Selection for and against pigmentation alleles in South Asia

Deepika Padukone

Recently some British friends were asking about what we knew about South Asian historical genetics now. I explained that it does look like there was some migration in from the Central Asian steppe and West Asia into South Asia during the Holocene. To which one friend responded, “that’s obvious though, many Indians look like brown white people.” Setting aside the semantic paradox (if you are brown, you are literally not white), it is clear what he is getting at: due to shared ancestry the facial structure of many South Asians is not that different from West Eurasians.

The Bollywood actress Deepika Padukone is an example of someone who is rather brown-skinned (naturally), but whose facial features are such that if she went with 100% skin-bleaching she would pass as white without too much trouble. For the purposes of this post, I Googled Indian albino…and came up with this family. You can make your own judgments. I don’t know what to think of that!

The reason for this post is a newly accepted paper, Ancestry-specific analyses reveal differential demographic histories and opposite selective pressures in modern South Asian populations:

Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations, and showed our approach to be robust via coalescent simulations.

Our f3 and f4 statistics based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex inter-population relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.

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Unleash the data kraken!

The Reich lab has done a mitzvah and released a huge merged dataset of their modern and ancient populations in a big tarball. Actually, there are two files. One of them is a larger number of individuals with 600,000 SNPs (includes “Human Origins Array”) and the other has 1,200,000 SNPs, but fewer individuals. It is in EIGENSTRAT format.

For the convenience of readers who are more comfortable in PLINK/PEDIGREE format, I’ve converted them, and replaced the family ID column with population labels. The links take to you a zip file that has the three files for the binary format.

You really can’t talk about shariah in 20 minutes

Vox‘s Worldly is a short (less than 30 minute) podcast on world-affairs. I listen to it because American politics is boring, and it’s not a major timesink. But, its brevity is something that has worried me, since this is not a long period of time, and it’s hard to address things in a subtle manner to a general audience in such a short segment.

The most recent one, Brunei just made gay sex punishable by death, illustrated to me a lot of the problems with trying to compress too much into 20 minutes. There are three hosts. A fair portion of the time they discussed Islam, and Islamic jurisprudence (shariah).

Though they didn’t mention it, one of the hosts is a convert to Islam. You can read about her in this article, How a Blonde Tattooed Texas Girl Became an ISIS Twitter Star.

I am a social constructivist when it comes to religion. That is, I don’t have a religion, do not believe in gods, and am willing to accede to a consensus of the believers as to what their religion is, as well as instrumentally taking into account what religious believers as a whole seem to think about their religion.

To give an example of what I mean,

  • I am fine with someone with a non-binary gender identity who rejects a great deal of hadith and is totally fine with apostasy from Islam, calling themselves a Sunni Muslim. I’m not invested in the idea that being a Sunni Muslim means anything more than a particular self-identification. I’m not a Sunni Muslim. I don’t care if you call yourself a Sunni Muslim.
  • But, I also assume that acceptance of non-binary gender identity and apostasy in Islam is not normative among the majority of the world’s Muslims, and as an apostate from Islam I am very cautious about going to Muslim-majority countries and expressing my beliefs. Apostates are still killed by mobs, and it is still against the law in many Muslim-majority nations.

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The growth of human genomics

Citation: Aylwyn Scally

The above figure is from Aylwyn Scally, or as I like to think of him, the Irish Matt Hahn. I’m not going to add any comments as the chart speaks for itself, doesn’t it?

Also, looks like my son is about the 10,000th person in the history of the human race who was whole-genome sequenced. That’s not a shabby record. First prenatal whole-genome sequence of a healthy born individual, and in the first ~0.000125% of the human race alive today to be sequenced.

Sydney Brenner: the passing of a giant

Nobel laureate Sydney Brenner, who helped place Singapore on biotech world stage, dies at 92. If you are in genetics and development you know who Brenner his, and what he meant to these fields. I happened to be in the room with Brenner once, in Berkeley in 2008 I believe. He was already quite an old curmudgeon, and I will say his comments were amusing and awkward!

Long-time readers of this weblog know that about fifteen years ago I dabbled in a little worm-work. At that time I read In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite. As Brenner was involved in promoting C. elegans as a model he occupies a lot of this book. I recommend it. It’s short and packed with historical nuggets that make the 21st-century trajectory of science more comprehensible.

The shadow of the Hun

Short of stature, with a broad chest and a large head; his eyes were small, his beard thin and sprinkled with grey; and he had a flat nose and tanned skin, showing evidence of his origin.

– Jordanes, describing Atilla the Hun

When I was younger (think age 10) I had a period when I read a lot of medieval and “Dark Age” history. Reading about the Huns was pretty scary…they were like the Mongols, but even more, cloaked in legend. I always remember the debates about the physical descriptions of the Huns. On the one hand, it could be plausibly asserted that their descriptions indicated an Asiatic people. But another argument was that the ancient writers were utilizing common tropes to describe barbaric peoples.

Today with DNA we can answer some of these questions with finality. Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin:

Hun, Avar and conquering Hungarian nomadic groups arrived into the Carpathian Basin from the Eurasian Steppes and significantly influenced its political and ethnical landscape. In order to shed light on the genetic affinity of above groups we have determined Y chromosomal haplogroups and autosomal loci, from 49 individuals, supposed to represent military leaders. Haplogroups from the Hun-age are consistent with Xiongnu ancestry of European Huns. Most of the Avar-age individuals carry east Eurasian Y haplogroups typical for modern north-eastern Siberian and Buryat populations and their autosomal loci indicate mostly unmixed Asian characteristics. In contrast the conquering Hungarians seem to be a recently assembled population incorporating pure European, Asian and admixed components.

I was curious about the Hun samples, and the autosomal results. There were only three Huns, but one of them carried haplogroup Q1a2. This is found at highest frequencies in Turkic and Siberian groups. The other individuals were R1b and R1a. R1a is common in Eastern Europe…but the particular variant this Hunnic male carried was of the Z93 branch comon in Central and South Asia, and in particular in places like the Altai.

As far as the autosomal results:

Samples from different archaological cultures and cemeteries showed a remarkable pattern of phenotypic distribution. All Hun and Avar age samples had inherently dark eye/hair colors, DK/701being the only exception (Table 2). Moreover 6/14 Avar age samples were characterized with >0,7 black hair; >0,99 brown eye….

Again, some historians have argued that the tropes that emerged to describe the Sarmatians and Scythians were recycled for the Huns. But we know what these groups looked like because we have ancient DNA from them: they were clearly West Eurasian people, with western populations heavily Europeanized. It is clear from these results that the Huns and Avars were physically reflective of their East Asian origin. The ancient authors describing them in exotic terms were describing reality, not a metaphor.

I look forward to discovering whether other “metaphors” of the descriptions of ancient peoples turn out to be literal and serious as well.

Denisovans’ biogeography is very different from Neanderthals’

I want to elaborate on my earlier post, Deep Denisovan Population Structure. Though I don’t put much stock in any particular result, including the most recent ones reported at a conference, I think that biogeography tells us a lot about what we should expect in the future.

First, notice that Neanderthals, Denisovans, and European hunter-gatherers have all exhibited evidence of being subject to massive bottlenecks and very low effective population sizes. Things changed in Europe with the arrival of Neolithic farmers, whose higher genetic diversity is in the range of modern people. I think this is indicative of the fact that abiotic factors, climatic shocks, drove down population sizes periodically consistently with all these northern hominins. I’m not saying that population sizes couldn’t get large periodically, but the fact that later Altai Neanderthals are genetically closer to Neanderthals from Croatia than earlier Altai Neanderthals indicate lots of local population extinction. It applied to Neanderthals, it applied to northern Denisovans, and, it applied to northern modern humans. Only with a change in the mode of production were higher long-term population sizes feasible.

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Open Thread, 04/01/2019

The Birth of Modern Belief: Faith and Judgment from the Middle Ages to the Enlightenment. An interesting book, especially paired with The Rise of Western Christendom.

A seismically induced onshore surge deposit at the KPg boundary, North Dakota. This paper is the basis for the article in The New Yorker, The Day the Dinosaurs Died. This paper and the piece in The New Yorker has gotten serious blowback on Twitter.

A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data.

A three-sample test for introgression.

This week on The Insight I’m going to talk to Cosimo Posth about the genetics of Ice Age Europe. I also recorded a podcast on evolutionary psychology, and will be recording one on the “missing heritability.”

Recovery of trait heritability from whole genome sequence data.

Extraordinary claims require extraordinary evidence in the case of asserted mtDNA biparental inheritance.

I will be devoting some time to improving the subscription option….

The social and demographic dynamics of Al-Andalus

A slight detour from Rulers, Religion, and Riches took me to Brian Catlos’ Kingdoms of Faith: A New History of Islamic Spain. I’ve enjoyed Catlos’ work before, and he has an engaging narrative style. His books are quick reading and I recommend them, incuding his monographs.

But, there is always a weird aspect to his work and analysis that has always struck me: his overall narrative often works at cross-purposes with specific assertions he makes in passing. As an example, Catlos rightly points out that in Spain under the rule of the Muslim Arabs particular and specific religious confession was not a major issue, since most people lived lives not dominated by religion. But as you keep reading you notice that the overall arc of history is strongly shaped by confessional identities.

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South Asian Genotype Project, Spring 2019 update

It’s been a while since I updated the South Asian Genotype Project. Well, I updated almost everyone (‘projectmembers v2’ tab is one what you want). A few people had strangely formatted text files, so I’ll go add them tomorrow. Thanks to everyone who has submitted so far!

One of the main things that I’ve been curious about is undersampled groups. I finally got an Uttar Pradesh Kayastha in the data set (well, technically my second…but the first is a friend). I also got a submission of a Bengali Brahmin with origins in the west, and another in the east (in fact, from Comilla, which is where my own family is from). And, I got the submission of another West Bengali Kayastha.

Finally, I got another Maharashtra Kayastha.

If you click the image above you see some obvious things:

  • Bengali Brahmins don’t seem to be geographically structured. The eastern and western individuals are near each other on the PCA. Additionally, they are very close to Uttar Pradesh Pradesh Brahmins. Not the main Bangladesh cluster.
  • In contrast, the West Bengal Kayastha is positioned close to the Bangladeshis, though outside of that particular cluster.

In other words, to some extent Bengal’s landscape reflects both aspects of the South Asian genetic variation: it is strongly structured by caste, and, geography also plays a role. People from western Bengal have less East Asian ancestry and more affinity with peoples to the west on the Gangetic plain. But Bengali Brahmins are genetically entirely dissimilar from other Bengalis.

The dissimilar position of Kayastha groups across South Asia is in contrast to Brahmins. Though Brahmin groups in Bengal and South India seem to have mixed with local groups (they are always somewhat shifted to the regional substrate), overall their genetic character indicates shared common ancestry. In contrast, the different Kayastha groups seem much more likely to be a case of local populations who arose to fill a particular occupational niche that emerged with polities which required a bureaucratic class.