The Genomic Formation of South and Central Asia

Abstract

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.One Sentence SummaryGenome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia

“…Ancient Iran/Caucasus populations and contemporary South Asians do not share more alleles with ACF (|D| < 3.3 SE). Likewise, qpAdm modeling suggests that the AAF gene pool still constitutes more than 3/4 of the ancestry of ACF 2,000 years later (78.7 ± 3.5 %; tables S4 and S7) with additional ancestry well modeled 15 by the Neolithic Levantines (χ 2 p = 0.115) but not by the Neolithic Iranians (χ 2 p = 0.076; the model estimated infeasible negative mixture proportions) (tables S4 and S7). These results Table 1 and data table S6).…”

“…These results support a late Pleistocene presence of both ancestries in a mixed form in central Anatolia. Notably, the genetic 15 connection with the Levant predates the advent of farming in this region by at least five millennia and potentially correlates with evidence of human interactions between central Anatolia and the Levant during the Epipalaeolithic 13 .…”

“…Central Anatolia has some of the earliest evidence of agricultural societies outside the Here, we report new genome wide data from eight prehistoric humans ( Fig.1A, Table 1, table S1), including the first Epipalaeolithic Anatolian hunter-gatherer sequenced to date (labeled 10 AHG; directly dated to 13,642-13,073 BCE, excavated from the site of Pınarbaşı, Turkey), 5 early Neolithic Aceramic Anatolian farmers (labeled AAF; c. 8300-7800 cal BCE, one directly dated to 8269-8210 cal BCE 3 , from the site of Boncuklu, Turkey), adding to previously published genomes from this site 7 , and two Early Neolithic (PPNB) farmers from the southern Levant (One labeled KFH2, directly dated to c. 7,700-7,600 BCE; from the site of Kfar 15 HaHoresh, Israel and the second labeled BAJ001, c. 7027-6685 BCE, from the site of Ba'ja, Jordan). This data comprises a genetic record stretching from the Epiplaeolithic into the Early Holocene, spanning the advent of agriculture in the region.…”

“…We estimated low mitochondrial contamination levels for all eight individuals (1-6%; Materials and Methods and table S2) and could further test the males for nuclear contamination, resulting in low estimates (0.05-2.23%; table S2). For population genetic analyses, we merged genotype data of the new individuals with previously published datasets from 587 ancient individuals and 254 present-day populations 15 (data table S2).…”

“…In turn, AAF is slightly shifted upwards compared to AHG in the PCA, to the direction where ancient and modern Caucasus and Iranian groups are located. Likewise, when compared 20 to AHG by D(AAF, AHG; test, Mbuti), the AAF early farmers show extra affinity with early Holocene populations from Iran or Caucasus and with present-day South Asians, who have also been genetically linked with Iranian/Caucasus ancestry 14,15 (Fig. 2A, fig.…”