Caste in India: genetics and heredity (easy reading)

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The origin of the caste-system

Genetics Proves Indian Population Mixture

A new study indicates that population admixture in the pre-caste era occurred, shedding light on our understanding of present-day Indian populations


August 8, 2013


Between 4,000 and 2,000 years ago, intermarriage in India was rampant. Figure by Thangaraj Kumarasamy

Scientists from Harvard Medical School and the CSIR-Centre for Cellular and Molecular Biology in Hyderabad, India, provide evidence that modern-day India is the result of recent population mixture among divergent demographic groups.

The findings, published August 8 in the American Journal of Human Genetics, describe how India transformed from a country where mixture between different populations was rampant to one where endogamy—that is, marrying within the local community and a key attribute of the caste system—became the norm.

“Only a few thousand years ago, the Indian population structure was vastly different from today,” said co–senior author David Reich, professor of genetics at Harvard Medical School. “The caste system has been around for a long time, but not forever.”

In 2009, Reich and colleagues published a paper based on an analysis of 25 different Indian population groups. The paper described how all populations in India show evidence of a genetic mixture of two ancestral groups: Ancestral North Indians (ANI), who are related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI), who are primarily from the subcontinent.

However, the researchers wanted to glean clearer data as to when in history such admixture occurred. For this, the international research team broadened their study pool from 25 to 73 Indian groups. The researchers took advantage of the fact that the genomes of Indian people are a mosaic of chromosomal segments of ANI and ASI descent. Originally when the ANI and ASI populations mixed, these segments would have been extremely long, extending the entire lengths of chromosomes. However, after mixture these segments would have broken up at one or two places per chromosome, per generation, recombining the maternal and paternal genetic material that occurs during the production of egg and sperm.

By measuring the lengths of the segments of ANI and ASI ancestry in Indian genomes, the authors were thus able to obtain precise estimates of the age of population mixture, which they infer varied about 1,900 to 4,200 years, depending on the population analyzed.

While the findings show that no groups in India are free of such mixture, the researchers did identify a geographic element. “Groups in the north tend to have more recent dates and southern groups have older dates,” said co-first author Priya Moorjani, a graduate student in Reich’s lab at Harvard Medical School. “This is likely because the northern groups have multiple mixtures.”

“This genetic datatells us a three-part cultural and historical story,” said Reich, who is also an associate member of the Broad Institute. “Prior to about 4000 years ago there was no mixture. After that, widespread mixture affected almost every group in India, even the most isolated tribal groups. And finally, endogamy set in and froze everything in place.”

“The fact that every population in India evolved from randomly mixed populations suggests that social classifications like the caste system are not likely to have existed in the same way before the mixture,” said co–senior author Lalji Singh, currently of Banaras Hindu University, in Varanasi, India, and formerly of the CSIR-Centre for Cellular and Molecular Biology. “Thus, the present-day structure of the caste system came into being only relatively recently in Indian history.”*

But once established, the caste system became genetically effective, the researchers observed. Mixture across groups became very rare.

“An important consequence of these results is that the high incidence of genetic and population-specific diseases that is characteristic of present-day India is likely to have increased only in the last few thousand years when groups in India started following strict endogamous marriage,” said co–first author Kumarasamy Thangaraj, of the CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.**

Mohan Rao, Director, CSIR-CCMB said, “CCMB's continuing efforts over a decade on this field had helped in understanding the complexity of Indian population history and social structure, such as caste systems.”

This study was funded by the NIH (GM100233); NSF (HOMINID grant 1032255); a UKIERI Major Award (RG-4772); the Network Project (GENESIS: BSC0121) fund from the Council of Scientific and Industrial Research, Government of India; a Bhatnagar Fellowship grant from the Council of Scientific and Industrial Research of the Government of India; and a J.C. Bose Fellowship from Department of Science and Technology, Government of India.

  • , ** Quotes adapted from American Journal of Human Genetics news release.

Caste linked to skin colour, marriage patterns, multi-layered endogamy

Skin colour tied to caste system, says study, Nov 21 2016 : The Times of India

Scientists from the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad recently discovered that genetic differences and caste system were the main reasons behind the region-wise variation in the skin colour of Indians.

The study , which was led by senior scientist Dr Kumarasamy Thangaraj in collaboration with Estonian Biocentre and five other research institutes, has been published in the Journal of Investigative Dermatology . It indicates that social structure defined by the caste system has a “profound influence on skin pigmentation“. The team had studied 1,825 individuals belonging to 52 diverse populations across India with regard to the caste-colour concept.

“Unlike Africans and Europeans, we do not have homogeneous skin colour throughout the country. This could be due to different waves of human migration into India and recent admixture of all Indian populations,“ Dr Thangaraj said, adding that skin colour was found to vary significantly among ethnic groups and social categories.

“We did extensive epidemiological survey of 1,167 individuals belonging to 27 populations and quantified melanin content at the mostexposed and least-exposed area of human body in the Gangetic plains (Uttar Pradesh and Bihar). We had selected 374 individuals for the first round of genetic study ,“ said Dr Anshuman Mishra, one of the researchers.

The researchers found that gene SLC24A5, which is known to make skin colour lighter, has two variants, which together contribute to the variation in skin colour among Indian populations.

“Our study clearly reflects the profound influence of strict marriage patterns and multi-layered endogamy adding further to the variation in skin colour,“ said another researcher Dr Chandana Basu.

“This is yet another effort of the Centre for Cellular and Molecular Biology in the field of genomics, which helped us in understanding the genetic link to skin colour,“ said CCMB director Dr Rakesh Mishra, adding that the study will help deliver individual specific lifestyle advisory and medical prescriptions.

Caste and Genetic Disease

STEPH YIN | In South Asian Social Castes, a Living Lab for Genetic Disease | JULY 17, 2017 | The New York Times

In certain states in southern India, anesthesiologists know to ask anyone undergoing surgery whether they belong to the Vysya, a regional group traditionally associated with traders and businesspeople.

Anecdotally, medical workers know that some people with Vysya ancestry — who live primarily in Andhra Pradesh and Telangana — have had fatal responses to common muscle relaxants, so doctors will use a different combination of drugs.

The Vysya may have other medical predispositions that have yet to be characterized — as may hundreds of other subpopulations across South Asia, according to a study published in Nature Genetics on Monday. The researchers suspect that many such medical conditions are related to how these groups have stayed genetically separate while living side by side for thousands of years.

South Asians should be viewed not as a single population but as thousands of distinct groups reinforced by cultural practices that promote marrying within one’s community. Although recent changes to cultural norms have resulted in more marriages between members of different groups like castes or subcastes, especially in some urban areas, gene flow between populations was restricted for millenniums, the authors report.

Marriage within a limited group, or endogamy, has created millions of people who are susceptible to recessive diseases, which develop only when a child inherits a disease-carrying gene from both parents, said Kumarasamy Thangaraj, an author of the study and a senior scientist at the Center for Cellular and Molecular Biology in Hyderabad.

Along with David Reich, a geneticist at Harvard Medical School, Dr. Thangaraj led an effort to analyze data from more than 2,800 individuals belonging to more than 260 distinct South Asian groups organized around caste, geography, family ties, language, religion and other factors. Of these, 81 groups had losses of genetic variation more extreme than those found in Ashkenazi Jews and Finns, groups with high rates of recessive disease because of genetic isolation.

In previous studies, Dr. Reich, Dr. Thangaraj and colleagues found that social groups in South Asia mixed between around 4,000 and 2,000 years ago. After that, the solidification of India’s caste system resulted in a shift toward endogamy. “You can see writ in the genome the effects of this intense endogamy,” Dr. Reich said.

Today, South Asia consists of around 5,000 anthropologically well-defined groups. Over 15 years, the researchers collected DNA from people belonging to a broad swath of these groups, resulting in a rich set of genetic data that pushes beyond the field’s focus on individuals of European ancestry, Dr. Reich said.

The scientists then looked at something called the founder effect. When a population originates from a small group of founders that bred only with each other, certain genetic variants can become amplified, more so than in a larger starting population with more gene exchange.

Most people carry some disease-associated mutations that have no effect because they’re present only in one parent’s genes. In an endogamous group, however, it’s more likely that two individuals carry the same mutation from a common founder. If they reproduce, their offspring have a higher risk of inheriting that disease.

Rare conditions are therefore disproportionately common in populations with strong founder events. Among Finns, for instance, congenital nephrotic syndrome, a relatively rare kidney disease, is uniquely prevalent. Similarly, Ashkenazi Jews are often screened for diseases like cystic fibrosis or Gaucher disease.

To measure the strength of different founder events, Dr. Reich and Dr. Thangaraj’s team looked for long stretches of DNA shared between individuals from the same subgroups. More shared sequences indicated a stronger founder event.

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The strongest of these founder groups most likely started with major genetic contributions from just 100 people or fewer. Today, 14 groups with these genetic profiles in South Asia have estimated census sizes of over one million. These include the Gujjar, from Jammu and Kashmir; the Baniyas, from Uttar Pradesh; and the Pattapu Kapu, from Andhra Pradesh. All of these groups have estimated founder effects about 10 times as strong as those of Finns and Ashkenazi Jews, which suggests the South Asian groups have “just as many, or more, recessive diseases,” said Dr. Reich, who is of Ashkenazi Jewish heritage himself.

The next step, the authors say, is to map out and study the genetic origins of diseases prevalent in different groups. As proof of concept, they screened 12 patients from southern India for a gene mutation known to cause a joint disease called progressive pseudorheumatoid dysplasia. Of the six people that had the mutation, five instances could be traced to founder effects, and one case could be traced to a marriage between close relatives.

This distinction is important because it’s well documented that marriage between close relatives can increase the possibilities of recessive disease. But many South Asians are not yet aware that they should also look out for genetic risks among broader populations, said Svati Shah, an associate professor of medicine at Duke University who was not involved in the research.

“There’s a tendency to think, ‘This will never happen to me because I will never marry my first cousin,’” Dr. Shah said. “But that’s not what’s happening here, according to the data.”

There are many other suspected examples of disease associations that have yet to be systematically studied in South Asia. Some medical caregivers speculate that people with the surname Reddy may be more likely to develop a form of arthritis affecting the spine, Dr. Thangaraj said. Others think people from the Raju community, in southern India, may have higher incidence of cardiomyopathy, which affects the heart muscle.

If recessive disease mutations are cataloged, they could potentially be used for prenatal or premarital screening programs, which can be “immensely powerful,” said Priya Moorjani, an author of the paper and a postdoctoral researcher at Columbia University.

An example of successful genetic cataloging can be found in Dor Yeshorim, a Brooklyn-based organization that screens Ashkenazi and Sephardi Jews for common disease-causing mutations to inform marriage matchmaking. The program is credited with virtually eliminating new cases of Tay-Sachs disease, a neurodegenerative disorder, from these communities.

Beyond rare diseases, groups with founder effects hold lessons about common diseases and basic biology, said Alan Shuldiner, a professor of medicine at the University of Maryland and a genetics researcher for Regeneron Pharmaceuticals, who was not involved in the study. He and his collaborators have gained new insights into heart disease and Type 2 diabetes, for instance, from studying Old Order Amish.

Scientists often try to manipulate, or knock out, genes in mice or flies to better understand human disease. But populations like those found across South Asia provide a powerful opportunity to study how gene changes manifest naturally in humans. These are “genetic experiments of nature that have occurred across the planet,” Dr. Shuldiner said.

The sheer number of people and different groups in South Asia means there’s a huge, untapped opportunity to do biological and genetic research there, Dr. Reich said.

He suggested that knockouts of almost every single gene in the genome probably exist in India.

“I would argue that it’s unequal to anywhere else,” he said.

See also

Caste in India: genetics and heredity (easy reading)

Caste among Hindus

Caste in India: genetics and heredity (academic studies)

Racial Classification of Indian People

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