The piece was about genetics and demography, not my opinions about culture. So I will say this:

  1. The “West” as an entity is no older that Classical Greece. 500 BC. My own personal position, strongly held, is that the West should indicate cultures and societies which descend from the European societies which adhered to the Western Church around ~1000 AD (some nations, like Lithuania, became absorbed into this cultural complex hundreds of years later). So Russia is not the West. And Merovingian Francia is not the West.
  2. Indian civilization of what we term the Hindu variety coalesced in the period between between 500 BC and 500 AD, from before the Mauryas, up to the Guptas. Obviously the period before 1000 BC was important in setting the ground-work, but I do not believe it was Indian as we’d understand it in anything but the geographical sense, nor was it Hindu in any way we’d recognize it today (similarly, Shang dynasty China was not China as we’d understand, which came into being after 500 BC).

These positions mean that I think nationalist passions are in the “not even wrong” category. Indian Hindu civilization is indigenous by definition, since it was synthesized in situ on the edge of historical perception and attestation (for the record, I think Adi Shankara was critical in the completion of a crystalized self-conception of Hindu religio-philosophical thought, but its origins predate him). Similarly, Indian civilization was not seeded by white Europeans because white Europeans were only coming into being in Europe when the Indus Valley civilization was collapsing.

That is all (for now).

Addendum: The first tranche of ancient DNA should be out in a few months. Also, there is another paper on Indian genetics in the work from the usual suspects. There won’t be anything totally surprising (or so I’ve been told).

* By lies, I mean the contention that intelligence is an “invalid” instrument in relation to predictiveness, or, if it is valid, it is not genetically heritable. People routinely lie about these facts in discussion or spread lies because there are socially preferred positions which they conform to. Similarly, many questions about Indian history seem to hinge on widely promoted lies.

** This model needs to also confront the massive mixing of the last 4,000 years. If it is true then it is ASI which is mostly likely intrusive, because it is not creditable that these two populations were in nearby proximity for tens of thousands of years without exchanging genes.

Indian genetics, the never-ending argument

I am at this point somewhat fatigued by Indian population genetics. The real results are going to be ancient DNA, and I’m waiting on that. But people keep asking me about an article in Swarajya, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe.

First, the article attacks me as being racist. This is not true. The reality is that the people who attack me on the Left would probably attack magazines like Swarajya as highly “problematic” and “Islamophobic.” They would label Hindu nationalism as a Nazi derivative ideology. People should be careful the sort of allies they make, if you dance with snakes they will bite you in the end. Much of the media lies about me, and the Left constantly attacks me. I’m OK with that because I do believe that the day will come with all the ledgers will be balanced. The Far Left is an enemy of civilization of all stripes. I welcome being labeled an enemy of barbarians. My small readership, which is of diverse ideologies and professions, is aware of who I am and what I am, and that is sufficient. Either truth or power will be the ultimate arbiter of justice.

With that out of the way, there this one thing about the piece that I think is important to highlight:

To my surprise, it turned out that that Joseph had contacted Chaubey and sought his opinion for his article. Chaubey further told me he was shocked by the drift of the article that appeared eventually, and was extremely disappointed at the spin Joseph had placed on his work, and that his opinions seemed to have been selectively omitted by Joseph – a fact he let Joseph know immediately after the article was published, but to no avail.

Indeed, this itself would suggest there are very eminent geneticists who do not regard it as settled that the R1a may have entered the subcontinent from outside. Chaubey himself is one such, and is not very pleased that Joseph has not accurately presented the divergent views of scholars on the question, choosing, instead to present it as done and dusted.

I do wish Tony Joseph had quoted Gyaneshwer Chaubey’s response, and I’d like to know his opinions. Science benefits from skepticism. Unfortunately though the equivocation of science is not optimal for journalism, so oftentimes things are presented in a more stark and clear manner than perhaps is warranted. I’ve been in this position myself, when journalists are just looking for a quote that aligns with their own views. It’s frustrating.

There are many aspects of the Swarajya piece I could point out as somewhat weak. For example:

The genetic data at present resolution shows that the R1a branch present in India is a cousin clade of branches present in Europe, Central Asia, Middle East and the Caucasus; it had a common ancestry with these regions which is more than 6000 years old, but to argue that the Indian R1a branch has resulted from a migration from Central Asia, it should be derived from the Central Asian branch, which is not the case, as Chaubey pointed out.

The Srubna culture, the Scythians, and the people of the Altai today, all bear the “Indian” branch of R1a. First, these substantially post-date 6000 years ago. I think that that is likely due to the fact that South Asian R1a1a-Z93 and that of the Sbruna descend from a common ancestor. But in any case, the nature of the phylogeny of Z93 indicates rapid expansion and very little phylogenetic distance between the branches. Something happened 4-5,000 years ago. One could imagine simultaneous expansions in India and Central Asia/Eastern Europe. Or, one could imagine an expansion from a common ancestor around that time. The latter seems more parsimonious.

Additionally, while South Asians share ancestry with people in West Asia and Eastern Europe, these groups do not have distinctive South Asian (Ancestral South Indian) ancestry. This should weight out probabilities as to the direction of migration.

Second, I read some of the papers linked to in the article, such as Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia and Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. The first paper has good data, but I’ve always been confused by the interpretations. For example:

A few studies on mtDNA and Y-chromosome variation have interpreted their results in favor of the hypothesis,70–72 whereas others have found no genetic evidence to support it.3,6,73,74 However, any nonmarginal migration from Central Asia to South Asia should have also introduced readily apparent signals of East Asian ancestry into India (see Figure 2B). Because this ancestry component is absent from the region, we have to conclude that if such a dispersal event nevertheless took place, it occurred before the East Asian ancestry component reached Central Asia. The demographic history of Central Asia is, however, complex, and although it has been shown that demic diffusion coupled with influx of Turkic speakers during historical times has shaped the genetic makeup of Uzbeks75 (see also the double share of k7 yellow component in Uzbeks as compared to Turkmens and Tajiks in Figure 2B), it is not clear what was the extent of East Asian ancestry in Central Asian populations prior to these events.

Actually the historical and ancient DNA evidence both point to the fact that East Asian ancestry arrived in the last two thousand years. The spread of the first Gokturk Empire, and then the documented shift in the centuries around 1000 A.D. from Iranian to Turkic in what was Turan, signals the shift toward an East Asian genetic influx. Alexander the Great and other Greeks ventured into Central Asia. The people were described as Iranian looking (when Europeans encountered Turkic people like Khazars they did note their distinctive physical appearance).

We have ancient DNA from the Altai, and those individuals initially seemed overwhelmingly West Eurasian. Now that we have Scythian ancient DNA we see that they mixed with East Asians only on the far east of their range.

The second paper is very confused (or confusing):

The time divergence between Indian and European Y-chromosomes, based on the closest neighbour analysis, shows two different distinctive divergence times for J2 and R1a, suggesting that the European ancestry in India is much older (>10 kya) than what would be expected from a recent migration of Indo-European populations into India (~4 to 5 kya). Also the proportions suggest the effect might be less strong than generally assumed for the Indo-European migration. Interestingly, the ANI ancestry was recently suggested to be a mix of ancestries from early farmers of western Iran and people of the Bronze Age Eurasian steppe (Lazaridis et al. 2016). Our results agree with this suggestion. In addition, we also show that the divergence time of this ancestry is different, suggesting a different time to enter India.

Lazaridis et al. accept a mass migration from the steppe. In fact, the migration is to such a magnitude that I’m even skeptical. Also, there couldn’t have been a European migration to South Asia during the Pleistocene because Europeans as we understand them genetically did not exist then!!!

I assume that many of the dates of coalescence are sensitive to parameter conditions. Additionally, they admit limitations to their sampling.

Ultimately the final story will be more complex than we can imagine. R1a is too widespread to be explained by a simple Indo-Aryan migration in my opinion. But we can’t get to these genuine conundrums if we keep having to rebut ideologically motivated salvos.

Related: Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts. I wish David would be a touch more equivocal. But I have to admit, if the model fits, at some point you have to quit.

Indian media is finally reporting on the Aryan migration into South Asia

For various ideological reasons in India there has been a strong resistance to the idea that Aryans came from outside of South Asia. When David Reich’s Reconstructing Indian Population History was published 2009 the Indian media had a weird response. For example, Aryan-Dravidian divide a myth: Study.

Though Reich’s paper was equivocal, it was clear to me that it was likely going to be the launching point for a resurrection of the Aryan migration theory. Now Tony Joseph in The Hindu has published a pretty good survey of the literature, How genetics is settling the Aryan migration debate. Nothing new for readers of this weblog, but he some good quotes:

The avalanche of new data has been so overwhelming that many scientists who were either sceptical or neutral about significant Bronze Age migrations into India have changed their opinions. Dr. Underhill himself is one of them. In a 2010 paper, for example, he had written that there was evidence “against substantial patrilineal gene flow from East Europe to Asia, including to India” in the last five or six millennia. Today, Dr. Underhill says there is no comparison between the kind of data available in 2010 and now. “Then, it was like looking into a darkened room from the outside through a keyhole with a little torch in hand; you could see some corners but not all, and not the whole picture. With whole genome sequencing, we can now see nearly the entire room, in clearer light.”

In relation to online debates I have had Indian interlocutors tell me flat out that they believe in the papers published between 2005 and 2010. It is nice to get the scientists who actually published this work now admit that new results overturn the older theories.

Note: I am going to refer to this as a migration, because “invasion” seems to connote too much specificity as to how it happened. But I have a difficult time imagining that it was a peaceful process.