The Genetic Origin of the Indo-Europeans

Abstract

The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.

Extended Data Figure 1:. The origin of Central Anatolian Bronze Age.

(a) Fitting models include Mesopotamian (Çayönü) and steppe ancestry. (b) Models with western sources from Southeastern Europe fail except those with Mayaky or Boyanovo EBA sources both of which are Yamnaya-derived. (c) The steppe (BPgroup)+Çayönü model fails all Chalcolithic/Bronze Anatolians except Central Anatolian Bronze Age. (d) Steppe (BPgroup) ancestry observed in all individuals of the Central Anatolian Bronze Age (±3s.e. shown). (e) BPgroup-related ancestry admixed with different substrata: Aknashen-related in the North Caucasus Maikop, Masis Blur-related in Chalcolithic Armenia, and Mesopotamian-related (Çayönü) in the ancestors of the Central Asian Bronze Age, following the route (f) from the North Caucasus to Anatolia.

Extended Data Figure 2:. Admixture time estimates.

We estimate admixture times for the Core Yamnaya as a mixture of European hunter-gatherer and West Asian populations (a), for the Don Yamnaya as a mixture of Core Yamnaya and UNHG (b), for the Bulgaria-Moldova-Romania-Serbia (BMRS) Yamnaya as a mixture of Core Yamnaya and European Neolithic/Chalcolithic farmers (c), for the Corded Ware as a mixture of Core Yamnaya and Globula Amphora (d), and for Caucasus-Anatolia populations (Maikop-Armenia_C-TUR_C_BA) as a mixture of European hunter-gatherer and West Asian populations which occurred ca. 4400BCE (e). The Core Yamnaya were formed ca. 4000BCE, followed by admixture ca. 3350 BCE with UNHG and European farmers in the east and west of the Dnipro-Don region and <3000BCE in central-eastern Europe.

Extended Data Figure 3:

A 4-way model for the entire Dnipro-Don-Volga-Caucasus region. Error bars show ±1 standard error.

Figure 1:. Three Eneolithic clines and their neighbors in space and time.

(a) Map with analyzed sites. (b) PCA analysis using axes formed by a set of ancient West European hunter-gatherer (WHG), Siberian, West Asian, and European farmer populations. Selected individuals relevant to this study are projected (Methods). (c) qpAdm models fitted on individuals of the populations of the three clines. The Volga Cline is generated by admixture between Lower Volga (BPgroup) people with upriver Eastern hunter-gatherers (EHG). Populations of the Dnipro Cline have UNHG or UNHG+EHG admixture relative to the Core Yamnaya (the hunter-gatherer source along this cline is significantly variable). The Caucasus-Lower Volga Cline is generated by admixture between lower Volga people with those from the Neolithic Caucasus (Aknashen-related).

Figure 2.. The three Eneolithic clines in the context of Eneolithic and Bronze Age admixture.

Six 3-source models elucidate a complex history of admixture. Individuals plotted at the triangle edge fit (p>0.05); the simpler 2-source model is plotted for individuals with a negative coefficient from one of the three sources. The corners of each triangle represent the sources. Unplotted individual all give fits at P<0.05 and so should be viewed as poorly described by the model. (a) Caucasus and European hunter-gatherer admixtures in the “Old Steppe”: Krivyansky on the Lower Don received much more CHG-related admixture than upriver people of the Middle Don at Golubaya Krinitsa. In the Middle and Upper Volga and the Kama River, populations belonged to the old EHG cline with negligible CHG-related influence. (b) The “Don-Volga” difference. On the Lower Volga and North Caucasus piedmont, the BPgroup did receive CHG-related ancestry like its western Lower Don counterpart at Krivyansky; but, unlike Krivyansky, it also received ancestry from Central Asia; this eastern influence was higher still in the Bronze Age Steppe Maikop. (c) The “Volga Cline” vis-à-vis the Don: populations at Khvalynsk, Klopkov Bugor, and Ekaterinovka are clinal between the Berezhnvoka cluster on the Lower Volga and the upriver EHG-like populations of the Middle Volga (Labazy and Lebyazhinka). (d) the “Volga Cline” vis-à-vis Central Asia: a slight excess of Central Asian ancestry in the Khi subset of Khvalynsk. (e) the “Dnipro” cline: the Core Yamnaya are on one end of a cline that also includes the Don Yamnaya and Serednii Stih populations. The cline is formed by admixture from the “Caucasus-Lower Volga” (CLV) cline that is formed by differential admixture of Neolithic Caucasus and BPgroup people. The CLV Cline includes diverse people buried in kurgans at Berezhnovka, Progress-2, Remontnoye, and Maikop sites Klady and Dlinnaya-Polyana ~5000–3000 BCE. (f) “West Asian”: CLV ancestry first appears in the Chalcolithic population at Areni-1 in Armenia and is also present in the Bronze Age at Maikop. The majority of the ancestry in both populations is from West Asian sources from the Mesopotamia-Caucasus (or Çayönü-Masis Blur-Aknashen) cline. Chalcolithic and Bronze Age Anatolians lack CLV ancestry but traces of it can be found in Bronze Age Central Anatolians.

Figure 3.. Patrilineal succession.

Temporal distribution of key Y-chromosome haplogroups from Kazakhstan, Kyrgyzstan, Mongolia, Russia, Turkmenistan, Ukraine, Uzbekistan, and comparative regions of Europe and West Asia 6000–1000 BCE. The Early and Middle Bronze Age group includes the Yamnaya, Afanasievo, Poltavka, Catacomb, Chemurchek, and North Caucasus cultures; the Middle and Late Bronze Age group individuals of diverse cultures down to 1000 BCE including those of the Sintashta, Andronovo, Potapovka, and Srubnaya cultures.

Figure 4:. Population structure in people with a Yamnaya cultural affiliation.

Individuals are projected in the same space as in Fig. 1. (a) showing that the Core Yamnaya cluster (black symbols) from diverse sites is differentiated from the Don Yamnaya (blue) who tend towards the UNHG. (b) Yamnaya individuals in the West (Ukraine, Hungary, Slovakia, and Southeastern Europe) include a tight cluster of individuals as well as others that tend towards the direction of European Neolithic and Chalcolithic groups from Romania and Hungary. Individuals from Russia are shown in grey circles in panel (b).

Figure 5:. Trajectory of the Yamnaya expansion.

We use HapNe-LD to estimate the changes in effective population size over time of Yamnaya ancestors, performing the computation separately for the individuals from the earlier three hundred years (a) of our sampling, and the later three hundred years (b); shading shows uncertainty intervals. We infer an extraordinary population expansion (c) after 3642–3374 BCE (intersection of 95% confidence intervals for the two analyses for the minimum), from a time when the effective size is a few thousand to an order of magnitude larger.

Figure 6:. IBD analysis of the Yamnaya and their predecessors.

Pairs of individuals linked by at least one IBD segment ≥20cM in length reveal a sparse and highly connected network in the Pre-Yamnaya (a) and Yamnaya (b) groups. No detectible IBD is found in the Pre-Yamnaya period beyond the scale of 1000km (c); Yamnaya share more IBD with each other at short distance scales but IBD sharing extends all the way to the ~6000km scale of their geographical distribution. However, closely related individuals only occur at short distance scales in both Pre-Yamnaya (e) and Yamnaya (f) groups, indicating that the IBD sharing in the Yamnaya was a legacy of their common origin. (g) In a set of 9 Yamnaya cemeteries, and a total of 25 kurgans closely or distantly related individuals are virtually absent in inter-cemetery comparisons, more are found in inter-kurgan/within-cemetery comparisons, and more still in intra-kurgan comparisons; nonetheless, most Yamnaya individuals in all comparisons were unrelated. Kurgan burial of close kin was less common than in the case of a local patrilineal dynasty as at a Neolithic long cairn at Neolithic Hazleton North, but more common than in Neolithic monuments of Neolithic Ireland.