The genetic history of admixture across inner Eurasia

Abstract

The indigenous populations of inner Eurasia, a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra, harbor tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine, and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 BP). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contribution from so-called “ancient North Eurasian” ancestry over time, detectable only in the northern-most “forest-tundra” cline. The intermediate “steppe-forest” cline descends from the Late Bronze Age steppe ancestries, while the “southern steppe” cline further to the South shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium BC. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.

A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

“…By the end of the Mongol period the genetic make-up of the Eastern Steppe had dramatically changed, retaining little of the ANE ancestry that had been a prominent feature during its prehistory. Today, ANE ancestry survives in appreciable amounts only in isolated Siberian groups and among the indigenous peoples of the Americas (Jeong et al, 2019). The genetic profile of the historic Mongols is still reflected among contemporary Mongolians, suggesting a relative stability of this gene pool over the last ∼700 years.…”

“…To analyse our dataset in the context of known ancient and modern genetic diversity, we merged it with previous published modern genomic data from i) 225 worldwide populations genotyped on the Human Origins array (Jeong et al, 2019; Lazaridis et al, 2014), ii) 300 high-coverage genomes in the Simons Genome Diversity Project (“SGDP”) (Mallick et al, 2016), and currently available ancient genomic data across Eurasian continent (Allentoft et al, 2015; de Barros Damgaard et al, 2018; Damgaard et al, 2018; Fu et al, 2014, 2016; Haak et al, 2015; Haber et al, 2017; Harney et al, 2018; Jeong et al, 2016, 2018; Jones et al, 2015; Kilinç et al, 2016; Lazaridis et al, 2016, 2017; Mathieson et al, 2015, 2018; McColl et al, 2018; Narasimhan et al, 2019; Raghavan et al, 2014, 2015; Rasmussen et al, 2010, 2014, 2015; Sikora et al, 2019; Unterländer et al, 2017; Yang et al, 2017). We obtained 1,233,013 SNP sites (1,150,639 of which on autosomes) across our dataset when intersecting with the SGDP dataset, and 597,573 sites (593,124 of which on autosomes) when intersecting with the Human Origins array.…”

The Genomic Formation of Human Populations in East Asia

“…We generated 94 direct AMS (Accelerator Mass Spectrometry) radiocarbon ( 14 C) dates as part of this study; 87 at Pennsylvania State University (PSU) and 7 at Poznan Radiocarbon Laboratory. The methods used at both laboratories are published, and here we summarize the methods from PSU.…”

“…Instead in the Late Bronze Age and Iron Age and afterward we have data from multiple Mongolian groups whose Yamnaya-related ancestry can only be modeled as deriving not from the initial Afanasievo migration but instead from a later eastward spread into Mongolia related to people of the Middle to Late Bronze Age Sintashta and Andronovo horizons who were themselves a mixture of ∼2/3 Yamnaya-related and 1/3 European farmer-related ancestry 5,7,8 . The Sintashta-related ancestry is detected in proportions of 5% to 57% in individuals from the Mongolia_LBA_6_Khovsgol (a culturally mixed group from the literature 14 ), Mongolia_LBA_3_MongunTaiga, Mongolia_LBA_5_CenterWest, Mongolia_EIA_4_Sagly, Mongolia_EIA_6_Pazyryk, and Mongolia_Mongol groups, with the most substantial proportions of Sintashta-related ancestry always coming from western Mongolia (Figure 3, Online Table 5). For all these groups, the qpAdm ancestry models pass when Afanasievo is included in the outgroups while models with Afanasievo treated as the source with Sintashta more distantly related outgroups are all rejected (Figure 3, Online Table 5).…”

Mitochondrial Genome Diversity in the Central Siberian Plateau with Particular Reference to Prehistory of Northernmost Eurasia

“…Hence, genetic and archeological evidence support a single/common origin of a population directly related to the maternal ancestors of some of the present-day Ket, Tofalar, Tuvan, Yakut, Buryat, as well as the Koryak individuals. It has been suggested that the Okunevo Culture derived ancestry from long-resident populations of the Altai-Sayan Upland whose roots may extend back to the Neolithic, if not before [35]. Supplementary Fig.…”