Social barriers to Indian public health & non-Aryan “invasions”

A reader points me to a talk given by David Reich at the Center for Human Genetic Research 2013 Retreat. One of the issues Reich brought up is old, but perhaps worth reemphasizing: due to endogamy many South Asians carry a higher load of recessive ailments. This is not due to recent inbreeding (which is barred by custom in many South Asian groups, which enforce kin-level exogamy), but long term genetic isolation. Over time even a moderate sized population can be affected by drift. This was one of the major points in the 2009 paper Reconstructing Indian History, but not one particularly emphasized in the press follow up. A major implication is that a relatively simple public health measure for South Asians would be to marry outside of their jati. The social or genetic distance need not be great. But one generation of outbreeding should “mask” many of the deleterious alleles. If this model is correct one should be able to track decreases in morbidity within the American South Asian population, where there are many inter-caste and inter-regional marriages (yes, this is between people of putative high status, but this doesn’t matter).

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We are Nature

There’s an interesting piece in Slate, The Great Schism in the Environmental Movement, which seems to be a distillation of trends which have been bubbling within the modern environmentalist movement for a generation now (I’ve read earlier manifestos in a similar vein). I can’t assess the magnitude of the shift, but here’s the top-line:

But that is a false construct that scientists and scholars have been demolishing the past few decades. Besides, there’s a growing scientific consensus that the contemporary human footprint—our cities, suburban sprawl, dams, agriculture, greenhouse gases, etc.—has so massively transformed the planet as to usher in a new geological epoch. It’s called the Anthropocene.

Modernist greens don’t dispute the ecological tumult associated with the Anthropocene. But this is the world as it is, they say, so we might as well reconcile the needs of people with the needs of nature. To this end, Kareiva advises conservationists to craft “a new vision of a planet in which nature—forests, wetlands, diverse species, and other ancient ecosystems—exists amid a wide variety of modern, human landscapes.”

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We don’t know why Ethiopians breathe easy

Most people are aware that altitude imposes constraints on individual performance and function. Much of this is flexible; athletes who train at high altitudes may gain a performance edge. But over the long term there are costs, just as there are with computers which are ‘overclocked.’ This is the point where you make the transition from physiology to evolution. Residence at high altitude entails strong selective pressures on populations. Over the past few years there has been a great deal of exploration of the genetics of long resident high altitude groups, the Tibetans, Peruvians, and Ethiopians.

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The origins of the Romani determined definitively

In many cases there are questions of a historical and ethnographic nature which are subject to controversy and debate. Scholarly arguments are laid out, and further dispute ensues. For decades progress seems fleeting, as one hypothesis is accepted, only to be subject to later revision. This sort of pattern gives succor to the most cynical and jaded of ‘Post Modern’ set, especially when the ‘discourse’ in question is in the domain of science.

But thankfully these debates can come to an end in some cases. So it is with the origins of the European Romani, better known as ‘Gypsies’ (though the Roma are the most well known of the Romani, other groups within Europe have different ethnonyms). Obviously many of the basic elements have long been there, but I think the most recent genetic work now establishes a level of closure. Taking a step back, what do we know?

1) The Romani language seems to be Indo-Aryan, with a likely affinity with the northwest group of Indo-Aryan languages

2) The Romani presence in Europe only dates to the past ~1,000 years, with an entry point in the Byzantine Empire

3) They are an admixture between an ancestral Indian element, and local populations

4) Their history of endogamy has resulted in a strong genetic drift effect

The two papers which seem to nail the coffin shut on these questions use somewhat different methodologies. One relies on Y chromosomal STRs (hypervariable repeat regions) to generate a paternal phylogeny. Focusing just on the paternal phylogeny allows for one to make very robust genealogical inferences. Additionally, the authors had a very large data set across India. Their goal was to ascertain the exact region of origin of the Romani before they left India. As noted in bullet #1 there is already some evidence from their language that this must be in northwest India. The second paper uses a SNP-chip; hundreds of thousands of autosomal markers. This has been done to death for other populations, so the method isn’t new. Rather, it is that it is now being applied to the Romani.

First, the Y chromosomal paper. The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations:

Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.

Two trees illustrate the results succinctly:

The bottom line:

- This particular Y chromosomal lineage which is highly diagnostic of South Asian origin in the Romani shows that the Romani seem to derive from the populations of northwest India

- Additionally, within these populations the Romani Y chromosomal lineages derive from the lower caste elements, the scheduled castes and scheduled tribes

But the above results don’t get directly at genome-wide admixture. The second paper does, using hundreds of thousands of markers to explore the Romani affinity to other populations. Reconstructing the Population History of European Romani from Genome-wide Data:

The Romani, the largest European minority group with approximately 11 million people…constitute a mosaic of languages, religions, and lifestyles while sharing a distinct social heritage. Linguistic…and genetic…studies have located the Romani origins in the Indian subcontinent. However, a genome-wide perspective on Romani origins and population substructure, as well as a detailed reconstruction of their demographic history, has yet to be provided. Our analyses based on genome-wide data from 13 Romani groups collected across Europe suggest that the Romani diaspora constitutes a single initial founder population that originated in north/northwestern India ∼1.5 thousand years ago (kya). Our results further indicate that after a rapid migration with moderate gene flow from the Near or Middle East, the European spread of the Romani people was via the Balkans starting ∼0.9 kya. The strong population substructure and high levels of homozygosity we found in the European Romani are in line with genetic isolation as well as differential gene flow in time and space with non-Romani Europeans. Overall, our genome-wide study sheds new light on the origins and demographic history of European Romani.

The plot to the left illustrates the relationship of the Romani to world-wide populations using multi-dimensional scaling, where genetic variation is decomposed into dimensions, and individuals are plotted on those dimensions. In short, the Romani exhibit a classic admixture cline pattern.That is, they are the products of a two-way admixture between populations which occupy distinct positions along a cline, and Romani individuals and populations are distributed along the cline in proportion to their admixture. One notable aspect is that the Romani are actually two clusters; one which manifests a strong ‘east’-'west’ distribution, and another which seems located purely within the European cluster. The latter seems to be the Welsh Romani, who in the neighbor-joining tree (see the supplements) fall on the same branch as European populations, as opposed to the other Romani, who form their own clade.

To drill down further you need to ascertain admixture with a model-based clustering algorithm. Ergo, ADMIXTURE. I’ve reedited the figure to illustrate the salient points. In particular, it is clear that the Roma populations except the Welsh have significant South Asian ancestry. The question is how much? To answer this question you need to know the source population in South Asia. A peculiar aspect of this plot is that the Romani have very little of the green ancestral component, which happens to be modal in the Middle East (not shown). This element happens to be highly enriched in many Pakistani populations, but not necessarily northwest Indian ones. Nevertheless, the issue that leaves me suspicious of this particular finding is that many of the European populations, in particular those groups (e.g., Balkans) which may have admixed with the Romani, have this element to extent not evident in one of their presumed ‘daughter’ populations. I wonder if perhaps the peculiarities of Romani inbreeding has skewed the allele frequency distribution so much that you get strangeness like this. I am not showing higher K’s because those break out with a Romani-cluster. Just like the Kalash-cluster this is to a great extent a feature of the long term endogamy of these communities. With high levels of drift the allele frequency of these groups moves into a very peculiar space in relation to their parental populations, but one must not become confused and assume that the Romani or Kalash are themselves appropriate independent clusters in the same way that Europeans or East Asians are.

Using various forms of admixture analysis the authors seem to conclude that the Balkan Romani are 30-50% South Asian. This seems in line with intuition. But that still leaves open the question of who those South Asians were. As I noted above the most thorough Y chromosomal data point to the lower caste elements of northwest India. What do the autosomes say?

I don’t want get into the technical details of how they tested the models, but it seems that one of the likely parental populations to the Romani had a close relationship to the Meghwal, a scheduled caste from northwest India. In other words, the autosome results align very well with the Y chromosomal inferences. Additionally, the models tested imply that the Romani likely left South Asian ~1,000 years before the present, which aligns well with what is known from the historical record (though this is a case where I put much more stock in the historical record than inferences from population genetic models; look at the intervals).

Finally, there is the question of inbreeding. One aspect of the Romani genome is jumps out you is that they have many long “runs-of-homozygosity” (ROH). This is totally expected, as decades of uniparental analyses suggested a great deal of population bottleneck events as the Romani spread throughout Europe. But the ROH patterns also unearth an interesting fact: some of the Balkan Romani clearly have recent European admixture, while the non-Balkan Romani had an initial period of admixture followed by endogamy. The latter scenario seems to resemble Askhenazi Jews, while the former would suggest that the boundary between Romani and non-Romani in the Balkans is more fluid than is sometimes portrayed.

So there we have it. The Romani derive from lower castes populations from the northwest Indian subcontinent who seem to have left ~1,000 years ago. Over time they admixed with local populations, and are now 50-70% non-South Asian, with some groups being ~90% European (e.g., Welsh Romani). And, they have a long history as an endogamous group, judging by their inbreeding.