Andronovo pastoralists brought steppe ancestry to South Asia (Narasimhan et al. 2018 preprint)

Over at bioRxiv at this LINK. Note that the Andronovo samples that are shown to be the best fit for the steppe ancestry in South Asians are labeled Steppe_MLBA_East (ie. Middle to Late Bronze Age eastern steppe). Below is the abstract and a couple of key quotes from the paper and its supp info PDF. Emphasis is mine:

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

...

Third, between 3100-2200 BCE we observe an outlier at the BMAC site of Gonur, as well as two outliers from the eastern Iranian site of Shahr-i-Sokhta, all with an ancestry profile similar to 41 ancient individuals from northern Pakistan who lived approximately a millennium later in the isolated Swat region of the northern Indus Valley (1200-800 BCE). These individuals had between 14-42% of their ancestry related to the AASI and the rest related to early Iranian agriculturalists and West_Siberian_HG. Like contemporary and earlier samples from Iran/Turan we find no evidence of Steppe-pastoralist-related ancestry in these samples. In contrast to all other Iran/Turan samples, we find that these individuals also had negligible Anatolian agriculturalist-related admixture, suggesting that they might be migrants from a population further east along the cline of decreasing Anatolian agriculturalist ancestry. While we do not have access to any DNA directly sampled from the Indus Valley Civilization (IVC), based on (a) archaeological evidence of material culture exchange between the IVC and both BMAC to its north and Shahr-i-Sokhta to its east (27), (b) the similarity of these outlier individuals to post-IVC Swat Valley individuals described in the next section (27), (c) the presence of substantial AASI admixture in these samples suggesting that they are migrants from South Asia, and (d) the fact that these individuals fit as ancestral populations for present-day Indian groups in qpAdm modeling, we hypothesize that these outliers were recent migrants from the IVC. Without ancient DNA from individuals buried in IVC cultural contexts, we cannot rule out the possibility that the group represented by these outlier individuals, which we call Indus_Periphery, was limited to the northern fringe and not representative of the ancestry of the entire Indus Valley Civilization population. In fact, it was certainly the case that the peoples of the Indus Valley were genetically heterogeneous as we observe one of the Indus_Periphery individuals having ~42% AASI ancestry and the other two individuals having ~14-18% AASI ancestry (but always mixes of the same two proximal sources of AASI and Iranian agriculturalist-related ancestry). Nevertheless, these results show that Indus_Periphery were part of an important ancestry cline in the wider Indus region in the 3 rd millennium and early 2 nd millennium BCE. As we show in what follows, peoples related to this group had a pivotal role in the formation of subsequent populations in South Asia.

...

These results—leveraging our rich data from ancient samples closer in time to the Bronze Age—show that the group(s) that contributed Iranian agriculturalist-related ancestry to South Asia shared more genetic drift with the Iranian agriculturalist-related groups in our dataset that are temporally and geographically closest, compared to Caucasus HGs (CHG) or early Zagros related agriculturalists previously shown to be related to source populations for South Asians (11, 81). We are not only able to exclude these early farming and hunter-gathering groups, but also Copper and Bronze Age groups in western Iran (Seh_Gabi_C and Hajji_Firuz_C), and even in eastern Iran and Turan (Tepe_Hissar_C, Gioksiur_EN, and BMAC). Our detailed analyses in Text S3 indicate that what is driving the failure of these models is an excess of Anatolian agriculturalist-related ancestry in all of these groups, suggesting that the Iranian agriculturalist-related population that mixed into South Asia had less Anatolian agriculturalist-related ancestry than all of these. However, we find that mixtures using the Indus_Periphery sample (a pool of three outlier individuals from the BMAC site of Gonur and from Shahr-i-Sokhta), provides an excellent source population for the Iranian agriculturalist-related ancestry in South Asia when combined with any individuals in the Steppe_MLBA cluster (Srubnaya, Sintashta_MLBA, Steppe_MLBA_West or Steppe_MLBA_East).

Narasimhan et al, The Genomic Formation of South and Central Asia, Posted March 31, 2018, doi: https://doi.org/10.1101/292581

Update 12/04/2018: The dataset from the prerprint has been made available early at the Reich Lab website here. I've already started analyzing it. You can see the results in several new threads, for instance here, here and here.

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Central Asia as the PIE urheimat? Forget it

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts