Open Thread, 6/24/2018

I recently read John Keay’s Midnight’s Descendants: A History of South Asia since Partition. No particular reason. But I’ve read earlier books on the history of India and China and I sort of wanted to fill a hole in my knowledge. I would recommend it if you don’t know much about this period and place. It’s probably somewhat important in the future.

Thanks to all the readers of this weblog who have given iTunes ratings to my podcast. We’re almost to 100 ratings, so you won’t be hearing me go on and on about it.

Though speaking of the podcast, we’re going to talk to Ian Morris, author of War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, soon. So subscribe now.

Erdogan’s Election Win Gives Him Vastly Expanded Powers in Turkey.

The Trailer for The Man Who Unlocked the Universe Is a Gorgeous Mixture of Science and Action. This looks like a good complement to Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane.

It’s curious how many Central Asian warlords were patrons of culture. Mahmud of Ghazni, for example, supported Ferdowsi.

Just found out that Reihan has a new book out this fall, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders.

Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise.

Bangladesh’s Secular Bloggers: Risking Their Lives for Freedom. A lot of atheist podcasts aren’t really “edgy” anymore. The Secular Jihadists is an exception.

Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise.

The citizen scientist who finds killers from her couch.

Human demographic history has amplified the effects of background selection across the genome.

Most people have always thought human sacrifice was bad

A few days ago a minor controversy about the cultural context of human sacrifice in Mesoamerica cropped up. A writer at Science, wrote a piece, Feeding the gods: Hundreds of skulls reveal massive scale of human sacrifice in Aztec capital. The article was good. But it elicited some emotional responses from readers. As one sees in the earliest writings of the Spanish, the Aztec penchant for human sacrifice often results in a moralistic reaction.

The writer of the piece took to Twitter to disagree with the moralistic tone of many who read her article. It being Twitter, her original series of comments were easy to misinterpret or exaggerate, and she had to post a follow-up clarifying some issues. Below is a response to one of her original assertions.

Basically, I agree that our feelings about sacrifice today are irrelevant to understanding it. To understand human history and something scientific that relates to humans it is important to set aside feelings, at least for the moment. That being said, let me remind the reader that this is not the attitude of many science writers when a story has a “social justice” angle. We all know if a science article has a social hook which appeals to emotional or moralistic impulses in the readership, it will probably be injected into it for purposes of clicks and adding an extra layer of meaning and relevance. For various reasons, Aztec human sacrifice is better presented in a dispassionate manner, as Mesoamerican human sacrifice doesn’t lend itself easily to a standard social justice narrative (i.e., the “villains” are not white).

The Aztec Empire, or the Triple Alliance if you prefer, was built on brutality. From what we can tell it was an analog in the New World to what the Assyrian Empire had been in Eurasian antiquity: a polity bound together through brutal coercion.

Here is one tale from Aztec history that is well known:

In 1323, they asked the new ruler of Culhuacan, Achicometl, for his daughter, in order to make her the goddess Yaocihuatl. Unknown to the king, the Mexica actually planned to sacrifice her. The Mexica believed that by doing this the princess would join the gods as a deity. As the story goes, during a festival dinner, a priest came out wearing her flayed skin as part of the ritual. Upon seeing this, the king and the people of Culhuacan were horrified and expelled the Mexica.

Note that the legend is recounted whereby the other native peoples of Mexico were horrified by the Aztec behavior. This highlights the reality that human sacrifice seems to elicit negative reactions generally. It’s not arbitrary. In Carthage Must Be Destroyed the author spends a great deal of time exploring the reality of child sacrifice in that society. A practice in decline in the Phoenician homeland, for some reason it reemerged in the western Mediterranean much more vigorously. Classical observers found the practice grotesque, and their descriptions of Carthaginian child sacrifice were suspected by many scholars as being scurrilous. Fortunately, or unfortunately, the truth has been established by the discovery of bones of children in urns. The key point to note is that ancient observers were just as judgemental as modern people.

Though human sacrifice persisted in some form in many antique societies, it is clear that what was once a common occurrence in the Bronze Age world became rarer with time, until it was no longer socially or ethically acceptable. Researchers in the field of cultural evolution have explored the emergence and decline of human sacrifice. Though there are no current definitive conclusions, it seems likely that it crops up in societies which have transitioned toward being highly inegalitarian. But, it declines again in societies which scale large enough to the point where more abstract ideological and political systems must bind groups of people together. The Classical Western world, India, and China, all seem to be marked by a recollection of normative human sacrifice (e.g., Iphigenia), and a turn away from it.

The inequality aspect is important. Though some people willingly gave themselves as human sacrifices, there are recurrent themes of low-status individuals within the group (e.g., slaves) or outsiders (prisoners of war) being given to the gods. There is debate as to the nature of the Aztec “flower wars”, but one traditional explanation is that they were driven by the need for victims of human sacrifices.

In other words, Aztec human sacrifice can be contextualized in a generalized framework. But that is not where the writer of the original piece went on the Twitter thread. Rather, she seems to have bracketed the practice by modern social and political considerations, “centuries of colonial oppression and destruction.” To be frank, it is a strongly Eurocentric narrative where everything before European colonialism is viewed as a prologue to the true story. The only story that matters. The context of Aztec human sacrifice that matters to many people steeped in this way of thinking is what the Spaniards did to the native peoples of the New World after the conquest of the Aztec Empire. Like ethical tachyons the present blasts back into the past, and reshapes our whole perception of it in current terms. The Aztec tendencies toward brutality, oppression and grotesque customs such as human sacrifice, are inconvenient to this framework.

The cultural conditioning isn’t that of a Western individual who lives in a consumer society at the tail end of a two-century path of growth, domination, and maturation. Rather, the cultural conditioning is of a whole class of intellectuals steeped in understanding all social and historical relations as but mirrors of the one which defined the 19th and 20th century. This viewpoint also asserts that this period, these people, are sui generis. It is profoundly Eurocentric to the bones.

To me when considering the ethical and historical frame of human sacrifice two facts jump out to me. First, it’s an empirical fact that at certain levels of social complexity human sacrifice seems to emerge, and at later levels of social complexity tends to be dampened and abolished.  The reason that it tends to be dampened and abolished is probably the reason that the Spanish found it easy to obtain native allies against the Aztec Empire: human sacrifice is a costly and brutal way to foster social cohesion. Across societies, there has been a general tendency to abandon the practice and create psychologically satisfying substitutes which don’t have the bloody downsides.

The second aspect is more primal: humans don’t like to die. It is true that humans will sacrifice themselves, or in the case of Carthaginian nobles, their own children, in exigent circumstances. Human nature exists, and many aspects are universal. The abhorrence of human sacrifice doesn’t emerge out of particular and unique elements of Western colonial culture,  it has cropped up in many societies, and I would suggest that the shoe is on the other foot here: those who argue for human sacrifice have to make the argument for it is necessary. And that is why so often humans who are sacrificed are those who can least choose to give their own lives. Slaves, children, prisoners, and criminals.

Unfortunately, the Western colonial narrative looms so large for many moderns that other cultures and other histories are erased in all their complexity. They gain depth and richness only as handmaids to the deconstruction and critique of the Western colonial narrative.

Beware scientists laundering their credentials

Recently Vox had a really bad piece up, How a pseudopenis-packing hyena smashes the patriarchy’s assumptions: Lessons from female spotted hyenas for the #MeToo era. The first thing you’ll notice is the crass inverse naturalistic fallacy that seems to be operating here. That is, you think of a state you’d find desirable (in this case, “matriarchy”), and then look at nature to find an illustrative instance to draw some lessons. I don’t always oppose this, but the people sharing the Vox piece are also the sort who’d find it “problematic” if others did the same (e.g., lobsters).

Reading the piece, I thought back to the fact that mammals as a whole tend to be rather polygynous, with males investing far less in their offspring than, for example, birds. This is why genomic imprinting and sexual genetic conflict is a thing for our broad class of tetrapods. I happen to believe humans are rather different in nature because of our evolutionary history from our mammalian cousins. Also, cultural forces are important to us. Our social complexity is hard to understand without acknowledging our plasticity, even though that plasticity is bounded by our dispositions.

But Katie Herzog in The Stranger reports that researchers who study hyena behavior are angry about the Vox piece because it gets the science all wrong.

This is entirely expected. The author is “a Ph.D. student in microbiology and immunobiology at Harvard University.” Someone who has this particular training can’t be expected to be up-to-date on the latest literature in zoology and behavioral ecology, let alone organismic knowledge about a particular species (usually, one might make an exception if she was studying the microbiome of hyenas!).

Science is very specialized. I can’t speak for others, but just because someone is a “biologist” doesn’t mean that they really know much about biology in a broad sense. Most biologists outside of population genetics have somewhat woolly intuitions about population genetics. I know the difference between a dendrite and an axon, but I don’t know much about neuroscience.

When a scientist opines on a field in which they have some distant relationship to, such as a microbiologist offering their thoughts on the relevance of the evolutionary and behavioral insights from hyenas, be very careful, because whether they know it or not they are laundering their authority from one discipline into another where it does not apply.  A few years ago a scientist on Twitter with a background in ecology was explaining to an undergraduate that “epigenetics has rewritten the genetics textbooks.” This was just flat out wrong.

Many ecologists have as much understanding of genetics as a layperson, and many geneticists have as much understanding of ecology as a layperson. Yes, most ecologists have probably taken a genetics class as an undergraduate, but they don’t know the literature, nor do they think much about genetics day to day. Similarly, most geneticists have probably taken an ecology class as an undergraduate, but they don’t know the literature, nor do they think much about ecology day to day. And really, classes aren’t worth much. I’ve taken introductory and advanced ecology courses on the undergraduate level, and graduate level ecology courses. I still don’t know much about ecology.

And these specializations are unfortunately quite narrow. I don’t study translational mechanisms in yeast. Talk to me about population genetic inference, especially in the context of diploid organisms which reproduce sexually.

It’s unfortunate that many science journalists are generalists who have a difficult time navigating specialized disciplines. But at least science journalists are not going to present themselves as experts. They are conscious of their limitations. I wish many people with a scientific background were too.

The fault in our parameters

Of the books I own, Elements of Evolutionary Genetics is one I consult frequently because of its range and comprehensiveness. The authors, Brian Charlesworth and Deborah Charlesworth’s encyclopedic knowledge of the literature. To truly understand the evolutionary process in all its texture and nuance it is important to absorb a fair amount of theory, and Elements of Evolutionary Genetics does do that (though it’s not as abstruse as something like An Introduction to Population Genetics Theory).

When I see a paper by one of the Charlesworths, I try to read it. Not because I have a love of Drosophila or Daphnia, but because to develop strong population-genetics intuitions it always helps to stand on the shoulders of giants. So with that, I pass on this preprint, Mutational load, inbreeding depression and heterosis in subdivided populations:

This paper examines the extent to which empirical estimates of inbreeding depression and inter-population heterosis in subdivided populations, as well as the effects of local population size on mean fitness, can be explained in terms of estimates of mutation rates, and the distribution of selection coefficients against deleterious mutations provided by population genomics data. Using results from population genetics models, numerical predictions of the genetic load, inbreeding depression and heterosis were obtained for a broad range of selection coefficients and mutation rates. The models allowed for the possibility of very high mutation rates per nucleotide site, as is sometimes observed for epiallelic mutations. There was fairly good quantitative agreement between the theoretical predictions and empirical estimates of heterosis and the effects of population size on genetic load, on the assumption that the deleterious mutation rate per individual per generation is approximately one, but there was less good agreement for inbreeding depression. Weak selection, of the order of magnitude suggested by population genomic analyses, is required to explain the observed patterns. Possible caveats concerning the applicability of the models are discussed.

Open Thread, 6/20/2018

I try to limit the shilling, but since readers of this weblog know what this means: Helix has a sale on kits until the end of the month. The three Insitome products can be purchased for app-only cost ($29.99) as an entrance into the ecosystem. In other words, for $29.99 you can get millions of markers in your exome sequenced, as well as some positions in the rest of your genome. Helix keeps the data, but there will be no kit cost if you see a future app that you want to purchase.

* Regional Ancestry
* Metabolism
* Neanderthal

If you are not subscribed to my total feed, you might not know that my review of She Has Her Mother’s Laugh went up at National Review Online. One thing that I’ve reiterated: it’s a very big book. A single review can’t really cover many aspects of what Carl touches on, and unfortunately even during the podcast I didn’t get to chimeras.

We’re almost at 100 reviews on iTunes on 10 on Sticher. I’ll stop bugging when we reach those milestones.

It’s been obvious to me that more and more people are protecting their Twitter accounts. Instead of a conversation the platform is about snooping on blow-ups and controversies.

In rapidly adapting asexuals, the orientation of G can reflect selection rather than functional constraints. Evolutionary, population, and quantitative genetics have been long-term interests of mine, so I love stuff like this. Adding a little genomics would be even better.

The most important study of the Mediterranean diet has been retracted and The collapse of a $40 million nutrition science crusade. Basically, it seems you should just eat what you want. Probably avoid processed food and trans-fats.

Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa. Centromeres are crazy.

Harvard Office of Institutional Research on Discrimination Against Asian-American Applicants. I will blog about this at some point…and I’ve been making semi-serious/jokey tweets. But people are probably not clear on my “position.” My main irritation about Harvard is the extent of the doublethink that they get away with. Drew Gilpin Faust’s pablum about inclusion and diversity being central values at Harvard is a classic “Shaggy defense”. Faust helms a finishing school for the overclass, and as such accepts the necessity of discrimination when it comes to anointing future overlords. Some hypocrisy is necessary for the ruling caste, but the juxtaposition between “neoliberal” reality of what Harvard is, and the “progressive” rhetoric of it presents to the gullible and ignorant public, is starting to become indecent.

Speaking of overclass, Tim Draper is a third generation member of the capital class, and still defends Elizabeth Holmes.

With tantalizing early results, Sarepta’s gene therapy for Duchenne raises hopes for ‘real change’.

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy.

Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors.

Population Genomics blog. The author is Chad Rohlfsen.

Re-identification of genomic data using long range familial searches.

Inference of species histories in the presence of gene flow.

How Much Does Education Improve Intelligence? A Meta-Analysis. It’s probably time to start reviewing stuff on psychometrics. The Ian Deary book is pretty good.

Why the world before 1450 matters

It is no surprise that I am not excited by the proposal to focus AP History in the United States on the period after 1450. Overall I agree with many of the comments made in T. Greer’s tweet thread. Though I have a concurrent opinion with many history teachers who oppose the change, my opposition is for different reasons. To be frank I don’t care about “showing our black and brown and native students that their histories matter—that their histories don’t start at slavery”.

Though my leanings are toward positivism, that is, I think history is an empirical discipline, even with a potential scientific scaffold, I understand that with finite time and resources your choices are conditional on your viewpoint. When I grew up in the American North the Civil War was taught with facts, but the arrangement and emphasis of those facts were not flattering to the Confederacy. I think objectively this isn’t hard from a modern perspective. But, the fact that some Union regiments were raised in the area where I grew up is certainly relevant

But this old-fashioned biased perspective still gave the nod to the importance of objectivity in some deep way. And though I was an immigrant who was routinely asked “where I was really from”, there was also an understanding that I needed to know this particular Union history, because it was the history which I inherited.  It was our history, which set the objective preconditions of the world in which we lived. The sharply critical cast of modern history teaching has its roots in this fundamental understanding. History may often have had propagandistic overtones, in that it inculcated, but the facts still mattered, and sometimes they were at counter-purposes to the narrative (e.g., the Abolitionists were clearly in the minority even in the North; good history teachers didn’t lie about this).

The idea that one’s history, “their” history, is rooted in descent is common sense. But it’s also an idea which brings together frog-Nazis and Critical Race Theorists. Because of the closeness of the past few hundred years, the histories will be contested on the grounds of ideology. All narratives are contested, but emotion and effort vary in the contestation. The way to push through the contestation is to flood the zone with facts, with robust models. But this isn’t feasible for high school students, many of whom simply want to obtain a good AP score so they never have to take a history course again.

Rather, I think history before 1450 is critical not because it is relevant to a diverse student body due to genealogical affinity, but because common human universal themes are easier to perceive in more distant peoples whose actions and choices don’t have as strong a direct connection to the lived present. Consider the Classical Greeks. It is reasonable to assert that the genesis of the West as we understand it has to be traced at least in part to the Ionian flowering of the 5th century, and to Athens in particular. But it is not reasonable to make Classical Greeks a stand-in for modern Europeans, whose Christianity (at a minimum culturally) would be alien, and whose origins are from peoples who the ancient Greeks would term barbarians.

The Classical Greeks are profoundly alien to moderns, rupturing excessive identity, though that didn’t stop 19th century Romantics! Athenian democracy is very different from the modern democracies, with its participatory character and the large class of excluded residents. But Athenian democracy, and Classical Greece more generally, also highlight deep universal aspects of the human condition. It speaks more forcefully to many students because the mental clutter of the past few centuries, and their ideological baggage, are removed from the picture.

Additionally, cross-cultural comparisons of similarities and differences in the ancient and medieval world are useful because they are less overshadowed by the “Great Divergence”, and the post-1800 European breakout. While the world before Classical Greece was one of strange and isolated polities in a vast barbarous world, the world after 1450 points strongly in our mind’s eye to a state where Europe occludes our entire view. The problem is not slavery, because the age of European supremacy saw the abolition of slavery.

Obviously, even the period before 1450 can be fraught. Consider the rise of Islam, and the crystallization of the West as Christian Europe in tension with the rising civilization to the south, and the receding pagan wilderness to the north and east. There are plenty of opportunities for debate, disagreement, and ideological axes to grind. But contrast the same argument around the Arab-Israeli conflict or Sykes-Picot Agreement.  The fact is that pushing the past further back into the past muddles modern preoccupations. And that’s a feature, not a bug.

Why the Y chromosome is coming back


Last week Spencer and I talked about chromosomes and their sociological import on The Insight. It was a pretty popular episode, but then again, my post on the genetics of Genghis Khan is literally my most popular piece of writing of all time which wasn’t distributed in a non-blog channel (hundreds of thousands of people have read it). Thanks to everyone who left a review on iTunes and Stitcher (well, a good review). We’re getting close to my goal of 100 reviews on iTunes and 10 on Stitcher so that I won’t pester you about it.

Of course the reality is that the heyday of  chromosomal population genetic studies was arguably about 15 years ago, when Spencer wrote The Journey of Man. I have personally constructed Y phylogenies before…but as you know from reading this weblog, I tend to look at genome-wide autosomal studies. There is a reason that why Who We Are and How We Got Here focuses on autosomal data.

All that being said, Y (and mtDNA) still have an important role to play in understanding the past: sociological dynamics. The podcast was mostly focused on star phylogenies, whether it be the Genghis Khan haplotype, or the dominant lineages of R1a and R1b. Strong reproductive skew does have genome-wide effects, but unless it’s polygyny as extreme as an elephant seal’s those effects are going to be more subtle than what you see in the Y and mtDNA.

Submitted for your approval, two recent preprints on bioRxiv: The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola and Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia. The future is going to be in understanding sexual dynamics and culture.

Burmese are a bit Bengali

About ten years ago I read the book The River of Lost Footsteps: Histories of Burma. Though I have read books where Burma figures prominently (e.g., Strange Parallels), this is the only history of Burma I have read. The author is Burmese, and provide something much more than a travelogue, as might have been the case if he was of Western background. By chance over the past month or so I’ve been in contact with the author, who made a few inquiries as to the genetics of his own family (he came with genotypes in hand). But this brought us to the issue of the genetics of the Burmese people, and their position in the historical-genetic landscape.

The author of The River of Lost Footsteps reminded me of something that’s curious about Southeast Asia: its Indic influences tend to be from the south of the subcontinent. In particular, the native scripts derive from a South Indian parent. Could genetics confirm this connection as well? Also, could genetics give some insights as to the timing of admixture/gene-flow?

In theory, yes.

I had a lot of Southeast Asian datasets to play with, and did a lot of pruning to remove outliers (e.g., people with obvious recent Chinese ancestry). First, comparing them to Bangladeshis it seems that even without local ancestry tract analysis that Burmese and Malays have more varied, and so likely recent, exogenous ancestry than Bangladeshis. At least this is evidence on the PCA plot, where these two groups exhibit strong admixture clines toward South Asians.

But what about the question of Southeast Asian affinities? This needs deeper analysis. Three-population tests, which measure admixture with outgroups when compared to a dyad of populations which are modeled as a clade, can be informative.

Outgroup Pop1 Pop2 f3 z
Bangladeshi Telugu Cambodians -0.00183999 -46.3322
Bangladeshi Telugu Han -0.00220121 -46.046
Burma Telugu Han -0.00406071 -51.0018
Burma Han Bangladeshi -0.00348186 -49.1398
Burma Han Punjabi_ANI_2 -0.00418193 -47.2351
Cambodians Telugu Viet -0.00126923 -16.91
Cambodians Punjabi_ANI_2 Viet -0.00129881 -15.6039
Cambodians Bangladeshi Viet -0.000970022 -14.5642
Malay Igorot Telugu -0.00249795 -18.758
Malay Igorot Bangladeshi -0.00223454 -18.5212
Malay Igorot Punjabi_ANI_2 -0.00250732 -18.3027
Malay Igorot Cambodians -0.00107817 -16.6214
Viet Han Cambodians -0.000569337 -13.1139

Bangladeshis show strong signatures with both Cambodians and Han. This is in accordance with earlier analysis which suggests Austro-Asiatic and Tibeto-Burman contributions to the “East Asian” element of Bengali ancestry. The Burmese always have Han ancestry, with a South Asian donor as well. This aligns with other PCA analysis which shows the Burmese samples skewed toward Han Chinese. Burma is a compound of different ethnic groups. Some are Austro-Asiatic. The Bamar, the core “Burman” group, have some affinities to Tibetans. And the Shan are a Thai people who are relatively late arrivals.

Cambodians have a weaker admixture signature and are paired with a South Asian group and their geographic neighbors the Vietnamese. The Malays are similar to Cambodians but have the Igorot  people from the Philippines as one of their donors. And finally, not surprisingly the Vietnamese show some mixture between Han-like and Cambodian-like ancestors.

Further PCA analysis shows that while Cambodians and Malays tend to skew somewhat neutrally to South Asians (the recent Indian migration to Malaysia is mostly Tamil), the Burmese are shifted  toward Bangladeshis:

Click to enlarge

Finally, I ran some admixture analyses.

First, I partitioned the samples with an unsupervised set of runs (K = 4 and K = 5). In this way I obtained reified reference groups as follows:

“Austronesians” (Igorot tribesmen from the Philippines)
“Austro-Asiatic” (a subset of Cambodians with the least exogeneous admixture)
“North Indians” (Punjabis)
“South Indians” (A subset of middle-caste Telugus highest on the modal element in South Indians)
“Han” (a proxy for “northern” East Asian)

The results are mostly as you’d expect. In line with three-population tests, the Vietnamese are Han and Austro-Asiatic. More of the former than latter. There is a minor Austronesian component. Notice there is no South Asian ancestry in this group.

In contrast, Cambodians have low levels of both North and South Indian. These out sample Cambodians are still highly modal for Austro-Asiatic though.

Malays are more Austro-Asiatic than Austronesian, which might surprise. But the Igorot samples are highly drifted and distinct. I think these runs are underestimating Austronesian in the Malays. Notice that some of the Malays have South Asian ancestry, but a substantial number do not. This large range in admixture is what you see in PCA as well. I think this strongly points to the fact that Malays have been receiving gene-flow from India recently, as it is not a well mixed into the population.

The Bangladeshi outgroup is mostly a mix of North and South Indian, with a slight bias toward the latter. No surprise. As I suggested earlier you can see that the Bangladeshi samples are hard to model as just a mix of Burmese with South Asians. The Austro-Asiatic component is higher in them than the Burmese. This could be because Burma had recent waves of northern migration (true), and, eastern India prior to the Indo-Aryan expansion was mostly inhabited by Austro-Asiatic Munda (probably true). That being said, the earlier analysis suggested that the Munda cannot be the sole source of East Asian ancestry in Bengalis.

Finally, every single Burmese sample has South Asian ancestry. Much higher than Cambodians. And, there is variance.  I think that leads us to the likely conclusion that Burma has been subject to continuous gene-flow as well as recent pulses of admixture from South Asia. The variation in South Asian ancestry in the Burmese is greater than East Asian ancestry in Bengalis. I believe this is due to more recent admixture in Burmese due to British colonial Indian settlement in that country.

The cultural and historical context of this discussion is the nature of South Asian, Indic, influence, on Southeast Asia. One can not deny that there has been some gene-flow between Southeast Asia and South Asia. In prehistoric times it seems that Austro-Asiatic languages moved from mainland Southeast Asia to India. More recently there is historically attested, and genetically confirmed, instances of colonial Indian migration. But, the evidence from Cambodia suggests that this is likely also ancient, as unlike Malaysia or Burma, Cambodia did not have any major flow of Indian migrants during the colonial period. One could posit that perhaps the Cambodian Indian affinity is a function of “Ancestral South Indian.” But the Cambodians are not skewed toward ASI-enriched groups in particular. And, I know for a fact that appreciable frequencies of R1a1a exist within the male Khmer population (this lineage is common in South Asia, especially the north and upper castes).

As far as Burma goes, I think an older period of South Indian cultural influence, and some gene-flow seems likely. But, with the expansion of Bengali settlement to the east over the past 2,000 years, more recent South Asian ancestry is probably enriched for that ethnolinguistic group.

I’m going to try and follow-up with some ancestry tract analysis….

The lost 50,000 years of non-African humanity

The figure above is from Efficiently inferring the demographic history of many populations with allele count data. This preprint came out a few months ago, but I was prompted to revisit it after reading Spectrum of Neandertal introgression across modern-day humans indicates multiple episodes of human-Neandertal interbreeding.

The latter paper indicates that there were multiple waves to Neanderthal admixture into both Europeans and East Asians. The motivation to do the analysis is that East Asians are about ~12 percent more Neanderthal than Europeans. The authors don’t reject the idea that there was ‘dilution’ of Neanderthal through selection and especially admixture with a “Basal Eurasian” group which didn’t have Neanderthal ancestry. I don’t want to get into the details of the results except for one thing: the preprint confirms a consistent finding over the past eight years that the Neanderthal contribution to the modern human genome is from a single population.

Perhaps it was a small population. Or perhaps it was a large population that had gone through a bottleneck and was genetically not very differentiated. But unlike Denisovans it seems that it was a particular Neanderthal lineage that interacted with modern humans.

Moving back to the “Basal Eurasians,” notice some details of the schematic above. The divergence of Basal Eurasians from other non-Africans was ~80,000 years ago, across an interval of 70 to 100 thousand years ago. The admixture of Basal Eurasians into the proto-LBK population occurred ~30,000 years ago, across an interval of 11 to 41 thousand years ago. Ancient DNA from North Africa indicates that Basal Eurasians were already well admixed well before 11 thousand years ago.

The other dates make sense. 50,000 years for Europeans-Han Chinese, 96,000 years for Mbuti-Eurasians, and 696,000 years for Neanderthal-modern humans.

Ancient modern humans were highly structured. We know this from within Africa. But it seems clear that modern humans who had crossed over the other side of the Sahara also exhibited the same tendency. Basal Eurasians did not mix with Neanderthal populations. I suspect that that might be due to the fact that they were in Northeast Africa. At some point in the Pleistocene a mixing event occurred. This may have been precipitated by drier conditions and human retreat into only a few habitable areas, and the original Basal Eurasian populations may have mixed into other Near Eastern groups, which were part of the broader Neanderthal-mixed populations.

No steppe ancestry in the the Rakhigarhi samples = non sequitur

Harappan site of Rakhigarhi: DNA study finds no Central Asian trace, junks Aryan invasion theory:

The much-awaited DNA study of the skeletal remains found at the Harappan site of Rakhigarhi, Haryana, shows no Central Asian trace, indicating the Aryan invasion theory was flawed and Vedic evolution was through indigenous people.

“The Rakhigarhi human DNA clearly shows a predominant local element — the mitochondrial DNA is very strong in it. There is some minor foreign element which shows some mixing up with a foreign population, but the DNA is clearly local,” Shinde told ET. He went on to add: “This indicates quite clearly, through archeological data, that the Vedic era that followed was a fully indigenous period with some external contact.”

I haven’t heard anything definitive, but this is what I have heard: that the genetics they could analyze indicates continuity, but none of the steppe element ubiquitous in modern North India (and that there was contamination in the Korean lab). The Rakhigarhi samples date to 2500 to 2250 BC last I checked. That means they shouldn’t have any steppe ancestry if the model of the relatively late demographic impact of Indo-Aryans after 2000 BC is correct.

Basically, the whole article is kind of a non sequitur. I do understand that many archaeologists think there was continuity culturally. And there could have been. But taking into account the genetics of the modern region of India where Rakhigarhi is located, there was a major demographic perturbation after 2250 BC.