Scientists have identified migrating humans from Africa, Iran and Central Asia over a period of 50,000 years

In addition to its vast patchwork of languages, cultures and religions, the Indian Subcontinent also harbours huge genetic diversity. Where did its peoples originate? This is an area of huge controversy among scholars and scientists. A University of Huddersfield PhD student is lead author of an article that tries to answer the question using genetic evidence.

A problem confronting archaeogenetic research into the origins of Indian populations is that there is a dearth of sources, such as preserved skeletal remains that can provide ancient DNA samples. Marina Silva and her co-authors have instead focused on people alive in the Subcontinent today.

They show that some genetic lineages in South Asia are very ancient. The earliest populations were hunter-gatherers who arrived from Africa, where modern humans arose, more than 50,000 years ago. But further waves of settlement came from the direction of Iran, after the last Ice Age ended 10-20,000 years ago, and with the spread of early farming.

These ancient signatures are most clearly seen in the mitochondrial DNA, which tracks the female line of descent. But Y-chromosome variation, which tracks the male line, is very different. Here the major signatures are much more recent. Most controversially, there is a strong signal of immigration from Central Asia, less than 5,000 years ago.

This looks like a sign of the arrival of the first Indo-European speakers, who arose amongst the Bronze Age peoples of the grasslands north of the Caucasus, between the Black and Caspian Seas. 

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A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

Marina Silva, Marisa Oliveira, Daniel Vieira, Andreia Brandão, Teresa Rito, Joana B. Pereira, Ross M. Fraser, Bob Hudson, Francesca Gandini, Ceiridwen Edwards, Maria Pala, John Koch, James F. Wilson, Luísa Pereira, Martin B. Richards  andPedro Soares(†Contributed equally)

BMC Evolutionary Biology
BMC series – open, inclusive and trusted 201717:88

DOI: 10.1186/s12862-017-0936-9 ©  The Author(s). 2017

Received: 15 December 2016, Accepted: 14 March 2017, Published: 23 March 2017

Background: India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called “Indo-Aryan invasions” from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging.

Results: We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55–65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems.

Conclusions: Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.

Keywords: Mitochondrial DNA Indian Subcontinent Genome-wide Y chromosome Neolithic Indo-European