None dare call it multiregionalism

Dienekes Pontikos resurfaces with a post, Out of Africa: a theory in crisis. The title is a bit hyperbolic. But in Dienekes’ defense, he’s been on this wagon for over ten years, and the evidence is moving in his direction, not against him. I think a little crowing is understandable on this part.

With that being said, I think the biggest rethinking that we’re doing is less about where modern humans arose (Sub-Saharan Africa, North Africa, the Middle East), but how they arose. Some geneticists are quite open to the idea of Eurasian (Neanderthal?) back-migration to Africa several times (and out of Africa several times). Others are positing that a “multiregional” model might actually be about the situation within Africa.

A simple stylized model of a rapid punctuated expansion of humanity which replaces other lineages in toto is no longer likely. There has been widespread admixture, even though the last major demographic wave seems to be overwhelmingly predominant, at least outside of Africa. But the whole process might result in a much more complex history than we had thought.

The multiregional model is probably wrong on the details. The history of our species is not really phyletic gradualism and anagenesis. But there are also many processes and dynamics which a multiregional model takes into account and anticipates that probably are important in a general sense toward understanding the origin of our species.

The rapid fading of information


In Robert Heinlein’s uneven late work Friday the mentor of the protagonist mentions that because of a possible collapse of technological civilization he maintains a collection of paper books.

This crossed my mind when I saw that Storify is shutting down. Or Kevin Drum’s reflections on the changes in blogging.

I’ve put a lot of content out there over the years. Probably on the order of 5 million words across my blogs. Some publications here and there. Lots of tweets. But very little of it will persist into future generations. Digital is evanescent.

But so is paper. I believe that even good hardcover books probably won’t last more than a few hundred years.

Perhaps we should go back to some form of cuneiform? Stone and metal will last thousands of years.

Open Thread, 01/28/2108

For various reasons we focus Classical Greece and Rome, but neglect the Hellenistic period, with the exception of the biography of Alexander. If you want to read something besides Alexander to Actium, check Dividing the Spoils.

A heads up, this week on The Insight we’ll be talking to Joe Pickrell of Gencove. The main topic will be DNA and ancestry.

Is the United States the new Saudi Arabia? This stuff is crazy if you read books about “Peak Oil” in the 2000s. Also, I really don’t ever want to hear about this stuff from random guys who read these books and thought they had all the answers ever again.

DNA Geeks is now gearing toward more general STEM and items for children. The 100x LED Microscope for Mobile Devices has been quite popular, and shipping is right now free. Also, we have European vendors for our t-shirts, so shipping is cheaper and faster.

Following many liberals on Twitter has confirmed my right-wing identity, though modified by policy beliefs. In particular, far Left people, such as Matt Stoller, seem to make coherent criticisms of capitalism and what it has wrought. Criticisms which I don’t always have a good answer for.

In contrast, moderate liberals, with their mild platitudes and thin policies are not persuasive, but their adherence to sex/race identity politics and smearing of all those to the Right of them as white supremacists means that it’s pretty obvious all of those who are “Other” need to band together as one when the time comes. We hang together, or we’ll go to the re-education camps separately.

The Follower Factory. This makes sense.

Why Ursula Le Guin Matters.

Nicholas Christakis is being treated pretty unfairly. I don’t expect that he’ll get satisfaction. This isn’t the age for honorable men.

Big Data Comes to Dieting.

The new gnomAD is pretty dope.

Dissecting historical changes of selective pressures in the evolution of human pigmentation. Not sure of the demographic model.

Sarah Haider on Secular Jihadists.

Punjabi genetic variation in 1000 Genomes: Hindu caste in the Land of the Pure?


In the 1000 Genomes, there is a Punjabi dataset. Here is the description:

These cell lines and DNA samples were prepared from blood samples collected in Lahore, Pakistan. The samples are from a mix of parent- adult child trios and unrelated individuals who identified themselves and their parents as Punjabi.

A few years ago I did an analysis of the population structure in the 1000 Genomes dataset. In the Chinese data, there seemed to be some curious structure (there were two clusters of South Chinese). But the biggest issues predictably were in the South Asians. To give concrete examples, there were a few Brahmins in the Telugu data. A subset of Tamils and Telugus were highly ASI shifted. The Gujurati were highly heterogeneous, and one subcluster were almost certainly Patels (the samples were collected in Houston). The ASI shifted groups were almost certainly Scheduled Castes (Dalits) because I could see that they clustered with those samples from Estonian Biocentre dataset.

There was something curious about the samples from Pakistan and Bangladesh. Aside from a small number of individuals, whose samples were collected at the same time judging by their IDs (these individuals cluster with Scheduled Castes), the Bangladeshi sample didn’t have much South Asian style structure. That is, there wasn’t a cline or lots substructure within the ethnicity.

As noted by some commenters, the Punjabi samples were very different. Like the Gujurati samples, there was a huge variance along the ANI-ASI cline. To me, this was somewhat surprising. To make the 1000 Genomes more useful I used PCA and divided both Gujuratis and Punjabis into groups based on their position on the ANI-ASI cline. So that ANI_1 is the subpopulation with the most ANI and ANI_4 the least.

Using Treemix produced some weird results. As you can see above Punjabi_ANI_1 looks like an Iranian population with gene flow from Punjabi_ANI_3. Punjabi ANI_2 looks like a North Indian population with Iranian gene flow (so it is more ASI). Punjabi_ANI_3 are less ANI shifted than Uttar Pradesh Brahmins, but more than Uttar Pradesh Kshatriya. Finally, Punjabi_ANI_4 actually is very similar to Punjabi_ANI_2, except it has gene flow from a Dalit-like population.

With the South Asian Genotype Project I have a few Punjabi samples. All of them are within Punjabi_ANI_1.

I don’t know what’s going on here. Is this really caste-like structure in Punjab? Or are we see lots of admixture of people who are called “Punjabi” today? For example, the gene flow edges suggest lots of mixing between quite South Asian types of groups and an Iranian sort. Perhaps this is the absorption of Pathans into South Asian groups? Could it be Muhajir people who mixed with local Punjabis and identified as such?

I was curious to see if I could find something similar in relation to the three Jatts. As you can see with Treemix, no. Jatts are just very ANI-shifted. I added Lithuanians and Georgians, and you can see that Uttar Pradesh Brahmins get gene flow from a Lithuanian shifted group, while South Indian Brahmins have a more Georgian gene flow. This is just an artifact I suspect of the fact that South Indian Brahmins have a lot of admixture from non-Brahmin South Indians, who are more Georgian than Lithuanian (Iran_N as opposed to Yamnaya).

Finally, going back to the Bengali (Bangladeshi) vs. Punjabi contrast, it is really interesting. If Punjab has such deep caste-like structures it really goes to show how within South Asia caste is a very very powerful institution, and ~1,000 years of Muslim rule and in western Punjab a majority Muslim population did not break down the institution. In contrast, in Bangladesh, there doesn’t seem to be much caste structure. I am routinely the most East Asian shifted Bengali in datasets, but my family is also from the eastern edge of eastern Bengal. Why the difference?

in The Rise of Islam and the Bengal Frontier the author posits that the Islamicization of eastern Bengal was to a great extent the function of the opening up of lands for cultivation under the supervision of Muslim elites under the rule of Afghans and later Mughals. This would explain the lack of caste structure because presumably, caste structure would be difficult to maintain in a frontier landscape, where the cultural elite does not promote or accept caste (though the elite West Asian Muslims were racially exclusive, they were also a very small minority).

In contrast, the Punjab has long been settled by Indo-Aryan peoples, and despite its long history of Islam, it was not recently a frontier society.

Anyway, that’s all I got to say for that. I’m sure readers will have more insight on this pattern than I do….

Anhui, in the shadow of Shanghai

Anhui is inland of the prosperous lower Yangzi river valley. According to Wikipedia this province is a recent creation, dating to the Kangxi Emperor. The northern part of the province is part of North China while the south closer to the Yangzi river valley regions.

It’s relatively poor in comparison to the provinces to the east and seems to be a mishmash of rural regions. But it has been close enough to cosmopolitan regions to be forward thinking in its political orientation.

Genetic distances across Eurasia

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 Fst. Fst 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 Fst 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 Fst.

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

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

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


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

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.