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October 6, 2018

The population genetic structure of China (through noninvasive prenatal testing)

Filed under: China genetics,Han genetics,Population genetics,Population genomics — Razib Khan @ 10:03 am


This week a big whole genome analysis of China was published in Cell, Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. The abstract:

We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses.

In The New York Times write-up there is an interesting detail, “This study served as proof-of-concept, he added. His team is moving forward on evaluating prenatal testing data from more than 3.5 million Chinese people.” So what he’s saying is that this study with >100,000 individuals is a “pilot study.” Let that sink in.

The PCA at the top of the post is a bit busy, so I want to highlight the salient aspect. These results confirm that 5-10% of the ancestry of the Hui, Chinese speaking Muslims, is West Eurasian. The Uygur and Kazakh are about ~40% on the left of the plot. The authors note that the Manchus overlapped almost perfectly with individuals sampled from Northern China. This is expected because by the end of the Ching dynasty most of the Manchus had been fully Sinicized, and in the 20th century fully assimilated. Recently due to an emphasis on “national minorities” and some privileges granted therein many people have identified as Manchu due to some ancestry who in all other ways simply northern Han (the Manchu language is moribund).

The sections on particular adaptations which vary by region are not surprising. In books like The Retreat of Elephants the slow, gradual, and inexorable expansion of the Chinese beyond the Yangzi basin is described in a way that makes it clear that southern diseases and climate were a major impediment. But through a process of acclimation, assimilation of local peoples, and adaptation, by 1000 AD the center of demographic gravity had shifted to the south.

There is a section of the text which I think will be falsified though:

After removing participants with 49bp read length and with sequencing error rate >0.00325, a principal component analysis of 45,387 self-reported Han Chinese from the 31 administrative divisions showed that the greatest differentiation of Han Chinese is along a latitudinal gradient (Figures S3E and S3F), consistent with previous studies (Chen et al., 2009, Xu et al., 2009). In contrast, there is, perhaps surprisingly, very little differentiation from East to West. This observation may be explained by the fact that a large proportion of the western Han populations in China are recent immigrants organized by the central government starting from 1949 when the People’s Republic of China was founded (Liang and White, 1996).

I don’t think there’s any need to make recourse to migration from 1949 and after. The argument in Guns, Germs, and Steel suffices: it’s just easier to move across latitudes than longitudes. The people of the north eat noodles made from wheat, and the people of the south eat rice. This is a big cultural transition for peasants to make, and so it didn’t happen as often as moving to the coast, or inland. We have documented instances of mass migrations from adjacent provinces due to famine and political instability. In the 17th century conflicts resulted in the depopulation of Sichuan and the arrival of large numbers of people from Hunan and Hubei to the east.

The plot below is one of the more interesting ones from the paper. From left to right, private alleles found in the HapMap Utah whites also found in all individuals in a given province, and then just Han, and then private alleles to ethnic Telugu Indians (from South India) found in all individuals in a given province, and then just Han.

Click to enlarge

The first thing to notice is that there is a correlation between the Han and non-Han. This shouldn’t be surprising. Plenty of ethnic groups have become Han through acculturation and become demographically absorbed. This is probably truer in parts of the south than in the north, but southern Chinese ethnic minorities are genetically and culturally much more like the Han in the first place.

Private alleles shared with Northern Europeans (CEU) almost certainly has to do with the interaction sphere of the steppe pastoralists, which extends from the Carpathians to Mongolia. The relatively high frequency of R1a, and to a lesser extent R1b, among many Turkic/Central Asian peoples is a pretty good sign of where this West Eurasian ancestry comes from.

The Indian affinity is perhaps more interesting. To be honest I was surprised at the high affinity in Yunnan and Hainan. Tibet has strong cultural connections to India through its form of Buddhism. But its interesting that Qinghai, where many Tibetans also live, does not have the affinity with India. What’s going on in the other provinces? I suspect that the aboriginal peoples assimilated by the Han and other groups in this region probably had some distant connections to the non-West Eurasian ancestry in South Asia.

September 25, 2018

The lineage of the ancient sage kings

Filed under: China genetics — Razib Khan @ 9:27 pm

After recording the “India genetics” podcast for The Insight and reading Early China: A Social and Cultural History, I wonder what surprises we’re going to get from China from ancient DNA when it comes online. If there is one thing we are learning by looking closely at DNA, modern and ancient, it’s that at least for humans there are very few ‘primal’ populations from the “Out of Africa” event which haven’t been threaded together from pulse admixtures of continuous gene flow across the landscape.

Early China makes it clear that Erlitou culture which dates from ~1900 to 1500 BC was almost certainly the legendary Xia dynasty. This means that the ethnogenesis of the modern Han Chinese probably dates to the latest ~4,000 years ago. This is centuries before the Indo-Aryans were likely arriving in South Asia, and around the same time that Indo-European groups were pushing into peninsular Southern Europe.

The Y chromosome data does not indicate a Bronze Age ‘star phylogeny’ expansion in East Asia that I know of, so the dynamics were not entirely similar to Western Eurasia. But, it seems quite plausible that the Han themselves are not a chrysalis from the late Pleistocene.

A cursory examination of the SNP data makes it clear that there is a north-south cline whereby the peoples north of the Yangzi have more West Eurasian admixture than those to the south. In fact, if you look at the PCA and admixture plot you notice that the Japanese have no West Eurasian ancestry. The Yayoi ancestry dominant among the Japanese probably arrived from southern Korea ~2,500 years ago. And, positioned away from the Chinese “mainland” southern Korea was relatively shielded from Inner Asian migrations (I am aware of Korea’s association with Manchuria and the extent of those early kingdoms).

In Empires of the Silk Road, Christopher Beckwith argues strongly for the role of Indo-Europeans in the ethnogenesis of the early proto-Han, through the influence of the Rong, Di, and Qiang. The Qiang were probably proto-Tibetan, but the genetically attested presence of people with overwhelmingly West Eurasian ancestry in areas like Dzungaria during the Bronze Age is well known. Y chromosome R1a1a is found at levels of a few percents among the northern Han, and perhaps as high as ~10% among the Mongolians (though R1b is found among many Uygurs, which is rare for Central Asia).

Beckwith points to the spread of chariot technology from Inner Asia ~1200 BC as strong evidence that Indo-Europeans were somehow involved with the rise of the Shang or Zhou, and so ties them into the emergence of Sinic civilization. Though it is clear that early Chinese chariots were originally derived from Inner Asian exemplars, as Egyptian chariots were, I think it is not unreasonable to suppose this was a case of genuine cultural diffusion and emulation of a useful weapon of war. Consider how quick native peoples in the New World adopted firearms and horses.

Within the next few years, we will have ancient DNA from a wide transect of Chinese history. Unlike some peoples the Chinese are highly historical people, so the genetics will not be stepping into the breach. We even have census records going back 2,000 years, and attempts of scholars to trace migrations based on the changing distribution of the taxable households (though note that some variation in the census count is due to tax dodging during times of political weakness).

I’ll hazard a prediction that most of the West Eurasian admixture into the North Chinese will be seen to be a function of the period after the fall of the Han dynasty and before the Sui-Tang, as well as the influx of Sogdians during the Sui-Tang, and later the arrival of large numbers of Muslims with the Mongolian Yuan. In other words, the shape of modern China on the edges came into being between 300 AD and 1300, as a small proportion of very exotic West Eurasian ancestry became the norm on the North China plain, while a large proportion of far less exotic and quite similar non-Chinese people were instrumental in the development of a distinctive southern Han people, based around particular localities and dialects.

The more interesting story will probably be in the Neolithic, around the time of the rise of agriculture on the North China plain (and in the Yangzi basin).

July 15, 2018

India vs. China, genetically diverse vs. homogeneous

Filed under: China,China genetics,Human Population Genetics,India,India Genetics — Razib Khan @ 1:50 pm

About 36% of the world’s population are citizens of the Peoples’ Republic of China and the Republic of India. Including the other nations of South Asia (Pakistan, Bangladesh, etc.), 43% of the population lives in China and/or South Asia.

But, as David Reich mentions in Who We Are and How We Got Here China is dominated by one ethnicity, the Han, while India is a constellation of ethnicities. And this is reflected in the genetics. The relatively diversity of India stands in contrast to the homogeneity of China.

At the current time, the best research on population genetic variation within China is probably the preprint A comprehensive map of genetic variation in the world’s largest ethnic group – Han Chinese. The author used low-coverage sequencing of over 10,000 women to get a huge sample size of variation all across China. The PCA analysis recapitulated earlier work. Genetic relatedness among the Han of China is geographically structured. The largest component of variance is north-south, but a smaller component is also east-west. The north-south element explains more than 4.5 times the variance as the east-west.

Click to enlarge

Another dimension of the of the variation is that different parts of China are character by different levels of admixture between the Han and other groups. In Northwest China, there is gene flow from West Eurasian sources. In all likelihood, this is through proxy populations, such as Mongols, who are about ~10% West Eurasian. Also, during the period between the fall of the Han Dynasty and the rise of the Sui-Tang Dynasty much of northern China was dominated by barbarian groups from the steppe, and these groups settled down and were absorbed. In Northeast China, the source of admixture is from Siberian and Tungusic group. Again, this makes geographical sense.

In contrast in South China, the gene flow is from indigenous Chinese national groups, such as Dai. This is in keeping with the historical record, whereby South China became Han in the period between 0 and 1000 AD through migration, intermarriage, and acculturation.

Click to enlarge

I have my own small private dataset of Chinese individuals. Some with provenance. Some without. But using known populations I was able to divide China along the north to south cline.  Individuals from Guangdong in the south, those from Shaanxi in the north, and from Zhejiang to Sichuan in the center.

Using Punjabis as a West Eurasian outgroup I was able to plot these individuals on a PCA. If you click to enlarge you will see that a substantial minority of the Han_N sample is shifted to the left of the plot. This is toward the Punjabis. This is not because they have Punjabi ancestry, but because Punjabis are reasonable proxies for West Eurasians.

Click to enlarge

More importantly, I want to compare South Asia to China. To do that I created a small dataset that merged the Han with representative South Asian groups. The first PC, 1 and 2, illustrate the contrast. All three Chinese groups, sampled from the north to the south, occupy a very tight cluster, while the South Asians span PC 2. The Bengalis are shifted a bit to the Chinese, but most of the variance is due to within-South Asian genetic differences.

Click to enlarge

I ran PCA to 10 dimensions. Only at PC 10 did the Han Chinese separate along the north-south access. Most of the earlier PC’s separated out specific castes (e.g, Patels because if their large number in the Gujurati sample were PC 3). Here are the eigenvalues: 53.0682, 2.5641, 2.31876
1.97058, 1.90652, 1.88879, 1.7935, 1.69375, 1.61516, and 1.54207. The large value for PC 1 is what you’d expect, it’s a continental scale difference. PC 2 differentiates South Asia from north to south. It’s much more modest. The other PCs get progressively smaller, but within the data, it’s clear that the continental size difference is the big one. The variance between north and south China is a small one in a South Asian scale.

Click to enlarge

Pairwise Fst is more ambiguous. That’s probably because most of the South Asian samples have structure within them. Merging them into one pooled population just confuses the issue.

Using a South Asian dataset where groups are disaggregated makes a lot more sense, and you see the structure between the different groups.

Click to enlarge

Running Treemix gives similar results. The South Asian groups exhibit a fan-shaped topology, where the Han cluster tightly together. Since I removed Bengalis from Treemix adding migration edges doesn’t do anything between the two clusters, so I omitted those results.

Click to enlarge

Finally, of course I ran some admixture analysis. Using South Asians + Han Chinese, I thought K = 4 would be reasonable. Even if you don’t enlarge, the results are straightforward: the Han Chinese have very little diversity in unsupervised mode. A small South Asian-like component, which has affinities with Punjabis, is found in northern Han. This confirms other results with other methods that the northern Han have some West Eurasian gene flow.  Some of the southern and central Han have an affinity with one of the South Indian clusters. I think is artifactual, due to deep structure within Eastern Eurasian populations and affinities between those groups that the Han absorbed as they moved south.

This post doesn’t really shed new light on anything we didn’t know. Rather, it’s just a review of what jumps out at anyone who works with genotype data: there is not very much genetic diversity in China and there is a great deal of genetic diversity in India. Why? These are not questions genetics can really answer directly, though it can give us clues and support certain models over others.

Anyone who has read much about Chinese history knows that the cultural ideal of meritocracy is deeply ingrained, even if it is honored in the breach quite often. Chinese civilizations has been characterized by the domination of extended pedigrees (e.g., the Xianbei-Han ruling faction among the Tang), but those pedigrees never become ethno-religious castes. The exception occurred during the Yuan (Mongol) period where Kublai Khan entered into a divide-and-rule policy. But that was a short period which had no longer term cultural consequences.

In contrast, South Asia is characterized by long-term endogamy. This is not surprising to anyone who knows anything about South Asian history. The genetic evidence suggests that modern jati-barriers emerged around ~2,000 years ago. Not only do South Asian groups differ a great deal in biogeographic ancestry (deep ancestry), but historical endogamy has resulted in further drift between these groups.

May 1, 2018

Hui have a lot of West Eurasian Y chromosomes

Filed under: China genetics,Hui — Razib Khan @ 1:26 am
O C R1a R1b R2 E1b G H I1 I2 J1 J2 L N Q T Total N
Han 258 12 2 2 2 1 1 2 1 1 7 9 2 300
Hui 24 7 21 1 9 1 3 1 1 4 1 11 1 3 14 4 106
Tibetan 49 11 18 1 1 3 3 3 3 7 1 100

It’s been a while since I checked in on the genetics of the Hui people. I found the paper, Analysis of 17 Y‐STR loci haplotype and Y‐chromosome haplogroup distribution in five Chinese ethnic groups. About 50% of the Y chromosomal haplogroups are normally classified as “West Eurasian” (R, E, G, I and J). But curious a fraction of the Han have these too, as do some Tibetans.

Additionally, know that some Mongols also have R1a1a. It’s hard to differentiate different periods of admixture. But to me the presence of R2 and J2 point to a Central/South Asian origin of a lot of the Hui R1a as well.

August 1, 2017

The great genetic map and history of China

Filed under: China genetics — Razib Khan @ 8:49 pm


About 20 percent of the world’s population is Chinese (and since over 90% of Chinese citizens are ethnically Han, so by Chinese here I mean Han to a first approximation). In comparison to other non-European groups a fair amount of genetics research has been done with Chinese populations. But in comparison to their overall numbers, not too much has really been done. That will change.

A new preprint, A comprehensive map of genetic variation in the world’s largest ethnic group – Han Chinese, aims to enrich our knowledge set somewhat. The authors used low coverage next generation sequencing to get increase their sample sizes greatly (cheaper). By low coverage, I mean instead of hitting each genetic position on average 30 times or more, as is in the norm in medical genomics, they sampled a position closer to twice.

But while any given genome was usually not given much close attention, their overall sample size of individuals was 11,670 Han Chinese women. Impressive This means that if they called a position as a variant, they could assess their confidence that it was a variant by looking at how many times it was called as a variant across their data set (as coverage declines one’s confidence that a call of a variant is a true call declines because there is a relatively high base rate of error set against the proportion of true expected polymorphisms; in contrast if you sample 30 times the error rate gets overwhelmed by repeated sampling). Overall they counted 25,057,223 variants, which sounds about right. They also found 548,401 novel variants with at least a count of 10 in the data set (a ~0.04% allele frequency, so a very low cut-off).

The most important thing about this preprint is not that the sample size is large enough that they could detect low frequency variants and add to the catalog. No, for me, it is that they sampled so many of the provinces. As you can see in the figure up top just like Europe China’s Han population recapitulate the map of China. That is, populations arrange themselves spatially when projected onto a principle components analysis plot in the same manner that they do geographically. This is a new finding in some ways because previous sampling strategies had not been robust enough to detect the east-west cline (though to be honest if you looked at the Chinese samples in the 1000 Genomes there was suggestion of this).

All that being said, please note that the PCA is not to scale, insofar as most of the variation is north-south (4 to 5 times more than east-west). Rather like Europe in this regard. Part of this difference is due to the fact that gene flow from non-Han populations, particularly in the South, inflate the genetic variation on the first dimension. Another aspect of interest is that genetic variation between Han populations is rather low to begin with.

One way to visualize this is a matrix like the one to the left. You see pairwise population Fst statistics. The largest is between Guangdong in the south, home to Hong Kong and Guangzhou (Canton), and the northern provinces. The Fst value between Guangdong and Shanxi in the center-north is 0.0029. You may know that the Fst value between Han Chinese and Northern Europeans is ~0.10. A 34 factor difference, more than one order of magnitude. As a point of comparison you can find Fst tables which show values between English and Croations and English and Spaniards are about the same as between Guangdong and Shanxi.

What is just as interesting is the very low genetic differentiation on the North China plain. Why is this? There are two reasons I can think of. The easy explanation is that across politically unified flat landscapes gene flow occurs so easily that genetic differences disappear over time.

But, this presupposes there were genetic differences in the first place. The reason I say this is that though there was a early period of migration from the north to the south (from the Han dynasty onward), and absorption of non-Chinese peoples, there were also periods when much of China north of the Yangtze river valley was under barbarian domination or politically unstable. Elite northern families fled to the south, and eventually when political stability reemerged migrated back to the north (similarly, persistent north-south migration occurred, as the Hakka people of South China are clearly of northern provenance).

The low genetic differentiation across northern China may then be thought of as the outcome of structural fixtures of the landscape (no mountains to obstruct gene flow), as well as possibly due to historical instances of copious back-migration from various regions of southern China (or perhaps more accurately Central China, as I’m presuming much of the settlement would come from the lower Yangtze river valley). Both of these dynamics may have led to little intra-regional structure. In contrast you notice that genetic distance between Fujian and Guangdong, two regions adjacent to each other in the South, is still higher than between any of the northern regions.

Again, this is not surprising due to both geography and history. The dialect map of China shows that southeast China is more fragmented than the north (or southwest). These differences are long-standing and date to the initial founding of Han communities in the south via migrants from the north. Unlike North China South China is a topographically diverse landscape, with beautiful escarpments and deep gorges. Fujian literally hugs the ocean, and has long had a relationship to overseas communities for this reason. Geographic barriers mean there are genetic barriers. Combined with admixture with local populations this means it is not surprising that there were greater genetic differences between southern regions than in the north.

Additionally, China south of the Yangtze has been relatively shielded from foreign conquest and invasion compared to the North China plain. Obviously events like the Taiping rebellion and famine more generally had impacts on South China, but North China has had more periods of domination in a destabilizing manner by non-Chinese invaders over the past 2,000 years.

Perhaps more intriguing than the modern genetic relationships within China are the relations with non-Chinese populations. It is not surprising that the South Chinese populations show evidence of admixture with Dai and Tawainese aboriginals (the basal group of the Austronesian migration). The genetics and cultural practices in parts of South China have long suggested relationships to indigenous groups, as well as Sinicization. Honestly I suspect many were surprised how similar North and South Chinese were, indicating either continuous gene flow or descent from a large demographic expansion.

More curious is that some North Chinese seem to show evidence of admixture with West Eurasians. In particular, they show affinities with European populations. Again, this is not surprising. Some earlier analyses have shown evidence of European-like admixture in northern China, and among ethnic groups like Mongolians. More precisely there are strong signals of European-like admixture in the northwestern provinces of Gansu, Shaanxi, and Shanxi.

The details here are important though. The authors note that Hellenthal et al. detected admixture in the from Northern Europeans into North China using haplotype based methods to around 1200 AD. This preprint finds a similar admixture date. But they caution that these admixture dates may only signal the latest of the events.

As for what that event could be, there was clearly turmoil on the Silk Road in the years around 1000 AD. After 750 AD for all practical purposes the Chinese lost control of their portion of the Silk Road, what is now Xinjiang. Turkic groups like Uyghurs and Iranian ones such as Sogdians were prominent in China due to a power vacuum (the Uyghurs were used by the Tang emperors like the Germans were used by the later Roman Emperors, as federates). Later on one saw the emergence of Tanguts, various groups from Manchuria, and finally the Mongols. Since both haplotype based methods and these preprint suggest something around 1000 AD, the most likely candidate was the absorption of Central Asians with some European-like ancestry into the Chinese substrate. The Uyghur conquest of the major cities of in the centuries before the rise of the Mongols famously resulted in the assimilation of a European-like population which had earlier spoken Indo-European languages.

But admixture was not a feature of just recent Chinese history. The figure to the right is somewhat difficult to read, but it shows on the y-axis variance in the f3 statistic. In short, how well does the Chinese data set here form a clade with the outgroup, and how much does that statistic vary between groups. The x-axis is for the D statistic, which measures the relationship of four populations, with two clades. On the bottom left you see the Siberian genome from 45,000 years ago. On the y-axis you can see all provinces show very little variation, and that’s because the Siberian genome is old enough that it is basal to all the Chinese and Europeans. The D statistic indicates no gene flow between the Siberian populations and modern groups. Not so with other populations. You see the Pleistocene European populations are shifted to the right, and that’s because they all contribute to later Europeans. The Chinese-European clade is not a good fit. This is true across the Chinese populations (so the variance of the f3 statistic is very low),.

Also in the text they note that there is high shared drift with the three “Ancient North Eurasian” (ANE) samples from Siberia. This is discussed extensively in the supplements to Lazaridis et al. 2016. Another replicated finding is that the Chinese share drift with ancient European hunter-gatherers. The drift declines later on, likely because the Chinese do not share as much drift with the early farmers. This is due in part to the “Basal Eurasian” (BEu) element. But in Fu et al. 2016 they observe that drift between East Eurasians and European hunter-gatherers increases after 15,000 years BP, when there was a genetic turnover, and the Villabruna cluster (in their terminology) came to dominate the landscape.

The most probable, though not certain, explanation for this pattern is that ANE populations contributed ancestry to both antipodes of Eurasia. To European hunter-gatherers, and, to the ancestors of the Chinese in Pleistocene East Asia (remember that there was a fusion between a proto-East Asian population and ANE to give rise to the ancestors of Amerindians 15-20,000 years ago). Another explanation could be East Asian gene flow rather early on into Europe, some time after the Last Glacial Maximum ~20,000 years ago. We don’t have the sample density outside of Europe to really say with certainty.

Finally, I have to mention that at SMBE Melinda Yang of Qiaomei Fu’s lab gave a talk about the Tianyuan genome. Their group has found that the Tianyuan individual, who dates to 40,000 years ago, is the likely ancestor of modern East Asians. That is, Tianyuan shares more drift with modern East Asians than Europeans. No huge surprise. What was surprising though is that Tianyuan also shared appreciable drift with GoyetQ116, a 35,000 year old sample from Belgium, whose descendants seem to have played a role in the emergence of the Magdalenian culture. But not later European hunter-gatherer populations. The Tianyuan sample also seemed to share some drift with Australasian samples (a possible resolution for why some Amerindians share drift with Oceanians presents itself here obviously). Overall, the group’s conclusion was that this might be evidence of ancient population structure rather early on in the “Out of Africa” populations, which eventually carried over as the groups dispersed (rather than each geographic region being direct descendants from a single panmictic “Out of Africa” group). The implications here are beyond the purview of Chinese genetics so I’ll address it in a later post.

I have to mention there is a fair amount within this paper on selection as well as medical genetics. I didn’t tackle that in this post since there’s so much phylogenomics one could talk about.

Charleston W. K. ChiangSerghei MangulChristopher R. RoblesWarren W.KretzschmarNa CaiKenneth S. KendlerSriram SankararamJonathan Flint

July 27, 2011

How Chinese genetics is like Chinese food

Representatives of Szechuan and Shangdong cuisine

The Pith: The Han Chinese are genetically diverse, due to geographic scale of range, hybridization with other populations, and possibly local adaptation.

In the USA we often speak of “Chinese food.” This is rather peculiar because there isn’t any generic “Chinese cuisine.” Rather, there are regional cuisines, which share a broad family similarity. Similarly, American “Mexican food” and “Indian food” also have no true equivalent in Mexico or India (naturally the novel American culinary concoctions often exhibit biases in the regions from which they sample due to our preferences and connections; non-vegetarian Punjabi elements dominate over Udupi, while much authentic Mexican American food has a bias toward the northern states of that nation). But to a first approximation there is some sense in speaking of a general class of cuisine which exhibits a lot of internal structure and variation, so long as one understands that there is an important finer grain of categorization.

Some of the same applies to genetic categorizations. Consider two of the populations in the original HapMap, the Yoruba from Nigeria, and the Chinese from Beijing. There are ~30 million ...

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