Ainash Childebayeva

Max Planck Institute for Evolutionary Anthropology

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Johannes Krause

Max Planck Institute for Evolutionary Anthropology

Adam B. Rohrlach

Max Planck Institute for Evolutionary Anthropology

Wolfgang Haak

Max Planck Institute for Evolutionary Anthropology

Harald Ringbauer

Max Planck Institute for Evolutionary Anthropology

Sandra Penske

Max Planck Institute for Evolutionary Anthropology

Svend Hansen

Deutsches Archäologisches Institut, Zentrale

Vanessa Villalba‐Mouco

Max Planck Institute for Evolutionary Anthropology

Franziska Aron

Max Planck Institute for the Science of Human History

Sabine Reinhold

Deutsches Archäologisches Institut, Zentrale

Stéphane Rottier

De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie

Cooperative Institutions

Max Planck Institute for the Science of Human History

Max Planck Institute for Evolutionary Anthropology

Centre National de la Recherche Scientifique

Harvard University

Deutsches Archäologisches Institut, Zentrale

Universitat Autònoma de Barcelona

University of Tübingen

Max Planck - Harvard Research Center for the Archaeoscience of the Ancient Mediterranean

De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie

Université de Bordeaux

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Blood lead levels in Peruvian adults are associated with proximity to mining and DNA methylation

Environment International (2021)

Ainash Childebayeva Jaclyn M. Goodrich Nathan Chesterman Fabiola Lèon‐Velarde Maria C. Rivera

Inorganic lead (Pb) is common in the environment, and is toxic to neurological, renal, and cardiovascular systems. Pb exposure influences the epigenome with documented effects on DNA methylation (DNAm). We assessed the impact of low levels of Pb exposure on DNAm among non-miner individuals from two locations in Peru: Lima, the capital, and Cerro de Pasco, a highland mining town, to study the effects of Pb exposure on physiological outcomes and DNAm.Pb levels were measured in whole blood (n = 305). Blood leukocyte DNAm was determined for 90 DNA samples using the Illumina MethylationEPIC chip. An epigenome-wide association study was performed to assess the relationship between Pb and DNAm.Individuals from Cerro de Pasco had higher Pb than individuals from Lima (p-value = 2.00E-16). Males had higher Pb than females (p-value = 2.36E-04). Pb was positively associated with hemoglobin (p-value = 8.60E-04). In Cerro de Pasco, blood Pb decreased with the distance from the mine (p-value = 0.04), and association with soil Pb was approaching significance (p-value = 0.08). We identified differentially methylated positions (DMPs) associated with genes SOX18, ZMIZ1, and KDM1A linked to neurological function. We also found 45 differentially methylated regions (DMRs), seven of which were associated with genes involved in metal ion binding and nine to neurological function and development.Our results demonstrate that even low levels of Pb can have a significant impact on the body including changes to DNAm. We report associations between Pb and hemoglobin, Pb and distance from mining, and between blood and soil Pb. We also report associations between loci- and region-specific DNAm and Pb.

dNaM

Epigenome

10.1016/j.envint.2021.106587

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Citations (16)

Extensive pedigrees reveal the social organization of a Neolithic community

Nature (2023)

Maïté Rivollat Adam B. Rohrlach Harald Ringbauer Ainash Childebayeva Fanny Mendisco

Abstract Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations 1–4 . However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic around 4850–4500 bc . We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality 5 . Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.

Exogamy

Pedigree chart

Lineage (genetic)

10.1038/s41586-023-06350-8

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Citations (45)

Ancient genomes reveal trans-Eurasian connections between the European Huns and the Xiongnu Empire

Proceedings of the National Academy of Sciences (2025)

Guido Alberto Gnecchi‐Ruscone Zsófia Rácz Salvatore Liccardo Juhyeon Lee Yilei Huang

The Huns appeared in Europe in the 370s, establishing an Empire that reshaped West Eurasian history. Yet until today their origins remain a matter of extensive debate. Traditional theories link them to the Xiongnu, the founders of the first nomadic empire of the Mongolian steppe. The Xiongnu empire dissolved, however, ~300 y before the Huns appeared in Europe, and there is little archaeological and historical evidence of Huns in the steppe during this time gap. Furthermore, despite the rich 5th to 6th centuries current era (CE) archaeological record of the Carpathian Basin, the cultural elements of connections with the steppe are limited to few findings and even fewer solitary eastern-type burials. In this study, we coanalyze archaeological evidence with 35 newly sequenced and published genomic data for a total of 370 individuals—from 5th to 6th century CE contexts in the Carpathian Basin including 10 Hun-period eastern-type burials, 2nd to 5th century sites across Central Asia and 2nd c. before current era (BCE) to 1st c. CE Xiongnu period sites across the Mongolian steppe. We find no evidence for the presence of a large eastern/steppe descent community among the Hun- and post-Hun-period Carpathian Basin population. We also observe a high genetic diversity among the eastern-type burials that recapitulates the variability observed across the Eurasian Steppe. This suggests a mixed origin of the incoming steppe conquerors. Nevertheless, long-shared genomic tracts provide compelling evidence of genetic lineages directly connecting some individuals of the highest Xiongnu-period elite with 5th to 6th century CE Carpathian Basin individuals, showing that some European Huns descended from them.

Steppe

Elite

10.1073/pnas.2418485122

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Early contact between late farming and pastoralist societies in southeastern Europe

Nature (2023)

Sandra Penske Adam B. Rohrlach Ainash Childebayeva Guido Alberto Gnecchi‐Ruscone Clemens Schmid

Abstract Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000–6000 bc (refs. 1–3 ) and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300 bc (refs. 4,5 ). The period between these events saw new economies emerging on the basis of key innovations, including metallurgy, wheel and wagon and horse domestication 6–9 . However, what happened between the demise of the Copper Age settlements around 4250 bc and the expansion of pastoralists remains poorly understood. To address this question, we analysed genome-wide data from 135 ancient individuals from the contact zone between southeastern Europe and the northwestern Black Sea region spanning this critical time period. While we observe genetic continuity between Neolithic and Copper Age groups from major sites in the same region, from around 4500 bc on, groups from the northwestern Black Sea region carried varying amounts of mixed ancestries derived from Copper Age groups and those from the forest/steppe zones, indicating genetic and cultural contact over a period of around 1,000 years earlier than anticipated. We propose that the transfer of critical innovations between farmers and transitional foragers/herders from different ecogeographic zones during this early contact was integral to the formation, rise and expansion of pastoralist groups around 3300 bc .

Pastoralism

Steppe

Human settlement

Demise

10.1038/s41586-023-06334-8

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Citations (25)

Ancient genomes reveal insights into ritual life at Chichén Itzá

Nature (2024)

Rodrigo Barquera Oana del Castillo-Chávez Kathrin Nägele Patxi Pérez-Ramallo Diana Iraíz Hernández-Zaragoza

Abstract The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods ( ad 600–1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica 1–4 . However, many questions about the social and cultural use of its ceremonial spaces, as well as its population’s genetic ties to other Mesoamerican groups, remain unanswered 2 . Here we present genome-wide data obtained from 64 subadult individuals dating to around ad 500–900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes 5 , but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.

Mesoamerica

Maya

Human settlement

Human migration

10.1038/s41586-024-07509-7

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Citations (4)

Kinship practices in the early state El Argar society from Bronze Age Iberia

Scientific Reports (2022)

Vanessa Villalba‐Mouco Camila Oliart Caravatti Cristina Rihuete Herrada Adam B. Rohrlach María Inés Fregeiro

Abstract The Early Bronze Age in Europe is characterized by social and genetic transformations, starting in the early 3rd millennium BCE. New settlement and funerary structures, artifacts and techniques indicate times of change with increasing economic asymmetries and political hierarchization. Technological advances in metallurgy also played an important role, facilitating trade and exchange networks, which became tangible in higher levels of mobility and connectedness. Archeogenetic studies have revealed a substantial transformation of the genetic ancestry around this time, ultimately linked to the expansion of steppe- and forest steppe pastoralists from Eastern Europe. Evidence for emerging infectious diseases such as Yersinia pestis adds further complexity to these tumultuous and transformative times. The El Argar complex in southern Iberia marks the genetic turnover in southwestern Europe ~ 2200 BCE that accompanies profound changes in the socio-economic structure of the region. To answer the question of who was buried in the emblematic double burials of the El Argar site La Almoloya, we integrated results from biological relatedness analyses and archaeological funerary contexts and refined radiocarbon-based chronologies from 68 individuals. We find that the El Argar society was virilocally and patrilineally organized and practiced reciprocal female exogamy, supported by pedigrees that extend up to five generations along the paternal line. Synchronously dated adult males and females from double tombs were found to be unrelated mating partners, whereby the incoming females reflect socio-political alliances among El Argar groups. In three cases these unions had common offspring, while paternal half-siblings also indicate serial monogamy or polygyny.

Steppe

10.1038/s41598-022-25975-9

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Citations (30)

Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia

Science Advances (2021)

Vanessa Villalba‐Mouco Camila Oliart Caravatti Cristina Rihuete Herrada Ainash Childebayeva Adam B. Rohrlach

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.

Grave goods

Social Organization

Steppe

Chalcolithic

10.1126/sciadv.abi7038

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Citations (56)

Kinship practices at the early bronze age site of Leubingen in Central Germany

Scientific Reports (2024)

Sandra Penske Mario Küßner Adam B. Rohrlach Corina Knipper Jan Nováček

Abstract With the beginning of the Early Bronze Age in Central Europe ~ 2200 BC, a regional and supra-regional hierarchical social organization emerged with few individuals in positions of power (chiefs), set apart by rich graves with extensive burial constructions. However, the social organization and stratification within the majority of people, who represent the non-elite, remain unclear. Here, we present genome-wide data of 46 individuals from the Early Bronze Age burial ground of Leubingen in today’s Germany, integrating archaeological, genetic and strontium isotope data to gain new insights into Early Bronze Age societies. We were able to reconstruct five pedigrees which constitute the members of close biological kinship groups (parents and their offspring), and also identify individuals who are not related to individuals buried at the site. Based on combined lines of evidence, we observe that the kinship structure of the burial community was predominantly patrilineal/virilocal involving female exogamy. Further, we detect a difference in the amount of grave goods among the individuals buried at Leubingen based on genetic sex, age at death and locality but see no difference in the types of grave goods.

Grave goods

Exogamy

Pedigree chart

Elite

Social Stratification

Genetic genealogy

Chiefdom

Paleoanthropology

10.1038/s41598-024-54462-6

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DNA methylation at stress‐related genes is associated with exposure to early life institutionalization

American Journal of Physical Anthropology (2016)

Amy L. Non Brittany M. Hollister Kathryn L. Humphreys Ainash Childebayeva Kyle Esteves

ABSTRACT Objectives Differences in DNA methylation have been associated with early life adversity, suggesting that alterations in methylation function as one pathway through which adverse early environments are biologically embedded. This study examined associations between exposure to institutional care, quantified as the proportion of time in institutional care at specified follow‐up assessment ages, and DNA methylation status in two stress‐related genes: FKBP5 and SLC6A4 . Materials and Methods We analyzed data from the Bucharest Early Intervention Project, which is a prospective study in which children reared in institutional settings were randomly assigned (mean age 22 months) to either newly created foster care or care as usual (to remain in their current placement) and prospectively followed. A group of children from the same geographic area, with no history of institutionalized caregiving, were also recruited. DNA methylation status was determined in DNA extracted from buccal epithelial cells of children at age 12. Results An inverse association was identified such that more time spent in institutional care was associated with lower DNA methylation at specific CpG sites within both genes. Discussion These results suggest a lasting impact of early severe social deprivation on methylation patterns in these genes, and contribute to a growing literature linking early adversity and epigenetic variation in children. Am J Phys Anthropol 161:84–93, 2016.. © 2016 Wiley Periodicals, Inc.

Institutionalisation

10.1002/ajpa.23010

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Citations (98)

The rise and transformation of Bronze Age pastoralists in the Caucasus

Nature (2024)

Ayshin Ghalichi Sabine Reinhold Adam B. Rohrlach Alexey Kalmykov Ainash Childebayeva

Abstract The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age 1 and the birthplace of the earliest steppe pastoralist societies 2 . Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies 3–5 . Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry 4,6 in the north, and a distinct Caucasus hunter-gatherer ancestry 7 with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex 8 . By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.

Steppe

Pastoralism

Chalcolithic

Kazakh

Bronze

Mesolithic

10.1038/s41586-024-08113-5

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