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Published in final edited form as: Science. 2022 Aug 26;377(6609):eabm4247. doi: 10.1126/science.abm4247

The genetic history of the Southern Arc: a bridge between West Asia and Europe

Iosif Lazaridis 1,2,*,†, Songül Alpaslan-Roodenberg 2,3,*,†, Ayşe Acar 4, Ayşen Açıkkol 5, Anagnostis Agelarakis 6, Levon Aghikyan 7, Uğur Akyüz 8, Desislava Andreeva 9, Gojko Andrijasevic 10, Dragana Antonović 11, Ian Armit 12, Alper Atmaca 13, Pavel Avetisyan 7, Ahmet İhsan Aytek 14, Krum Bacvarov 15, Ruben Badalyan 7, Stefan Bakardzhiev 16, Jacqueline Balen 17, Lorenc Bejko 18, Rebecca Bernardos 2, Andreas Bertsatos 19, Hanifi Biber 20, Ahmet Bilir 21, Mario Bodružić 22, Michelle Bonogofsky 23, Clive Bonsall 24, Dušan Borić 25, Nikola Borovinić 26, Guillermo Bravo Morante 3, Katharina Buttinger 3, Kim Callan 2,27, Francesca Candilio 28, Mario Carić 29, Olivia Cheronet 3, Stefan Chohadzhiev 30, Maria-Eleni Chovalopoulou 19, Stella Chryssoulaki 31, Ion Ciobanu 32,33, Natalija Čondić 34, Mihai Constantinescu 35, Emanuela Cristiani 36, Brendan J Culleton 37, Elizabeth Curtis 2,27, Jack Davis 38, Tatiana I Demcenco 39, Valentin Dergachev 40, Zafer Derin 41, Sylvia Deskaj 42, Seda Devejyan 7, Ruben Davtyan 7, Vojislav Djordjević 43, Kellie Sara Duffett Carlson 3, Laurie R Eccles 44, Nedko Elenski 45, Atilla Engin 46, Nihat Erdoğan 47, Sabiha Erir-Pazarcı 48, Daniel M Fernandes 3,49, Matthew Ferry 2,27, Suzanne Freilich 3, Alin Frînculeasa 50, Michael L Galaty 42, Beatriz Gamarra 51,52,53, Boris Gasparyan 7, Bisserka Gaydarska 54, Elif Genç 55, Timur Gültekin 56, Serkan Gündüz 57, Tamás Hajdu 58,59, Volker Heyd 60, Suren Hobosyan 7, Nelli Hovhannisyan 61, Iliya Iliev 16, Lora Iliev 2,27, Stanislav Iliev 62, İlkay İvgin 63, Ivor Janković 29, Lence Jovanova 64, Panagiotis Karkanas 65, Berna Kavaz-Kındığılı 66, Esra Hilal Kaya 67, Denise Keating 3, Douglas Kennett 37,68, Seda Deniz Kesici 69, Anahit Khudaverdyan 7, Krisztián Kiss 58,59, Sinan Kılıç 20, Paul Klostermann 70, Sinem Kostak Boca Negra Valdes 69, Saša Kovačević 71, Marta Krenz-Niedbała 72, Maja Krznarić Škrivanko 73, Rovena Kurti 74, Pasko Kuzman 75, Ann Marie Lawson 2,27, Catalin Lazar 76, Krassimir Leshtakov 77, Thomas E Levy 78, Ioannis Liritzis 79,80, Kirsi O Lorentz 81, Sylwia Łukasik 72, Matthew Mah 2,27,82, Swapan Mallick 2,27, Kirsten Mandl 3, Kristine Martirosyan-Olshansky 83, Roger Matthews 84, Wendy Matthews 84, Kathleen McSweeney 24, Varduhi Melikyan 7, Adam Micco 2, Megan Michel 1,2,27, Lidjia Milasinovic 85, Alissa Mittnik 1,2, Janet M Monge 86, Georgi Nekhrizov 15, Rebecca Nicholls 87, Alexey G Nikitin 88, Vassil Nikolov 15, Mario Novak 29, Iñigo Olalde 2,89, Jonas Oppenheimer 2,27, Anna Osterholtz 90, Celal Özdemir 13, Kadir Toykan Özdoğan 3, Nurettin Öztürk 66, Nikos Papadimitriou 91, Niki Papakonstantinou 92, Anastasia Papathanasiou 93, Lujana Paraman 94, Evgeny G Paskary 95, Nick Patterson 1,82, Ilian Petrakiev 45, Levon Petrosyan 7, Vanya Petrova 77, Anna Philippa-Touchais 96, Ashot Piliposyan 97, Nada Pocuca Kuzman 75, Hrvoje Potrebica 98, Bianca Preda-Bălănică 60, Zrinka Premužić 99, T Douglas Price 100, Lijun Qiu 2,27, Siniša Radović 101, Kamal Raeuf Aziz 102, Petra Rajić Šikanjić 29, Kamal Rasheed Raheem 102, Sergei Razumov 103, Amy Richardson 84, Jacob Roodenberg 104, Rudenc Ruka 74, Victoria Russeva 105, Mustafa Şahin 57, Ayşegül Şarbak 106, Emre Savaş 69, Constanze Schattke 3, Lynne Schepartz 107, Tayfun Selçuk 69, Ayla Sevim-Erol 108, Michel Shamoon-Pour 109, Henry M Shephard 110, Athanasios Sideris 111, Angela Simalcsik 32,112, Hakob Simonyan 113, Vitalij Sinika 103, Kendra Sirak 2, Ghenadie Sirbu 114, Mario Šlaus 115, Andrei Soficaru 35, Bilal Söğüt 116, Arkadiusz Sołtysiak 117, Çilem Sönmez-Sözer 108, Maria Stathi 118, Martin Steskal 119, Kristin Stewardson 2,27, Sharon Stocker 38, Fadime Suata-Alpaslan 120, Alexander Suvorov 60, Anna Szécsényi-Nagy 121, Tamás Szeniczey 58,59, Nikolai Telnov 103, Strahil Temov 122, Nadezhda Todorova 77, Ulsi Tota 74,123, Gilles Touchais 124, Sevi Triantaphyllou 92, Atila Türker 125, Marina Ugarković 71, Todor Valchev 16, Fanica Veljanovska 122, Zlatko Videvski 122, Cristian Virag 126, Anna Wagner 3, Sam Walsh 84, Piotr Włodarczak 127, J Noah Workman 2, Aram Yardumian 128,129, Evgenii Yarovoy 130, Alper Yener Yavuz 131, Hakan Yılmaz 20, Fatma Zalzala 2,27, Anna Zettl 3, Zhao Zhang 2, Rafet Çavuşoğlu 20, Nadin Rohland 2, Ron Pinhasi 3,132,*, David Reich 1,2,27,82,*
PMCID: PMC10064553  NIHMSID: NIHMS1873728  PMID: 36007055

Abstract

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic and Bronze Ages (~5000-1000BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southwards: into the Balkans, and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

One-Sentence Summary:

Web of migrations between Anatolia, its neighbors, and the Steppe suggests a West Asian origin of Indo-Anatolian languages.

Print page summary

Introduction

Humans moved, for thousands of years, across the “Southern Arc,” the area bridging Europe through Anatolia with West Asia. We report ancient DNA data from 727 individuals of this region over the last 11,000 years, which we co-analyse with the published archaeogenetic record to understand the origins of its people. We focus on the Chalcolithic and Bronze Age periods ~7,000-3,000 years ago, when Indo-European language speakers first appeared.

Rationale

Language is not encoded in the genome. But genetic data are relevant to understanding linguistic evolution because they may identify population movements that were opportunities for language spread. How does the changing ancestral landscape of the Southern Arc revealed by ancient DNA correspond to the structure inferred by linguistics, which links Anatolian (such as Hittite and Luwian) and Indo-European (such as Greek, Armenian, Latin, and Sanskrit) languages as twin daughters of a common Proto-Indo-Anatolian parent?

Results

Steppe pastoralists of the Yamnaya culture initiated a chain of migrations across Eurasia, linking Europe in the west to China and India in the east. We find people throughout the Balkans who traced almost all their ancestry to this Yamnaya expansion (~5,000-4,500 years ago). These steppe migrants soon admixed with locals to create a tapestry of diverse ancestry from which speakers of Greek, Paleo-Balkan, and Albanian languages emerged.

The Yamnaya expansion also crossed the Caucasus and by ~4,000 years ago, Armenia had become an enclave of low but pervasive steppe influence in West Asia, where the patrilineal descendants of Yamnaya men, virtually extinct across Europe and the steppe, persisted. The Armenian language was born there and its relationship with faraway Indo-European languages of Europe such as Greek reflects their shared Yamnaya heritage.

Neolithic Anatolia (Turkey) was home to diverse populations descended from both local hunter- gatherers and eastern populations of the Caucasus, Mesopotamia, and the Levant. By ~6,500 years ago and thereafter, Anatolians became more similar to each other, a process driven substantially by the flow of eastern ancestry across the breadth of the peninsula. The numerous languages revealed by archaeology, both Anatolian, but also non-Indo-European ones like Hattic and Urartian, are likely to be those of locals and migrants who participated in this great mixture.

Anatolia is remarkable for its lack of steppe (Yamnaya or earlier) ancestry down to the Bronze Age. The ancestors of the Yamnaya were, however, substantially drawn from West Asia, mainly from the Caucasus, a process that had started by ~7,000 years ago, but also from the more southern Anatolian-Levantine continuum. The Bronze Age expansion of the Yamnaya into the Caucasus can thus be seen as a return to the homeland of about half their ancestors.

Conclusion

All ancient Indo-European speakers can be traced back to the Yamnaya culture, whose southern expansions into the Southern Arc left a trace in the DNA of the Bronze Age people of the region. But, the link connecting the Proto-Indo-European speaking Yamnaya with the speakers of Anatolian languages was in the highlands of West Asia, the ancestral region shared by both.

Graphical Abstract

Many partings, many meetings—how migration and admixture drove early language spread. Westward and northward migrations out of the West Asian highlands split the Proto- Indo-Anatolian language into Anatolian and Indo-European branches. Yamnaya pastoralists, formed on the steppe by a fusion of newcomers and locals, admixed again as they expanded far and wide, splitting the Proto-Indo-European language into its daughter languages across Eurasia. Locations and routes are approximate.

graphic file with name nihms-1873728-f0001.jpg

The Balkans and Anatolia are often portrayed as geographically peripheral to Europe and Asia, rather than as central to an interconnected region spanning both continents. Here we take a different view by providing a systematic genetic history of what we refer to as the “Southern Arc”, a region (Fig. 1A) centered on the large Anatolian peninsula (Turkey), including in the west (in Europe) the Balkans and the Aegean, and in the south and east, Cyprus, Mesopotamia, the Levant, Armenia, Azerbaijan, and Iran. We present new genome-wide DNA data from 777 individuals from the SA: 727 previously unsampled and 50 previously published for which we report new data from 1,094 newly reported ancient DNA libraries (1). As a resource to guide future sampling efforts, we also report negative results for 476 samples that we screened using 537 libraries and that failed to yield ancient DNA data passing criteria for authenticity (1). We finally provide 239 new radiocarbon dates on the same skeletal elements analyzed for DNA (1). We study these along with previously published individuals for a total sample size of 1,317 ancient individuals in the region (Fig. 1B) (1).

Fig. 1. Studied individuals and PCA analysis.

Fig. 1.

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(A) The geography of the Southern Arc; Sampling locations of previously published individuals (grey circle), new data on published individuals (pink square), and new individuals (yellow circle); convex hulls of individuals from each present-day country are also shown. (B) Timeline of studied individuals (random uniform jitter applied to the vertical dimension). (C) Principal components analysis of ancient individuals projected on modern West Eurasian variation. Country names represented by 3-letter ISO codes.

Our newly reported data fills many sampling gaps in space and time in the Southern Arc. In Turkey our new sampling has a particular focus on the western (Aegean, Marmara), northern (Black Sea) and eastern (Eastern Anatolia, Southeastern Anatolia) regions connecting it with the rest of the Southern Arc. Another area of high-density sampling is Armenia with substantial coverage of the Bronze and Iron Ages representing an order of magnitude more individuals than previously available. Many individuals of Bronze-to-Iron Age timeframe are also sampled from the Iranian highlands at Hasanlu, where only a single individual has previously been studied (2), and Dinkha Tepe, neighboring Anatolia, Mesopotamia, Armenia and the Caucasus. In the southern part of Southeastern Europe, we sample Mycenaean-era individuals from multiple regions of the Aegean. From the southern Balkans, we present a full time transect of Albania, numerous individuals from North Macedonia where previously data from only a single Neolithic individual had been published (3), and more than double the previously available body of ancient DNA data from Bulgaria. Further north, at the western wing of the Southern Arc, we sample individuals from Croatia, Montenegro, and Serbia in the west; and Romania and Moldova in the east; which interface with the extensively studied worlds of Central Europe and the Eurasian steppe. This dataset includes >100 Bronze Age individuals, including many from Cetina Valley and Bezdanjača Cave in Croatia which we add to only 5 previously published from the entire area (3, 4). Some of the Balkan individuals include culturally Yamnaya individuals from Serbia and Bulgaria, allowing us to compare them with those of the Eurasian steppe. With this greatly enhanced dataset across the entire region, we are able to fill in major gaps in sampling in time, space, and cultural context. Our large sample sizes also allow us to identify main clusters as well as genetic outliers, providing insights about within-population patterns of variation and contact networks with neighboring groups. Details of all studied individuals can be found in (1) (Figs. S5-S21).

To discuss the geographic distribution of these individuals, we take a flexible approach, in some cases using the names of ecological or topographical regions and in others the names of present-day countries depending on how well these align with genetic patterns. In some cases, we also use more specific regional location information to be more precise (5). In the interest of having a uniform nomenclature that is easily accessible to readers familiar with the current political map of the Southern Arc, we also refer to groups of individuals with labels prefixed with 3-letter International Standards Organization (ISO) codes for countries, as in Fig. 1. Multiple toponyms have been used for the same sites during the Southern Arc’s long history, and we typically choose labels appropriate for the period and/or present-day usage. To designate the period in which individuals lived, we use conventional archaeological designations for each region, e.g., Eneolithic and Chalcolithic both denote copper-using cultures in different parts of the archaeological literature. We caution that the transition between the Eneolithic or Chlacolithic and Bronze Ages did not occur simultaneously in different parts of the Southern Arc. Detailed archaeological information for each individual is presented in (1) specifying the analysis labels we use integrating information from chronology, geography, archaeology, and genetics.

Overview of genetic variation in the Southern Arc

To understand genetic variation in the Southern Arc, we began with ADMIXTURE (Fig. S1) analysis, which allowed us to detect individuals with non-West Eurasian-associated ancestry (7) and to appreciate the broad pattern of variation in terms of the four West Eurasian components that appear in the ADMIXTURE analysis: Iran/Caucasus-related, “Eastern hunter-gatherer”, Anatolian/Levantine-related, and “Balkan hunter-gatherer”. Principal components analysis (Fig. 1C) of Southern Arc individuals together with other West Eurasian individuals demonstrates the central position of the Southern Arc within the continuum of West Eurasian variation, with a long “bridge” of individuals joining Europe (left) to West Asia (right), but with individuals spread across the entire range of variation.

To quantify the ancestry of Southern Arc individuals, we developed a 5-source modeling framework (using qpAdm and F4admix) (1) that allows a high-resolution description of the ancestry of the Southern Arc population as a whole and as individuals. To generate this model, we used an automated procedure that did not pre-select a specific set of surrogates for the source populations, but instead explored many possible sets and identified those that, for as many individuals as possible, maximized the quality of the statistical fit of the model while minimizing the standard errors in inferences of ancestry proportions (Tables S1-S21, Figs. S22-S27). After applying this procedure, the five sources of ancestry we used are: Caucasus hunter-gatherers (8), Eastern hunter-gatherers (9, 10), Levantine Pre-Pottery Neolithic (11), Balkan hunter-gatherers from the Iron Gates in Serbia (3), and Northwestern Anatolian Neolithic from Barcın (10); these correspond to the 4-source ADMIXTURE model, with further distinction between the Anatolian and Levantine ends of the “Mediterranean” interaction zone (6). These five sources should not be unduly emphasized beyond their utility as a descriptive convenience, as they: (i) could be swapped for related ones (e.g., Neolithic Iran captures much of the same deep ancestry as Caucasus hunter-gatherers do (6, 11)), (ii) were themselves derived from earlier (more “distal”) populations (e.g., Levantine PPN from earlier Natufian hunter-gatherers (11)), and (iii) transmitted their ancestry via later (more “proximal”) sources (e.g., Eastern hunter-gatherers via Yamnaya steppe pastoralists (9)). The inferred proportions of ancestry for individuals are summarized in Figs. S2-S4 and Figs. S28-S76, and discussed in detail in (1).

The Anatolian core of the Southern Arc

When we apply our 5-way model to individuals from Anatolia (Fig. 2A-E), it is immediately apparent that prior to ~3,000 years ago, virtually all ancestry there is drawn from local West Asian sources (northwest Anatolian Neolithic hereafter called “Anatolian”, Levantine, Caucasus) with negligible contribution from the two European (Balkan and Eastern hunter-gatherer) sources of our model. Broadly speaking, the temporal trend is one of increasing Caucasus/Levantine-related ancestry between the Neolithic and Chalcolithic periods with a corresponding decrease of the Anatolian-related ancestry. To better understand this process in the Anatolian peninsula, we examined geographical sub-populations of the Chalcolithic and Bronze Age in comparison to the Neolithic ones that preceded them (Fig. 2F). We observed that northwest Anatolian-related ancestry varied between ~100% (at Barcın, Menteşe, and Ilıpınar in the Marmara region; we use the high quality data we have from Barcın to define this component of ancestry) to ~16% (the Pre-Pottery Neolithic individual from Mardin in SE Anatolia/North Mesopotamia). Conversely, Caucasus/Levantine ancestry varied between ~50/~32% in North Mesopotamia to ~0% in northwest Anatolia.

Fig. 2: The Anatolian heartland.

Fig. 2:

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Panels (A-E) show five components of ancestry in Anatolia from the Pottery Neolithic to the Roman/Byzantine period. Boxes in this and subsequent figures indicate the temporal extent (horizontal) and 95% confidence interval (±1.96s.e.) for each period; we also show the fit (solid line) and 5/95% (dotted lines) of the fit of a heteroskedastic Gaussian process (55) on the individuals without any assignment to populations, which allows us to appreciate the degree of variation in ancestry in each time period. The results show that across the peninsula the post-Neolithic period was characterized by expansion of Caucasus hunter-gatherer (CHG)-related ancestry (A) and dilution of northwest Anatolian-related ancestry (E). European hunter-gatherer-related ancestry from both the steppe/eastern Europe (B) and the Balkans (D) was insignificant until the last 3,000 years. A detailed look at the Chalcolithic/Bronze Age period (F) shows that populations there had ancestry intermediate between early farmers from western/central Anatolia (Barcın(10), Tepecik-Çiftlik(13), and Çatalhöyük(12)) and southeastern Anatolia (northern Mesopotamia at Mardin) on the other, the result of admixture between the preceding Neolithic populations, without discernible external influences (that would have elevated any of the five components above their Neolithic levels).

The Chalcolithic period in Anatolia has a wide temporal range (Fig. 2) that spans from the end of the Neolithic (~6000BCE) to the beginning of the Bronze Age (~3000BCE). Individuals in our analysis are mostly from the Late Chalcolithic (post ~4500BCE) and from the entirety of the Bronze Age (down to 1300BCE). Both Chalcolithic and Bronze Age populations from all regions generally had intermediate admixture proportions within the Neolithic ranges of ancestry. This suggests that they could be modeled as drawn from mixtures of the preceding Neolithic populations. In the Marmara region, Caucasus hunter-gatherer ancestry increased from ~0% to ~33% between the Neolithic and Chalcolithic periods (to defined the Chalcolithic we added four individuals from Ilıpınar to a single one from Barcın previously published(11)). In the Central region, we document an increase from ~10-15% at Neolithic Çatalhöyük (12) and Tepecik-Çiftlik (13) to a similar ~33% at Chalcolithic Çamlıbel Tarlası(14) and ~42% at Bronze Age Kalehöyük and Ovaören(15). In the Mediterranean region (southwest Anatolia) the same ~1/3 proportion was present at Harmanören Göndürle (16) in the Bronze Age. In the Aegean region (western Anatolia) we observe a similar ~29% in the Bronze Age. Thus, individuals from more western regions of Anatolia (Marmara, Aegean, Central, and Mediterranean) all had more Caucasus-related ancestry (and correspondingly less Anatolian-related ancestry) during the Chalcolithic and Bronze Age than the preceding Neolithic populations of the area, suggesting a spread of this ancestry westward across the peninsula occurred after the Neolithic, a pattern also observed in the Levant (6). In the more eastern regions of Anatolia (East, in Arslantepe (14); Southeast, from Batman, Gaziantep, Kilis, and Şırnak (new data) and Titriş Höyük (14); Black Sea, from Devret Höyük in Amasya, Samsun (new data), and İkiztepe (14)), populations of the Chalcolithic and Bronze Age periods had, conversely, more western Anatolian Neolithic-related, and less Caucasus-related ancestry, than the Pre-Pottery Neolithic individual from Mardin. This pattern is also observed when we compare the Chalcolithic with the Bronze Age. Differences are small but all in the direction of more western Anatolian Neolithic-related ancestry (an increase of ~3-7% in the East, Southeast, and Black Sea regions) except in the Hatay province (14) where western Anatolian Neolithic-related ancestry decreased and Caucasus-related ancestry increased (from ~14% to 43%) between the Early Chalcolithic (~5500BCE) and Middle to Late Bronze Age (post ~2000BCE).

Taken as a whole, the genetic history of Anatolia during the Chalcolithic and Bronze Age can be characterized as one of homogenization. Neolithic populations differed by as much as ~80% in terms of western Anatolian Neolithic-related and ~50% in terms of Caucasus-related ancestry. In the Chalcolithic and Bronze Age, the range of these differences narrowed substantially: that of western Anatolian Neolithic-related ancestry halved to ~40% (becoming ~20-60%) and that of Caucasus-related ancestry to ~15% (becoming ~30-45% except in the Hatay province). Despite this homogenization, some ancestry differences persisted: the eastern regions retained more Caucasus-related ancestry than the western ones, but the overall pattern was one of attenuated differentiation following intra-Anatolian gene flow stemming from the highly differentiated Neolithic populations of western/central Anatolia on the one hand and northern Mesopotamia on the other (as well as hitherto unsampled others).

Homogenization in Anatolia was coupled by impermeability to exogenous gene flow from Europe, which could be explained by either a large and stable population base that attenuated the demographic impact of external immigration, or cultural factors impeding it. The asymmetry of gene flow between Anatolia and its neighbors is evident for example in the fact that Caucasus hunter-gatherer-related ancestry flowed westward across Anatolia into the Balkans and northward into the Eurasian steppe, but Balkan hunter-gatherer ancestry did not flow into Anatolia or further eastward, and Eastern hunter-gatherer ancestry entered West Asia only as far south as Armenia and to a lesser extent Iran (as we will see below), even down to the Urartian period of the Iron Age, where a population lacking Eastern hunter-gatherer ancestry still existed in the center of the Kingdom of Van (7).

The origin and expansion of steppe pastoralists

The absence of European hunter-gatherer admixture in Anatolia during the Chalcolithic and Bronze Age periods contrasts with developments to the north of the Southern Arc, and north of the Black and Caspian Seas, which saw the formation of Eneolithic (a term used instead of Chalcolithic for this area) and Bronze Age pastoralist populations that harbored a mixture of populations from Eastern Europe and the Southern Arc (9, 10, 17). Examining individuals from the steppe (Fig. 3), we observe that in the post-5000BCE period, Caucasus-related ancestry is added to the previous Eastern hunter-gatherer population, forming the Eneolithic populations at Khvalynsk (10) and Progress-2 (17); this ancestry persisted in the Steppe Maykop population of the 4th millennium BCE (17). Yet, all these populations prior to ~3000BCE lack any detectible Anatolian/Levantine-related ancestry, contrasting with all contemporaneous ones from the Southern Arc, which possess at least some such ancestry at least since the Neolithic (6). In all later periods in the Southern Arc, Caucasus hunter-gatherer-related ancestry is never found by itself, but always admixed, to various degrees, with Anatolian/Levantine-ancestry. This suggests that whatever the source of the Caucasus-related ancestry in the Eneolithic steppe, it cannot have been from the range of variation sampled in the Southern Arc, as this would have introduced Anatolian/Levantine-related ancestry. This implies that the proximal source of the Caucasus-related ancestry in the Eneolithic steppe should be sought in an unsampled group that did not experience Anatolian/Levantine-related gene flow until the Eneolithic. Plausibly this population existed in the North Caucasus, from which Caucasus hunter-gatherer-related but not Anatolian/Levantine-related ancestry could have entered the Eneolithic steppe.

Fig. 3: Yamnaya origins and expansions.

Fig. 3:

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(A) The earliest inhabitants of the steppe (Eastern hunter-gatherers; EHG) were followed by Caucasus hunter-gatherer (CHG)-admixed populations by ~5000BCE and by Anatolian/Levantine-admixed populations by ~3000BCE with the emergence of the Yamnaya-Afanasievo genetic cluster. The proportion of Balkan hunter-gatherer-related ancestry (not shown) is 0.8±0.6% in the Yamnaya cluster and −0.5±0.5% in the Afanasievo. (B) The Yamnaya had nearly half their ancestry from CHG, higher than any Bronze Age Europeans from the Balkans, Italy, or central-northern Europe, but their CHG-EHG balance was equal, similar to the Corded Ware/Beaker clusters of central/northern Europe and contrasting with Southeastern and Mediterranean Europe where CHG was significantly higher than EHG. (95% confidence intervals of ±1.96s.e. are shown.)

The Eneolithic steppe population contrasts with that of the Yamnaya cluster of individuals ~3000BCE, which does have significant Anatolian (3±1%) and Levantine (3.5±1%)-related ancestry (Fig. 3A; steppe individuals in this analysis listed in (1) ). This inference is further supported by detailed analysis of Yamnaya ancestry at different time depths (Tables S22-S28) (1) which indicates that they derived from at least two southern sources. The first source dates to the Eneolithic and includes Caucasus hunter-gatherer ancestry only. The second source dates to prior to the formation of the Yamnaya cluster, and includes Anatolian/Levantine-related ancestry in addition to Caucasus hunter-gatherer (as deep sources), ancestry related to Neolithic people of Armenia (more proximally), or ancestry related to Chalcolithic people of the Caucasus to SE Anatolia (even more proximally). A more direct and geographically proximate source in the Maykop population of the North Caucasus of the 4th millennium BCE has also been proposed (18). While the exact source cannot be at present determined (all of the candidates have different combinations of the same Anatolian/Levantine/Caucasus ancestry; Fig. S1), it was people drawn from this meta-population in the Chalcolithic Caucasus and SE Anatolia that must have been responsible for the second pulse of Southern Arc ancestry into the precursors of Yamnaya steppe pastoralists. The genetic contribution of the second pulse may have been as low as 6.5%, the sum of Anatolian and Levantine ancestry in the Yamnaya, or as high as 53.1%, the totality of the combined Caucasus hunter-gatherer and Anatolian/Levantine ancestry. The low end is unlikely, as Caucasus hunter-gatherer ancestry was ubiquitous in West Asia during the Chalcolithic period and some of it should be added to the 6.5% figure. The high end is also unlikely, as it suggests that all Caucasus hunter-gatherer ancestry flowed northwards with the second pulse, thus ignoring the evidence for its independent flow into the Eneolithic steppe. Our modeling suggests intermediate values of ~21-26% (Table S28), in the middle of the 6.5-53.1% range, an estimate that may be updated in the future as better proximate sources in both West Asia and the steppe come to light.

Archaeological evidence documents how western steppe populations interacted with European farmer groups such as the Tripolye-Cucuteni and Globular Amphora, and it was previously suggested that ancestry from such groups contributed to the ancestry of the Yamnaya (17). Our genetic results contradict this scenario, as European farmers were themselves a mixture of Anatolian Neolithic and European hunter-gatherer ancestry, but the Yamnaya: (i) lacked the European hunter-gatherer ancestry differentiating European from West Asian farmers, and (ii) had an approximately 1:1 ratio of Levantine-to-Anatolian ancestry in our 5-way model, contrasting with the overwhelming predominance of Anatolian ancestry in European farmers. The Caucasus hunter-gatherer/Eastern hunter-gatherer/Western hunter-gatherer/Anatolian Neolithic model of (17) fails (p<1e-10) because it underestimates shared genetic drift with Levantine farmers (Z=5.6), whose contribution into the Yamnaya cannot be explained under that model. These results shift the quest for the ancestral origins of a component of Yamnaya ancestry firmly to the south of the steppe and the eastern wing of the Southern Arc. Determining the proximate source of the two movements into the steppe from the south will depend on further sampling across the Anatolia-Caucasus-Mesopotamia-Zagros area where populations with variations of the three components existed. Similarly, on the steppe side, study of Eneolithic (pre-Yamnaya) individuals could disclose the source dynamics of Caucasus hunter-gatherer infiltration northwards and identify the likely geographical region for the emergence of the distinctive Yamnaya cluster which we show has an autosomal signal of admixture dating to the mid-5th millennium BCE (Fig. S5 and (19)), coinciding with the direct evidence of the first southern influence provided by the Eneolithic individuals of the steppe.

The role of Yamnaya-like populations in spreading both Eastern hunter-gatherer and West Asian ancestry into mainland Europe has been previously recognized (9), but it has also become apparent that some of the latter entered Europe independently of steppe expansions into the Aegean (10, 16), Sicily (20), and even as far west as Iberia (21) by the Bronze Age. We observe that the Caucasus minus Eastern hunter-gatherer ancestry difference in the Yamnaya is ~0% (Fig. 4B) and this allows us to both (a) test whether steppe migrants into mainland Europe may have originated from a different steppe population (with a non-equal balance of Caucasus and Eastern hunter-gatherer components), and (b) test whether additional migrations (with either more Eastern or Caucasus hunter-gatherer ancestry, thus shifting the difference away from zero) occurred. We find that the Corded Ware and Bell Beaker complex individuals from Europe are all consistent with a balanced presence of the two components (consistent with having been transmitted via a Yamnaya-like population). Even the early Corded Ware from Bohemia where a third “northern” source has been suggested to have been substantially involved (22), the difference is one of a small 3.1±2.1% excess of Eastern hunter-gatherer ancestry, which is entirely consistent with being transmitted entirely by the Yamnaya to the limits of the resolution of our statistical analysis. This is not the case for Southeastern Europe where Bronze Age individuals had an excess of Caucasus over Eastern hunter-gatherer ancestry not only in the Aegean (~17% in both Minoans and Mycenaeans) (16), but throughout the Balkan peninsula (Fig. 3B) where the overall Bronze Age excess is 7.4±1.7% (with by-country estimates of ~4-13%). A possible explanation for this excess is the existence of a small 5.2±0.6% Caucasus hunter-gatherer component in the Neolithic substratum of Southeastern Europe (Fig. 4A); we estimated that this proportion is ~0-1% in four separate Early Neolithic populations from Hungary (Starčevo-Körös cultural complex), France, Spain, and the Linearbandkeramik of Austria, Germany and Hungary(3, 23-30). Thus, the Bronze Age Caucasus hunter-gatherer ancestry in Southeastern Europe compared to central-northern-western Europe may continue this contrast from the Neolithic. However, the even higher levels observed in the Aegean (Fig. 3B and (7)) suggest additional gene flow after the Neolithic by the time of the Early Bronze Age(31).

Fig. 4: Genetic heterogeneity in Southeastern Europe following the Yamnaya expansion.

Fig. 4:

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Panels (A-E) show five components of ancestry in Southeastern Europe. The replacement of hunter-gatherer by early farmer ancestry (panels D and E) was followed by the rise of Caucasus hunter-gatherer (CHG) and Eastern hunter-gatherer (EHG) ancestry over the last 5,000 years (panels A and B) with Levantine ancestry being relatively unimportant and showing no discernible temporal pattern (C). In panel (F) we show a linear regression of population dates (using directly radiocarbon dated individuals for each population) on admixture times in generations; more recent populations have older admixture times, and the regression places admixture between populations related to the southeast European Neolithic and Yamnaya at 4853±205 years ago and the generation length at 28±4 years, virtually identical to its independent empirical estimation of 28 years.

Interplay of Local, Steppe, and West Asian ancestries in Southeastern Europe

Southeastern Europe interfaces geographically with both the Eurasian steppe and with Anatolia and its genetic history (Fig. 4) bears traces of both connections, starting from the partial replacement of its local Balkan hunter-gatherers by Anatolian Neolithic farmers beginning ~8,500 years ago, followed by the expansion of Eastern hunter-gatherer-ancestry bearing steppe populations ~5,000 years ago (3). While the Bronze Age was a period of partial homogenization in Anatolia as we have seen, in Southeastern Europe it was a time of remarkable contrasts.

One aspect of this heterogeneity was the retention of the local Balkan hunter-gatherer ancestry itself; this was detected only in the Balkans (within the SA), thus precluding any substantial migration from the area to the rest of the Southern Arc. Balkan hunter-gatherer ancestry was variable during the Bronze Age and related to geography. A striking contrast is found within Romania where our new data shows that it makes up ~12% of the ancestry of 42 individuals from the Bodrogkeresztúr Chalcolithic, and ~24-30% in 10 Bronze Age individuals from Cârlomăneşti (Arman), and in Ploieşti and Târgşoru Vechi south of the Carpathian Mountains. Together with another Bronze Age individual from Padina in Serbia (2460-2296 calBCE) near the Iron Gates, whose Balkan hunter-gatherer ancestry was ~37%, these results prove remarkable hunter-gatherer ancestry preservation in the North Balkans postdating the arrival of both Anatolian Neolithic and steppe ancestry in the region. This contrasts with the southern end of the Balkan peninsula in the Aegean (7) where neither the Neolithic nor the Bronze Age populations had any significant Balkan hunter-gatherer ancestry, raising the question of whether the region’s pre-Neolithic population was more similar to that of the North Balkans (Balkan hunter-gatherer-like) or western Anatolia (and thus similar to the Neolithic population).

The key driver of the Bronze Age heterogeneity was the appearance of Eastern hunter-gatherer ancestry that became ubiquitous in Southeastern Europe after its sporadic Chalcolithic appearance (3). This is most evident (~31-44%) in Moldova at several Bronze Age sites including those of the Catacomb and Multi-cordoned Ware cultures, and individuals from Romania (Trestiana and Smeeni) on the eastern/southeastern slopes of the Carpathians which contrast with the high-Balkan hunter-gatherer group from Arman. We also detect a contrast between Catacomb culture individuals from Moldova and those from the Caucasus(17), driven by an individual from Purcari with substantial (17±4%) Anatolian Neolithic ancestry, suggesting some heterogeneity within this culture on opposite sides of the Black Sea. For the rest of the Balkans, the amount of Eastern hunter-gatherer ancestry is ~15% and drops to ~4% in Mycenaean Greece and to negligible levels in Minoan Crete (7, 16).

Our study identifies a “High-steppe ancestry” set of individuals, a term we use to refer to individuals from the Balkans during the Early Bronze Age who had unusually high proportions of Eastern hunter-gatherer ancestry compared to their contemporaries (Fig. 4B). This includes two previously published individuals from Nova Zagora in Bulgaria and Vucedol in Croatia (3), as well as five newly reported individuals, including an Early Bronze Age individual from Çinamak in Albania (2663-2472 calBCE) and four that are culturally Yamnaya: one from Vojlovica-Humka in Serbia, and two from Boyanovo and one from Mogila in Bulgaria. In aggregate, this group of Balkan individuals has 35.9±2.5% Eastern hunter-gatherer, 36.4±1.9% Caucasus hunter-gatherer, and 23.0±1.9% Anatolian Neolithic ancestry in comparison to the Yamnaya cluster individuals (46.1±1.0%, 46.6±1.6%, and 3.0±1.0% respectively), i.e., the same Caucasus/Eastern hunter-gatherer balance as the Yamnaya but diluted by about one-fifth by local Neolithic ancestry of ultimately Anatolian origin.

When we use DATES (19) to date the admixture of steppe ancestry in populations of Southeastern Europe (Fig. 5F; Fig. S6), we arrive at an estimate that this took place ~4850 years ago, i.e., precisely following the Yamnaya expansion, and within the timeframe of our “High-steppe” cluster individuals. This suggests that (as a first approximation) steppe ancestry in Southeastern Europe from the Bronze Age onward was largely mediated by descendants of Yamnaya and local Balkan populations and not by earlier waves out of the steppe that affected the region sporadically. This admixture need not have taken place in one locality, as indicated by the presence of Yamnaya-like individuals in several regions of the Balkans, spatially beyond both the cultural transition zone between steppe pastoralist and settled populations(32), and the geographical one from the eastern European flatlands into mountainous areas.

Fig. 5: A genetic history of Armenia.

Fig. 5:

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Panels (A-D) show changes in the four components of ancestry. (A) Caucasus hunter-gatherer (CHG) is the most important component in all ages, rising to its maximum in the Kura-Araxes culture of the Early Bronze Age. (B) Eastern hunter-gatherer (EHG) ancestry first appears in the Chalcolithic at Areni Cave, disappears during the Kura-Araxes period, re-appears strongly in the Middle-Late Bronze Age period and decreases to ~1/3 of its peak value by ~2,000 years ago. (C, D) Levantine and Anatolian ancestry were present in all periods as minority components. Balkan hunter-gatherer ancestry (not shown) is <1% in all periods. (All individuals shown are from Armenia save for two Neolithic and a Chalcolithic individual previously published from Azerbaijan). (E) During the Middle-to-Late Bronze Age peak, Armenia had more EHG ancestry than its neighbors in West Asia (Anatolia, the Levant, and Iran), (F) C14-dated Bronze-to-Iron Age individuals from Armenia admixed 52.2±8.0 generations (1460±224 years) prior to their average date of 1119BCE, or ~2579BCE (mid-3rd millennium BCE), assuming a generation length of 28 years(56) (we use Early Bronze Age Armenia and Yamnaya cluster individuals from Russia as proxy sources).

Armenia: fluctuating steppe ancestry against a persistent West Asian genetic background

Armenia is situated in the highlands of West Asia to the east of Anatolia and to the south of the Caucasus mountains separating West Asia from the Eurasian steppe to the north. When we examine the trajectory of ancestry there (Fig. 5), we observe that the local Caucasus hunter-gatherer-related ancestry (Fig. 5A) has always been the most important component of the population from the Neolithic to the present, making up ~50-70% of ancestry over the last 8,000 years. As in Anatolia, the two other components of West Asian ancestry had a strong presence as well making up most of the remainder.

The most striking feature of the history of Armenia compared to all other Asian regions of the Southern Arc is the tentative appearance of Eastern hunter-gatherer ancestry in the Chalcolithic at Areni-1 Cave (11) ~6,000 years ago (Fig. 5B) followed by its disappearance ~5,000 years ago with the Early Bronze Age Kura-Araxes culture and its reappearance at the Middle Bronze Age where a level of ~14% was followed by ~10% in the Late Bronze Age and Iron Age and then diluted to ~7% by the Urartian period of the first half of the 1st millennium BCE and to the ~1-3% levels observed since the second half of that millennium at sites like Aghitu and through the medieval period (at Agarak) down to present-day Armenians. When we compare the Middle/Late Bronze Age individuals from Armenia (when Eastern hunter-gatherer ancestry was highest and from which we have individuals from more than twenty sites) with other West Asian European and steppe populations (Fig. 5E) it is evident that Armenia is an outlier. Populations from Armenia have significantly more such ancestry than all surrounding populations: Anatolia and the Levant where this ancestry is undetected during the Bronze Age, Iran where it makes up ~2% overall, and even the Maykop cluster populations of the North Caucasus (17) where it reaches ~3%. These analyses in Armenia show that Eastern hunter-gatherer ancestry flowed from the steppe not only west of the Black Sea into southeastern Europe attaining its minimum in the Aegean and east of it, but also across the Caucasus into Armenia. However, significant proportions of Steppe ancestry spread no further into Anatolia from either west or east.

The appearance of Eastern hunter-gatherer ancestry at Areni-1 Cave is the first known genetic influence of peoples of the Eurasian steppe on West Asia, although with our current sparse sampling of the Eneolithic steppe we do not know the precise geographical source of this ancestry within the steppe. The Areni individuals date to the same 5th millennium BCE in which we saw that the Eneolithic steppe came to be influenced by Caucasus hunter-gatherer-related ancestry from the south and to which our admixture dating of Yamnaya origins also points. However, it was only during the Middle/Late Bronze Age that Eastern hunter-gatherer ancestry became entrenched in Armenia, at least for a while, forming an “enclave” of Steppe influence in West Asia that eventually dissipated during the 1st millennium BCE. This period of relatively high steppe ancestry corresponds to the “Lchashen-Metsamor” culture of the Bronze-to-Iron Age (1). Linkage disequilibrium dating of steppe admixture (Fig. 5F) in our extensive set of individuals of average late 2nd millennium BCE date suggests it occurred a millennium and a half earlier, at the middle of the 3rd millennium BCE and thus in parallel with the transformation of mainland Europe and the Balkans. In Armenia itself, the mid-3rd millennium BCE corresponds to the demise of the Kura-Araxes culture and its succession by the “Early Kurgan” culture, followed during the end of that millennium by the “Trialeti-Vanadzor” complex from which an individual from Tavshut (2127-1900 calBCE) already has the ~10% Eastern hunter-gatherer ancestry of the Lchashen-Metsamor population, the first documented steppe descendant in Armenia two millennia after the Chalcolithic. The analysis of Y-chromosomes to which we now turn provides an independent line of evidence for a link between the Yamnaya and populations of Armenia following this 3rd millennium BCE re-appearance of Eastern hunter-gatherer ancestry.

Y-chromosome links between the Steppe and West Asia in their genome-wide context

Y-chromosome variation (Tables S29-S34; Figs. S77, S79)(1) can be used to provide confident upper bounds on the date when two populations shared ancestors as the large number of mutations that can be analyzed over almost ten million nucleotides of alignable sequence means that the split times in the genealogy are accurately known. When the ancient individuals Y-chromosome analysis also has the potential to provide insight into the social processes.

Subclades of Y-chromosome haplogroup R-L389 are particularly informative for tracing connections between the Southern Arc and the Eurasian steppe (Fig. 6). First, haplogroup R-V1636 with an inferred common ancestor in the 5th millennium BCE documents gene flow between the steppe and the Southern Arc in the Eneolithic/Chalcolithic period (Fig. 6B). R-V1636 is present in two individuals from the Late Chalcolithic at Arslantepe (Turkey) (14) and the Early Bronze Age in Armenia at Kalavan (11). It is also found in the piedmont of the North Caucasus at Progress-2 (17), the open steppe at Khvalynsk II (10), and the Single Grave Culture of northern Europe (Gjerrild) (33). Importantly, the individuals from Armenia and Arslantepe lack any detectible Eastern hunter-gatherer autosomal ancestry (Fig. 6C) which is maximized in the Khvalynsk individuals, an observation that provides some evidence for a southern origin for the R-V1636 haplogroup (we caution, however, that the haplogroup occurs earlier in several sites in the north, which could be consistent with an alternative scenario in which male migrants from the steppe introduced it into Southern Arc populations during the Chalcolithic but their autosomal genetic legacy was diluted by the much more numerous locals). The earliest individuals from the R-L389 clade belong to the R-P297 sister clade of R-V1636, including the hunter-gatherer from Lebyazhinka IV(9, 10) and hunter-gatherers from the Baltic region (3), both without Caucasus hunter-gatherer ancestry, suggesting an eastern European origin of this clade which would eventually give rise to the R-M269 clade that spread extremely widely in the Bronze Age.

Fig. 6: Y-chromosome links between the Southern Arc and the Eurasian steppe.

Fig. 6:

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(A) Phylogeny of haplogroup R-L389 (R1b1a1) with TMRCA estimates of yfull.com. (B) Caucasus hunter-gatherer (CHG)/Eastern hunter-gatherer (EHG) ancestral composition of R-L389 Y-chromosome individuals. (C) R-L389 individuals from the Southern Arc, representing a subset of the individuals plotted in panel B. Individuals more than 2,000 years old are shown.

Haplogroup R-M269, which is inferred to have a shared common ancestor in the 5th millennium BCE is crucial for understanding steppe expansions as it was the dominant lineage of the Yamnaya-Afanasievo group (4, 9, 34), in its 4th millennium BCE R-Z2103→R-M12149 sub-lineage. In the Balkans, a group of six Bronze Age individuals from the 3rd millennium BCE carrying R-M269 (Fig. 6C) are associated with >30% Eastern hunter-gatherer ancestry and this includes not only Catacomb and Multi-cordoned Ware individuals from Moldova, adjacent to the steppe, but also from further south, including two Yamnaya males from Bulgaria (Boyanovo and Mogila, the latter associated with Yamnaya burial custom and with the R-Z2103 haplogroup typical of the steppe Yamnaya) and one from Albania (Çinamak) belonging to the “High steppe” ancestry group. By the Late Bronze Age (late 2nd millennium BCE), as well as later, no high-steppe ancestry individuals are observed, but steppe-associated Y-chromosomes persist, including R-Z2106, a lineage that links North Macedonia (Ulanci-Veles), Albania (Çinamak), the steppe, and Armenia. The population of Southeastern Europe contrasts strongly with those of the central/northern Europe and Eurasian steppe archaeological cultures of ~3000-2000BCE that were strongly associated with particular Y-chromosome lineages: Afanasievo (4, 34) with the same R-Z2103 as the Yamnaya, Corded Ware/Fatyanovo/Sintashta (4, 9, 34, 35) with R-M417, and Beaker (36) with R-L51. In Southeastern Europe during the Bronze Age we detect 32/30/21/11 Y-chromosomes belonging to haplogroups R/J/I/G linking it with central-northern Europe and the steppe/West Asia/local hunter-gatherers/Anatolian-European Neolithic farmers respectively. Together with the extraordinary heterogeneity in autosomal ancestry in the Balkans, a picture emerges of a fragmented genetic landscape that may well parallel the poorly understood linguistic diversity in the ancient Balkans which among IE languages includes Paleo-Balkan speakers prior to the spread of Latin and Slavic, with Albanian the only surviving representative. Did early Indo-European become successful in Southeastern Europe because it functioned as a “lingua franca”, facilitating communication among speakers of the diverse languages of previous farmer and hunter-gatherer populations?

Our newly reported data reveals that a large proportion of individuals in Armenia and northwest Iran belonged to the R-Z2103→R-M12149 haplogroup during the 2nd and early 1st millennium BCE, providing a genetic link with the Yamnaya in these regions where no archaeological presence of the Yamnaya culture itself is attested. It definitely represents a more direct link than either R-V1636 or the early appearance of Eastern hunter-gatherer ancestry at Areni-1 cave in Armenia (11) during the Chalcolithic at the end of the 5th millennium BCE which provides evidence of converse movement of Caucasus hunter-gatherer ancestry into the steppe Eneolithic.

Despite the Y-chromosome movement southward attested by our data, any association between R-haplogroup bearers and Eastern hunter-gatherer ancestry was lost south of the steppe as these had similar proportions of Eastern hunter-gatherer ancestry as I-Y16419 bearers (the second most prevalent lineage in Armenia). Two Bronze-to-Iron Age sites with substantial sample sizes (Bagheri Tchala, n=7 and Noratus, n=12 unrelated males) have contrasting haplogroup distributions dominated by R-M12149 and I-Y16419 respectively (Fisher’s exact test p<0.001), suggesting the existence of a patrilocal mating system ~1000BCE in Armenia. During the same period at Hasanlu in northwest Iran many individuals have no trace of Eastern hunter-gatherer ancestry at all despite the presence of R-M12149 there(7), suggesting that the initial association of this lineage with Eastern hunter-gatherer ancestry on the steppe had vanished as R-M12149 bearers reproduced with Southern Arc individuals without Eastern hunter-gatherer ancestry (Fig. 6C).

We observe that, on the steppe, R-M12149 Y-chromosomes (within haplogroup R1b) at the beginning of the 3rd millennium BCE, associated with the Yamnaya, were replaced by the beginning of the next millennium by R-Z93 Y-chromosomes (within haplogroup R1a), associated with Corded Ware/Fatianovo (35) steppe descendants such as those of the Sintashta culture (34). It is important to emphasize that the genetic data cannot distinguish whether this Y chromosome replacement was the result of competition between patrilineal groups from the steppe, one of which may have had cultural adaptations such as usage of an improved variety of domesticated horse (37), or whether one group simply filled in an ecological niche vacated by earlier groups. A fuller understanding of the reason for this profound genetic change requires combined analysis of genetic and archaeological data.

Whatever the reason for their demise on the steppe itself, the Yamnaya-descended R-Z2103 patrilineages survived in Armenia, down to the present-day where this clade is present in appreciable frequencies in all studied Armenian groups (38), despite the substantial dilution of autosomal steppe ancestry inferred in our study. The persistent and lasting presence of Yamnaya patrilineal descendants in Armenia contrasts with mainland Europe and South Asia where steppe ancestry was introduced by people who were not patrilineal descendants of the dominant R-M12149 lineage of the Yamnaya population. Instead, they belonged to different descent groups that had received autosomal steppe admixture while carring different predominant Y-chromosome lineages. Armenia also contrasts with Anatolia for which no R-M269 Y-chromosomes are observed at all during the Chalcolithic, Bronze Age, or Ancient (pre-Roman) periods (n=80 unrelated individuals; 95% C.I.: 0-4.5%) and in which haplogroups J (36 individuals) and G (17 individuals) are most common with the former—also still most common, at a frequency of ~1/3, in present-day people from Turkey (39)—achieving such prominence despite occurring in only in 1/18 Neolithic male individuals from Barcın and Ilıpınar in the Marmara region during the pre-Chalcolithic period. A likely explanation for the haplogroup J increase is that it accompanied the spread of Caucasus hunter-gatherer ancestry inferred by our admixture analysis (Fig. 2). This inference is made plausible by the fact that both Caucasus hunter-gatherer individuals from Kotias and Satsurblia (7) and a Mesolithic individual from Hotu Cave (11, 34) in Iran belonged to this lineage, suggesting its very old presence in the Caucasus/Iran region, and contrast it with haplogroup G which occurred in the majority (10/18) individuals from the Neolithic Marmara region. By the Chalcolithic, haplogroups G and J were ubiquitous in Anatolia, each making up 10/28 males from that period, paralleling the homogenization that had occurred by that time.

The Indo-Hittite hypothesis in the light of genetic data

In what follows we discuss the implications of our genetic findings for hypotheses about the origins and spread of Indo-European and Anatolian languages. We also highlight a caveat: in contrast to findings about movements of people, the relevance of genetics to debates about language origins is more indirect, as languages can be replaced with little or no genetic change, and populations can migrate and mix with little or no linguistic change. Nevertheless, the detection of migration is important as it identifies a plausible vector for language change(40).

The discoveries of massive migrations from the steppe both westwards into central and western Europe (4, 9) and eastwards into South Siberia (4) and Central/South Asia (34) have provided powerful evidence for the theory of steppe Indo-European origins by linking populations all the way from northwest Europe (36) to India via common steppe ancestry. The present paper adds further support to the theory by the discovery of ubiquitous ancestry from the steppe in the Bronze Age Balkans (where indubitably Indo-European Paleo-Balkan languages such as Thracian and Illyrian (41) were spoken), including individuals of predominantly steppe ancestry; by documenting the ubiquity of steppe ancestry in Bronze and Iron Age Armenia where Armenian is first attested and links between Armenia, the steppe, and the Balkans; and by the further documentation of steppe ancestry in the Aegean (7) during the Mycenaean period when the Greek language is first attested, albeit at lower levels. All ancient and present-day branches of the Indo-European language family can be derived or at least linked to the early Bronze Age Yamnaya pastoralists of the steppe or genetically similar populations.

A link to the steppe cannot be established for the speakers of Anatolian languages due to the absence of Eastern hunter-gatherer ancestry in Anatolia (4, 11, 14, 16) which our study reinforces in three ways: (i) first, by documenting its paucity in ~100 new Anatolian individuals from the Chalcolithic to pre-Roman antiquity, (ii) by contrasting western parts of Anatolia with its immediate Aegean-Balkan neighbors to the west, and (iii) by contrasting eastern/northern parts of Anatolia with its neighbors in Armenia in the east. Certainly, the absence of Eastern hunter-gatherer ancestry in Anatolia can never be categorically proven (as more sampling can always disclose some such ancestry); however, at present, and despite extensive sampling, such ancestry is not detected either at possible entry points (west and east by land, or even north by sea), or in the population as a whole.

The Indo-Hittite hypothesis, first proposed by E.H. Sturtevant in 1926 (42), has been supported by more modern phylolinguistic analyses that indicate that Anatolian languages such as Hittite are basal to the rest of the Indo-European family tree (43), suggesting an early split between the two. We have shown that Anatolia was indeed transformed by the Late Chalcolithic by the spread of Caucasus hunter-gatherer-related ancestry to its westernmost edges, as were apparently Eneolithic populations of the steppe, which included also Anatolian/Levantine-related ancestry by the time of the formation of the Yamnaya pastoralists. It is premature to identify the proximate sources of these movements before all the candidate source populations of Anatolia, north Mesopotamia, western Iran, Armenia, Azerbaijan, and the Caucasus have been adequately sampled.

Our analyses show that there were at least two gene flows from two group related to West Asians into the steppe, which transformed the steppe’s population and may have induced linguistic change there; the reverse movement is more tentative, with early influences from the north such as at Areni Cave (11) or possibly associated with R-V1636 Y-chromosomes not making a sizeable genetic impact on the population of Anatolia. The evidence is consistent with two hypotheses: Hypothesis A postulates that Proto-Indo-Anatolian (including both Anatolian languages and Proto-Indo-European) was spoken by a population with high Eastern hunter-gatherer ancestry which had a disproportionate linguistic impact on Anatolia while contributing little if any ancestry. In the post-Bronze Age landscape of Anatolia, we do find outliers marked by European or steppe influence (7), but this is a period when Anatolia is influenced by numerous linguistically non-Anatolian Indo-European populations, including Phrygians, Greeks, Persians, Galatians, and Romans, to name only a few. Yet in individuals from Gordion, a Central Anatolian city that was under the control of Hittites before becoming the Phrygian capital and then coming under the control of Persian and Hellenistic rulers, the proportion of Eastern hunter-gatherer ancestry is only ~2%, a tiny proportion for a region controlled by at least four different Indo-European speaking groups. In medieval times, Central Asian ancestry associated with Turkic speakers was added to the population (7), which persists to the present. Clearly, Anatolia has not been impervious to linguistic change during its recorded history, and the harbingers of that change are also detected genetically, even if as outliers. By contrast, the complete absence of Eastern hunter-gatherer ancestry in the Chalcolithic and Bronze Age either as isolated outliers or as a general low-level presence challenges the steppe theory to suggest a plausible mechanism of how a population that made little-if-any genetic impact could nonetheless effect large-scale linguistic change. A common vocabulary for wheeled vehicles is not attested for both Anatolian languages and the rest of Indo-European (44), thus potentially removing a technological advantage regarded as potentially crucial in the dissemination of Indo-European languages (45).

Hypothesis B postulates that Proto-Indo-Anatolian was spoken by a population of West Asia and the Caucasus, with low or no Eastern hunter-gatherer ancestry which affected both Anatolia and the steppe. Hypothesis B may help explain the linguistic diversity observed in Bronze Age Anatolia in which both Anatolian (Hittite, Luwian, and Palaic) speakers, as well as speakers of other languages including Hattic (a non-Indo-European linguistic isolate of central-northern Anatolia), and Hurrian (a non-Indo-European language from eastern Anatolia and north Mesopotamia related to the later Iron Age Urartian language(7)) co-existed. The non-Indo-European Hattic language, attested only in Anatolia, would most economically represent the linguistic substratum, spoken by a population of high Anatolian-related ancestry, while the Indo-European Anatolian languages would be spoken by a population of high Caucasus hunter-gatherer-related ancestry. The spread of people of high Caucasus hunter-gatherer ancestry across the peninsula from the east, at least some of which may have spoken early forms of Anatolian languages, would simultaneously explain both the genetic homogenization prior to the Late Chalcolithic (Fig. 2) and the co-existence of the two linguistic groups. How many of the people associated with the spread of Caucasus hunter-gatherer ancestry spoke Anatolian languages? Other languages, related to the diverse non-Indo-European language families of the Caucasus, such as Kartvelian and Northwest/Northeast Caucasian, may have also participated in the westward movements.

As for the steppe, at least two streams of migration from the south (Eneolithic and Yamnaya-specific) present the opportunity for an early (Chalcolithic) split of Yamnaya linguistic ancestors from the Anatolian linguistic ancestors, followed 1000-2000 years later by the dispersal of Indo-European languages from the steppe with the expansion of the Yamnaya culture. Linguistic borrowings (46) between Proto-Indo-European and other language families such as Kartvelian (spoken primarily in Georgia) could be useful for localizing the Proto-Indo-Anatolian homeland, but these may have alternatively come about by long-range mobility since the Chalcolithic, proven by such evidence as the presence of R-V1636 descendants ~3000km apart from Khvalynsk to Anatolia during this period. Contributions of Indo-European to Uralic (spoken in the forest-zone of eastern Europe and Siberia) appears to have involved only Indo-Iranian speakers around 4200 years ago (47); this is important as it constrains the migratory history of Proto-Indo-Iranian, suggesting that it spread through the Steppe to South Asia and ruling out the possibility it spread from West Asia to South Asia over the Iranian plateau. However, the contribution of Indo-Iranian to Uralic languages does not shed light on the deeper question of early Indo-Anatolian origins. A challenge for the theory that Proto-Indo-Anatolian was formed in the south in a Caucasus hunter-gatherer-rich population will be to trace the origins of the autosomal ancestry of the Yamnaya in the Caucasus or West Asia (where some existing proposals place the Proto-Indo-Anatolian homeland (48, 49)) and to identify the place where the R-M269 ancestral lineage expanded from, as this will be a most plausible secondary homeland of Indo-European expansion outside Anatolia.

The scenario of a West Asian source of Proto-Indo-Anatolian is consistent with a linguistic analysis (50) which places the split of Tocharian from the remaining (Inner Indo-European) languages ~3000BCE associated with the Yamnaya expansion and the disintegration of the remaining languages during the 3rd millennium BCE, in line with our inferences of major steppe admixture into the Balkans and Armenia for the subset of Indo-European languages of these regions. The Anatolian split is placed by that study at ~3700BCE (4314–3450 BC, 95% Highest Posterior Density interval), a period during which the Caucasus hunter-gatherer ancestry first appears as far west as the Chalcolithic individuals from northwest Anatolia (at Ilıpınar) sampled in our study and during which the flow of Caucasus hunter-gatherer ancestry into the steppe had already commenced.

Overall we suggest that a scenario in which Anatolian and Indo-European languages are descended from a common West Asian progenitor matches the evidence of population change provided by ancient DNA for four reasons. First, the genetic transformation of Anatolia between the Neolithic and before the Late Chalcolithic (Fig. 2) was a clear opportunity for linguistic spread resulting in the co-existence of Hattic and Anatolian languages. Second, the two transformations of steppe populations during the Chalcolithic and before the Bronze Age, with their strong south-north directionality (Fig. 3) were opportunities for linguistic spread and match exactly the Anatolia/Indo-European split inferred by linguists. Third, steppe migrations into regions where Indo-European daughter languages were spoken, such as the Balkans (Fig. 4), Armenia (Fig. 5), central-northern Europe(4, 9, 36) and Central/South Asia(4, 34) were clear opportunities for the disintegration of Proto-Indo-European and the dispersal of its daughter languages across Eurasia. Fourth, the absence of such migrations into Anatolia (Fig. 2F), in contrast to both neighboring Armenia and Southeastern Europe (Fig. 4, 5 and (7)), makes Anatolia the only exception in the association of steppe ancestry with Indo-Anatolian languages.

This outline of events points toward a concrete research program of investigating the archaeological cultures of West Asia, the Caucasus, and the Eurasian steppe to identify a population driving both transformations (i) and (ii) above, thus linking Anatolia and the steppe. The discovery of such a “missing link” (corresponding to Proto-Indo-Anatolians if our reconstruction is correct) would bring to an end the centuries-old quest for a common source binding through language and some ancestry many of the peoples of Asia and Europe (41, 51)

Supplementary Material

Supplementary Materials
DataS1(individuals.with.newly.reported.data)
DataS2(libraries.from.individuals.with.newly.reported.data)
DataS3(newly.reported.C14.dates)
DataS4(full.list.of.analyzed.inds)
DataS5(ancestry.and.phenotypes)

Ethics Statement and Acknowledgments:

This study was carried following the principles for ethical DNA research on human remains laid out in (52). We are grateful to the authorities and sample stewards including museums, museum curators, and archaeologists, for providing written permission to sample each human remain. We acknowledge the ancient individuals whose genetic data we analyzed and whose permission we could not directly ask. We aimed to write a manuscript that was respectful of the ancient individuals, treating samples from them as derived from real people whose memories must be respected. We sought to reflect the perspectives of people from the diverse geographic regions and cultural contexts from which the sampled individuals came by having each sample be represented by at least one co-author who was a sample steward and was part of a network engaged with local communities. We thank J. Bennett, V. Narasimhan, H. Ringbauer; J. Sedig, A. Shaus, L. Vokotopoulos, M. Wiener, and several anonymous reviewers for critical comments; D. Mitrevski, M. Pantelidou-Gofa for archaeological work; G. Rollefson for support for publishing additional data from ‘Ain Ghazal and advising on archaeological contextualization; V. Urasin for technical help with the yfull.com phylogeny; and N. Adamski for lab work. Most of the samples from Albania (sites of Podgorie; Tren Cave 2; Dukat; Çinamak; Kënetë; Bardhoc; Shtikë, Barç and Pazhok) were included in this study as part of the project "The paleogenetics of southeastern Europeans, admixture, selection and transformations: the case of Albania", a joint-collaboration between the Albanian Institute of Archaeology (Tirana) and the Anthropology Department of the University of Vienna (principal investigators R.P, R.K. and R.R). We thank the National Museum of Bosnia and Herzegovina and its staff. We honor the memories of Gregory Areshian, Milos Bilbija, Edgar Peltenburg, who would have been our co-authors if they had not passed away in the course of this study.

Funding:

The ancient DNA work for this study was supported by the National Institutes of Health (NIGMS GM100233), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, and by the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation and the Howard Hughes Medical Institute (DR). We acknowledge European Research Council (ERC) Starting Grant Project HIDDEN FOODS (Grant No. 639286) (ECr); two grants of the Romanian Ministry of Research, Innovation, and Digitization (CNCS, CNFIS, CCCDI – UEFISCDI), project numbers 351PED (PN-III-P2-2.1-PED-2019-4171), and CNFIS-FDI-2021-0405 D6/ 2021, within PNCDI III (CL)’ support from the FF-MAC project (Face to Face: Meet an Ancient Cypriot; Grant No. INTEGRATED/0609/29) and the BioMERA project (Platform for Biosciences and Human Health in Cyprus: MicroCT and Synchrotron Radiation Enabled Analyses; Grant No. INFRASTRUCTURES/1216/09) co-financed by the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation (KOL); a grant of the Hungarian Research, Development and Innovation Office (FK128013) (TH, TSz, KK); Croatian Science Foundation grant HRZZ IP-2016-06-1450 (MN, IJ, JB); Grant NCN 2015/17/B/HS3/01327 (PW); and a Bursa Uludağ University (Turkey) General Research Project Grant SGA-2021-389 (project title ‘Early Christian Martyriums in the Light of the Basilica Church of the Lake of Iznik) (MŞa).

Footnotes

Competing interests: The authors declare that they have no competing interests.

Data and Materials availability: Genotype data for individuals included in this study can be obtained from the Harvard Dataverse repository through the following link (doi to be added upon publication). BAM files of aligned reads can be obtained from the European Nucleotide Archive (Accession number PRJEB54831).

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Materials
NIHMS1873728-supplement-Supplementary_Materials.pdf (59.9MB, pdf)
DataS1(individuals.with.newly.reported.data)
NIHMS1873728-supplement-DataS1_individuals_with_newly_reported_data_.xlsx (203.7KB, xlsx)
DataS2(libraries.from.individuals.with.newly.reported.data)
NIHMS1873728-supplement-DataS2_libraries_from_individuals_with_newly_reported_data_.xlsx (466.3KB, xlsx)
DataS3(newly.reported.C14.dates)
NIHMS1873728-supplement-DataS3_newly_reported_C14_dates_.xlsx (46.8KB, xlsx)
DataS4(full.list.of.analyzed.inds)
NIHMS1873728-supplement-DataS4_full_list_of_analyzed_inds_.xlsx (689.6KB, xlsx)
DataS5(ancestry.and.phenotypes)
NIHMS1873728-supplement-DataS5_ancestry_and_phenotypes_.xlsx (272.8KB, xlsx)

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