India's evolutionary past tied to huge migration 50,000 years ago and to now-extinct human relatives

Live Science ^ | March 11, 2024 | Emily Cooke

[SunkenCiv]

Scientists analyzed more than 2,700 modern Indian genomes from 17 states, including DNA from individuals from most geographic regions, speakers of all major languages, tribal and caste groups.

They revealed that one of the three main ancestral groups in India — ancient Iranian farmers — can be traced back to a group of agricultural farmers from Sarazm in modern-day Tajikistan. They also uncovered the extraordinary diversity of DNA inherited from Neanderthals and Denisovans, the closest, now-extinct relatives of modern humans.

Additionally, the team found that most of the genetic variation within the current Indian population stems from a single, major migration event of modern humans to India from Africa around 50,000 years ago...

To paint a clearer picture of genetic variation in India, the authors of the new study analyzed the genomes of thousands of individuals who participated in the Longitudinal Aging Study in India-Diagnostic Assessment of Dementia (LASI-DAD). Participants were over the age of 60 and agreed to have blood samples taken for analysis...

In one analysis in the new study, the team compared the DNA of modern Indians to that of Iranian-related individuals from the Neolithic, or New Stone Age, to the Iron Age. They found that ancient Iranian-related DNA inherited by Indian populations originated from individuals from Sarazm from the early Neolithic.

In a separate analysis, the researchers compared the DNA of modern Indians to that of sequenced Neanderthal and Denisovan genomes and found that Indians, like most non-Africans, inherited between 1% and 2% of their DNA from these groups. This DNA is highly diverse: Almost 90% of all known Neanderthal genes found in humans outside of Africa were detected in the Indian genomes studied...

[SunkenCiv]

Abstract: India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India––including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups––providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry through gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ∼1.5 Gb (or 50%) of the introgressing Neanderthal and ∼0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.

50,000 years of Evolutionary History of India: Insights from ∼2,700 Whole Genome Sequences
Elise Kerdoncuff, Laurits Skov, Nick Patterson, Wei Zhao, Yuk Yee Lueng, Gerard D. Schellenberg, Jennifer A. Smith, Sharmistha Dey, Andrea Ganna, AB Dey, Sharon L.R. Kardia, Jinkook Lee, Priya Moorjani

[SunkenCiv]

...The team discovered that modern Japanese people mostly descended from three ancestral groups: Neolithic Jomon hunter-gatherers; a group believed to have been the ancient predecessors of the Han Chinese; and an unidentified group with ties to Northeast Asia. This finding further challenges a contested, three-decades-long hypothesis that Japanese people originated from the Jomon people and, later, rice-farming Yayoi migrants from continental Asia.

The new analysis also revealed 42 pieces of DNA that Japanese people inherited from Neanderthals and two from Denisovans that could be linked to complex traits, meaning those that are encoded by multiple genes...

Denisovan-derived DNA within a gene called NKX6-1 was associated with the development of type 2 diabetes (T2D), and within the gene POLR3E, it was tied to height, the authors found. Eleven Neanderthal-derived DNA sequences were found to be associated with seven diseases, including T2D, coronary artery disease, prostate cancer and the inflammatory disorder rheumatoid arthritis. Most of these 44 chunks of ancient DNA are unique to East Asians, the authors said.

Modern Japanese people arose from 3 ancestral groups, 1 of them unknown, DNA study suggests | Emily Cooke | April 17, 2024 | LiveScience

[Angelino97]

They also uncovered the extraordinary diversity of DNA ...

Seems that every scientific study of, practically anything, discovers "diversity." Not just of people or DNA, but of everything. Journalists and historians are also always discovering that this or that culture or country was a place of extraordinary "diversity," of far more diversity that previously believed.

They drop that word into everything.

[SunkenCiv]

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[SunkenCiv]

[whoops] The other GGG topics added since the previous digest ping, alpha:

[SunkenCiv]

“They” again? “They” sure get around. What do we really need diversity for anyway? No one needs to have more than one choice of food, political party, toothpaste...

[Thommas]

Again, one might surmise that 50 thousand years ago another melanin challenged group of Africans beat feet out of the dark continent.

[Angelino97]

The word "diversity" was little used 30 or 40 years ago.

Then, in the 1990s, it was applied to demographics -- and the word took off. Suddenly, the word appeared everywhere, in all articles, on every subject.

I saw an article on a new park opening. A typical headline, 30 years ago, would have been "City Opens New Park." Instead the headline was "New Park Attracts a Diversity of People."

The word is being injected into everything because it's associated with demographic diversity, so even when we talk about a store offering a diversity of products, it creates a subconscious sense that (demographic) diversity is good and necessary.

For that same reason, the use of the word is a form of virtue signaling. Using it, in any contexts, signals "I am a good person because I love demographic diversity."

[SunkenCiv]

IOW, your comments don’t have anything to do with the actual information in the article.

[nwrep]

another melanin challenged group of Africans

Hardly "melanin-challenged". Some South Asian Indians are blacker and darker than Africans. They have distinct aboriginal or African features.

[blam]

"Hardly "melanin-challenged". Some South Asian Indians are blacker and darker than Africans. They have distinct aboriginal or African features."

Racial Groups of India

"1. The Negritos-Perhaps they were the first of the racial groups that came to India. They got settled in the hilly areas of Kerala and the Andaman Islands. Kadar, Irula and Puliyan tribes of Kerala resemble to a great extent with the Negritos. They are related to Africa, Australia and their neighbouring islands. The Negritos have black (dark) skin, woolly hair, broad and flat nose and slightly protruded jaws."

[mistfree]

“we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago,”

50,000 yrs ago the continents were where they are now. That said, how did the majority of Indian people “migrate” across that territory? Little land to cross the red sea, lots of desert, more ocean or a huge detor to get around it? Askin for a friend

[Mr. Blond]

Neanderthal traces may just have come from the proto-European invasion of the Indus Valley.