Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine

www.nature.com/scientificreports OPEN Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine Pere Gelabert1,2,13*, Ryan W. Schmidt3,4,13*, Daniel M. Fernandes1,2,5, Jordan K. Karsten6, Thomas K. Harper7, Gwyn D. Madden8, Sarah H. Ledogar9, Mykhailo Sokhatsky10, Hiroki Oota11, Douglas J. Kennett12 & Ron Pinhasi1,2* The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the CucuteniTrypillia cultural complex (CTCC, ~ 5000–3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935–825 cal BCE). Results reveal that the CTCC individuals’ ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980–825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE. The Neolithisation process in Europe resulted in dramatic technological and cultural shifts, which included novel subsistence practices1. There are two major groups of models that explain the Neolithisation process: demic diffusion models describe Neolithisation as a colonisation process by farmers which is propelled by exponential population growth characteristic of the Neolithic, whereas acculturation models outline the process as one in which at least some of the transition entails indigenous hunting-foraging groups that adopt farming following periods of variable length during which they interact with neighbouring exogenous f armers2. Across most of Europe, the Neolithic transition was genetically defined by a profound population replacement, consistent with the demic diffusion of peoples from Anatolia3–5. The Anatolian farmers reached the Balkans and other regions of Southeast Europe in the seventh millennium B CE6,7 and subsequently spread further via the Mediterranean and later through the Danube, substantially replacing indigenous Mesolithic European p opulations8,9. In contrast to Central Europe10,11, areas of Eastern Europe including Ukraine, Moldova, Western Russia, and Romania did not adopt agriculture until the Late Neolithic (~ 4500 BCE), although various sedentary and semisedentary hunter-gatherers Mesolithic groups in these regions began using pottery as early as 8500 B CE12,13. 1 Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. 2Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. 3University of Porto, CIBIO-InBIO, Rua Padre Armando Quintas, nº 7, 4485‑661 Vairão, Portugal. 4School of Archaeology & Earth Institute, University College, Dublin, Belfield, Dublin 4, Ireland. 5CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. 6Department of Anthropology, Global Religions, and Cultures, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA. 7Institute for European and Mediterranean Archaeology, State University of New York at Buffalo, Buffalo, NY 14260, USA. 8Department of Anthropology, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA. 9Department of Archaeology, Classics, and History, University of New England, Armidale, NSW 2351, Australia. 10Borschiv Regional Museum of Local Lore, Borschiv, Ternopil Oblast, Ukraine. 11Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7‑3‑1 Hongo, Bunkyo‑ku, Tokyo 113‑0033, Japan. 12Department of Anthropology, University of California, Santa Barbara, CA 93106, USA. 13These authors contributed equally: Pere Gelabert and Ryan W. Schmidt. *email: pere.gelabert@ unive.ac.at; ; Scientific Reports | (2022) 12:7242 | https://doi.org/10.1038/s41598-022-11117-8 1 Vol.:(0123456789) www.nature.com/scientificreports/ Figure 1.  (A) Location of Verteba cave in Ternopil Oblast, Ukraine, plotted against the overall distribution of CTCC sites. (B) Map of sites within Verteba cave; individuals included in this publication were found at sites 7, 17 and 20, Adapted from Ledogar et al.31. The Cucuteni-Trypillia cultural complex (CTCC) is a grouping of several interrelated Middle Neolithic/Eneolithic archaeological cultures in parts of Ukraine, Moldova, and R omania14,15. This complex stretches from the Transylvanian Alps to the Dnieper River and is named for the type-sites of Cucuteni in Iași County, Romania and Trypillia (also known as Tripolye, in Russian) in Kyiv oblast, Ukraine. The Cucuteni and Trypillia cultures have common roots in the Precucuteni culture; the earliest CTCC sites are found in the piedmont of the Carpathian Mountains and the earliest radiocarbon dates (from the Precucuteni 2 period) date to around 4800 B CE16,17. The CTCC originated from the interaction of several Danubian Neolithic groups, with evidence for similarities in house construction, ceramic styles, and lithic artifact p roduction10,16,18,19. Following the origin of this cultural complex in the Carpathian piedmont, the CTCC eventually occupied a territory covering much of the modern territories of Ukraine, Moldova, and Romania. The first diagnostically Early Trypillia (Trypillia A) sites diverged from the Precucuteni culture ~ 4500 BCE in the Dniester River valley. Later population movements, occurring from the middle period (Trypillia BI) onward, saw the Trypillia culture expand to Volhynia in the west and the Dnieper River in the east. This territorial expansion is believed to have resulted primarily from demographic increases associated with a successful agropastoral subsistence strategy, and the search for new arable land for cultivation18. However, some population growth may have been the product of Trypillian populations incorporating indigenous hunting and gathering (HG) groups, such as members of the Bug-Dneister culture. Another mode of population increase could have been the acculturation of refugees following the collapse of the Neolithic in Romania, Hungary, and Bulgaria. During the middle-to-late periods of the Trypillia culture (Trypillia BII to CI; 4100–3400 BCE), some CTCC groups established extremely large settlements in Central Ukraine, often referred to as “giant-settlements’’ or “me (...truncated)