Genetic distances across Eurasia

Posted on January 27, 2018January 27, 2018 by Razib Khan

I feel that for whatever reason that over the past few years that many people have started to exhibit weak intuitions about the magnitude of between population differences on this weblog. Two suggestions for why this might occur.

* First, the proliferation of PCA plots with individuals can make it hard to discern averages

* Second, model-based admixture plots don’t explicitly quantify the differences between the different clusters

To get a better sense of between-group differences I decided to take a step back and look at F_st. F_st basically looks all the genetic variance between groups and quantifies the proportion that can be attributed to differences between groups.

The plot at the top of this post is from an F_st matrix I generated with Plink (I wrote a script to do the pairwise comparison). I did some PCA pruning of the populations to be clear (e.g., with both Cambodians and Filipinos I made them more distinct than they would otherwise be). The goal was to give people a sense of genetic distances within regions and between them.

I also generated a PCA plot and a Treemix plot, for the sake of comparison.

It’s also useful to look at a few group comparisons and judge them in a global context.

		Fst
Tamil	Telugu	0.0011
Tamil	Tamil Scheduled Caste	0.0016
Tamil	Bangladeshi	0.0024
Tamil	South Indian Brahmin	0.0031
Tamil	Uttar Pradesh Brahmin	0.0041
Tamil	Sindhi	0.0087
Tamil	Vietnamese	0.0668
Southern Chinese	Northern Chinese	0.0033
Southern Chinese	Vietnamese	0.0034
Southern Chinese	Korea	0.0045
Southern Chinese	Japanese	0.0087
Southern Chinese	Tamil	0.0711
Southern Chinese	Polish	0.1141
Gujurati_Patel	Telugu	0.0062
Gujurati_Patel	Uttar Pradesh Brahmin	0.0065
Gujurati_Patel	Bangladeshi	0.0069
Gujurati_Patel	Velama	0.0094
Gujurati_Patel	Sindhi	0.0104
Gujurati_Patel	Polish	0.0405
Gujurati_Patel	Japanese	0.0781
GreatBritain	Ireland	0.0015
GreatBritain	Polish	0.0043
GreatBritain	Sicily	0.0077
GreatBritain	Uttar Pradesh Brahmin	0.0264
GreatBritain	Tamil	0.0430
GreatBritain	Korea	0.1130

The non-Brahmin and non-Dalit samples in the 1000 Genomes are not much partitioned much by geography. The Tamil vs. Telugu difference is smaller than that between the British and Irish. Within Tamil Nadu Brahmins though are nearly as different from typical Tamils as Poles are from the English (most of the British sample is English). The biggest differences in Europe are between Sicilians and Northern European groups, which similar in a degree to that between South Indians and Pakistanis. The South Chinese sample is nearly as close to Vietnamese as it is to a North Chinese group, while the difference between Koreans and Chinese is relatively small when compared to the variance you see in South Asia and Europe.

Note: Drift tends to inflate F_st.

Out of Africa to Out of Eden (well, perhaps not yet)

Posted on January 25, 2018January 25, 2018 by Razib Khan

The recent African origins hypothesis for modern humans had several things going for it. First, most of the old fossils that look like modern humans were in Africa. Chris Stringer and others were pushing the African origins of our modern lineage before genetics came to the fore. But of course, you also have DNA. The mtDNA, Y, and autosomal DNA, which tends to show a pattern where Africans are more diverse, and non-Africans are nested within phylogenies of Africans.

In the 2000s the “Out of Africa” model got a little out of control. The stylized narrative was that a small tribe of East Africans developed some genetic mutation that allowed them to exterminate all other human lineages (e.g., language). This is best encapsulated in Richard Klein’s The Dawn of Human Culture. The British science fiction author Stephen Baxter used this idea as a frame in his novel Evolution (the innovation in this novel was religion though). In this view modern humanity was an African saltation, a great leap forward.

We’re at a different point now. The idea of admixture and/or introgression from non-African lineages into African modern humans is widely accepted. Additionally, both genomic inference and paleontology are pushing the roots of modern humanity much further than ~50,000-60,000 years before the present.

So it’s not as surprising to see a paper like this, The earliest modern humans outside Africa:

To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.

Now, the reality is that Israel is arguably part of “Greater Africa” biogeographically. So it isn’t that surprising. Or it shouldn’t be.

But, this reinforces the reality that anatomically modern humans were geographically already widespread ~200,000 years ago. I would say that this informs and updates our estimation of the plausibility of the Jebel Irhoud modern humans in Morocco, who flourished ~300,000 years ago. It also makes more sense of the reality that most of the ancestors of the Khoisan likely diverged from other modern lineages ~200,000 years ago (or more, depending on who you talk to). Finally, it makes recent archaeological finds of modern humans or their artifacts in East Asia tens of thousands of years before the great expansion of neo-African humanity50,000-60,000 years before the present much more plausible.

There has been some genetic evidence for modern(ish) human expansion before the 50,000 year date. So this isn’t resting only on paleontological evidence.

Where does this leave us? In The Guardian David Reich observes that ‘It’s important to distinguish between the migration out of Africa that’s being discussed here and the “out-of-Africa” migration that is most commonly discussed when referring to genetic data. This [Misliya] lineage contributed little if anything to present-day people.’

Obviously, this is an important point. But we know that the first modern humans to settle Europe did not leave any descendants either. The modern human settlement of Europe was still nevertheless important. Second, these early wave humans may have given modern populations adaptive variants that are present at high frequencies in modern lineages.

Finally, there’s the issue that this may reorient our understanding about the demographic origins of human populations. Ever so slightly our priors as to an African genesis for our modern lineage are getting weaker. You have two very old modern fossils on the northwest and northeast fringe of the continent. Ten years back the arguments was between those who argued for an East African origin (most), or a minority who favored a Southern Africa one. Now the whole continent, and perhaps even Arabia, are game.

Ultimately, as always, ancient DNA is going to be the final arbiter.

How South Asian populations relate to each other

Posted on January 25, 2018January 25, 2018 by Razib Khan

Since people asking me about this, and I’m running the South Asian Genotype Project, I thought I would post two non-PCA visualizations of how various South Asian groups relate to each other (along with a few outgroups).

The radial plot above is a neighbor-joining tree visualized from pairwise Fst statistics (basically a proxy for genetic distance).

I also used Treemix to generate a plot. You see the similar patterns as the one above, though the two methods are different. Treemix tests a bunch of models and sees how the data fit those models. The visualization of Fst is just a way of representing the summary statistic.

I added 5 migration edges to the plot to the right. Not sure if they add anything, but you can see that some of the nodes move around because they are so mixed.

It isn’t what you say, it’s who you are

Posted on January 24, 2018January 24, 2018 by Razib Khan

Sarah Haider in the talk above outlines the reality that she has particular privileges in regards to talking skeptically and critically of Islam because of who she is, not the force of her arguments. More precisely, her status as an immigrant, woman, and a person with brown skin, inoculates her against the reflexive charges of racism or bigotry which get leveled against those who dare challenge Islam and the cultures with which it is associated.

And yet even here Sarah observes that she gets attacked and dismissed, whether through undermining her credibility, or suggesting that she’s a “native informant”.

I’ve been writing on the internet for 15 years. Long enough to see some trends emerge. This pattern of dismissal-by-identity has become much more noticeable on the Left over the past few years. Left-wing thought policing is operationalized through enforcing informational hygiene by segregation from unclean persons. I don’t know where it’s going, but I’m not optimistic.

But there is another group that engages in the same thing: the racist Right, what is now called the Alt-Right. In the early years of this weblog, most of the attempts of dismissal-by-identity came from this sector. Basically, the thesis is that nonwhites are constitutionally not intellectually creative, so their arguments were better than mine because they were white and I was not (this is a real position that was staked out by people who kept reading my writing).

A milder form of this stance would be that of a long-time reader, who I will not name in this post, who suggested that he understood the Bible better than I did because he was a white American and it was part of his culture, and not mine (nevermind that I grew up around white Americans and in white American culture, so he probably confused my brown skin for my cultural identity; again, something common among the identity politics Left and the racist Right).

Ultimately this form of argument-by-identity goes nowhere. Arguments are won through positional rank status within the tribe (you all know what “oppression Olympics” are), so they’re not arguments at all, but restatements of the nature of identity and its determinative character. If you are a white male, your job is to listen and learn, not talk back. If you are a white male and Alt-Right it is the job of others to listen and learn from you. If two people are of different tribes there is suspicion and incommensurability. I, for example, am suspicious of engaging in discussions with liberals who I don’t know because tribalized arguments are usually just a waste of time (once they realize I’m not on their tribe they’ll just go full identity and everything will collapse). Similarly, many liberals probably feel the same way about #MAGA types.

The future seems to be more about power than persuasion. You are either in the Elect, or you are among the damned.

Meanwhile, someone like Sarah, who exhibits an old-fashioned fidelity and adherence to the idea and execution of truth is caught in the cross-fires of the two ascendent barbarian tribes.

The conversos in the Spanish Empire and undoing anthropological mythologists

Posted on January 24, 2018January 25, 2018 by Razib Khan

A new preprint in bioRxiv reports on the high likelihood if elevated Sephardic Jewish ancestry in New World populations, Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance:

…Using novel haplotype-based methods here we infer the sub-populations involved in admixture for over 6,500 Latin Americans and evaluate the impact of sub-continental ancestry on the physical appearance of these individuals. We find that pre-Columbian Native genetic structure is mirrored in Latin Americans and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming from the clandestine colonial migration of Christian converts of non-European origin (Conversos)….

I’ll not focus too much on the genetics in this post. The haplotype-based methods are very good, and these researchers have access to a massive genotype database. The results are also not entirely surprising to people in the genetic genealogy community. As direct-to-consumer genomics has become more popular, suggestions of Jewish ancestry in Latino customers were not uncommon. Showing enrichment via haplotype-based methods really hammers home the nail (I myself when I consulted with FamilyTree DNA analyzed customers who seemed to show patterns that genuinely indicated affinity to our Sephardic samples, though they were from mestizo families with deep roots in the New World).

The historical reason why this might occur is well known to anyone familiar with this period of history: migration to the New World was one way “New Christians,” some of whom were crypto-Jews in reality, could avoid social opprobrium and the attention of the inquisition. The author of the paper notes that with the methods they used it’s hard to dispute a greater representation of Sephardic ancestry in these populations than Spain proper.

Additionally, there are cultural and historical suggestions that some of these conversos settled in the Southwest of the United States when it was Spanish territory, and maintained Jewish traditions. Some of these people are now coming back to Judaism.

But over 15 years ago The Atlantic published a piece, Mistaken Identity? The Case of New Mexico’s “Hidden Jews, which presented a revisionist argument that these people were not the descendants of conversos at all. Rather, they were Judaizers who created a history out of their yearnings.

Here’s a representative portion:

Neulander thinks they are doing it because they are, in effect, racists. Colonial Spaniards were obsessed with proving they had “pure” blood, untainted by that of what they regarded as inferior peoples. The same has been true for many New Mexicans, and Neulander believes that the concern for purity — limpieza de sangre — is intensifying, now that Hispanos are being boxed in by Anglo newcomers and Mexican immigrants. As noted, Hispanos have always been loath to be called Mexicans. But that is how Anglos in the region have identified anyone who speaks Spanish. So, Neulander theorizes, some Hispanos are using crypto-Jewish identity as a postmodern marker for ethnic purity. What better way to be a noble Spaniard than to be Sephardic, since Sephardim almost never marry outside their own narrow ethnic group — and would certainly not intermarry with Native Americans? Neulander also comes at the racism issue from another, not quite compatible angle. She stresses that Protestant lost-tribes logic is deeply anti-Semitic. Below its Judeophilic veneer lies the belief that because they reject Jesus, most of today’s ethnic Jews will in fact go up in flames at the Apocalypse.

The thesis is a mishmash of what are now fashionable ideas that one can understand the culture of people like the Hispanos of the Southwest in postcolonial terms, that is, how they reacted and engaged with white Anglo oppression, and also the internalized racism inherited from the Spanish.

The irony is that I believe in fact the American anthropologists and journalists were the ones engaging in myth-creation, sweeping aside the reality of genuine Sephardic Jewish cultural traits in New World Latinos, and putting in its place the idea that these post-converso people were really just indigenous Americans who had adopted a Spanish culture and adapted to American racism. They erased the likely real history of American conversos and substituted something that was more intelligible to white Americans (non-white history as a great chain of reactions to the agency of white people).

We can’t know if these methods will vindicate the conversos of the Southwest, though I’m 95% confident that the signal of enriched Sephardic ancestry south of the Rio Grande is correct. But at this point, the converso model seems far more likely on genetic grounds than the anthropological revisionism.

I await the piece from The Atlantic vindicating the cultural traditions and memories of the Hispanos.

A commentary on the current year

Posted on January 23, 2018January 23, 2018 by Razib Khan

Function & phylogeny, where the twain shall diverge

Posted on January 23, 2018January 23, 2018 by Razib Khan

Every few years I get asked about Nuristanis and Kalash. The reason is that these people are often white. By white, I mean that some Nuristanis and Kalash are fair-skinned, blonde-haired, and blue-eyed. Entering “Nuristani” into Google images returns some very white faces. And you have weird news stories about ‘white’ Taliban, because non-locals don’t realize that some Nuristanis look like Northern Europeans.

Since the vast majority of people who look like white Northern Europeans are white Northern Europeans, many people assume that the Nuristanis and Kalash must have some kinship to white Northern Europeans. More precisely, many have spread the legend that these people have some relationship to the soldiers of Alexander the Great (even though Macedonians are Southern European…details).

As it turns out, they do have some kinship to Europeans…but not inordinately more than any of the other peoples of the region. The TreeMix plot at the top of this post shows that Greeks are far closer to Iranian Jews than they are to Kalash. In fact, the Kalash clearly have a non-trivial proportion of “Ancestral South Indian” South Asian ancestry.

Because of their high genetic drift (they’re endogamous and kind of inbred) a lot of population genetic analyses are a bit more difficult with the Kalash samples that are out there. But their genetic affinities are clear:

Table S4 show highly significant evidence (p value < 10−10) in the Kalash when using Armenia and Chamar as surrogates. Eight other pairings of surrogates give p values < 10−5. In all cases, the surrogate pairs include one group from South Asia (Chamar, Kol) and the other from West Eurasia (Armenia, Adygei, Brahui, Hungarians, Palestinians, Tuscans), consistent with admixture from a West Eurasian source.

Chamar are a Dalit caste of Northern India if you don’t know.

So what’s going on with the Kalash and Nuristanis? Appreciable frequencies of alleles which are correlated with traits like blue-eyes are found amongst them. Though the frequencies are much lower than in Northern Europeans. Very white looking Nuristanis and Kalash may be highly salient to photographers and the Western media, but it turns out most Nuristanis and Kalash look West Asian, with a minority who are dark-skinned enough that their South Asian ancestry is also quite clear.

This disjunction between appearance and ancestry should not surprise us. There has been a lot of recent change in physical appearance across populations over the last 10,000 years. Europeans themselves have changed in appearance. Similarly, other populations have as well. Some of them look similar to Europeans due to happenstance or convergence.

Another case are the Ainu of Japan. Though as an unadmixed group they no longer exist, old photos show some of them exhibiting an appearance not typical of East Asians. This led early anthropologists to posit that the Ainu were a “lost white race.” And yet to my knowledge, no European ancestry is found in Hokkaido, or in the Tohoku region, where Ainu-like people lived down to the early medieval period.

The moral of the story: don’t judge the contents of the book by its cover.

On the passing of Ursula K Le Guin

Posted on January 23, 2018January 24, 2018 by Razib Khan

About four months ago Jerry Pournelle died. He and Ursula K Le Guin did not get on, in part because of their political differences. And despite my differences with both, I read them with appreciation.

Well, Le Guin passed away today. A science fiction and fantasy great she was. I appreciate especially her defenses of “genre fiction,” since she received admiration from the literary mainstream.

That is probably because her prose was more writerly than most science fiction, which came out of the adolescent male pulp tradition, long on plot, short on turn of phrase.

If I had to pick a work of Le Guin’s to reread, it has to be The Tombs of Atuan. Earthsea was not a Middle Earth rip-off, and her quasi-Daoist philosophical framework was genuinely novel.

(when I lived in Berkeley I would regularly pass the building named after her father)

Populism leads to tyranny

Posted on January 22, 2018January 22, 2018 by Razib Khan

I just listened to the authors of How Democracies Die on NPR. First, the book might well have been titled “The necessity of liberalism.” Basically, democracy without liberalism is clearly not democracy in their judgment.

But second, I was struck by their emphasis on the role of elites in dampening and diminishing the passions of the masses in a functioning modern democratic system. To a great extent, the authors were simply warning about what Fareed Zakaria termed “illiberal democracy” in The Future of Freedom over ten years ago.

Without elites acting as structural guardrails on the atavistic passions of the masses charismatic figures who channel their basest impulses can arise and gain popular approval of their autocratic behavior. The ancient Greeks could have told you that. Some things never change.

The rise of Chinese science and CRISPR

Posted on January 22, 2018January 22, 2018 by Razib Khan

So as of now China is producing more scientific publications than the United States of America. But there’s quality and there’s quantity. I think most people would still American science is more cutting edge than Chinese science. And for cultural reasons that may stay true for a while longer.

But there is one area where China seems to be forging ahead and likely will make advances earlier than the USA: genetics, and genetic engineering in particular. The Wall Street Journal has a long piece, China, Unhampered by Rules, Races Ahead in Gene-Editing Trials. It turns out that Chinese have been doing human trials since 2015. Meanwhile, in the USA the greenlight has still not been given (though it seems close).

Honestly how quickly the Chinese are moving in human trials is alarming. Then again, this is a country with the highest number of executions in the world (some of this is sheer size, but it’s higher per capita than the USA). So we should keep perspective. There are many worse things that the Chinese are doing in relation to human rights that moving too fast in trials with cancer patients.

In any case, this comment jumped out at me:

In traditional drug development, too, human-trial rules can differ among countries. But China’s foray into human Crispr trials has some Western scientists concerned about the unintended consequences of using the wholly new tool—such as harm to patients—which could set back the field for everyone.
Western scientists the Journal interviewed didn’t suggest America’s stringent requirements should be weakened. Instead, many advocate an international consensus on ethical issues around a science that makes fundamental changes to human DNA yet still isn’t completely understood.

As a descriptive matter, I am highly skeptical of the possibility that “international standards” is going to involve the Chinese adhering to Western standards. If a genuine international consensus is going to emerge there has to be a give and take, which means that the very high threshold set for safety in human trials in the West may not apply in China.