Where did India’s people come from? Massive genetic study reveals surprises

Amazing stuff! Amazing Neanderthals!

"South Asia is home to one of the most diverse assemblages of people in the world. A mélange of different ethnic identities, languages, religions, castes, and customs makes up the 1.5 billion humans who live here. Now, scientists have revealed the most detailed look yet of how this population took shape.

In the largest ever modern whole-genome analysis from South Asia—published as a preprint last month on bioRxiv—researchers reveal new details about the origin of India’s Iranian ancestry and when ancient hunter-gatherers settled the region. The study also turns up a surprise: an unexpectedly rich diversity of genes from Neanderthals and their close evolutionary cousins, the Denisovans. Because no fossils of these ancient human relatives have been found in India, researchers are speculating about how these genes got there—and why they stuck around. ..."

From the 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."

Where did India’s people come from? Massive genetic study reveals surprises | Science | AAAS

50,000 years of Evolutionary History of India: Insights from ∼2,700 Whole Genome Sequences (open access)

Figure 1 Population structure and admixture in India.
(A) We show the sampling locations of individuals in the DAD study. States are colored by region (North, North-east, Central, South, East and West) used for analysis.
(B) n Principal component analysis (PCA) for Indians in LASI-DAD and 1000G individuals of European (EUR), East (EAS) and South Asian (SAS) ancestry. We show the projection of the first two principal components, colored by of birth.
(C) Using qpAdm, we inferred the ancestry proportions for each individual on the ‘Indian cline’ using m_EN as a proxy for Iranian farmer-related, Central_Steppe_MLBA as a proxy for Steppe pastoralist-related and (Onge) as a proxy for AASI-related ancestry. We compared AHG-related ancestry proportion by region (left), ge family (middle), and caste group (right) of each individual.