Genetic variation in South Asia

I don’t have too much time right now. So a quick data post. The map above shows India’s scale in relation to Europe.

Below is an NJ tree that shows pairwise Fst values (genetic distance):

Please notice the small genetic difference between Britain/Spain/Poland. Compare to Gujrati vs. Sindhi, let alone Gujrati vs. Telegu.

Now, PCA:

Genetically Sindhis occupy a place between South Indians and Iranians. Some Gujaratis are nearly where Sindhis are, but many are far more shifted toward South Indians. The Fst display masks this since it aggregates populations.

Treemix shows the relationships and their scale. South Asians have a lot of drift between them.

Some of you are probably bored by this post and wonder about it’s practical implication. If so, keep on paging down (or up).

Genetical observations on caste

One of the more interesting and definite aspects of David Reich’s Who We Are and How We Got Here is on caste. In short, it looks like most Indian jatis have been genetically endogamous for ~2,000 years, and, varna groups exhibit some consistent genetic differences.

This is relevant because it makes the social constructionist view rather untenable. The genetic distinctiveness of jati groups is very hard to deny, it jumps out of the data. The assertions about varna are fuzzier. But, on the whole Brahmins across South Asia have the most ancestry from ancient “steppe” groups, while Dalits across South Asia have the least. Kshatriya is closer to Brahmins. Vaisya has lower fractions of “steppe”. And so on. These varna generalizations aren’t as clear and distinct as jati endogamy. Sudras from Punjab may have as much or more “steppe” than South Indian Brahmins. But the coarse patterns are striking.

As a geneticist, and as an irreligious atheist, a lot of the conversations about “caste” are irrelevant to me. They’re semantical.

You can tell me that true Hinduism doesn’t have caste, that it was “invented” by Westerners. They may not have had caste, but the genetical data is clear that South Asians were endogamous for 2,000 years to an extreme degree. Additionally, the classical caste hierarchy seems to correlate with particular ancestry fractions.

Second, you can say Islam, Sikhism, Jainism, and Buddhism don’t have caste. That they picked it up from Hinduism. Or Indian culture. That’s true. But I think Islam, Sikhism, Jainism, and Buddhism are all made up, just like Hinduism. I don’t care if made up ideologies don’t have caste in their made up religious system. I am curious about the revealed patterns genetically.

I have a pretty big data set of South Asians. Some of them are from the 1000 Genomes. Here is where the 1000 Genomes South Asians were collected:

Gujarati Indians from Houston, Texas
Punjabi from Lahore, Pakistan
Bengali from Dhaka, Bangladesh
Sri Lankan Tamil from the UK
Indian Telugu from the UK

Some of the groups showed a lot of genetic variation, so I split them based on how much “Ancestral North Indian” (ANI) they had. So Gujurati_ANI_1 has more ANI than Gujurati_ANI_2 and so forth.

Continue reading “Genetical observations on caste”

American Caste

Our featured post modernist scholar Daria Roithmayr appears to believes that America has four castes: caucasions, latinos, blacks, asians; and emphasizes the importance of caste (which she calls “race”) over class in understanding how the world works and changing societal socio-economic outcomes. And our featured hero, leader of the intellectual dark web, global respected elder, and leading global intellectual Glenn Loury believes in emphasizing class over caste. I am 200% with my hero Glenn Loury on emphasizing class over caste.

Discussions at Brown Pundits seem to be overrun with discussions on caste that I don’t fully understand. The parallels of caste in the muslim world (various different sects of Islam), Arya societies (Iran, Hindu Jain Buddhist influenced societies) and America are uncannily similar. Perhaps a discussion of American caste might help lower extreme passions and facilitate a more productive discussion of caste in muslim societies and Arya influenced societies.

Start watching 35 minutes in if interested.

Daria Roithmayr believes that due to a series of historical events humans are not born with the same social capital. This inequality in social capital is inherited across generations and she believes drives differences in average socio-economic outcomes between America’s four castes. The way she believes social capital in inherited across generations is:

  1. Inter-generational wealth transfer from parents to children [I think this is easily overcome]
  2. Rich kids go to better public schools funded by high property tax revenues [I don’t think school funding matters as much as she does. Expensive versus cheaper public schools matter far less than the power of “good company”, or the effect of kids being surrounded by other amazing kids.]
  3. Social networks [this or the power of “good company” is even more important and valuable than she thinks]
  4. Leadership of or influence on social networks [I don’t think I understand this point]

Daria Roithmayr is right that social capital advantage is inherited across generations. My belief is the way social capital transfers across generations is through affecting four types of privilege:

  1. Physical health [Sharira Siddhi in Sanskrit]
  2. Mental health [Chitta Shuddhi in Sanskrit]
  3. Intelligence [Buddhi in Sanskrit] {Intelligence is affected by physical and mental health as well as by meditation in eastern philosophy}
  4. Good company [This is the least important of the four and primarily works via the influence good company has on physical and mental health and intelligence. There is an eastern saying: “tell me your company and I will tell you who you are”. Social networks or what Glenn Loury calls “relations over transactions” is part of “good company”.]

The other issues Daria is discussing has a far smaller effect on inter-generational social capital transfer than these four.

Is American culture sharply increasing crime?

The US is currently experiencing the second largest increase in crime since statistics began to be tabulated, the largest increase in crime being in the 1960s and 1970s. From “Crime in California 2016” Table 5, page 9 in document, page 13 in PDF, the total number of forcible rapes in California increased by 49.3% between 2014 (8,562) to 2016 (12,785). From Table 1, page 5 in the document, page 9 in the PDF:

  • Homicides increased 13.7% between 2014 (1,697) and 2016 (1,930)
  • Robberies increased 12.6% between 2014 (48,650) and 2016 (54,769)
  • Aggravated Assault increased 13.8% between 2014 (91,681) and 2016 (104,307)

To better understand the massive US crime wave, I decided to calculate crimes committed  by various ethnic groups.

This article will use California crime data since US national level data on crime for Latino Americans and Asian Americans is usually not publicly released by the US government; perhaps for fear of what such data would show. I suspect that US and Canadian nationwide data would show similar trends. California demographic data by ethnicity is taken from 2015 US Census Bureau estimates. From “Crime in California 2016” Table 30, page 33 in document, page 37 in PDF, “Felony and Misdemeanor Arrests” 2016:

  • Caucasions were 4.99 times more likely to be arrested than Asians
  • Hispanics were 5.91 times more likely to be arrested than Asians
  • Blacks were 17.04 times more likely to be arrested than Asians
  • Non Asian Others (mostly native Americans) were 3.38 times more likely to be arrested than Asians

Arrest data by Asian country are also available; but Asians commit so few crimes that such data would be skewed by the law of small numbers. However you are free to research it yourself. The spreadsheet used for these calculations is available upon request.

Total crimes committed by caucasions, hispanics, blacks and “other” are released by category. “Other” is not broken down into Asian and non Asian other. However if we assume that non Asian others commit 3.38 times as much crime as Asians (a stretch to be sure), then:

Total homides by race from “Crime in California 2016” Table 31, page 34 in document, page 38 in PDF:

  • Caucasions were 2.44 times more likely to commit homicide than Asians
  • Hispanics were 4.44 times more likely to commit homicide than Asians
  • Blacks were 17.23 times more likely to commit homicide than Asians

Total robbery by race:

  • Caucasions were 4.63 times more likely to commit robbery than Asians
  • Hispanics were 7.96 times more likely to commit robbery than Asians
  • Blacks were 44.19 times more likely to commit robbery than Asians

Total rape by race:

  • Caucasions were 3.13 times more likely to commit rape than Asians
  • Hispanics were 5.44 times more likely to commit rape than Asians
  • Blacks were 12.24 times more likely to commit rape than Asians

Total assault by race:

  • Caucasions were 4.44 times more likely to commit assault than Asians
  • Hispanics were 5.48 times more likely to commit assault than Asians
  • Blacks were 15.44 times more likely to commit assault than Asians

Total kidnapping by race:

  • Caucasions were 3.92 times more likely to commit kidnapping than Asians
  • Hispanics were 6.52 times more likely to commit kidnapping than Asians
  • Blacks were 18.42 times more likely to commit kidnapping than Asians

If we assume that non Asian others are 3.38 times more likely to be incarcerated than Asians, then from 12.31.2.10:

  • Caucasions were 4.18 times more likely to be incarcerated than Asians
  • Hispanics were 5.8 times more likely to be incarcerated than Asians
  • Blacks were 25.2 times more likely to be incarcerated than Asians

Continue reading “Is American culture sharply increasing crime?”

Intellectual Dark Web

I would define the “intellectual dark web” as the confluence and convergence of leaders from classical European enlightenment, hard sciences, technology (including neuroscience, bio-engineering, genetics, artificial intelligence), and east philosophy streams. Among the intellectual dark web’s many members are Dr. Richard Haier, Jordan Peterson, Jonathan Haidt, Ben Shapiro, Weinstein brothers, Sam Harris, Glenn Loury, John McWhorter, Yuval Noah Harari, Thomas Friedman, Maajid Nawaz, Neil deGrasse Tyson, Michio Kaku , Dr. VS Ramachandran, Steven Pinker, Armin Navabi, Ali Rizvi, Farhan Qureshi, Peter Beinart, Gad Saad, Nassim Nicholas Taleb, Dave Rubin, Joe Rogan, Russell Brand.  If Steve Jobs were still alive, I would include him among them. They defy easy labels and are high on openness. I hesitate to label others without their permission, but our very own Razib Khan strikes me as a potential leader of the “intellectual dark web”; although I will withdraw this nomination if he wishes. 😉

Some see the intellectual dark web as the primary global resistance to post modernism. I don’t agree. Rather I see them as ideation and intuition leaders thinking different:

Continue reading “Intellectual Dark Web”

Closing the genetic chapter

Indus Valley People Did Not Have Genetic Contribution From The Steppes: Head Of Ancient DNA Lab Testing Rakhigarhi Samples:

In other words, the preprint observes that the migration from the steppes to South Asia was the source of the Indo-European languages in the subcontinent. Commenting on this, Rai said, “any model of migration of Indo-Europeans from South Asia simply cannot fit the data that is now available.”

Some more comments at my other weblog.

At this point, we need to move to other things. I think the broad genetic framework is pretty clear.

1) The Indus Valley Civilization (IVC) people were a mix of eastern West Asian (from modern Iran) people and native South Asian peoples (~80% of South Asian mtDNA are haplogroup M).

2) ~1500 BC a major incursion from the steppe occurred and overlaid upon #1 to various extents as a function of region, language, and caste.

3) ~0 to 500 AD the strong endogamy that characterizes modern South Asians seems to have established itself.

Ancient Egyptian, Arya and Greek history part 2

This article is a continuation of previous articles on ancient history from Zachary, Razib, Omar and myself:

Continue reading “Ancient Egyptian, Arya and Greek history part 2”

The water rises and Canute drowns

The Genetic History of Indians: Are We What We Think We Are?. The answer is that people of all races have always been what they always were. What we think about what we were…well, that changes.

“I KNOW PEOPLE won’t be happy to hear this,” geneticist Niraj Rai says over the phone from Lucknow. “But I don’t think we can refute it anymore. A migration into [ancient] India did happen.” As head of the Ancient DNA Lab at Lucknow’s Birbal Sahni Institute of Palaeosciences (BSIP), he earlier worked at the CCMB in Hyderabad and has been part of several studies that employed genetics to examine lineages. “It is clear now more than ever before,” he says, “that people from Central Asia came here and mingled with [local residents]. Most of us, in varying degrees, are all descendants of those people.”

Some researchers, even those associated with the current study like Shinde, aren’t quite convinced that an ancient influx of people into the subcontinent from the northwest has finally been established by the latest findings. Shinde does not like the word ‘migration’. “It is better to say movement,” he says, implying a two-way pattern. “Everyone back then was moving to and fro. Some people were moving here and some were moving out. There was contact, yes. There was trade. But local people were involved in the development of several things. So I am not very sure of the interpretation.”

As Rai points out, the analysis of the DNA sample they will present will be of a period before the Steppe people supposedly arrived in India. If R1a is absent in the Indus Valley sample, it suggests that it was brought into South Asia, perhaps by a proto-Indo- European speaking group, from elsewhere. “How do I say it? See, I am a nationalist,” Rai says over the phone. “People will be upset. But that’s how it is. All the studies are showing that people came here from elsewhere.”

I’ve been hearing from Indian journalists that some of these researchers have only “evolved” over the last few months. First, it’s a credit to them if they changed their views on the new data. If the above is correct they got usable DNA from one Rakhigarhi sample. I predict it will be like “Indus Periphery”, but with more AASI. It seems rather clear they’re going to submit a preprint within a month or so (that’s the plan, but it’s been the plan for a year!), but the results are being written up now.

Meanwhile, the ancient DNA tsunami is going to come in further waves in the near future. Various groups have huge data sets from Central Eurasia that are going to surface. Unfortunately, samples are going to be thin on the ground from India, but we have enough now that in broad sketches most people are now falling in line with what happened demographically from the northwest. The “AASI” ancestry is deeply rooted in South Asia, and it doesn’t look like there’s much of an impact of this outside of the subcontinent aside from nearby regions.

The real action is now in understanding the cultural and archaeological processes involved in the perturbation in the years after 2000 BCE. I’ve talked to a few of the geneticists working in this area over the past month or so, and they agree.

South Asian genetics, the penultimate chapter

A long post at my other blog, The Maturation Of The South Asian Genetic Landscape, a reflection on the important preprint The Genomic Formation of South and Central Asia. Shorter:

  1. The original inhabitants of the Indian subcontinent who descent from the “out of Africa” migration separated very quickly, ~50,000 years ago, from other eastern populations (East Asians, Andaman Islanders, Papuans, etc.). These are the “Ancient Ancestral South Indians” (AASI).
  2. Agriculturalists from what is today Iran seem to have entered and mixed with the AASI in the Indus Valley earlier than 5,000 years ago, and possibly as early as 9,000 years ago. The only samples they have are from extra-Indian sites, in Central Asia and eastern Iran, as outlier individuals. They call these “Indus_Periphery” (I call then InPe).
  3. The “Ancestral South Indians” (ASI) were created from a mixing of InPe with AASI still extant in much of South Asia ~4,000 years ago.
  4. Between ~4,000 and ~3,200 years ago populations from the steppe arrive, carrying admixture from Iranian farmers, as well as people from the steppe (Andronovo-Sintashta?). They mix with the ASI population, though a few groups, such as the Kalash, mix directly with InPe, and create unmixed “Ancestral North Indian” (ANI).
  5. Subsequent mixing between ASI and ANI populations in various fractions accounts for most of the variation in South Asia.
  6. Some groups are enriched for “steppe” as opposed to the Iranian agriculturalist that first came with InPe. In particular, Brahmins. The hypothesis then is differential ancestry of Indo-Aryan heritage persists to this day.
  7. The Munda of northeast India have a somewhat different origin, mixing Southeast Asian ancestry with ASI and further AASI. The fact that unmixed AASI were present in South Asia indicates that the Munda arrived before the full mixture was complete. Though Austro-Asiatic expansion into northern Vietnam dates to ~4,000 BC, so I think it can’t be that early.

Things I now think are unlikely:

  • Indo-Aryan interpenetration with non-Indo-Aryans in the IVC before 4,000 years ago (I was somewhat agnostic on this). The date for migration now seem very close to the “Classical Model” of arrival around 1500 BC.
  • The AASI is very diverged from the Onge, who form a clade with mainland Southeast Asian Negritos. I now think it is likely that the AASI were primal, and not migrants from Southeast Asia.

It would be nice if the results were published from the Rakhigarhi site, which dates to 4,600 years ago. But it seems less and less necessary. Perhaps at some point we’ll get enough samples from Pakistan to generate a reasonable model….

Neoliberalism

Thomas Friedman is one of the world’s greatest champions of neoliberalism. Neoliberalism works great when most people have high levels of physical health, mental health (called Chitta Shuddhi in Sanskrit) and intelligence (called Buddhi in Sanskrit).  In my opinion human beings can acquire these things through their own effort. [Many neuroscientists disagree with me that “environment” can appreciably increase measured IQ.]

Listening to Thomas Friedman makes clear how much new technologies such as AI benefit those with physical, mental health and intelligence. In my view countries with less post modernist syndrome (which colonizes the mind with inferiority complex, a lack of self confidence, and a lack of freedom of thought, intuition and feeling) especially benefit from globalized neoliberalism and technological innovation. Implicitly this benefits Asians. Very soon China will have more billionaires than America; India too will follow in less than a generation. How will post modernists react?

Continue reading “Neoliberalism”