Razib Khan One-stop-shopping for all of my content

July 31, 2018

Documentary on the arrival of R1a1a-Z93 to South Asia (scions of the all-father!)

Filed under: Humor — Razib Khan @ 12:17 am

July 30, 2018

Ancient India, archaeology, etc.

Filed under: ancient india,Prehistory — Razib Khan @ 11:43 pm

I think I have asked before, but I’m soliciting suggestions about a book on Indian prehistory, with a focus on the period between 10 and 2 thousand years ago. India: The Ancient Past: A History of the Indian Subcontinent from c. 7000 BCE to CE 1200 looks decent, but I don’t have an ability to evaluate this stuff.

The reason is pretty simple. I’ve been asked to write a book chapter on the genetics of India. The draft is written, and I think we’re 80-90% done with the genetic “big picture.” The real work is going to be in synthesizing with archaeology. To be entirely frank I’m not sure how open Indian archaeologists are going to be to the new genetics, which is not stopping at any time in the near future. So I think perhaps I should see what I can snap together myself.

Anyway, suggestions appreciated. Though keep in mind that I don’t know much archaeology and don’t care that much about ancient village plans….

Open Thread

Filed under: Open Thread — Razib Khan @ 11:00 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

Bubba has the babies

Filed under: Culture,Fertility,GSS — Razib Khan @ 10:32 pm

Today Colin Woodward, author of American Nations: A History of the Eleven Rival Regional Cultures of North America, has an op-ed up, The Maps That Show That City vs. Country Is Not Our Political Fault Line: The key difference is among regional cultures tracing back to the nation’s colonization. Woodward’s thesis is basically that the modern shape of American cultural and political conflict has deep structural roots in American history. This is the same argument that David Hackett Fischer makes in Albion’s Seed: Four British Folkways in America, and Kevin Phillips more broadly about the Anglo-world in The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America. These perspectives are useful because there is a tendency in modern American discussion to reduce the sum totality of the dynamic to the white supremacist order, as opposed to the “rising tides of color.” There is an area where the cult-of-Pepe and the identity Left agree descriptively (they just flip the good guys and the bad guys).

There is some of this in the Ezra Klein Vox piece, White threat in a browning America. There are the whites. And there are the non-whites. And never the twain shall meet.

On a side note, Klein’s reliance on social psychological research about white racial anxiety being elicited by priming or information which makes non-whites salient should be critiqued more thoroughly. I suspect most of us find the argument intuitively believable, but the past five years of the replication crisis in psychology, where social psychology was ground-zero, should really make us put our guards up about evidentiary claims which support views we already have a bias toward accepting.

In any case, Klein cites research which shows that non-Hispanic whites are now less than 50% of the births in this country. Rather than arguing about the future of racial identification, I was curious about which whites were giving birth. The problem with raw average total fertility rates is that they mask underlying variance. For example, in Britain the majority of Jews are non-observant, but the majority of Jews under the age of five are from observant families. This is a function of the extremely low fertility of the non-observant majority, and the very high fertility of observant Jews in Britain.

The reason I bring this up is that the different subcultures of the United States have different fertility rates. David Hacket Fischer posits four major Anglo-American streams which date to before the Revolutionary War: New England Yankees, Tidewater and lowland Southerners, Scots-Irish highlanders, and the diverse polyglot Mid-Atlantic region, from Quakers to Dutch. Woodward and others have a somewhat different taxonomy, but the broad sketch aligns.

The curious fact is that up between the 1640s and 1840s New England Yankees were the most fecund of the American Anglo-cultures. The fertility of New England was such that the region began to colonize parts of the United States which had heretofore been dominated by other groups. The eastern half of Long Island was taken over by New Englanders, and they became prominent in New York’s merchant class (there was also a Yankee migration into the Canadian Atlantic provinces). New England farmers swept past the Dutch dominated lower Hudson Valley and overwhelmed the rest of upstate New York, creating a cultural fission that persisted up to the Civil War between the pro-Southern city of New York and the fiercely Republican upstate areas.

In contrast, the population growth rate in the South was depressed compared to the North. Much of this probably can be accounted for by endemic disease.

Things are different now.

The CDC has data on total births by race and ethnic identity by state. I pulled the data and plotted them. The correlation between the number of births and the number of people in the states by race and ethnicity were very high (0.98 and such). Also, I removed about the bottom five states in total population. The data are from ACS sample surveys, and it is pretty clear that small sample sizes are a problem in some of the cross-tabs/states.

In any case,

1) everyone seems to have lower fertility in California
2) Texas is good for whites and Hispanics in terms of having children
3) blacks have very high relative fertility in Florida

Yes, you can see Utah has elevated fertility. No surprise there. Here are the ten states in my data with the highest number of white births to their white population from top to bottom:

Utah
Hawaii
Nebraska
Kansas
Idaho
Louisiana
Kentucky
Oklahoma
Missouri
Iowa
Indiana

Here are the states with a relatively low number of white births to total white population (Connecticut has the lowest number of white births to white population):

Connecticut
Rhode Island
Massachusetts
New Hampshire
Florida
California
New Jersey
Nevada
New Mexico
Arizona
Maine

California is expensive. Florida and Arizona are filled with old white people. Many of the rest are Yankee.

The General Social Survey allows me to look at white ethnicities. I wanted to look at the number of children of various white ethnicities. I limited the sample to Protestants and Catholics.

Here are the results:

In the early 20th century Nordicists like Madison Grant were worried about the fact that Southern and Eastern European ethnics were going to overwhelm the Nordic stock of this country. But take a look at Italian and Polish fertility. People in urban areas have fewer children, and presumably white ethnics who remained identified by their ancestral heritage are disproportionately urban. When the Irish are split up by religion, Catholics tend to be more childless, and also have a minority with large families. This is probably tracking the intense secularization of white Catholics over the last generation, but the persistence of a traditionalist minority. Protestant Irish, who are probably often Scots-Irish, are similar to the other British Americans.

Finally, the ideological differences are really striking but unsurprising:

Left-liberal dominance of cultural institutions such as the media and academia are essential in part because it allows them to generate defections from people raised conservative. They can’t maintain their numbers through “natural increase” alone.

We’ll see what 2050 is life. I hope to be alive. But I think we’ll all be surprised in some ways by some of the defections and realignments. Michael Dukakis won West Virginia in 1988.

Open Thread

Filed under: Open Thread — Razib Khan @ 9:14 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

The HGDP in the post-ascertainment era

Filed under: HGDP,Human Population Genetics — Razib Khan @ 6:45 pm

In the 1990s there was a huge debate around the “Human Genome Diversity Project” (HGDP). By the HGDP I don’t mean what you probably know as the HGDP panel, but a more ambitious attempt to genotype tens of thousands of individuals across the world. In the end activists “won”, and the grand plans came to naught. If you want to read about it, The Human Genome Diversity Project: An Ethnography of Scientific Practice has a scholarly viewpoint, though you can also just ask someone who was involved with the human population genetics community in the 1990s (this not a large set of scholars).

Ultimately the HGDP became the samples from L. L. Cavalli-Sforza’s dataset which you read about in The History and Geography of Human Genes. This is what drives the HGDP Browser. It’s also the data set at the heart of papers like Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Here is the abstract:

Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.

These SNPs though were ascertained on European populations. That is, the genetic variation tended to be genetic variation found in Europe. This is a problem, and one reason that the Human Origins Array was developed. The ascertainment problem was really obvious when researchers were looking at Khoisan genomes, and noticed how much variation they had that wasn’t being captured on SNP-arrays.

Today, we’ve finally moving beyond the era where ascertainment is so much of an issue. At the SMBE meeting earlier this month Anders Bergstrom presented results from the HGDP using whole-genome analysis. When you look at the whole genome, you obviate the problem with selecting a biased subset of the variation. You can look at all the variation, or vary the variation you want to look at.

Bergstrom & company will have a paper on the whole-genome analysis of the HGDP in the near future. I assume it will be somewhat like the 1000 Genomes paper, but I bet you the SNP count will be higher, because they have Khoisan in their samples (along with Mbuti, etc.). Anders shared with me some of the preliminary data that the Sanger Institute has generated.

Below the fold I plotted a PCA of the HGDP data. First, the classic SNP-chip data. Second, SNPs pulled out of the WGS which are very high quality calls (though they may still have wrong calls), but have a minor allele frequency of at least 1% (~1.5 million). You immediately notice the Eurasian compression along PC 1. Finally, using ~15 million SNPs that had no missingness in the data, you see you PC 2 being defined by San Bushmen vs. non-San-Bushmen, while Mbuti Pygmies along with Biaka clearly are the furthest along PC 1 excepting the San. There are 6 San Bushmen in the data. If there are SNPs which are very distinct to this group, and not polymorphic in other populations, then my 1% cut-off would actually remove that variation.

It’s an interesting world we live in, thanks to research groups like the Sanger Institute, Estonian Biocentre, and the 1000 Genomes Project, as well as tools such as PLINK. Analysis that took decades in the 20th century can now be whipped out in a matter of hours. Better analyses in fact.

650,000 SNPs (European ascertained)

 

1.5 million SNPs, 1% or more minor allele frequency

15 million SNPs, 0 “no calls”

 

July 29, 2018

Open Thread, 07/29/2018

Filed under: Open Thread — Razib Khan @ 10:38 pm

Reading Imperial China 900–1800 it is interesting how the Khitan seem to have chosen to develop a written script that was not based on that of the Chinese, to resist the cultural assimilation that would have inevitably occurred. Through that choice they reduced their short-term efficiency, but probably enabled their long-term persistence as a people. Certainly the Khitan seem to have remained less Sinicized on the even of Jurchen conquest than the Jurchen were on the eve of the Mongol conquest (though the Jurchen conquered North China, so they had a bigger demographic imbalance). That the Khitan continued nomadic ways is clear as they managed to reassemble to the west and fond the Qara-Khitai. The Manchu descendants of the Jurchen who conquered China seem to have been thoroughly Sinicized after a few centuries as well.

DNAGeeks going “full nerd”. If you don’t know why UGA is funny, learn some genetics! Trust me, it’s good for you. Look how I turned out.

Last Friday for whatever reason I watched Mission Impossible: Fallout. I don’t really watch films except for Marvel and DCEU stuff (I need to keep up with the culture). But I was in the mood, and I hadn’t watched a Mission Impossible since the 1996 one. Apparently Tom Cruise is really into parkour. And though Cruise has aged really well, so has Michelle Monaghan. At least Ving Rhames is still around.

I used to listen to Chapo Trap House now and then. Still do now and then. There is some stuff I agreed with, some stuff I don’t agree with that I think needs to be said, and, they are often kind of funny. But unless you are on the same political wavelength I think they do get a little stale, because they’ve got an agenda, and they need to keep revisiting the same themes. It’s a feature, not a bug.

But listen below where they contextualize the “supposed crimes” of Communism:

The issue isn’t that avowed socialists are engaging in whataboutism in relation to Communism. That’s kind of what I expect. It’s that Chapo Trap House is still part of the respectable broader Left to center-Left cultural Zeitgeist. And they’re contextualizing literal Communism.

This is the sort of stuff that pisses conservatives off whenever we point out double-standards of respectability of radical Left politics as opposed to the radical Right. If someone contextualized Nazism as a reaction to Versailles and hyper-inflation they’d be de-platformed in a second. Meanwhile, Chapo pulls in $100,000 per month on Patreon.

A special treat this week on The Insight (Apple Podcasts, Stitcher and Google Play). We talked with James Lee, lead author of Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. In the next few months we have at least one more interview relating to behavior genomics work. This is a field where stuff is happening.

Though I hope ancient DNA will start popping back up in the fall.

Big Pharma Would Like Your DNA: 23andMe’s $300 million deal with GlaxoSmithKline is just the tip of the iceberg. This was always the plan.

Out of Africa by spontaneous migration waves. Not sure if I buy this model, but we’re at more model-building stage.

A Large Body of Water on Mars Is Detected, Raising the Potential for Alien Life. This is cool.

Episode 856: Yes In My Backyard. I relate to the NIMBY activist. It’s a generational and local vs. migrant issue. Not a typical class one.

I’ve been asked to submit a chapter on a book on Indian genetics, primarily relating to the “Aryan question.” I’ve gotten most of it written, but it’s really annoying to have to wait until the Rakhigarhi preprint/paper is out. The general finding will be no surprise to a reader of this weblog. Don’t think it will be published in the USA. Perhaps I’ll post the draft at some point if the copyright allows.

Replicability of introgression under linked, polygenic selection. “Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.”

July 28, 2018

On ethnicity

Filed under: Ethnicity — Razib Khan @ 3:29 pm


A really strange conversation on ethnicity broke out below. The primacy of lots of different variables was argued.

My family arrived in the USA ~1980 when there were not too many South Asians compared to today. Additionally, they have lived in major urban areas, small towns, and medium-sized cities. My parents grew up in (East) Pakistan, married and had their first children in Bangladesh, but have spent most of their lives now in the United States of America. Both speak English with a strong accent and are moderately religious Muslims. You wouldn’t call them secular, but neither are they visibly or ostentatiously Muslim. In American politics, they are staunch Democrats, while if they have an opinion on Bangladeshi politics they are Awami League (the ratio of discussion of American to Bangladesh politics in my family growing up was about 100 to 1 in favor the former).

Today my parents’ social circle, in a relatively large urban area, are Bangladeshis. Most of these people (almost all in fact) arrived in the United States much later than they did. But in the 1980s my parents had a much smaller pool of social acquaintances who were Bangladeshi. In the early 1980s, there were 15,000 Bangladeshis in New York City. Today there are probably closer to 200,000.

Here are some things I will observe in relation to my parents’ more diverse social circles in the 1980s. First, they were overwhelmingly South Asian. Those who were not South Asian were usually married in, and usually white. Second, a core group consisted of Bangladeshis. But the next group probably consisted by Indian Bengalis. A somewhat more established community. In fact, the boundary between Bangladeshis and Indian Bengalis were somewhat fluid. The two groups spoke the same language, and there was a large dietary overlap.

Next in order to the Indian Bengalis were a variety of other social clusters of South Asians that they met through various acquaintances and friends. For example, one cluster of friends consisted mostly of people from the Indian state of Andhra Pradesh, but with a large minority from other parts of India. Because there was ethnolinguistic diversity in this social group generally everyone spoke English, rather than Telugu, which was the most numerous language.

Another group consisted of people from Pakistan and Indian Muslims. This group also had some other token Bangladeshis. The unifying factor in this group was that all were South Asian Muslims. The de-unifying factor in this group is that the non-Bengalis would sometimes make the proactive case for Urdu as a unifying language, which my parents and the other Bengalis always objected to (because of their age, almost all the Bengalis in the group could follow the conversation in Urdu, since they grew up in Pakistan).

One issue in social circumstances with Pakistanis is that my parents found the food less palatable. This was a very important criterion for them for social interactions and a primary reason why sometimes they preferred going to parties thrown by their Hindu Bengali friends in preference to their Pakistan Muslim friends. By “less palatable”, I mean here that Pakistani cuisine was not “comfort food” for them.

My parents went to a multi-ethnic mosque several times a year. From what I could tell the South Asians kept to themselves, the Arabs kept to themselves, the Turks kept to themselves, etc. There was no real deep interaction. My parents never had any close Muslim friends who were not South Asian. In fact, we went to dinner with Chinese people (my father’s colleagues) more often than we went to dinner at a non-South Asian Muslim’s house.

That’s about it from me. Below are some genetic plots.

South Asian nationalism

Filed under: Nationalism — Razib Khan @ 2:01 pm


I happen to have Saloni’s genotype and she is certainly closer genetically to Sindhis than to most other South Asians. That being said, my own response to her tweet is this: my personal experience is that many liberal Pakistani & Indian Americans are highly nationalistic.

To be honest, it’s mostly Indian Americans. I don’t know too many hyper-nationalistic Pakistani Americans. I think that has to do with the fact that despite India’s social-political problems, its democratic and pluralist history, along with the international appeal of Mahatma Gandhi, makes it easier to be an Indian nationalist than a Pakistani nationalist if you are an American.

Also, there is a cultural “code-switching” that is common among Indian Americans, where they are fluent in, and totally embedded within, a Left-of-centre cultural zeitgeist in the American landscape. But, they also are comfortable switching into their parents’ more Indian nationalist views in different contexts. Rather than synthesizing the two worldviews (which may not be possible), Indian Americans just switch facultatively between the two, because the two social milieus never really engage each other.

Because I am Bangladeshi American it is hard for me to relate. Bangladesh is a very young nation. Both my parents have spent more than 3.5 times of their life living in the United States than an independent Bangladesh. In fact, both lived as Pakistanis for far longer than they lived as Bangladeshis! Additionally, it is not a major geopolitical player, and there are ambiguities with the relationship to both India and Pakistan enough that socially my family has felt comfortable with both Indians and Pakistanis in the USA.

P.S. I do get annoyed when I’m identified as Pakistani American by people just because of my last name. Since I am not vocal about being a “Bangladeshi American” I only find out later people had assumed I was Pakistani. Apparently, in some Indian circles, I am known as a “Pakistani American geneticist”, albeit not a particularly nationalistic Pakistani (told to me by an Indian journalist friend).

Complex evolution of pigmentation in modern humans

Filed under: Human Population Genetics,Pigmentation — Razib Khan @ 1:49 pm

Last fall Crawford  et al.Loci associated with skin pigmentation identified in African populations, was published in Science and made a huge splash. As I’ve been saying recently, and most people agree, much of the remaining “low hanging fruit” in human evolutionary genomics, and to some extent, human medical genetics, is going to be in Africa on Africans. From an evolutionary perspective, that’s probably because from a gene-centric viewpoint most of our recent evolutionary history was within Africa. As a friend once told me, “most of the last 200,000 years is about the collapse of ancient population structure.” This goes too far, but at least it gets at something we’ve not been too conscious of.

Top left clockwise: Luo Kenya, Khoisan, South Asian, Arrernte Australia

Crawford  et al. was important because it was a deep dive into a topic which has been understudied, the variation of pigmentation genetics within Africa (also see Martin et al.). The fact that there is variation in pigmentation within Africa should not be surprising, though some people are surprised that there is variation in pigmentation within Sub-Saharan Africa. But anyone who has seen photos of San Bushmen, knows they are very distinct from South Sudanese, who are very distinct from West Africans. As documented by both Crawford  et al. and Martin et al. some of this variation is likely novel.

By this, I mean there has been backflow of the derived Eurasian variant of a mutation on SLC24A5. Arguably the first major human pigmentation locus of the “post-genomic era”, its discovery was enabled by its huge effect in explaining variation among Eurasian populations and their differences from African groups. In Crawford  et al. the author observes within Africans nearly ~30% of the trait variance was due to four loci, with ~13% due to SLC24A5. In earlier work comparing just people of European and African descent, SLC24A5 variance explains closer to 30% of the pigmentation difference. It seems that pigmentation effects genetically exhibit an exponential distribution. A small number of loci have a large effect, and a numerous number of loci have small effects.

Distribution of rs1426654 at SLC24A5

The results from Crawford  et al. and Martin et al., a naive inspection of the modern distribution of the derived rs1426654 allele, and ancient DNA, seem to indicate a mutation associated with lighter skin emerged after 40,000 years ago. After the expansion of non-African humans, and, the divergence between eastern and non-eastern branches of non-Africans. A common haplotype around this mutation suggests that it wasn’t part of the ancestral “standing variation” of the human lineage. Ancient samples from Scandinavia, the Caucasus, and modern samples from Eurasia and from Africa, all exhibit the same pattern, suggesting recent common descent.

And though a mutation on rs1426654 is associated with lighter skin, it does not produce white skin. I have the homozygote derived genotype on rs1426654, as does my whole nearby pedigree. All of us have brown skin, to varying degrees. And interestingly, the locus around rs1426654 seems to be under strong selection in both South Asia and Africa, including East Africa. This makes me somewhat skeptical that there is a simple story to tell on this locus in relation to skin pigmentation being the driver here.

Let me quote from  Crawford  et al.:

Most alleles associated with light and dark pigmentation in our dataset are estimated to have originated prior to the origin of modern humans ~300 ky ago (26). In contrast to the lack of variation at MC1R, which is under purifying selection in Africa (61), our results indicate that both light and dark alleles at MFSD12, DDB1, OCA2, and HERC2 have been segregating in the hominin lineage for hundreds of thousands of years (Fig. 4). Further, the ancestral allele is associated with light pigmentation in approximately half of the predicted causal SNPs…These observations are consistent with the hypothesis that darker pigmentation is a derived trait that originated in the genus Homo within the past ~2 million years after human ancestors lost most of their protective body hair, though these ancestral hominins may have been moderately, rather than darkly, pigmented (63, 64). Moreover, it appears that both light and dark pigmentation has continued to evolve over hominid history….

For over ten years it has been clear that very light skin in eastern and western Eurasia are due to different mutational events. Crawford  et al. give us results that indicate this pattern of evolutionary complexity is primal and ancient.

But there is often a tacit understanding that the selection process is the same over time and space. Something to do with protection from UV light and also synthesization of vitamin D at higher latitudes. So this paper that just came out definitely piqued my interest, Darwinian Positive Selection on the Pleiotropic Effects of KITLG Explain Skin Pigmentation and Winter Temperature Adaptation in Eurasians. The authors looked at a lot of variants in KITLG with a focus on East Asians. They confirmed that there were at least two selection events, one just around the “Out of Africa” period, and possibly another one later, during a period when West and East Eurasians were genetically distinct.

This section is very intriguing: “Besides pigmentation, KITLG is also involved in mitochondrial function and energy expenditure in brown adipose tissue under cold condition (Nishio et al. 2012; Huang et al. 2014). We demonstrated that winter temperature showed a much stronger correlation than UV for rs4073022.” Earlier the authors review work which suggests that large melanocytes are much more susceptible to damage due to cold than than smaller ones. Dark-skinned individuals tend to have large melanocytes (and more of them!). The KITLG locus does a lot of things; some of you may know its relationship to testicular cancer.

What  Crawford  et al. tells us that there seems to have been recurrent and sometimes balancing selection around loci implicated in pigmentation for hundreds of thousands of years. What ancient DNA is telling us is that the genetic architectures we take for granted as typical across much of Eurasia are relatively novel. But, I think people are perhaps taking the implications of modern genetic architecture too far in predicting the variation of characteristics in the past. Even the best genomic predictors seem to account for only around half the variance in pigmentation. “Ancestry” accounts for the rest, which basically means there are many other loci which are not accounted for. It is not unreasonable to suppose that ancient northern Eurasian populations may have been light-skinned due to genetic variants which we are not aware of.

Of course, there are people at high latitudes who retain darker complexions. From what we know the Aboriginal people of Tasmania were isolated for about 10,000 years at the same latitude as Beijing and Barcelona, and yet their skin color remained dark brown. In contrast, Martin et al. report that Khoisan people who lived 10 degrees further north, in a much sunnier climate, were selected at loci that strongly correlate with lighter skin.

I think it is safe to say that in the near future we will close in on much of the reamining genetic factor accounting for variation in pigmentation in modern populations. It is polygenic, but almost certainly far less polygenic and more tractable than height or intelligence. But the story of why humans have varied so much over time, and why loci implicated in pigmentation are so often targets of selection in some many contexts, remains to be told.

July 26, 2018

Local ancestry deconvolution made simpler (?)

Filed under: Local ancestry,Population genetics — Razib Khan @ 11:37 pm

I’ve been waiting for a local ancestry deconvolution method to come out of Simon Myers’ group for a few years. Well, I think we’re there, Fine-scale Inference of Ancestry Segments without Prior Knowledge of Admixing Groups. Here’s the abstract:

We present an algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary number of genetically differentiated groups coming together. This allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping. The algorithm employs nested hidden Markov models to obtain local ancestry estimation along the genome for each admixed individual. In a range of simulations, the accuracy of these estimates equals or exceeds leading existing methods that return local ancestry. Moreover, and unlike these approaches, we do not require any prior knowledge of the relationship between sub-groups of donor reference haplotypes and the unseen mixing ancestral populations. Instead, our approach infers these in terms of conditional “copying probabilities”. In application to the Human Genome Diversity Panel we corroborate many previously inferred admixture events (e.g. an ancient admixture event in the Kalash). We further identify novel events such as complex 4-way admixture in San-Khomani individuals, and show that Eastern European populations possess 1-5% ancestry from a group resembling modern-day central Asians. We also identify evidence of recent natural selection favouring sub-Saharan ancestry at the HLA region, across North African individuals. We make available an R and C ++ software library, which we term MOSAIC (which stands for MOSAIC Organises Segments of Ancestry In Chromosomes).

The truth is I’ve only done a quick skim of the preprint and not run the method myself to see how it works. But to be honest I can’t see where the part about Eastern Europeans is in the manuscript (I checked the supporting text)? That being said, if you run a PCA many Northern and most Eastern Europeans are clearly shifted toward East Asians compared to Southern Europeans. So I accept it.

In any case, always remember, all models are wrong. But some of them have insight.

Render unto Caesar worldly goods

Filed under: History,Religion,Secularism — Razib Khan @ 11:11 pm

At Tanner Greer’s recommendation, I purchased a copy of Imperial China 900-1800. Now that I’ve received it I realize that I read a few chapters of Imperial China 900-1800in 2008, before abandoning the project due to sloth. Older and wiser.

As I’m reading this book, I’ve been giving thought how I would respond to this comment:

…not only were priests an independent power source from kings, but no matter how deeply interrelated each was in principle independent of the other, with their own independent spheres: the secular sphere and the religious sphere. This fact too was important in shaping the modern world, in that modernity assumes that government is fundamentally secular in a way that would have been unfamiliar to pre-moderns outside of Latin Christendom.

This is a common view. Fareed Zakaria, for example, expresses something similar in The Future of Freedom, whereby the emergence of an independent Western Church after the Fall of Rome created space for secularization and the development of liberal democratic institutions through decentralization of power.

And yet after having just read History of Japan, and reading again about the Battle of Anegawa, where Oda Nobunaga completed a chapter of his crushing of institutional Buddhism as an independent power in Japan, I wonder what the above even means. A standard model would argue that in East Asia religion suffused life, philosophy tended toward monism, and there was no separation between this world and that. The Emperor of Japan descended from the Sun Goddess. The Emperor of China was the Son of Heaven, though Heaven was not conceived of in an anthropomorphic sense. And yet the kingship of nations such as France and England have exhibited a sacral nature, and to this day the monarch of England is also the head of its established religion.

About when I abandoned my plan to read Imperial China I read Jay Winik’s The Great Upheaval: America and the Birth of the Modern World, 1788-1800. One of the many things that stuck with me from that book was just how radical in regards to religion the federal government established by the American Founders was at the time. While the American states had all had an established religion, due to the pluralism of the new nation, and the personal secularism of many of the Founders, no consideration was given to privileging religion on the national level. This concerned many leading thinkers, some of whom suggested that simply declaring Christianity in the general sense the national religion would have been sufficient (and for all practical purposes Protestant Christianity was the national religion, even though church-state separationists such as Andrew Jackson were punctilious in making this not a de jure matter).

With hindsight, it seems clear that having a “national religion” only makes sense in the aftermath of the Protestant Reformation, and the collapse of the religious system of Western Christendom during the medieval period. The medieval Western Church was characterized by a great deal of diversity and variation. But something happened during early modernity, whereby that variation produced too many tensions and factionalized. Eventually, this shattered the tacit understandings and compromises which allowed for external unity. In nations where monarchs supported Protestant Reformers, national churches emerged, and become official arms of the state for all practical purposes. In Catholic Europe, a reaction produced a newly muscular and standardized church, which stood opposed to the new official Protestantism on very similar terms. The Roman Catholic church remained international, but it also became the national churches of nations as diverse as Poland, Ireland, and Spain.

Though many people assert that the Roman Empire became “officially” Christian with the conversion of Constantine, or perhaps during the reign of Theodosius the Great at the end of the 4th century, the reality is that the Roman Empire was not a totalitarian state. The dissolution of paganism occurred more through slow decay and death, as the cessation of subsidies from the state starved elite paganism, and persistent missionary efforts blanketed the population with nominal Christianity.

The assertion above that “government is fundamentally secular in a way that would have been unfamiliar to pre-moderns outside of Latin Christendom” always strikes me as strange because of my familiarity with Chinese history and philosophy, and the interpretation of how the Chinese seem to have viewed “church”-state relations. It is often said that the Chinese are superstitious, but not religious. In other words, what China lacked in the vigor of organized religion, it made up for in widespread belief in supernaturalism. This is broadly correct, but the same could be said for the West for most of its history. That is, many pre-modern peasants were not religious as much as they were superstitious, and their Christianity was a thin skein upon folk beliefs.

The issue rather is with the cultural elite, and what their beliefs were. There is a line of argument that philosophical dualism, and a particular sort of disenchantment with the world and a rationalism, was pregnant within Western Christianity, and came to fruition with Calvinism and modern forms of Catholicism. In the ancient world, Christians believed that magic was real, and that the pagans worshipped true supernatural forces, but that these were rooted in the devil. The argument proceeds that in early modernity this belief gave way to more rationalist views, whereby God remained true, but non-Christian beliefs were rooted in falsehood, rather than demons. Magic was now simply trickery.

And yet History of Japan notes that even before Oda Nobunaga’s crushing of the Buddhist clerical powers of the 16th century the society was going through broad secularization, as popular and elite enthusiasm for religion abated. Though the Tokugawa regime enforced Buddhist registration by families across Japan, this was a measure that enabled control and regulation, not one which promoted religion as such. Japanese intellectuals during this period were influenced by currents skeptical of supernaturalism that had its roots in Chinese Confucianism, and this in its turn can be found to have prefigured by anti-supernaturalist threads as far back as Xunzi.

Curiously, the Japanese system after the decline of the Fujiwara and the rise of the Shogun dynasties recollects the mythologies of dual kingship, with a sacred and a secular king, in other societies. To me, this reinforces my own current position that all the semantical distinction between secular and sacred power and how they differ between societies elides more than it illuminates. My own materialist bent leads me to suggest that in fact, secularization in early modernity at the two antipodes of Eurasia were natural and likely inevitable developments with mass societies and more powerful states. A coercive state did not need to rely on supernatural power to persuade a populace, and the workaday nature of bureaucratic governance, in any case, would not reflect positively upon a religious order that was fused with that state.

Naturally, others will have different views. But one of the reasons I am such a fan of Peter Turchin’s project is that I tire of semantic definitions as the axis around which arguments hinge. I am usually unconvinced by the erudition of my interlocutors because in most cases I don’t get a sense that they know more than I do, even though perhaps they may, in fact, be in the right. Rather than calculating, argumentation is often a way for two individuals to assess each other’s knowledge base and sophistication. If there is parity, there will never be a resolution, because personal qualities are more relevant than reality.

July 25, 2018

East Bengal/Pakistan catches up to West Bengal/Pakistan

Filed under: Economics — Razib Khan @ 9:48 pm


Today I was looking on the internet to get some more information on the Pakistan election. Honestly, I don’t have a strong opinion….

But by chance, I ended up stumbling on articles like this, When East overtakes West:

…a recent article, “East overtakes West,” in The Economist has thrown a spanner in the works. The east is the erstwhile East Pakistan and the west is today’s Pakistan. It shows that the GDP per capita of Bangladesh is $1,538 and that of Pakistan lags behind at $1,470. This is the result of a GDP growth rate of over six per cent per annum in the past 12 years. One-third of the GDP is contributed by industry and the value-added garments exports are larger than India and Pakistan put together.

The truth is that Bangladesh’s better statistics in some measures are due to demographics. Per capita values will change in opposite directions if nation underestimated its population (as Bangladesh did), and another nation overestimated its population (as Pakistan did). Using PPP corrections and such Pakistan is still a more prosperous land per person. But it’s getting close. The trendline is definitely pointing in one direction. A piece at Brookings asks “Why is Bangladesh booming?” The author notes:

Once one of the poorest regions of Pakistan, Bangladesh remained an economic basket case—wracked by poverty and famine—for many years after independence in 1971. In fact, by 2006, conditions seemed so hopeless that when Bangladesh registered faster growth than Pakistan, it was dismissed as a fluke.

But I’ve always thought that the infant mortality and life expectancy statistics in Bangladesh were things that were more important to be proud of (and on this score Bangladesh does indisputably better than Pakistan). And curiously, on this measure, Bangladesh does even better than India! But to a great extent, that’s not a fair comparison, as India is a coalition of regions, while Bangladesh would just be a very populous Indian state.

More comparable is West Bengal. Bangladesh and West Bengal look to be at parity in terms of life expectancy and per capita GDP. And metropolitan Dhaka and Kolkotta now have about the same population, at ~15,000,000.

We live in interesting times.

The Insight show notes: episode 30, Genetics and educational attainment

Filed under: Education,Genetics,Psychology — Razib Khan @ 3:47 pm

This week Razib and Spencer discussed the relationship between educational attainment and genetics on The Insight (Apple Podcasts, Stitcher and Google Play) with James Lee, lead author of Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals (published in Nature Genetics).

Here are some more resources: FAQs about “Gene discovery and polygenic prediction from a 1.1-million-person GWAS of educational attainment”. The Atlantic and The New York Times also covered the paper. An op-ed in The New York Times, Why Progressives Should Embrace the Genetics of Education.

The three laws of behavior genetics and the fourth law of behavior genetics are both mentioned. The study was a meta-analysis of genome-wide associations (GWAS), and may have been the largest GWAS published to date.

Much of the discussion centered around intelligence. The podcast with Stuart Ritchie was cited as a useful primer (remember to subscribe with Apple Podcasts, Stitcher and Google Play). You might want to check out Ritchie’s book, Intelligence.

Population stratification was mentioned. Martin et al., and two preprints, Berg et al. and and Sohail et al., tackle this issue in relation to disease and height, and how it confounds our understanding. Lee discussed LD score regression as a way to account for stratification in this particular analysis..

There was extensive discussion of the concept of heritability, where genetics explains variation in a trait.

The Social Science Genetic Association Consortium (SSGAC) and its research projects were referenced extensively.

Each allele seems to effect ~1 week of education. The authors returned more than 1,000 statistically significant markers.

Spencer brought up the “omnigenetic” model. This comes from Boyle et al., An Expanded View of Complex Traits: From Polygenic to Omnigenic.

James mentioned some of Camille Benbow’s work, in particular Life Paths and Accomplishments of Mathematically Precocious Males and Females Four Decades Later.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight show notes: episode 30, Genetics and educational attainment was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

July 23, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 9:12 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

The genetics of education

Filed under: Education,Genetics,Intelligence,Psychology — Razib Khan @ 11:49 am
Yale University

In the modern world, obtaining an education is a rite of passage. Not only does education provide one with skills useful for the modern economy, but it also helps to form one’s values and socializes one with peers who go through the same life experiences. Education isn’t just learning about various disciplines, it is a way to learn how to live in the modern world.

It is a topic which intersects with sociology, politics, and even ethics. As it turns out, education, or the attainment thereof, also intersects with genetics. This follows naturally from the first law of behavior genetics, “all human behavioral traits are heritable.” By “heritable,” geneticists refer to the fact that variation of a trait correlates with variation in genes. That variation tracks a causal relationship — so that genetic variants in some way cause a particular outcome.

This is easy enough to illustrate with an example. Imagine a genetic variant that changes the production of a biochemical that impacts whether someone is hyperactive or not. Hyperactivity is a behavioral characteristic with a lot of variables. Someone who drinks too much coffee will exhibit hyperactivity. But, it is surely true that some of the variation on these personality traits are due to cognitive neurological differences — some of which are then due to genetic differences between people. We may not be “born that way,” but we are probably “disposed to be that way.”

That’s a lot of caveats, and that is accounted for in the third law of behavior genetics: “a substantial portion of the variation in complex human behavioral traits is not accounted for by the effects of genes or families.” When it comes to behavior, environment matters. Although, what constitutes “environment” is not always clear, but any understanding of the genetic basis of behavioral variation needs to account for the fact that much of behavioral variation has nothing to do with genetics.

Galton’s classic illustration of parent-child correlation on height

And a when it comes to educational attainment, there is obviously no one “gene for education.” Whether or not you obtain a degree is impacted by many factors: from family encouragement and resources, inspirational teachers, intelligence, and your own conscientiousness. But, some of these characteristics, in particular the ones having to do with intelligence and personality, are impacted by your genes.

It has long been known through indirect methods that intelligence and personality are heritable. Identical twins are much more similar on these characteristics than conventional siblings, and relatives are much more similar than non-relatives. But, finding the biophysical genetic basis has been difficult because of the fourth law of behavior genetics: “A typical human behavioral trait is associated with very many genetic variants, each of which accounts for a very small percentage of the behavioral variability.”

A traditional way for geneticists to discover the cause of a trait is to target particular genetic locations and see if they are associated with the trait in question. This “candidate gene” method has been useful for many diseases, where a single defective mutation is responsible for much of the cause of the disease. But, it has been an utter failure in behavior genetics because of the fourth law of behavior genetics. To establish a connection between a genetic variant and a behavioral trait requires enormous sample sizes and a good knowledge of the human genome.

Until the year 2000, we didn’t have the sequence of a human genome, and until the past decade, dense assays of human genomic variation were expensive — this meant that studies were limited to small sample sizes and only a few genes. Most of the published results did not replicate, because they were not true in terms of the effect of the gene on the trait in question.

Recently, all that has changed. Thanks to “next generation sequencing” and “chip technology” researchers now have access to hundreds of thousands of markers in any given person — and cheaply at that. This cost-effectiveness allows for an increase in sample size; as many more people can be tested. This shatters the barriers implied by both the third and fourth laws of behavior genetics: small effect sizes no longer impede discovering ‘the needles in the haystack’ of complex traits. Bigger sample sizes and more subtle statistical methods are producing results that only a few years ago would have seemed fantastical.

A new paper in Nature Genetics illustrates this starkly, Gene discovery and polygenic prediction from a genome-wide association study of educational
attainment in 1.1 million individuals
. The authors identified 1,271 independent genome-wide-significant SNPs. This is a big achievement, considering that five years ago a paper with ~125,000 individuals identified just 3 SNPs that were significant for this trait!

Though it is hard to generalize about 1,000+ genetic variants, the figure to the left illustrates that the genes that these variants are found in are highly over-expressed in the nervous system. This is exactly what you see in most genetic analyses of complex traits that are behavioral. The genetic “hits” are found disproportionately in genes that control variation in neurological function because behavior is downstream of brain function. To be fair, many genes express in the brain, so that’s not a surprise. Rather, the authors compared the gene’s expression level to the typical gene.

Curiously these hits are not particularly over-expressed in genes associated with the development of glial cells, those cells in the central nervous system which are not neurons. Because these cells form the tissue which scaffolds the connections between neurons, the authors suggest that this might mean that differences in cognitive ability between individuals may not be a function of “transmission speed.” This highlights the fact that the these sorts of abstruse statistical analyses ultimately aim to uncover underlying biological phenomena.

And yet such a paper, with over 1 million samples from numerous cohorts, will have to get into the statistical weeds. One of the major issues that crops up in these analyses is “stratification.” This means that the genetic variation in the sample is correlated with variables such as geographical population structure. Therefore, some of the positive hits for any of these sorts of analyses might easily be picking up the overall population genetic variation and differences between groups, which may not have a genetic basis at all (e.g., British tend to drink tea, Americans tend to drink coffee).

Empirical genetic relationship of siblings

To get around this, the authors look at a sub-sample of 20,000 sibling-pairs. Many of the issues presented by population stratification do not apply within families. Families have the same broad genetic background, and also control for many environmental differences (since siblings are raised in the same family and socioeconomic context). But, there is still genetic variation among siblings, and some of this variation is responsible for variation in traits between siblings. After all, height tends to run in families, but the difference in height between same-sex siblings is not usually due to differences in nutrition (at least in the developed world).

Looking at the associations between genetic variation and educational attainment within families the authors found “that within-family
effect sizes are roughly 40% smaller than GWAS effect sizes.” In other words, there are factors that seem to result in the overestimation of the genetic effects on educational attainment within the broader population. The authors note that the same does not apply to height.

What might account for this then? One possibility is that some of the genes that a parent has, but does not transmit to the offspring, might result in a more beneficial environment. This is often termed the “parental effect.”

The paper looked are more than just educational attainment. With sample sizes in the hundreds of thousands they also looked at cognitive performance and mathematical ability (self-reported). Using the same methods as for educational attainment, the authors predicted around 10% of the variance.

Of course there are limitations. The sample size is large, but not diverse genetically. Overwhelmingly of European origin, the authors found that their method could predict less than 5% of the variance in African Americans. This is not surprising, because genome-wide associations often do not predict well across different populations.

Additionally, there is the reality that these methods focus on common variation within populations. The heritability of most behavioral traits using more indirect classical methods is much higher than this ~10% of variation explained would imply, so there is still a genetic component to be accounted for. Perhaps this variation is found in rare genetic variants, which are not explored in this sort of research.

Ultimately, we may look back at this 1 million-person analysis as the first in a scholarly tradition of massive GWAS sample sizes. Genomics is cheap enough that it is possible that genetic sample sizes in the range of a billion are feasible within 15 years. That will probably require a whole different set of esoteric methods but will probably yield many novel results.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The genetics of education was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Open Thread, 07/23/2018

Filed under: Open Thread — Razib Khan @ 3:12 am
Sale Code: GET20

Doing a Summer Sale at DNAGeeks, 20% off with the GET20 code. I believe GNXP-helix themed stuff is still the most consistent/popular item.

Reading T. N. Ninian’s Turn of the Tortoise: The Challenge and Promise of India’s Future. It’s a relatively dry book with an academic orientation. No complaint from me. So far the most interesting, and unfortunate, thing I’ve learned is that Indian men will take a 50% pay cut to work in a white-collar as opposed to blue-collar manufacturing job. Ninan contends that this may be due to caste aversion to manual labor. Men who have lower-paying white-collar jobs have better marriage prospects than those who have higher-paying blue-collar jobs.

James Gunn Fired From ‘Guardians Of The Galaxy’ Franchise Over Offensive Tweets. I’ve seen some people suggesting that you need to evaluate the “whole person” and that “people grow.” These are almost always the same people who gleefully crucify anyone to the Right of Alexandria Ocasio-Cortez for anything they’ve ever said in any context. I see no end to this cyber-Maoism until cultural “mutually assured destruction” becomes reality. To maintain civilization we must be barbarians!

Someone on Twitter suggested replacing libraries with bookstores and Amazon. This elicited outrage. I have opinions on this because I’m confident that among the population I’ve been a top 1% utilizer of libraries over my lifetime. I’ve seen slowly as libraries transform from book repositories to internet access portals and community centers. But, a minority of the population using the library is still using it for books.

And of that minority, many are nerdy kids for whom the library is a window upon the whole world. True, the internet is great, but the internet is broad and shallow. The minority of overutilizers of the book lending function of the library probably make a big impact in other ways later on in their life.

Before the age of 12, I probably had my parents buy me about a half a dozen books, ever. I bought more as a teen, and as an adult, I probably buy/purchased half the books I’ve read. This is a “think of the children” issue. Libraries are distribution centers for essential free “gateway drugs” of cognition. Not for most. But for those who care.

Last week on Secular Right I wrote On the semiotics of secularism and nakedness of village atheism in the culture war. As I told a friend of mine, people were tweeting almost word-for-word the exact same Islamophilic sentiments in the Left-progressive Twittersphere (he was one of them). Reactions to Richard Dawkins have become tribal measuring sticks. It’s tiresome for many apostates from the Islamic religion. Most Left-progressives don’t care about Islam or Muslims that much. They just care that they’re “tolerant” and follow their crowd as to who is, and isn’t, marginalized (1.8 billion Muslims, marginalized!).

Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians.

If you liked the Stuart Ritchie podcast from a few months back, you need to listen this week. If you subscribed I don’t need to remind you. Also, if you are subscribed to my total content RSS or follow my “gnxp posts” Twitter, you know I’ve been pushing my work-blog content into those feeds now (since people keep complaining that they’re missing them). Initially, I kept my work-blogs more “lay-friendly,” and they are still more soft-touch than the stuff I put here, but I’ve noticed that the more technical one still get shared a lot. I’ll have a write-up of a paper that’s going to be quite big (mega-sample size) out on the work-blog this week.

Looks like a justification for the two-fold cost of sex (the male part):

Inferring Continuous and Discrete Population Genetic Structure Across Space. This was out as a preprint a while back. These issues require more thought than people in pop-genomics have been doing.

Here’s What Happens To Your Body When You Eat Super Hot Peppers.

Neandertal fire-making technology inferred from microwear analysis.

Black American Culture and the Racial Wealth Gap:

… Consistent with the Nielsen data, they found that blacks with comparable incomes to whites spent 17 percent less on education, and 32 percent more (an extra $2300 per year in 2005 dollars) on ‘visible goods’—defined as cars, jewelry, and clothes….

Next, they asked if education accounted for the differences in financial habits by limiting the comparison to middle-aged families with advanced degrees. Surprisingly, they found that the racial gap in financial health-scores didn’t shrink; it widened. Highly-educated Asian families scored 3.49, comparable whites scored 3.38, comparable Hispanics scored 2.94, and comparable blacks remained far behind at 2.66. Thus, the study authors concluded, neither “periodic shortages of time or money” nor “lower educational attainment” were the driving forces behind the differences in financial decision-making.

Elizabeth Holmes’ Downfall Has Been Explained Deeply-By Men. The author of this Wired piece is Virginia Heffernan, who I know for having an impeccable pedigree, but whose writings are substantively often total tripe. Heffernan, who has a Ph.D. in English from Harvard, once wrote a weird piece titled Why I’m a creationist, which begins “As a child I fell in love with technology, but I have to admit I never fell in love with science.”

In any case, Holmes’ case is clearly one where a person from a upper-class WASP background with Stanford connections leveraged all that into a lot of money. Heffernan’s attempt to transform it into a gendered issue is totally predictable, but also incredibly reductive.

New criteria for sympatric speciation in the genomic era.

Gene expression drives the evolution of dominance. Old debates made new.

Nathan Lents’ new book, Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, looks interesting. Here’s a write-up by Lents’ in Skeptic.

Though I do wonder if Creationism as a cultural force has lost some steam. After all, conservative Protestants are probably more worried about their catastrophic losses in the culture wars right now than somewhat abstruse meta-scientific questions. I mean, I have more Twitter followers than The Discovery Institute!

If you want to analyze Tibetan genotypes, I converted some files I found in the Jorde lab website to plink. It has an OK overlap with HGDP.

What podcasts do you listen to?

Also, the India ancient DNA story should get a major breakthrough within the next week or so. “Watch this space” and all that.

July 22, 2018

Why moderating this weblog has become more difficult

Filed under: Blog — Razib Khan @ 11:36 pm

This is still a modest weblog. But engagement is high (average time on the website is 4+ minutes). And the proportion of Indian readers getting is higher and higher. At some point in 2019, conservatively, I think this weblog will have more Indian readers than American.

That is a problem for me because I have a hard time understanding a lot of the references or anticipating triggers. So flame-wars are getting common as I’m not sanitizing much….

Wolves out of Beringia!

Filed under: Canids,Canine Evolution,Dog Evolution,Wolves — Razib Khan @ 9:05 pm
Citation: Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Do Eurasian and North American wolves come from Beringia? That’s the conclusion of a new preprint, Modern wolves trace their origin to a late Pleistocene expansion from Beringia. The figure above is the main result, using ancient and modern mitochondrial genomes to construct a phylogeny. It’s not surprising that the ancient lineages are basal. Y and mtDNA lineages have a tendency to go extinct (lower effective population, etc.). But it’s a surprising result that the older Beringian individuals are distributed basal to the modern lineages, as opposed to more of the ancient samples from Europe and the Middle East.

The basic argument here is very similar to “mitochondrial Eve.” If Beringian lineages tend to be basal to modern wolves, then the former is likely to be ancestral to the latter. Additionally, as noted in the preprint there is whole-genome inference which indicates that modern gray wolves across the Palearctic ecozone underwent a rather recent demographic expansion, in particular, after the Last Glacial Maximum (~20,000 years BP). That being said, I am curious if modern Alaskan and (east) Siberian wolves exhibit greater mtDNA diversity than elsewhere, in keeping with the human analogy.

Needless to say, mtDNA has limitations. It’s a single locus, and in other animal research, there have been confusions and misunderstandings due to the usage of mtDNA. The authors did some explicit formal demographic modeling using their data. It’s fine, but generally, I ignore this stuff because it rarely tells us things we don’t know to a high degree of certainty.  Rather, I would rather focus on paleoclimate data and a model where coexistence with Beringian humans might explain a possible break-out of Beringian wolves to the west and the east after the Pleistocene. The Beringian landscape may have been particularly fertile territory for the Palearctic wolf. Though modern wolves seem to prefer some forest, rather than open territory.

One thing human evolutionary genomics has taught us is that the first-pass story is always far simpler than reality. I think this is a decent framework to start with, though it may still turn out to be wrong. But in the preprint, the authors note some peculiarities in South Asians and Tibetan wolves. So peculiar that they were discarded from the analysis. We know wolves hybridize with both jackals and coyotes, so the emergence of the modern lineages are likely more complex than a simple expansion and replacement. The whole-genome analysis will probably offer up curious wrinkles.

Though the preprint tries to put the emergence of the wolf from Beringia in the context of the domestication of the dog, I suspect we’ll find that the dog derives from an extinct Eurasian wolf lineage. This was the implication of Freedman et al., and ancient canine genomics is producing some erratic finds which are in keeping with a possible complex divergence of the dog lineage from wolves.

Japan as a natural cultural experiment

Filed under: History,Japan,Japanese — Razib Khan @ 6:59 pm

History of Japan is a good survey for anyone curious about the topic because it is short enough to not be intimidating (this was a complaint from friends who I recommended read The Making of Modern Japan), but dense enough to actually be much more informative than a Wikipedia entry. Unlike many surveys of Japanese history, it does not operationally begin with Oda Nobunaga. The extensive treatment of the Nara and Heian period is something that I particularly appreciated since often these are explored only in specialist monographs with any depth.

One of the curious things about Japan is that since the conquest of the Emishi of northern Honshu around 800 AD, the Japanese lost an external frontier with another people. True, there were periods of endemic warfare between Japanese when central authority collapsed, but by and large, these conflicts were arguably less destructive than shocks from without would have been. Wars within cultural groups are highly destructive, but often they are governed by unified cultural scripts and mores.

In Strange Parallels: Mainland Mirrors: Europe, Japan, China, South Asia, and the Islands, the historian Victor Lieberman examines Japan as a case study of a “protected-zone” civilization. In Lieberman’s framework, the emergence of organized steppe nomadism in the years after the fall of Rome and China caused stress and chaos across what Nichols Spyman would term the “Eurasian rimland,” and what the ancients would have termed the civilized oikoumene. The same model crops up in Ian Morris’ War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots.

The development of the chariot during the Bronze Age was arguably an integrative force in the evolution of agricultural polities. Chariots were useful for the transport and deployment of elite warriors and archers. But, they were not utilized as shock troops, as would be the case with the rise of mounted cavalry. First emerging around 1000 BC on the western edge of the Eurasian steppe, by 0 AD the mounted cavalry had given birth to full-blown nomadism from Europe to China. To some extent, the only way that core civilizations on the Eurasian rimland could maintain themselves in the face of the pure nomadic assault was through co-option and assimilation. Arabs, Turks, and Mongols all swallowed up earlier settled civilizations. In the Near East, China, and India,  peoples of nomadic origin became the ruling classes, synthesizing and integrating with the traditions of those they conquered.

In contrast, much of Western Europe and Southeast Asia were protected from these incursions due to distance, topography, and climate. The German barbarians who took over the reins of power in the post-Roman world were agro-pastoralists, not nomads. In mainland Southeast Asia, the Tai incursions was a migration of agriculturalist warrior elites. The modern states of Cambodia, Vietnam, and Burma withstood the assaults and maintained cultural continuity with their past. In Western Europe, Ireland can be thought of as an analogous case, though the Viking shocks, and later Anglo-Normand conquest, disrupted its continuity.

Lieberman argues in Strange Parallels that these protected-zone societies are much more natural nation-states than elsewhere, in part because their organic identity from earlier cultural traditions persisted down to the modern era, as opposed to having been created anew through novel ideologies. And is it a surprise that of the European nations England, which has not undergone a mass invasion since 1066*, has one of the deepest self-conceptions as a nation-state?

Which brings us back to Japan: its imperial family dates at least the early 6th century AD. Though we don’t have verified dates before the Emperor Kinmei, it seems likely that the Imperial House of Yamato is quite a bit older than that. Unlike in the West then the Japanese have a much easier line of descent from antiquity for its elites. The persistence of the Japanese imperial family is a testament to the cultural prominence that the Yamato lineage has, with all of its ups and downs. In contrast, the arrival of waves of barbarians in other regions of the Eurasian rimlands produces a situation where taboos against taking official power eventually broke down. In the 5th century West Roman Empire, there was a taboo against barbarians or people of part-barbarian ancestry from becoming Emperor. Eventually, the barbarians got rid of the Emperor, and over the centuries became Emperors themselves. The same process is evident in the Islamic world, where the Arab Caliphs remained figureheads for Persian and Turkic potentates until they took over both de jure and de facto roles.

The Japanese have a different experience. At the beginning of their history, they were a cohesive culture expanding into the post-Jomon frontier. Though reinforced with an elite migration of Koreans and Chinese prior to the Fujiwara period, unlike polities across Eurasia the Japanese ruling class have been uniformly and continuously of the same ethnicity and identity as the populace which it ruled.** And, unlike the Vietnamese or Koreans, they have not been subjected to conquest and hegemony by China. They have long been of the Sinic sphere, not within the Sinic sphere.

Between Korea and Japan, there is a 200 km distance by water. In contrast, between England and France, there are about 30 km. This greater distance explains the relative isolation of Japan in comparison to England when it comes to continental affairs. Proto-historical expeditions in Korea, or Hideyoshi’s adventure, are exceptions, not the rule.  Official contacts between Japan and China often had gaps of centuries.

This is not to say that Japan was not influenced by the continent. Obviously, Buddhism, Chinese writing, and the wholesale transplantation of Tang culture during the Fujiwara period attest to the early influences, while later on even during the Tokugawa era there were influences from Western thought via the Dutch. Rather, the Japanese are a natural experiment of a people who have repeatedly engaged with the world on their own terms, and developed their own culture organically to such an extent that they put their ancient tribal animism, Shinto, as the state religion during their phase of modernization!

In answer to the question “why is Japan different?” I would say this is a peculiarity of geography, close enough to be influenced culturally, but distant enough to be politically isolated.

* I think the Dutch invasion under William of Orange really was an invasion. But its impact was mild due to broad local support.

** Contrast this with ethnically distinct ruling elites in the Near East, India, and China, as well as cosmopolitan ruling families in Europe. Even England was for several centuries ruled by a nobility which spoke French.

 

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