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

February 5, 2018

In the long run sex always wins

Filed under: Uncategorized — Razib Khan @ 7:33 pm

Carl Zimmer has an incredible piece up, This Mutant Crayfish Clones Itself, and It’s Taking Over Europe:

All the marbled crayfish Dr. Lyko’s team studied were almost genetically identical to one another. Yet that single genome has allowed the clones to thrive in all manner of habitats — from abandoned coal fields in Germany to rice paddies in Madagascar.

In their new study, published in the journal Nature Ecology and Evolution, the researchers show that the marbled crayfish has spread across Madagascar at an astonishing pace, across an area the size of Indiana in about a decade.

Basically, it looks like a crayfish mutated and now is able to reproduce clonally. That is, it’s asexual. Also, because of its chromosomal structure, it’s no longer inter-fertile with the species from which it emerged.

As it happens there are a fair number of lineages which have sexual and asexual species. Asexual species seem to be much younger. The implication then is that they’re going extinct and emerging over and over again.

February 4, 2018

Open Thread, 2/4/2018

Filed under: Open Thread — Razib Khan @ 9:56 pm

One of the things that reading Land of Liberty has prompted in me is the need to read Matt Stoller’s book, when it comes out. Land of Liberty in many ways was a historical foil of Stoller’s article, How Democrats Killed Their Populist Soul.

And yet both exhibit an intellectual honesty which I generally find lacking in the modern pundit class, agree or disagree.

Steven Pinker’s new book, Enlightenment Now: The Case for Reason, Science, Humanism, and Progress, is now being published a few weeks earlier. Apparently this now one of Bill Gates’ favorite books.

I’m a big fan of Steven Pinker. But I’ve become much more pessimistic than him over the past few years. Here’s hoping that Enlightenment Now turns that around.

DNA Geeks has a total site redesign! Check it out.

I haven’t been saying this on the podcast yet, but you should be subscribing to it on iTunes, Stitcher, and Google Play, and review and rate it. Spencer and I have a certain audience already, and we’d like to expand it.

This has probably always been so, but I’m really getting tired by the emergence of different verbal ticks in various socio-political subcultures. For example, when liberals say “my dude” -“bros”, it’s dismissal-by-identity. Both NRx, and what is now called the Altright, also have their own subculture languages, which makes understanding what they’re trying to say hard for outsiders. A feature or a bug?

Taking a Twitter break for a week.

February 3, 2018

Why the Chinese don’t buy deodorant

Filed under: earwax,Human Population Genetics — Razib Khan @ 11:30 pm

 
In human populations a SNP in ABCC11 is correlated with two salient traits: 1) wet or dry earwax 2) body odor. When I had my first son sequenced before his birth the main variant of phenotypic consequence that I noticed (aside from him being a heterozygote on KITLG), was that he carried a derived mutation on this position. Meaning that he was going to have dry earwax and fewer issues with body odor.

My wife and I are both heterozygotes. This is not too surprising. The derived variant is actually greater than 50% in Bengalis in the 1000 Genomes (in South India the derived variant is also around ~50%), while about ~25% of Northern Europeans are heterozygotes.

This genetic story came to my mind again because of this article in The New York Times, Aiming at China’s Armpits: When Foreign Brands Misfire:

There’s another reason few Chinese consumers buy deodorant: basic biology.

Scientists in recent years have shown that many East Asians, a group that includes China’s ethnic Han majority, have a gene that lowers the likelihood of a strong “human axillary odor” — scientist-speak for body stink.

That lowers the likelihood that they will use deodorant to begin with, according to a 2013 study by researchers at the University of Bristol and Brunel University in Britain, after a survey of nearly 6,500 women of various backgrounds.

“It is likely that deodorant usage is not widely adopted because there is, for much of the East Asia population, no need for it,” it said. (For those curious about such matters, that same genetic difference also leads to drier earwax.)

A friend of mine in undergrad of East Asian background told me once that she had never worn deodorant. So this shouldn’t be very surprising.

Today I found a paper, A missense variant of the ABCC11 gene is associated with Axillary Osmidrosis susceptibility and clinical phenotypes in the Chinese Han Population, which explicitly probes the correlation between body odor (“Axillary Osmidrosis”) and the SNP in question in the Han Chinese population.

The chart below makes the association obvious:

The correlation between carrying the G, ancestral, allele, and body odor is very strong. Though it is imperfect. Going through this literature human smells are clearly a polygenic trait (see The effect of ethnicity on human axillary odorant production). That being said, this case-control study in a Han population shows ABCC11‘s importance in at least East Asian populations (earlier work in Japan showed that those with body odor tended to have wet earwax and carry the G allele as well).

In regards to the genotype proportions the authors observe:

The excessive heterozygosity observed in AO individuals is probably due to the effect of selection, particularly nonrandom mating against AO phenotype.

This doesn’t make sense to me. Wouldn’t people who have body odor tend to pair up in a society where they are a minority? The authors note that the excess of heterozygotes was observed in earlier studies too.

If you dig into the frequencies it seems that the derived mutation is absent among populations in Africa without recent Eurasian back-migration. I looked it up, and it’s segregating in ancient Eurasian samples, with Ust Ishim being a heterozygote. It is curious that in no population has the derived frequency swept to fixation, nor has the ancestral variant fixed in other groups (such as in Europe).

I strongly doubt that there is any selection on this locus due to earwax or body odor. It is a pleiotropic locus, there are other effects from the mutation. One of those other effects is probably the target of any selection. And in regards to selection, it seems likely that that would be a balancing sort since neither the ancestral nor the derived variant are fixed in most populations.

Perhaps the Genghis Khan modal haplotype is not Genghis Khan’s?

Filed under: Genghis Khan,Genghis Khan Genetics — Razib Khan @ 3:57 pm

Literally hundred of thousands of people have read my post, 1 in 200 men direct descendants of Genghis Khan, since 2010. It was based on the paper The Genetic Legacy of the Mongols*, which reported that one particular Y chromosomal lineage was very common in Central Asia, and, that it exhibited hallmarks of explosive growth over the last thousand years.

A new paper suggests that this inference is wrong, Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan:

The Y-chromosome haplogroup C3*-Star Cluster (revised to C2*-ST in this study) was proposed to be the Y-profile of Genghis Khan. Here, we re-examined the origin of C2*-ST and its associations with Genghis Khan and Mongol populations. We analyzed 34 Y-chromosome sequences of haplogroup C2*-ST and its most closely related lineage. We redefined this paternal lineage as C2b1a3a1-F3796 and generated a highly revised phylogenetic tree of the haplogroup, including 36 sub-lineages and 265 non-private Y-chromosome variants. We performed a comprehensive analysis and age estimation of this lineage in eastern Eurasia, including 18,210 individuals from 292 populations. We discovered that the origin of populations with high frequencies of C2*-ST can be traced to either an ancient Niru’un Mongol clan or ordinary Mongol tribes. Importantly, the age of the most recent common ancestor of C2*-ST (2576 years, 95% CI = 1975–3178) and its sub-lineages, and their expansion patterns, are consistent with the diffusion of all Mongolic-speaking populations, rather than Genghis Khan himself or his close male relatives. We concluded that haplogroup C2*-ST is one of the founder paternal lineages of all Mongolic-speaking populations, and direct evidence of an association between C2*-ST and Genghis Khan has yet to be discovered.

The primary aspect here seems to be pushing the age back. The Mongols, or what became the Mongols, were a marginal group of tribes when this variant arose. There is some citation of the fact that some putative descendants of Genghis Khan don’t even carry the “Star Cluster”, but there are other papers which report even different haplotypes! So I’m not sure that that is dispositive in any sense.

Perhaps the true question now is why this cluster expanded so much over the past 2,500 years or so? There are plenty of candidates historically, but being Bayesians we should be cautious about overturning prior hypotheses on new data. Coalescence dating in particular is often an art as opposed to a science (I don’t mean this literally, but anyone who has used the programs mentioned in the paper knows what I mean).

An alternative model is that as a null we should expect star clusters now and then. But most people don’t seem to think that rapid expansion of Y chromosomes during the Holocene is simply a matter of chance as opposed to necessity.

* My boss and friend, Spencer Wells, was a coauthor on the paper.

January 31, 2018

My top posts?

Filed under: GNXP — Razib Khan @ 8:56 pm

The fact that platforms tend to disappear has started to make me wonder: what posts should I figure out a way to preserve for posterity?

Do any long-time readers have opinions? I’m not talking popular posts necessarily even, that I can find through google analytics.

(note that I have my full archives on this site, so if you want to some for something that you vaguely remember that should be doable)

Facebook AMA with Spencer Wells & myself

Filed under: AMA,Media,Podcast — Razib Khan @ 8:02 pm

Spencer and I are doing a Facebook live AMA at 2 PM EDT/1 PM CDT/12 PM MDT/11 AM PDT on the 1st of February (tomorrow as of when I’m writing this). People will ask us questions, and the questions will be relayed to us, and we’ll answer live on video.

In other ‘media’ news our podcast with Joe Pickrell of Gencove, Ancestry Deconvoluted, is now live.

Finally, there has been some talk about me doing a Reddit AMA. Thoughts?

January 30, 2018

The “Finns” are probably an Iron Age intrusion into the East Baltic

Filed under: Finns,Historical Population Genetics — Razib Khan @ 10:23 pm

One of the first things I wrote at length about historical population genetics, in late 2002, happened to be a rumination on the Y chromosomal phylogeography of Finnic peoples. At the time there was debate as to the provenance of the N1c Y chromosomal haplotype (this is the haplotype of the Rurikids by the way). Just as R1b is ubiquitous in Western Europe, and R1a in Eastern Europe (and to some extent in Indo-Iranian lands), N1c has an extensive distribution in the northern zone of Eurasia.

The question at the time was whether N1c was from Europe and in particular the Finnic peoples, or, whether it was from Siberia.

NJ Tree of Pairwise Fst

Today we have many of the questions resolved. At this point, we know that the Finns, Sami, and Estonians, all exhibit evidence of gene flow from a Siberian-like population. This is clear on any genome-wide analyses. Though this is very much a minority component, even among the Sami, because it is genetically very different from the Northern European background, it is clear on any analysis.

Ancient DNA has also established the likelihood that this Siberian-like element is relatively new to the Baltic region. In a recent paper, The genetic prehistory of the Baltic Sea region:

We suggest that the Siberian and East Asian related ancestry in Estonia, and Y-haplogroup N in north-eastern Europe, where it is widespread today, arrived there after the Bronze Age, ca. 500 calBCE, as we detect neither in our Bronze Age samples from Lithuania and Latvia.

This is not the only ancient DNA paper that shows this. Of course, sampling is imperfect, and perhaps they’ve missed pockets of ancient Finnic peoples. But the most thorough analysis of Mesolithic hunter-gatherers in Scandinavian does not pick them up either, Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. Populations, such as the Comb Ceramic Culture, which have been identified as possible ancestors of the modern Finnic culture and ethnicity, lack the distinctive Siberian-like component.

At the SMBE 2017, I saw a poster which had results that were sampled from Finland proper, and distinctive ancestry of Siberian-like peoples was present in an individual who lived after 500 AD. This means that in all likelihood the circumpolar Siberian population which introduced this new element into the East Baltic arrived in the period between 500 BC and 500 AD.

Someone with more knowledge of paleoclimatology and archaeology needs to comment at this point. Something happened in this period, and it probably left a big ethno-linguistic impact. But I don’t know enough detail to say much (the Wikipedia entries are out of date or don’t illuminate).

I will add when I run Treemix Finns get the Siberian gene flow you’d expect. But the Lithuanians get something from the Finns. Since the Lithuanians have appreciable levels of N1c, that is not entirely surprising to me (the basal flow from the Yakut/European region to Belorussians may be more CHG/ANE).

Additionally, I will note that on a f-3 test Lithuanians have nearly as high a z-score (absolute) as Swedes (i.e., Finn; Swede/Lithuanian, Yakut), indicating that the predominant Northern European ancestry isn’t necessarily Scandinavian, as much as something between Lithuanian-like and Swedish-like (on Admixture tests the Finns do seem to have less EEF than Swedes, and Lithuanians probably the least of all among non-Finn peoples).

Addendum: I should note here that the genetics is getting clearer, but I have no great insight into the ethno-linguistic aspect. Perhaps the Siberian-like people did not introduce Finnic languages into the Baltic. Perhaps that was someone else. But I doubt it. That being said, though the Siberian-like component adds great distinctiveness to the Finns, it is important to add that by and large Finns are actually generic (if highly drifted) Northern Europeans.

 

January 29, 2018

Variation with the 1000 Genomes data set in China

Filed under: China,Human Population Genetics,Human Population Genomics — Razib Khan @ 10:09 pm


I have mentioned before that the 1000 Genomes Chinese are heterogenous. Many of the ones sampled in Beijing are North Chinese. But there is structure within the South Chinese samples as well. The PCA above shows it. I’ve pruned some of the data for clarity (it’s probably a cline really, with cut-offs and breaks happening because of variation in population density)

Nothing surprising in the Fst matrix. The two South Chinese groups are close to each other, while the North Chinese are shifted toward the Koreans, who are shifted toward the Japanese.

Admixture analysis shows that the two South Chinese groups can be modeled as a mix of North Chinese and the Dai people of southern China, who are ancestral to the Tai people of Southeast Asia. The “South China 2” cluster is somewhat more Dai than the “South China” cluster proper.

The Miao/Hmong samples from the HGDP are very similar to the South China cluster in admixture analysis (and less Dai than the South China 2 cluster). This is not surprising, as the Miao/Hmong are relatively recent migrants into Southeast Asia from China.

What does Treemix say? Basically, the two South Chinese clusters seem to differ mainly in their Dai proportions (as admixture would imply).  They could be on the same cline, and the perception of structure might be an artifact.

Species are what you want them to be

Filed under: Speciation,species,Species concepts — Razib Khan @ 8:55 pm

What is a species? I don’t know. And honestly, I don’t really care too much.

Species is just a semantic label I place on a set of individuals related to a phylogeny. There tends to be a correlation in genetic variants between these creatures. For sexual organisms, which does not include all organisms, it generally denotes the ability to produce fertile offspring between any two pairs of the opposite sex.

Over ten years ago I read Speciation by Jerry Coyne and H. Allen Orr. As evolutionary geneticists with an interest in taxonomy they take the “species problem” somewhat seriously, but ultimately they’re instrumentalists. “Species” are not the ultimate goal of their scholarship from what I can tell. Rather, species are instruments, semantic tools to smoke out evolutionary processes which shape and determine the pattern of biological variation we see around us. The “origin of species” is less important in relation to the species themselves, as opposed to why we can create categories of species out of the specialized morphological diversity around us.

Not everyone agrees with this position. And not everyone has the same opinion about species. On the whole plant systematists and ecologists will take a different tack on the species problem than evolutionary geneticists. Evolutionary geneticists who work with plants will have a different view from those who work on animals, let alone those who work with bacteria.

The point then is that species are social constructs whose utility and nature varies by discipline. I’m not being a solipsist here. Nature is real. And genetic and phenotypic variation is real. But in some ways the labels we give it can become matters of emphasis.

Of course, I am aware this is an idiosyncratic view. For Carl Linnaeus, the cataloging of species, natural kinds, was cataloging the Creation of God. If you are a Creationist, as most pre-modern people were, then species in their variety and number reflect the will and intention of God. Their study and enumeration would be a glimpse into the mind of the divine.

This doesn’t come out of a vacuum. The religious and Creationist thought simply systematized deep intuitions about the nature of things and biological categories. One doesn’t have to be a genius to make a story about why it would be adaptive to promiscuously and compulsively categorize nature around you. Religious thinkers were simply reshaping and firming up ideas which were in the air.

And this probably brings up why questions about “species” crop up over and over in the comments. And this is why a few times a year I have to put this post up….

Caste in Punjab

Filed under: Genetics,Punjab — Razib Khan @ 9:17 am

Punjabi Genetic Variation In 1000 Genomes: Hindu Caste In The Land Of The Pure?.

I don’t know much about caste in Punjab (Pakistan) at all. But there’s a lot of genetic structure in this Lahore sample (these are people who claim their parents are Punjabis).

January 28, 2018

None dare call it multiregionalism

Filed under: Paleoanthropology,Paleogenetics — Razib Khan @ 11:22 pm

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, and not against it. 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. Others are positing that a “multiregional” model might actually about 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 predominant, at least outside of Africa. But, the whole process might be more much more complex history than we had thought.

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

The rapid fading of information

Filed under: Technology — Razib Khan @ 10:32 pm


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

Filed under: Open Thread — Razib Khan @ 10:07 pm

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.

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

Filed under: Genetics,Punjabi,South Asian Genetics — Razib Khan @ 8:58 pm


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….

January 27, 2018

Anhui, in the shadow of Shanghai

Filed under: China,Province — Razib Khan @ 10:34 pm

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

Filed under: Human Population Genetics,Population genetics — Razib Khan @ 10:00 pm

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.

January 25, 2018

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

Filed under: Human Evolution,Out-of-Africa — Razib Khan @ 10:05 pm

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.

South Asian genetic relationships

Filed under: Genetics — Razib Khan @ 9:37 am

At my other blog. Some charts.

How South Asian populations relate to each other

Filed under: Population genetics,South Asian Genetics — Razib Khan @ 12:45 am

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.

January 24, 2018

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

Filed under: Identity Politics,Politics — Razib Khan @ 11:36 pm


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).

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 it’s determinative character. Or, if 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.

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