1
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Krettek KL, Casas-Vargas A, Mas-Sandoval A, Alvis LA, Reiter E, Madero JM, Urban M, Vargas JCN, Usaquén W, Cuenca JVR, Posth C. A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia. SCIENCE ADVANCES 2025; 11:eads6284. [PMID: 40435234 PMCID: PMC12118548 DOI: 10.1126/sciadv.ads6284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 04/18/2025] [Indexed: 06/01/2025]
Abstract
Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.
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Affiliation(s)
- Kim-Louise Krettek
- Senckenberg Centre for Human Evolution and Paleoenvironment at the University of Tübingen, Tübingen, Germany
| | - Andrea Casas-Vargas
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Alex Mas-Sandoval
- Dipartimento di Scienze Statistiche “Paolo Fortunati,” Universitá di Bologna, Bologna, Italy
| | - Leonardo Arias Alvis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Leiden University Centre for Linguistics, Leiden, Netherlands
| | - Ella Reiter
- Archeo- and Paleogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Julie Moncada Madero
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Matthias Urban
- Centre National de la Recherche Scientifique “Dynamique du Langage” (UMR5596) and Université Lumière Lyon 2, Lyon, France
| | - Juan Camilo Niño Vargas
- Department of Anthropology, Faculty of Social Sciences, Universidad de los Andes, Bogotá, Colombia
| | - William Usaquén
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Jose Vicente Rodríguez Cuenca
- Grupo de Investigación en Antropología Biológica, Departamento de Antropología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Cosimo Posth
- Senckenberg Centre for Human Evolution and Paleoenvironment at the University of Tübingen, Tübingen, Germany
- Archeo- and Paleogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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2
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Huang Z, Gao J, Ma M, Hu W, Xiao X, Li H. Ancient genomes reveal complex population interactions in the middle Yellow River basin during the Late Neolithic period. Genomics 2025; 117:111061. [PMID: 40449690 DOI: 10.1016/j.ygeno.2025.111061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 04/01/2025] [Accepted: 05/26/2025] [Indexed: 06/03/2025]
Abstract
The middle reaches of the Yellow River in the Late Neolithic period were the frontier of cultural communication between the Central Plains and the northern steppe. The remarkable sites that emerged during this period, such as Taosi, Shimao, and Lushanmao, played important roles in the formation of early Chinese civilization. Here we report ancient genomic data from 8 individuals from the three sites. Population genetics analysis revealed that the ancestries of these individuals were mainly related to the Yangshao culture populations from the Central Plains, supplemented by Northeast Asian ancestry. We also found an individual who was a genetic outlier at the Lushanmao site who carried excess Northeast Asian ancestry and harbored a genetic background similar to that of the Hongshan culture population. These findings provide a more detailed picture of genetic interactions and population migrations in northern China of Late Neolithic period and suggest potential cross-regional population interactions.
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Affiliation(s)
- Zishuai Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiaqi Gao
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Mingzhi Ma
- Shaanxi Provincial Institute of Archaeology, Xi'an 710001, China
| | - Wengao Hu
- Shenmu Baoyuan Museum, Shaanxi 719300, China
| | - Xin Xiao
- The Department of Sociology, University of the Witwatersrand, Wits 2050, South Africa
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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3
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Kristensen NP, Chisholm RA, Ohtsuki H. Many-strategy games in groups with relatives and the evolution of coordinated cooperation. J Theor Biol 2025; 605:112089. [PMID: 40157047 DOI: 10.1016/j.jtbi.2025.112089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 03/03/2025] [Accepted: 03/05/2025] [Indexed: 04/01/2025]
Abstract
Humans often cooperate in groups with friends and family members with varying degrees of genetic relatedness. Past kin selection can also be relevant to interactions between strangers, explaining how the cooperation first arose in the ancestral population. However, modelling the effects of relatedness is difficult when the benefits of cooperation scale nonlinearly with the number of cooperators (e.g., economies of scale). Here, we present a direct fitness method for rigorously accounting for kin selection in n-player interactions with m discrete strategies, where a genetically homophilic group-formation model is used to calculate the necessary higher-order relatedness coefficients. Our approach allows us to properly account for non-additive fitness effects between relatives (synergy). Analytical expressions for dynamics are obtained, and they can be solved numerically for modestly sized groups and numbers of strategies. We illustrate with an example where group members can verbally agree (cheap talk) to contribute to a public good with a sigmoidal benefit function, and we find that such coordinated cooperation is favoured by kin selection. As interactions switched from family to strangers, in order for coordinated cooperation to persist and for the population to resist invasion by liars, either some level of homophily must be maintained or following through on the agreement must be in the self-interests of contributors. Our approach is useful for scenarios where fitness effects are non-additive and the strategies are best modelled in a discrete way, such as behaviours that require a cognitive 'leap' of insight into the situation (e.g., shared intentionality, punishment).
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Affiliation(s)
- Nadiah P Kristensen
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore. https://nadiah.org/
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
| | - Hisashi Ohtsuki
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193, Japan.
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4
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Beneker O, Molinaro L, Guellil M, Sasso S, Kabral H, Bonucci B, Gaens N, D'Atanasio E, Mezzavilla M, Delbrassine H, Braet L, Lambert B, Deckers P, Biagini SA, Hui R, Becelaere S, Geypen J, Hoebreckx M, Berk B, Driesen P, Pijpelink A, van Damme P, Vanhoutte S, De Winter N, Saag L, Pagani L, Tambets K, Scheib CL, Larmuseau MHD, Kivisild T. Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden. Genome Biol 2025; 26:127. [PMID: 40390081 PMCID: PMC12090598 DOI: 10.1186/s13059-025-03580-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/16/2025] [Indexed: 05/21/2025] Open
Abstract
BACKGROUND Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration, and disease pandemics during and after the Middle Ages had on these processes. RESULTS We perform low-coverage sequencing of the genomes of 338 individuals spanning the eighth to the eighteenth centuries in the city of Sint-Truiden in Flanders, in the northern part of Belgium. The early/high medieval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less genetic relatedness than observed today between individuals in present-day Flanders. We find differences in gene variants associated with high vitamin D blood levels between individuals with Gaulish or Germanic ancestry. Although we find evidence of a Yersinia pestis infection in 5 of the 58 late medieval burials, we were unable to detect a major population-scale impact of the second plague pandemic on genetic diversity or on the elevated differentiation of immunity genes. CONCLUSIONS This study reveals that the genetic homogenization process in a medieval city population in the Low Countries was protracted for centuries. Over time, the Sint-Truiden population became more similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the high medieval period, and the continuous process of local admixture of Germanic and Gaulish ancestries which formed the genetic cline observable today in the Low Countries.
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Affiliation(s)
- Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | | | - Meriam Guellil
- Department for Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Stefania Sasso
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Kabral
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Noah Gaens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | | | - Linde Braet
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Bart Lambert
- SHOC Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Simone Andrea Biagini
- Department of Archaeology and Museology, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Sara Becelaere
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | - Birgit Berk
- Birgit Berk Fysische Anthropologie, Meerssen, Netherlands
| | | | - April Pijpelink
- Crematie en Inhumatie Analyse (CRINA) Fysische Antropologie, 's-Hertogenbosch, Netherlands
| | - Philip van Damme
- Department of Neurology, University Hospitals Leuven and Department of Neuroscience, KU Leuven, Leuven, Belgium
| | | | | | - Lehti Saag
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Institute of Genomics, University of Tartu, Tartu, Estonia.
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5
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Amjadi MA, Özdemir YC, Ramezani M, Jakab K, Megyes M, Bibak A, Salehi Z, Hayatmehar Z, Taheri MH, Moradi H, Zargari P, Hasanpour A, Jahani V, Sharifi AM, Egyed B, Mende BG, Tavallaie M, Szécsényi-Nagy A. Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plateau, from the Copper Age to the Sassanid Empire. Sci Rep 2025; 15:16530. [PMID: 40360796 PMCID: PMC12075576 DOI: 10.1038/s41598-025-99743-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 04/22/2025] [Indexed: 05/15/2025] Open
Abstract
In this study, we present new ancient DNA data from prehistoric and historic populations of the Iranian Plateau. By analysing 50 samples from nine archaeological sites across Iran, we report 23 newly sequenced mitogenomes and 13 nuclear genomes, spanning 4700 BCE to 1300 CE. We integrate an extensive reference sample set of previously published ancient DNA datasets from Western and South-Central Asia, enhancing our understanding of genetic continuity and diversity within ancient Iranian populations. A new Early Chalcolithic sample, predating all other Chalcolithic genomes from Iran, demonstrates mostly Early Neolithic Iranian genetic ancestry. This finding reflects long-term cultural and biological continuity in and around the Zagros area, alongside evidence of some western genetic influence. Our sample selection prioritizes northern Iran, with a particular focus on the Achaemenid, Parthian, and Sassanid periods (355 BCE-460 CE). The genetic profiles of historical samples from this region position them as intermediates on an east-west genetic cline across the Persian Plateau. They also exhibit strong connections to local and South-Central Asian Bronze Age populations, underscoring enduring genetic connections across these regions. Diachronic analyses of uniparental lineages on the Iranian Plateau further highlight population stability from prehistoric to modern times.
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Affiliation(s)
- Motahareh Ala Amjadi
- Doctoral School of Biology, ELTE-Eötvös Loránd University, Budapest, Hungary.
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary.
| | - Yusuf Can Özdemir
- Doctoral School of Biology, ELTE-Eötvös Loránd University, Budapest, Hungary
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | | | - Kristóf Jakab
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Melinda Megyes
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Arezoo Bibak
- Department of Archaeology, University of Tehran, Tehran, Iran
| | | | - Zahra Hayatmehar
- Faculty of Management and Financial Science, Department of Management, Khatam University, Tehran, Iran
| | - Mohammad Hossein Taheri
- Laboratoire Archéorient, Université Lumière Lyon 2, Maison de l'Orient et de la Méditerranée, Lyon, France
| | - Hossein Moradi
- Iranian Centre for Archaeological Research (ICAR), Tehran, Iran
| | - Peyman Zargari
- Department of Biology, Science and Research branch, Islamic Azad University, Tehran, Iran
| | - Ata Hasanpour
- Research Institute for Cultural Heritage and Tourism, Lurestan, Iran
| | - Vali Jahani
- Research Institute for Cultural Heritage and Tourism, Gilan, Iran
| | | | - Balázs Egyed
- Department of Genetics, ELTE-Eötvös Loránd University, Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | | | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary.
- MTA-BTK Lendület 'Momentum' Bioarchaeology Research Group, Budapest, Hungary.
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6
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Hernández CL, Sánchez-Martínez LJ, Ceballos FC, Dugoujon JM, Pereira L, Calderón R. A genomic tale of inbreeding in western Mediterranean human populations. Hum Genet 2025:10.1007/s00439-025-02747-9. [PMID: 40347250 DOI: 10.1007/s00439-025-02747-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Accepted: 04/19/2025] [Indexed: 05/12/2025]
Abstract
Consanguineous marriages are common in many worldwide human populations, and the biological consequences for offspring can be relevant at the biomedical level. The current genomic revolution displayed through genome-wide studies is challenging the paradigm in the analysis of consanguinity. Here, we analyzed genomic inbreeding patterns in human populations located at the western edge of the Mediterranean region (Iberia and Morocco). Runs of Homozygosity (ROH) (autozygosity fragments) were identified in 139 autochthonous individuals originating from southern Iberia and Morocco via microarray data. All individuals analyzed carried at least one ROH in their genomes. The genomic inbreeding coefficient (FROH) and the presence of ROH islands (ROHi) revealed interesting patterns in the target populations as well as in the rest of the Mediterranean basin. Moroccan Berbers presented signals of recent inbreeding, relying on high coverage of long ROH (> 5 Mb) and FROH. The location and structure of ROHi among people in the western Mediterranean could be interpreted as a signature of common genetic links across the Strait of Gibraltar. We found a significant enrichment of some relevant biological functions in the estimated ROHi hotspots associated with the immune system and chemosensation. Genomic inbreeding approaches allow us to understand past population histories and can be used as a proxy to scan the genome in search of selection signals.
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Affiliation(s)
- Candela L Hernández
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
| | - Luis J Sánchez-Martínez
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Jean M Dugoujon
- CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
| | - Luisa Pereira
- i3S, Instituto de Investigação e Inovaçãao em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Rosario Calderón
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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7
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Salem N, van de Loosdrecht MS, Sümer AP, Vai S, Hübner A, Peter B, Bianco RA, Lari M, Modi A, Al-Faloos MFM, Turjman M, Bouzouggar A, Tafuri MA, Manzi G, Rotunno R, Prüfer K, Ringbauer H, Caramelli D, di Lernia S, Krause J. Ancient DNA from the Green Sahara reveals ancestral North African lineage. Nature 2025; 641:144-150. [PMID: 40175549 PMCID: PMC12043513 DOI: 10.1038/s41586-025-08793-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/14/2025] [Indexed: 04/04/2025]
Abstract
Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch1. DNA rarely preserves well in this region, limiting knowledge of the Sahara's genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals' ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco2, associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.
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Affiliation(s)
- Nada Salem
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany.
| | - Marieke S van de Loosdrecht
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
| | - Arev Pelin Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Alexander Hübner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Peter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raffaela A Bianco
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | | | | | - Abdeljalil Bouzouggar
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut National des Sciences de l'Archéologie et du Patrimoine, Origin and Evolution of Homo sapiens Cultures, Rabat, Morocco
| | - Mary Anne Tafuri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Rocco Rotunno
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy.
| | - Savino di Lernia
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy.
- School of Geography, Archaeology and Environmental Studies (GAES), University of Witwatersrand, Johannesburg, South Africa.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany.
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8
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Lipson M, Ringbauer H, Lucarini G, Aouadi N, Aoudia L, Belhouchet L, Cheronet O, Dahmani AR, Genchi F, La Pastina F, Lucci M, de Lumley H, Mansouri N, Nava A, Touj F, Mallick S, Rohland N, Coppa A, Pinhasi R, Reich D. High continuity of forager ancestry in the Neolithic period of the eastern Maghreb. Nature 2025; 641:925-931. [PMID: 40074896 PMCID: PMC12094895 DOI: 10.1038/s41586-025-08699-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 01/24/2025] [Indexed: 03/14/2025]
Abstract
Ancient DNA from the Mediterranean region has revealed long-range connections and population transformations associated with the spread of food-producing economies1-6. However, in contrast to Europe, genetic data from this key transition in northern Africa are limited, and have only been available from the far western Maghreb (Morocco)1-3. Here we present genome-wide data for nine individuals from the Later Stone Age through the Neolithic period from Algeria and Tunisia. The earliest individuals cluster with pre-Neolithic people of the western Maghreb (around 15,000-7,600 years before present (BP)), showing that this 'Maghrebi' ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to around 8,000 years BP, harboured ancestry from European hunter-gatherers, probably reflecting movement in the Early Holocene across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry, together with smaller contributions from European farmers (by around 7,000 years BP) and Levantine groups (by around 6,800 years BP), and were thus far less impacted by external gene flow than were populations in other parts of the Neolithic Mediterranean.
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Affiliation(s)
- Mark Lipson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Giulio Lucarini
- National Research Council of Italy, Institute of Heritage Science (CNR-ISPC), Rome, Italy.
- ISMEO - The International Association for Mediterranean and Oriental Studies, Rome, Italy.
| | - Nabiha Aouadi
- Institut National du Patrimoine (INP), Tunis, Tunisia
| | - Louiza Aoudia
- UMR 7206 Éco-Anthropologie, équipe ABBA, CNRS-Muséum National d'Histoire Naturelle, Musée de l'Homme, Paris, France
- Centre National de Recherche Préhistorique, Anthropologique et Historique (CNRPAH), Algiers, Algeria
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | | | - Francesco Genchi
- Italian Institute of Oriental Studies, Sapienza University of Rome, Rome, Italy
| | - Francesco La Pastina
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, STEBICEF, University of Palermo, Palermo, Italy
| | - Michaela Lucci
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Henry de Lumley
- Institut de Paléontologie Humaine (IPH), Fondation Albert-1Er Prince de Monaco, Paris, France
- Centre Européen de Recherches Préhistoriques de Tautavel (CERPT), Tautavel, France
| | | | - Alessia Nava
- Department of Odontostomatological and Maxillo Facial Sciences, Sapienza University of Rome, Rome, Italy
| | - Fatma Touj
- Institut National du Patrimoine (INP), Tunis, Tunisia
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
- Department of Law and Digital Society, Unitelma Sapienza, Rome, Italy.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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9
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Oteo-Garcia G, Silva M, Foody MGB, Yau B, Fichera A, Alapont L, Justeau P, Rodrigues S, Monteiro R, Gandini F, Rovira Gomar ML, Ribera I Lacomba A, Pascual Beneyto J, Mattiangeli V, Bradley DG, Edwards CJ, Pala M, Richards MB. Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa. Genome Biol 2025; 26:108. [PMID: 40296056 PMCID: PMC12036142 DOI: 10.1186/s13059-025-03570-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 04/07/2025] [Indexed: 04/30/2025] Open
Abstract
BACKGROUND The Islamic influence on the Iberian Peninsula left an enduring cultural and linguistic legacy. However, the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late medieval period through ancient DNA. RESULTS Our comprehensive genomic analysis uncovers gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncover one of the earliest dated Islamic burials in Spain, which shows high levels of consanguinity. For the first time, we also demonstrate the persistence of North African ancestry in a Christian cemetery until the seventeenth century, in addition to evidence of slave trafficking from North Africa. CONCLUSIONS This study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade, underscores the low impact of the Reconquista in the genetic landscape, and shows the lasting impact of post-medieval events, such as the Expulsion of the Moriscos in 1609 CE, on the region's genetic and cultural landscape, through mass population displacement and replacement.
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Affiliation(s)
- Gonzalo Oteo-Garcia
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy.
- Centre for Palaeogenetics & Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
| | - Marina Silva
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - M George B Foody
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Bobby Yau
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Alessandro Fichera
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Llorenç Alapont
- Department of Prehistory, Archaeology and Ancient History, University of Valencia, Valencia, Spain
| | - Pierre Justeau
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Simão Rodrigues
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Rita Monteiro
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Francesca Gandini
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | | | | | | | - Valeria Mattiangeli
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
| | - Ceiridwen J Edwards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
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10
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Ringbauer H, Salman-Minkov A, Regev D, Olalde I, Peled T, Sineo L, Falsone G, van Dommelen P, Mittnik A, Lazaridis I, Pettener D, Bofill M, Mezquida A, Costa B, Jiménez H, Smith P, Vai S, Modi A, Shaus A, Callan K, Curtis E, Kearns A, Lawson AM, Mah M, Micco A, Oppenheimer J, Qiu L, Stewardson K, Workman JN, Márquez-Grant N, Sáez Romero AM, Lavado Florido ML, Jiménez-Arenas JM, Toro Moyano IJ, Viguera E, Padilla JS, Chamizo SL, Marques-Bonet T, Lizano E, Riaza AR, Olivieri F, Toti P, Giuliana V, Barash A, Carmel L, Boaretto E, Faerman M, Lucci M, La Pastina F, Nava A, Genchi F, Del Vais C, Lauria G, Meli F, Sconzo P, Catalano G, Cilli E, Fariselli AC, Fontani F, Luiselli D, Culleton BJ, Mallick S, Rohland N, Nigro L, Coppa A, Caramelli D, Pinhasi R, Lalueza-Fox C, Gronau I, Reich D. Punic people were genetically diverse with almost no Levantine ancestors. Nature 2025:10.1038/s41586-025-08913-3. [PMID: 40269169 DOI: 10.1038/s41586-025-08913-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 03/18/2025] [Indexed: 04/25/2025]
Abstract
The maritime Phoenician civilization from the Levant transformed the entire Mediterranean during the first millennium BCE1-3. However, the extent of human movement between the Levantine Phoenician homeland and Phoenician-Punic settlements in the central and western Mediterranean has been unclear in the absence of comprehensive ancient DNA studies. Here, we generated genome-wide data for 210 individuals, including 196 from 14 sites traditionally identified as Phoenician and Punic in the Levant, North Africa, Iberia, Sicily, Sardinia and Ibiza, and an early Iron Age individual from Algeria. Levantine Phoenicians made little genetic contribution to Punic settlements in the central and western Mediterranean between the sixth and second centuries BCE, despite abundant archaeological evidence of cultural, historical, linguistic and religious links4. Instead, these inheritors of Levantine Phoenician culture derived most of their ancestry from a genetic profile similar to that of Sicily and the Aegean. Much of the remaining ancestry originated from North Africa, reflecting the growing influence of Carthage5. However, this was a minority contributor of ancestry in all of the sampled sites, including in Carthage itself. Different Punic sites across the central and western Mediterranean show similar patterns of high genetic diversity. We also detect genetic relationships across the Mediterranean, reflecting shared demographic processes that shaped the Punic world.
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Affiliation(s)
- Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Ayelet Salman-Minkov
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Dalit Regev
- Israel Antiquities Authority, Jerusalem, Israel
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | - Tomer Peled
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
| | - Luca Sineo
- Dept. STEBICEF, Laboratory of Anthropology, University of Palermo, Palermo, Italy
| | | | - Peter van Dommelen
- Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, USA
| | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Maria Bofill
- Archaeological Museum of Ibiza and Formentera, Eivissa, Spain
| | - Ana Mezquida
- Archaeological Museum of Ibiza and Formentera, Eivissa, Spain
| | - Benjamí Costa
- Archaeological Museum of Ibiza and Formentera, Eivissa, Spain
| | - Helena Jiménez
- Archaeological Museum of Ibiza and Formentera, Eivissa, Spain
| | - Patricia Smith
- Faculties of Medicine and Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Arie Shaus
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Archaeology and Ancient Near Eastern Civilizations, Tel Aviv University, Tel Aviv, Israel
- Department of Data Science, Mount Holyoke College, South Hadley, MA, USA
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | | | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG, Centro Nacional de Analisis Genomico, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Esther Lizano
- Institut Català de Paleontologia Miquel Crusafont (ICP-CERCA), Universitat Autònoma de Barcelona, Barcelona, Spain
- Unidad de Paleobiología, ICP-CERCA, Unidad Asociada al CSIC por el IBE UPF-CSIC, Barcelona, Spain
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | - Pamela Toti
- The Giuseppe Whitaker Foundation, Motya, Italy
| | | | - Alon Barash
- Bar Ilan University, The Azrieli Faculty of Medicine, Safed, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elisabetta Boaretto
- Weizmann Institute of Science, Scientific Archaeology Unit, D-REAMS Radiocarbon Dating Laboratory, Rehovot, Israel
| | - Marina Faerman
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michaela Lucci
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Francesco La Pastina
- Dept. STEBICEF, Laboratory of Anthropology, University of Palermo, Palermo, Italy
- Dept. Culture e Società, University of Palermo, Palermo, Italy
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Alessia Nava
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesco Genchi
- Italian Institute of Oriental Studies, Sapienza University of Rome, Rome, Italy
| | - Carla Del Vais
- Department of Literature, Languages and Cultural Heritage, University of Cagliari, Cagliari, Italy
| | - Gabriele Lauria
- Dept. STEBICEF, Laboratory of Anthropology, University of Palermo, Palermo, Italy
| | - Francesca Meli
- Dept. Culture e Società, University of Palermo, Palermo, Italy
| | - Paola Sconzo
- Dept. Culture e Società, University of Palermo, Palermo, Italy
| | - Giulio Catalano
- Dept. STEBICEF, Laboratory of Anthropology, University of Palermo, Palermo, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | | | - Francesco Fontani
- Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Brendan J Culleton
- Institute of Energy and the Environment, Penn State University, University Park, PA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadin Rohland
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lorenzo Nigro
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of History, Anthropology, Religion, Arts and Performing Arts, Sapienza University of Rome, Rome, Italy
- Department of Law and Digital Society, Unitelma Sapienza, Rome, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences - HEAS, University of Vienna, Vienna, Austria
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Natural Sciences Museum of Barcelona, Barcelona, Spain
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel.
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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da Silva NA, Özer O, Haller-Caskie M, Chen YR, Kolbe D, Schade-Lindig S, Wahl J, Berszin C, Francken M, Görner I, Schierhold K, Pechtl J, Grupe G, Rinne C, Müller J, Lenz TL, Nebel A, Krause-Kyora B. Admixture as a source for HLA variation in Neolithic European farming communities. Genome Biol 2025; 26:43. [PMID: 40022192 PMCID: PMC11869582 DOI: 10.1186/s13059-025-03509-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/14/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherers forming late farmers, from around 6200 years before present. The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. RESULTS We analyzed genome-wide data of 125 individuals from seven archeological early farmer and late farmer sites located in present-day Germany. The late farmer group studied here is associated with the Wartberg culture, from around 5500-4800 years before present. We note that late farmers resulted from sex-biased admixture from male western hunter-gatherers. In addition, we observe Y-chromosome haplogroup I as the dominant lineage in late farmers, with site-specific sub-lineages. We analyze true HLA genotypes from 135 Neolithic individuals, the majority of which were produced in this study. We observe significant shifts in HLA allele frequencies from early farmers to late farmers, likely due to admixture with western hunter-gatherers. Especially for the haplotype DQB1*04:01-DRB1*08:01, there is evidence for a western hunter-gatherer origin. The HLA diversity increased from early farmers to late farmers. However, it is considerably lower than in modern populations. CONCLUSIONS Both early farmers and late farmers exhibit a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time.
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Affiliation(s)
| | - Onur Özer
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | | | - Yan-Rong Chen
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Daniel Kolbe
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Sabine Schade-Lindig
- Landesamt für Denkmalpflege Hessen, hessenARCHÄOLOGIE, Schloss Biebrich, Wiesbaden, Germany
| | - Joachim Wahl
- Institute for Archaeological Sciences, Palaeoanthropology Working Group, University of Tübingen, Tübingen, Germany
| | - Carola Berszin
- Anthropologische Dienstleistungen Konstanz, Constance, Germany
| | - Michael Francken
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Constance, Germany
| | - Irina Görner
- Museumslandschaft Hessen Kassel, Sammlung Vor- und Frühgeschichte, Kassel, Germany
| | | | - Joachim Pechtl
- Institut für Archäologien, Universität Innsbruck, Innsbruck, Austria
| | - Gisela Grupe
- Biocenter of the Ludwig Maximilian University, Munich, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Johannes Müller
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
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12
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Fang H, Liang F, Ma H, Wang R, He H, Qiu L, Tao L, Zhu K, Wu W, Ma L, Zhang H, Chen S, Zhu C, Chen H, Xu Y, Zhao Y, Liu H, Wang CC. Dynamic history of the Central Plain and Haidai region inferred from Late Neolithic to Iron Age ancient human genomes. Cell Rep 2025; 44:115262. [PMID: 39893638 DOI: 10.1016/j.celrep.2025.115262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 12/04/2024] [Accepted: 01/13/2025] [Indexed: 02/04/2025] Open
Abstract
The peopling history of the Yellow River basin (YR) remains largely unexplored due to the limited number of ancient genomes. Our study sheds light on the dynamic demographic history of the YR by co-analyzing previously published genomes and 31 newly generated Late Neolithic to Iron Age genomes from Shandong in the lower YR and the Central Plain in the middle YR. Our analysis reveals the population structure in Shandong and the Central Plain in the Late Neolithic Longshan cultural period. We provide a genetic parallel to the observation of a significant increase in rice farming in the middle and lower YR in the Longshan period. However, the rice-farmer-related gene flow in the Longshan period did not arrive in groups from the Yuzhuang sites in the Central Plain or previously published groups in Shandong. The Bronze Age Erlitou culture genomes validate the genetic stability in the Central Plain and the relative genetic homogeneity between the Central Plain and Shandong.
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Affiliation(s)
- Hui Fang
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China.
| | - Fawei Liang
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China.
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Limin Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Weihua Wu
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China
| | - Long Ma
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China
| | - Huazhen Zhang
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China
| | - Shuqing Chen
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China; Ministry of Education Key Laboratory of Archaeological Sciences and Technology, Shandong University, Qingdao 266237, China
| | - Chao Zhu
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Haodong Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yu Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yongsheng Zhao
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China; Ministry of Education Key Laboratory of Archaeological Sciences and Technology, Shandong University, Qingdao 266237, China.
| | - Haiwang Liu
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China.
| | - Chuan-Chao Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China.
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13
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Wang R, Liu W, Wu Y, Ma H, Lv J, He H, Qiu L, Chen H, Zhao Y, Sun B, Wang CC. East and West admixture in eastern China of Tang Dynasty inferred from ancient human genomes. Commun Biol 2025; 8:219. [PMID: 39934375 PMCID: PMC11814302 DOI: 10.1038/s42003-025-07665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Accepted: 02/04/2025] [Indexed: 02/13/2025] Open
Abstract
The ancestry composition and Sinicisation process of the descendants of the immigrants of Hu people living in ancient China are largely unknown due to the lack of genetic evidence. Tang Dynasty people in Fudamen cemetery () excavated from Shandong province in eastern China are believed to be related to the descendants of Hu people, as some of the individuals with the surnames An (). The genetic origin of the Fudamen population requires genetic clarification using ancient DNA data. Here we successfully obtain genome-wide SNP data for 17 Tang dynasty individuals from Fudamen cemetery. Based on autosomal data, although all Fudamen individuals show high levels of middle reaches of Yellow River-related ancestry as previously published historical period Shandong populations, 2 Fudamen individuals require ~5% Western Eurasian/Central Asian-related ancestry to describe their ancestry composition best. To the best of our knowledge, it is the first evidence of such ancestry in Shandong, the eastern part of today's China. Moreover, the admixture pattern is also reflected by the presence of both west and east Eurasian-specific mtDNA and Y chromosomal haplogroups in Fudamen people. The estimated admixture time is also consistent with periods when Sogdians and other non-Han populations were active in ancient China. These genomic findings suggest that intermarriage with Han Chinese involved the Sinicization process of the Hu people.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Wentao Liu
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, 250012, China
| | - Yiting Wu
- Institute of Cultural Heritage, Shandong University, Qingdao, 266237, China
- Ministry of Education Key Laboratory of Archaeological Sciences and Technology, Shandong University, Qingdao, 266237, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jing Lv
- Institute of Cultural Heritage, Shandong University, Qingdao, 266237, China
- Ministry of Education Key Laboratory of Archaeological Sciences and Technology, Shandong University, Qingdao, 266237, China
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Limin Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Haodong Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yongsheng Zhao
- Institute of Cultural Heritage, Shandong University, Qingdao, 266237, China.
- Ministry of Education Key Laboratory of Archaeological Sciences and Technology, Shandong University, Qingdao, 266237, China.
| | - Bo Sun
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, 250012, China.
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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14
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Sümer AP, Rougier H, Villalba-Mouco V, Huang Y, Iasi LNM, Essel E, Bossoms Mesa A, Furtwaengler A, Peyrégne S, de Filippo C, Rohrlach AB, Pierini F, Mafessoni F, Fewlass H, Zavala EI, Mylopotamitaki D, Bianco RA, Schmidt A, Zorn J, Nickel B, Patova A, Posth C, Smith GM, Ruebens K, Sinet-Mathiot V, Stoessel A, Dietl H, Orschiedt J, Kelso J, Zeberg H, Bos KI, Welker F, Weiss M, McPherron SP, Schüler T, Hublin JJ, Velemínský P, Brůžek J, Peter BM, Meyer M, Meller H, Ringbauer H, Hajdinjak M, Prüfer K, Krause J. Earliest modern human genomes constrain timing of Neanderthal admixture. Nature 2025; 638:711-717. [PMID: 39667410 PMCID: PMC11839475 DOI: 10.1038/s41586-024-08420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 11/18/2024] [Indexed: 12/14/2024]
Abstract
Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals1-4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia3 and Bacho Kiro, Bulgaria2. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany4, and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.
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Affiliation(s)
- Arev P Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Hélène Rougier
- California State University Northridge, Northridge, CA, USA
| | - Vanessa Villalba-Mouco
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Yilei Huang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Leonardo N M Iasi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alba Bossoms Mesa
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anja Furtwaengler
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam B Rohrlach
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Federica Pierini
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Francis Crick Institute, London, UK
- University of Bristol, Bristol, UK
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of California, Berkeley, CA, USA
| | - Dorothea Mylopotamitaki
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB, Collège de France, Paris, France
| | - Raffaela A Bianco
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Zorn
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Patova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology, University of Reading, Reading, UK
| | - Karen Ruebens
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB, Collège de France, Paris, France
- Department of Archaeology, University of Reading, Reading, UK
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248 and Bordeaux Proteome Platform, Bordeaux, France
| | - Alexander Stoessel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Zoology and Evolutionary Research, Jena, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt-Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt-Landesmuseum für Vorgeschichte, Halle, Germany
- Prähistorische Archäologie, Freie Universität, Berlin, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Karolinska Institutet, Stockholm, Sweden
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB, Collège de France, Paris, France
| | | | | | - Benjamin M Peter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Rochester, Rochester, NY, USA
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt-Landesmuseum für Vorgeschichte, Halle, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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15
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Wang K, Tobias B, Pany-Kucera D, Berner M, Eggers S, Gnecchi-Ruscone GA, Zlámalová D, Gretzinger J, Ingrová P, Rohrlach AB, Tuke J, Traverso L, Klostermann P, Koger R, Friedrich R, Wiltschke-Schrotta K, Kirchengast S, Liccardo S, Wabnitz S, Vida T, Geary PJ, Daim F, Pohl W, Krause J, Hofmanová Z. Ancient DNA reveals reproductive barrier despite shared Avar-period culture. Nature 2025; 638:1007-1014. [PMID: 39814885 PMCID: PMC11864967 DOI: 10.1038/s41586-024-08418-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 11/18/2024] [Indexed: 01/18/2025]
Abstract
After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry1,2. We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century CE neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter1,2. We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture3,4. We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier.
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Affiliation(s)
- Ke Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Bendeguz Tobias
- Institute of Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Doris Pany-Kucera
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Margit Berner
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Sabine Eggers
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czech Republic
| | - Denisa Zlámalová
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czech Republic
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pavlína Ingrová
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czech Republic
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Computer and Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - Jonathan Tuke
- School of Computer and Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - Luca Traverso
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paul Klostermann
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
- Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Robin Koger
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | | | | | - Sylvia Kirchengast
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- HEAS Human Evolution and Archaeological Science Network, University of Vienna, Vienna, Austria
| | - Salvatore Liccardo
- Institute of Medieval Research, Austrian Academy of Sciences, Vienna, Austria
- Institute for Austrian Historical Research, University of Vienna, Vienna, Austria
| | - Sandra Wabnitz
- Institute of Medieval Research, Austrian Academy of Sciences, Vienna, Austria
- Institute for Austrian Historical Research, University of Vienna, Vienna, Austria
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE-Eötvös Loránd University, Budapest, Hungary
- Institute of Archaeology, Research Centre for the Humanities, HUN-REN-Hungarian Research Network, Budapest, Hungary
| | | | - Falko Daim
- Institute of Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Walter Pohl
- Institute of Medieval Research, Austrian Academy of Sciences, Vienna, Austria.
- Institute for Austrian Historical Research, University of Vienna, Vienna, Austria.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czech Republic.
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16
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Weber GW, Šimková PG, Fernandes DM, Cheronet O, Úry E, Wilfing H, Matiasek K, Llano-Lizcano A, Gelabert P, Trinks I, Douka K, Ladstätter S, Higham T, Steskal M, Pinhasi R. The cranium from the Octagon in Ephesos. Sci Rep 2025; 15:943. [PMID: 39794407 PMCID: PMC11723936 DOI: 10.1038/s41598-024-83870-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 12/18/2024] [Indexed: 01/13/2025] Open
Abstract
During excavations in 1929, a well-preserved skeleton was discovered in a sarcophagus in the Octagon at Ephesos (Turkey). For the following century, archaeologists have speculated about the identity of this obviously notable person. Repeated claim is that the remains could represent Arsinoë IV, daughter of Ptolemy XII, and younger (half-)sister of Cleopatra VII. To address these questions we undertook state-of-the-art morphological, genetic and dating analyses of the cranium and further analyses of bone samples from a femur and a rib of the skeleton found in the same tomb. We confirm based on genetic analyses from the cranium and the femur that they derive from the same person. 14C-dating of the cranium provides a most likely time range between 205-36 BC. The connection with Arsinoë IV can be excluded because we confirmed that the individual is a male. The cranium represents an 11-14-year-old boy who suffered from significant developmental disturbances. Genetics suggest an ancestry from the Italian peninsula or Sardinia. The fate of the body of Arsinoë IV, who reportedly was killed in 41 BC in Ephesos, remains open. In contrast, investigations regarding the fate and social background of the boy from the Octagon can now proceed free of speculation.
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Affiliation(s)
- Gerhard W Weber
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria.
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria.
| | - Petra G Šimková
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Daniel M Fernandes
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
- Department of Life Sciences, CIAS, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Előd Úry
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Harald Wilfing
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Katarina Matiasek
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Alejandro Llano-Lizcano
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Immo Trinks
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
- Vienna Institute for Archaeological Science (VIAS), University of Vienna, Vienna, Austria
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Sabine Ladstätter
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
- Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Tom Higham
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
| | - Martin Steskal
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
- Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS), University of Vienna, Vienna, Austria
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17
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Derkx I, Ceballos F, Biagini SA, Subedi S, Rajbhandari P, Gyawali A, Bosch E, Vinicius L, Migliano AB, Bertranpetit J. The genetic demographic history of the last hunter-gatherer population of the Himalayas. Sci Rep 2025; 15:1505. [PMID: 39789000 PMCID: PMC11718311 DOI: 10.1038/s41598-024-80156-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 11/15/2024] [Indexed: 01/12/2025] Open
Abstract
Nepal, largely covered by the Himalayan mountains, hosts indigenous populations with distinct linguistic, cultural, and genetic characteristics. Among these populations, the Raute, Nepal's last nomadic hunter-gatherers, offer a unique insight into the genetic and demographic history of Himalayan foragers. Despite strong cultural connections to other regional foragers, the genetic history of this population remains understudied. This study presents newly genotyped genome-wide SNP data of the Raute to explore their genetic isolation, their origins and potential as an older foraging lineage, and their genetic connections to other regional foragers. Our results show that high levels of inbreeding in the Raute indicate recent genetic isolation. Effective population size estimates suggest a dramatic population decline around 50 generations ago. Strong genetic similarity to Nepalese populations of various subsistence styles highlights a dynamic history of genetic interactions prior to isolation, with particular closeness to historical foragers like the Kusunda and Tharu, but excludes an ancient foraging lineage origin. The study underscores the complexity of human population dynamics in the Himalayas, suggesting a history of extensive interaction between foragers and farmers, followed by isolation and demographic decline among the Raute.
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Affiliation(s)
- Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland.
| | - Francisco Ceballos
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Simone Andrea Biagini
- Department of Archaeology and Museology, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medicine and Life Sciences, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | - Anita Gyawali
- Committee to study the social, cultural, economic and geographical and habitat of Raute community, Surkhet, Nepal
| | - Elena Bosch
- Department of Medicine and Life Sciences, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lucio Vinicius
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | | | - Jaume Bertranpetit
- Department of Medicine and Life Sciences, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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18
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Quilter J, Harkins K, Fanco Jordan R, Marsh E, Prieto G, Verano J, LeBlanc S, Broomandkhoshbacht N, Krigbaum J, Fehren-Schmitz L. Family relations of Moche elite burials on the North Coast of Peru (~500 CE): Analyses of the Señora de Cao and relatives. Proc Natl Acad Sci U S A 2025; 122:e2416321121. [PMID: 39715432 PMCID: PMC11725780 DOI: 10.1073/pnas.2416321121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 11/04/2024] [Indexed: 12/25/2024] Open
Abstract
The Moche archaeological culture flourished along Peru's North Coast between the 4th and 10th centuries CE and was characterized by a complex social hierarchy dominated by political and religious elites. Previous archaeological evidence suggests kinship was a key factor in maintaining political authority within Moche society. To test this hypothesis, we applied archaeological, genetic, and isotopic methods to examine familial relationships between six individuals, including the prominent Señora de Cao (~500 CE), buried together in a pyramid-like, painted temple, Huaca Cao Viejo, in the Chicama Valley, Peru. Our findings reveal that all six individuals were biologically related, with varying degrees of kinship. The Señora de Cao was interred with a sacrificed juvenile, identified as a possible niece, and at least one, and potentially two siblings and a grandparent in separate tombs nearby. One of the male siblings was accompanied in death by his sacrificed son. Isotopic analysis indicates that while most individuals had diets rich in maize and animal protein and spent their childhoods in or near the Chicama Valley, the sacrificed juvenile accompanying the Señora had a distinct diet and geographic origin. These results demonstrate that Moche elites were interred with family members, including some raised far from their parental homes. This supports the hypothesis that kinship was central to transmitting status and authority. Moreover, sacrificing family members to accompany deceased elites underscores the significance of ritual sacrifice in reinforcing familial ties and linking the deceased to both ancestors and the divine.
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Affiliation(s)
- Jeffrey Quilter
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA02138
| | - Kelly Harkins
- UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA95064
| | - Régulo Fanco Jordan
- Régulo Franco Jordán, Parque Arqueológico Nacional de Machupicchu, Ministerio de Cultura, Cusco, Peru
| | - Erik Marsh
- CONICET, Laboratorio de Paleoecología Humana, Instituto Interdisciplinario de Ciencias Baásicas, Universidad Nacional de Cuyo, MendozaM5500, Argentina
| | - Gabriel Prieto
- Department of Anthropology, University of Florida, Gainesville, FL32611
| | - John Verano
- Department of Anthropology, Tulane University, New Orleans, LA70118
| | - Steven LeBlanc
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA02138
| | | | - John Krigbaum
- Department of Anthropology, University of Florida, Gainesville, FL32611
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA95064
- UCSC Genomics Institute, University of California, Santa Cruz, CA95064
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19
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Gelabert P, Bickle P, Hofmann D, Teschler-Nicola M, Anders A, Huang X, Hämmerle M, Olalde I, Fournier R, Ringbauer H, Akbari A, Cheronet O, Lazaridis I, Broomandkhoshbacht N, Fernandes DM, Buttinger K, Callan K, Candilio F, Bravo Morante G, Curtis E, Ferry M, Keating D, Freilich S, Kearns A, Harney É, Lawson AM, Mandl K, Michel M, Oberreiter V, Zagorc B, Oppenheimer J, Sawyer S, Schattke C, Özdoğan KT, Qiu L, Workman JN, Zalzala F, Mallick S, Mah M, Micco A, Pieler F, Pavuk J, Šefčáková A, Lazar C, Starović A, Djuric M, Krznarić Škrivanko M, Šlaus M, Bedić Ž, Novotny F, D Szabó L, Cserpák-Laczi O, Hága T, Szolnoki L, Hajdú Z, Mirea P, Nagy EG, Virág ZM, Horváth M A, Horváth LA, T Biró K, Domboróczki L, Szeniczey T, Jakucs J, Szelekovszky M, Zoltán F, Sztáncsuj SJ, Tóth K, Csengeri P, Pap I, Patay R, Putica A, Vasov B, Havasi B, Sebők K, Raczky P, Lovász G, Tvrdý Z, Rohland N, Novak M, Ruttkay M, Krošláková M, Bátora J, Paluch T, Borić D, Dani J, Kuhlwilm M, Palamara PF, Hajdu T, Pinhasi R, Reich D. Social and genetic diversity in first farmers of central Europe. Nat Hum Behav 2025; 9:53-64. [PMID: 39613963 PMCID: PMC11774665 DOI: 10.1038/s41562-024-02034-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/26/2024] [Indexed: 12/01/2024]
Abstract
The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of Europe. We report genome-wide data for 250 individuals: 178 individuals from whole-cemetery surveys of the Alföld Linearbankeramik Culture eastern LBK site of Polgár-Ferenci-hát, the western LBK site of Nitra Horné Krškany and the western LBK settlement and massacre site of Asparn-Schletz, as well as 48 LBK individuals from 16 other sites and 24 earlier Körös and Starčevo individuals from 17 more sites. Here we show a systematically higher percentage of western hunter-gatherer ancestry in eastern than in western LBK sites, showing that these two distinct LBK groups had different genetic trajectories. We find evidence for patrilocality, with more structure across sites in the male than in the female lines and a higher rate of within-site relatives for males. At Asparn-Schletz we find almost no relatives, showing that the massacred individuals were from a large population, not a small community.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - Penny Bickle
- Department of Archaeology, University of York, York, UK
| | | | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Xin Huang
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Michelle Hämmerle
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Iñigo Olalde
- BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | | | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | | | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Swapan Mallick
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Matthew Mah
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Adam Micco
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Franz Pieler
- Collection of Prehistory and Historical Archaeology, State Collections of Lower Austria, Asparn an der Zaya, Austria
| | - Juraj Pavuk
- Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, Bratislava, Slovak Republic
| | - Catalin Lazar
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | | | - Marija Djuric
- Faculty of Medicine, Center of Bone Biology, University of Belgrade, Belgrade, Serbia
| | | | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Željka Bedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Friederike Novotny
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | | | | | | | | | | | - Pavel Mirea
- Teleorman County Museum, Alexandria, Romania
| | | | - Zsuzsanna M Virág
- Department for Prehistory and Migration Period, Budapest History Museum, Budapest, Hungary
| | - Attila Horváth M
- Department for Prehistory and Migration Period, Budapest History Museum, Budapest, Hungary
| | - László András Horváth
- Department for Prehistory and Migration Period, Budapest History Museum, Budapest, Hungary
| | | | | | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - János Jakucs
- HUN-REN Research Centre for the Humanities, Institute of Archaeology, Budapest, Hungary
| | | | | | | | | | | | - Ildikó Pap
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | | | | | - Branislav Vasov
- Museum Unit of Public Library 'Branko Radičević', Odžaci, Serbia
| | | | - Katalin Sebők
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, Hungary
| | | | - Zdeněk Tvrdý
- Anthropos Institute, Moravian Museum, Brno, Czechia
| | - Nadin Rohland
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Matej Ruttkay
- Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Maria Krošláková
- Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jozef Bátora
- Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Tibor Paluch
- Department of Antiquities and Museum, Ras al Khaimah, United Arab Emirates
| | - Dušan Borić
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Department of Anthropology, New York University, New York, NY, USA
| | - János Dani
- Déri Museum, Debrecen, Hungary
- Department of Archaeology, Faculty of Arts and Social Sciences, University of Szeged, Szeged, Hungary
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Pier Francesco Palamara
- Department of Statistics, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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20
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Gerber D, Csáky V, Szeifert B, Borbély N, Jakab K, Mező G, Petkes Z, Szücsi F, Évinger S, Líbor C, Rácz P, Kiss K, Mende BG, Szőke BM, Szécsényi-Nagy A. Ancient genomes reveal Avar-Hungarian transformations in the 9th-10th centuries CE Carpathian Basin. SCIENCE ADVANCES 2024; 10:eadq5864. [PMID: 39693417 DOI: 10.1126/sciadv.adq5864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 11/14/2024] [Indexed: 12/20/2024]
Abstract
During the Early Medieval period, the Carpathian Basin witnessed substantial demographic shifts, notably under the Avar dominance for ~250 years, followed by the settlement of early Hungarians in the region during the late 9th century CE. This study presents the genetic analysis of 296 ancient samples, including 103 shotgun-sequenced genomes, from present-day Western Hungary. By using identity-by-descent segment sharing networks, this research offers detailed insights into the population structure and dynamics of the region from the 5th to 11th centuries CE, with specific focus on certain microregions. Our evaluations reveal spatially different histories in Transdanubia even between communities in close geographical proximity, highlighting the importance of dense sampling and analyses. Our findings highlight extensive homogenization and reorganization processes, as well as discontinuities between Hun, Avar, and Hungarian conquest period immigrant groups, alongside the spread and integration of ancestry related to the Hungarian conquerors.
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Affiliation(s)
- Dániel Gerber
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Bea Szeifert
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Noémi Borbély
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Kristóf Jakab
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - György Mező
- Konkoly Observatory, HUN-REN Research Centre for Astronomy and Earth Sciences, Budapest, Hungary
- Wigner Data Center, HUN-REN Wigner Research Centre for Physics, Budapest, Hungary
| | | | | | | | | | - Piroska Rácz
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Krisztián Kiss
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
- Hungarian Natural History Museum, Budapest, Hungary
- Faculty of Health Sciences, University of Miskolc, Miskolc, Hungary
- Department of Biological Anthropology, Eötvös Loránd University (ELTE), Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
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21
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Wakano JY, Aoki K. Forward and backward modeling of cultural evolutionary processes. Proc Natl Acad Sci U S A 2024; 121:e2322880121. [PMID: 39556749 PMCID: PMC11621620 DOI: 10.1073/pnas.2322880121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 10/21/2024] [Indexed: 11/20/2024] Open
Abstract
Modern cultural evolution theory adopts a variety of concepts and methods developed in mathematical biology, in particular population genetics theory. In addition to forward-looking approaches such as two-locus models, backward-looking approaches such as coalescent theory, which describe ancestral states of the current population, have played an important role in population genetics. Here, we show how forward and backward approaches can be applied to two examples in cultural evolution. The first example deals with the number of cultural traits, which can be analyzed by a backward approach. Cultural coalescent theory illustrates many unique aspects of cultural processes such as information transfer (i.e., social learning) from many donors ("cultural parents"), including or excluding the biological parents. Theory predicts that many cultural traits of intermediate (or higher) frequency (popularity) can exist that are surprisingly old. Many unsolved issues remain, however, such as how to incorporate social structure as well as natural and/or cultural selection, which we believe to be an urgent agenda. The second example is the punishment of sibling incest, a problem to which cultural coalescent theory cannot currently be usefully applied. By analyzing forward recursions, we show that punishment is ineffective in suppressing incest, unless the incestuous inclination is diminished by the presence of punishers. Based on these examples, we discuss the merits and demerits of forward and backward approaches.
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Affiliation(s)
- Joe Y. Wakano
- Department of Mathematical Sciences Based on Modeling and Analysis, School of Interdisciplinary Mathematical Sciences, Meiji University, Nakano, Tokyo164-8525, Japan
| | - Kenichi Aoki
- Graduate School of Science, University of Tokyo, Hongo, Tokyo113-0033, Japan
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22
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Ravasini F, Kabral H, Solnik A, de Gennaro L, Montinaro F, Hui R, Delpino C, Finocchi S, Giroldini P, Mei O, Beck De Lotto MA, Cilli E, Hajiesmaeil M, Pistacchia L, Risi F, Giacometti C, Scheib CL, Tambets K, Metspalu M, Cruciani F, D'Atanasio E, Trombetta B. The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy. Genome Biol 2024; 25:292. [PMID: 39567978 PMCID: PMC11580440 DOI: 10.1186/s13059-024-03430-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 10/29/2024] [Indexed: 11/22/2024] Open
Abstract
BACKGROUND The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focus on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9th and the 3rd century BCE, until the Roman colonization. RESULTS More than 50 samples are reported, spanning more than 1000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to different population dynamics in the two sides of Italy and/or genetic contacts across the Adriatic Sea. Additionally, we identify several individuals with ancestries deviating from their general population. Lastly, in our Late Antiquity site, we observe a drastic change in the genetic landscape of the Middle Adriatic region, indicating a relevant influx from the Near East, possibly as a consequence of Romanization. CONCLUSIONS Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlight the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impact the Italian peninsula.
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Affiliation(s)
- Francesco Ravasini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Helja Kabral
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Luciana de Gennaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Chiara Delpino
- Superintendence Archaeology, Fine Arts and Landscape for the Provinces of Frosinone and Latina, Ministry of Cultural Heritage, Rome, Italy
| | - Stefano Finocchi
- Superintendence Archaeology, Fine Arts and Landscape of Ancona, Ministry of Cultural Heritage, Ancona, Italy
| | - Pierluigi Giroldini
- Superintendence Archaeology, Fine Arts and Landscape for the Metropolitan City of Florence and the Provinces of Pistoia and Prato, Ministry of Cultural Heritage, Florence, Italy
| | - Oscar Mei
- Department of Communication Sciences, Humanities and International Studies, University of Urbino, Urbino, Italy
| | | | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Mogge Hajiesmaeil
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Letizia Pistacchia
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Flavia Risi
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Chiara Giacometti
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Christiana Lyn Scheib
- Department of Zoology, University of Cambridge and St John's College, University of Cambridge, Cambridge, UK
| | | | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fulvio Cruciani
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | | | - Beniamino Trombetta
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
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23
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Pilli E, Vai S, Moses VC, Morelli S, Lari M, Modi A, Diroma MA, Amoretti V, Zuchtriegel G, Osanna M, Kennett DJ, George RJ, Krigbaum J, Rohland N, Mallick S, Caramelli D, Reich D, Mittnik A. Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts. Curr Biol 2024; 34:5307-5318.e7. [PMID: 39515325 PMCID: PMC11627482 DOI: 10.1016/j.cub.2024.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 09/13/2024] [Accepted: 10/01/2024] [Indexed: 11/16/2024]
Abstract
The eruption of Somma-Vesuvius in 79 CE buried several nearby Roman towns, killing the inhabitants and burying under pumice lapilli and ash deposits a unique set of civil and private buildings, monuments, sculptures, paintings, and mosaics that provide a rich picture of life in the empire. The eruption also preserved the forms of many of the dying as the ash compacted around their bodies. Although the soft tissue decayed, the outlines of the bodies remained and were recovered by excavators centuries later by filling the cavities with plaster. From skeletal material embedded in the casts, we generated genome-wide ancient DNA and strontium isotopic data to characterize the genetic relationships, sex, ancestry, and mobility of five individuals. We show that the individuals' sexes and family relationships do not match traditional interpretations, exemplifying how modern assumptions about gendered behaviors may not be reliable lenses through which to view data from the past. For example, an adult wearing a golden bracelet with a child on their lap-often interpreted as mother and child-is genetically an adult male biologically unrelated to the child. Similarly, a pair of individuals who were thought to have died in an embrace-often interpreted as sisters-included at least one genetic male. All Pompeiians with genome-wide data consistently derive their ancestry largely from recent immigrants from the eastern Mediterranean, as has also been seen in contemporaneous ancient genomes from the city of Rome, underscoring the cosmopolitanism of the Roman Empire in this period.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Victoria C Moses
- Department of History, Harvard University, Cambridge, MA 02138, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stefania Morelli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | | | | | | | - Massimo Osanna
- Ministry of Cultural Heritage and Activities and Tourism, 00197 Rome, Italy
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Richard J George
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - John Krigbaum
- Department of Anthropology, University of Florida, Gainesville, FL 32611, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy.
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA.
| | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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24
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Ghalichi A, Reinhold S, Rohrlach AB, Kalmykov AA, Childebayeva A, Yu H, Aron F, Semerau L, Bastert-Lamprichs K, Belinskiy AB, Berezina NY, Berezin YB, Broomandkhoshbacht N, Buzhilova AP, Erlikh VR, Fehren-Schmitz L, Gambashidze I, Kantorovich AR, Kolesnichenko KB, Lordkipanidze D, Magomedov RG, Malek-Custodis K, Mariaschk D, Maslov VE, Mkrtchyan L, Nagler A, Fazeli Nashli H, Ochir M, Piotrovskiy YY, Saribekyan M, Sheremetev AG, Stöllner T, Thomalsky J, Vardanyan B, Posth C, Krause J, Warinner C, Hansen S, Haak W. The rise and transformation of Bronze Age pastoralists in the Caucasus. Nature 2024; 635:917-925. [PMID: 39478221 PMCID: PMC11602729 DOI: 10.1038/s41586-024-08113-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/25/2024] [Indexed: 11/04/2024]
Abstract
The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age1 and the birthplace of the earliest steppe pastoralist societies2. 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 societies3-5. 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 ancestry4,6 in the north, and a distinct Caucasus hunter-gatherer ancestry7 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 complex8. 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.
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Affiliation(s)
- Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany.
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Austalia, Australia
| | | | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - He Yu
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Natalia Y Berezina
- Research Institute and Museum of Anthropology of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Yakov B Berezin
- Research Institute and Museum of Anthropology of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Nasreen Broomandkhoshbacht
- UCSC Paleogenomics Lab, Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alexandra P Buzhilova
- Research Institute and Museum of Anthropology of Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Lars Fehren-Schmitz
- UCSC Paleogenomics Lab, Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Irina Gambashidze
- Otar Lordkipanidze Centre of Archaeological Research, Georgian National Museum, Tbilisi, Georgia
| | - Anatoliy R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosovsky Moscow State University, Moscow, Russian Federation
| | | | - David Lordkipanidze
- Archaeology Department, Tbilisi State University, Tbilisi, Georgia
- Georgian National Museum, Tbilisi, Georgia
| | - Rabadan G Magomedov
- Institute of History, Archaeology and Ethnography DFRC, Russian Academy of Sciences, Makhachkala, Russian Federation
| | - Katharina Malek-Custodis
- Brandenburg Authorities for Heritage Management and State Archaeological Museum, Zossen, Germany
| | - Dirk Mariaschk
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Levon Mkrtchyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Anatoli Nagler
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | | | - Maria Ochir
- Kalmyk Scientific Center of the Russian Academy of Sciences, Elista, Russian Federation
| | - Yuri Y Piotrovskiy
- Archaeological Department, The State Hermitage Museum, St Petersburg, Russian Federation
| | - Mariam Saribekyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | | | - Thomas Stöllner
- Institut für Archäologische Wissenschaften, Ruhr-Universität Bochum, Bochum, Germany
- Forschungsstelle Archäologie und Materialwissenschaften, Abteilung Forschung, Deutsches Bergbau-Museum Bochum, Bochum, Germany
| | - Judith Thomalsky
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Benik Vardanyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
- Shirak Armenology Research Center, National Academy of Sciences of the Republic of Armenia, Gyumri, Armenia
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Cambridge, MA, USA
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Cambridge, MA, USA
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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25
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Mekonnen KT, Lee DH, Cho YG, Son AY, Seo KS. Genome-Wide Association Studies and Runs of Homozygosity Reveals Genetic Markers Associated with Reproductive Performance in Korean Duroc, Landrace, and Yorkshire Breeds. Genes (Basel) 2024; 15:1422. [PMID: 39596622 PMCID: PMC11594135 DOI: 10.3390/genes15111422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/22/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND Reproductive performance is critical in the pig industry, and improved sow performance could lead to increased economic benefits. GWAS and ROH analyses based on SNP array data were conducted to identify the breed-specific genetic architecture underlying the variation in NBA and TNB. METHODS A total of 7488 breeding pigs with phenotypic data from 1586 Duroc, 2256 Landrace, and 3646 Yorkshire breeds, along with 76,756 SNP markers from Korean grand-grand-parent (GGP) breeding farms, were used. RESULTS In the Duroc breeds, SNPs on SSC 9 and 17 were found to be associated with the SIDT2 and TGM2 genes, respectively. In the Landrace breed, PPP1R9A, LMTK2, and GTF2H3 on SSCs 9, 3, and 14, respectively, were associated with both TNB and NBA. With the Yorkshire breed genome, GRID1, DLGAP2, ZZEF1, PARG, RNF17, and NDUFAF5 in SSCs 14, 15, 12, 14, 11, and 17, respectively, were associated with NBA and TNB traits. These genes have distinct functions, ranging from synaptic transmission and cytoskeletal organization to DNA repair and cellular energy production. In the Duroc breed, six genes identified in the ROH islands were associated with various biological pathways, molecular functions, and cellular components. NT5DC1 was associated with metaphyseal chondrodysplasia, CRTAC1 with ion binding, CFAP43 with spermatogenic failure, CASC3 with intracellular mRNA localization, ERC2 with cellular component organization, and FOCAD with Focadhesin. In the Landrace and Yorkshire breeds, PDE6D was associated with GTPase inhibitor activity. CONCLUSIONS Through GWAS and ROH analyses, we identified breed-specific SNP markers associated with NBA and TNB in three breed genotypes, providing insights for improving reproductive performance efficiency and contributing to future breeding strategies.
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Affiliation(s)
- Kefala Taye Mekonnen
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea; (K.T.M.)
- Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella 193, Ethiopia
| | - Dong-Hui Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea; (K.T.M.)
| | - Young-Gyu Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea; (K.T.M.)
| | - Ah-Yeong Son
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea; (K.T.M.)
| | - Kang-Seok Seo
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea; (K.T.M.)
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26
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Higgins OA, Modi A, Cannariato C, Diroma MA, Lugli F, Ricci S, Zaro V, Vai S, Vazzana A, Romandini M, Yu H, Boschin F, Magnone L, Rossini M, Di Domenico G, Baruffaldi F, Oxilia G, Bortolini E, Dellù E, Moroni A, Ronchitelli A, Talamo S, Müller W, Calattini M, Nava A, Posth C, Lari M, Bondioli L, Benazzi S, Caramelli D. Life history and ancestry of the late Upper Palaeolithic infant from Grotta delle Mura, Italy. Nat Commun 2024; 15:8248. [PMID: 39304646 PMCID: PMC11415373 DOI: 10.1038/s41467-024-51150-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/30/2024] [Indexed: 09/22/2024] Open
Abstract
The biological aspects of infancy within late Upper Palaeolithic populations and the role of southern refugia at the end of the Last Glacial Maximum are not yet fully understood. This study presents a multidisciplinary, high temporal resolution investigation of an Upper Palaeolithic infant from Grotta delle Mura (Apulia, southern Italy) combining palaeogenomics, dental palaeohistology, spatially-resolved geochemical analyses, direct radiocarbon dating, and traditional anthropological studies. The skeletal remains of the infant - Le Mura 1 - were directly dated to 17,320-16,910 cal BP. The results portray a biological history of the infant's development, early life, health and death (estimated at ~72 weeks). They identify, several phenotypic traits and a potential congenital disease in the infant, the mother's low mobility during gestation, and a high level of endogamy. Furthermore, the genomic data indicates an early spread of the Villabruna-like components along the Italian peninsula, confirming a population turnover around the time of the Last Glacial Maximum, and highlighting a general reduction in genetic variability from northern to southern Italy. Overall, Le Mura 1 contributes to our better understanding of the early stages of life and the genetic puzzle in the Italian peninsula at the end of the Last Glacial Maximum.
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Affiliation(s)
- Owen Alexander Higgins
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, Rome, Italy.
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy.
| | | | | | - Federico Lugli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefano Ricci
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Valentina Zaro
- Department of Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Antonino Vazzana
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Matteo Romandini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - He Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Francesco Boschin
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Luigi Magnone
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Matteo Rossini
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | | | - Fabio Baruffaldi
- Laboratory of Medical Technology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Gregorio Oxilia
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Elena Dellù
- Institute Villa Adriana e Villa d'Este, Superintendence of Archeology, Fine Arts and Landscape for the metropolitan city of Bari - Ministry of Culture, Bari, Italy
| | - Adriana Moroni
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Annamaria Ronchitelli
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Müller
- Institut für Geowissenschaften, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Frankfurt Isotope and Element Research Center (FIERCE), Goethe University Frankfurt, Frankfurt, Frankfurt am Main, Germany
| | - Mauro Calattini
- Department of History and Cultural Heritage, University of Siena, Siena, Italy
| | - Alessia Nava
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, Rome, Italy
| | - Cosimo Posth
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Luca Bondioli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Cultural Heritage, University of Padua, Padova, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
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27
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Slimak L, Vimala T, Seguin-Orlando A, Metz L, Zanolli C, Joannes-Boyau R, Frouin M, Arnold LJ, Demuro M, Devièse T, Comeskey D, Buckley M, Camus H, Muth X, Lewis JE, Bocherens H, Yvorra P, Tenailleau C, Duployer B, Coqueugniot H, Dutour O, Higham T, Sikora M. Long genetic and social isolation in Neanderthals before their extinction. CELL GENOMICS 2024; 4:100593. [PMID: 39265525 PMCID: PMC11480857 DOI: 10.1016/j.xgen.2024.100593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/23/2023] [Accepted: 06/05/2024] [Indexed: 09/14/2024]
Abstract
Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed "Thorin," from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.
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Affiliation(s)
- Ludovic Slimak
- Centre d'Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Faculté de Santé, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France.
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Faculté de Santé, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, BP 647, 5 rue du Château de l'Horloge, 13094 Aix-en-Provence Cedex 2, France; University of Connecticut, College of Liberal Arts and Sciences, 215 Glenbrook Road, U-4098, Storrs, CT 06269-4098, USA
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600 Pessac, France
| | - Renaud Joannes-Boyau
- Geoarchaeology & Archaeometry Research Group (GARG), Southern Cross University, Military Rd., Lismore, NSW 2480, Australia
| | - Marine Frouin
- Department of Geosciences, Stony Brook University, 255 Earth and Space Sciences Building, Stony Brook, NY 11794-2100, USA; Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | - Lee J Arnold
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Martina Demuro
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Thibaut Devièse
- CEREGE, Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Technopôle de l'Arbois, Aix-en-Provence, France
| | - Daniel Comeskey
- Syft Technologies Ltd., 3 Craft Place, Middleton, PO Box 28 149, Christchurch 8242, New Zealand
| | - Michael Buckley
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Hubert Camus
- PROTEE-EXPERT, 4 rue des Aspholdèles, 34750 Villeneuve-lès-Maguelone, France
| | - Xavier Muth
- Get in Situ, 1091 Bourg-en-Lavaux, Switzerland
| | - Jason E Lewis
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA; Chronicle Heritage, 319 E Palm Lane, Phoenix, AZ 85004, USA
| | - Hervé Bocherens
- Fachbereich Geowissenschaften Forschungsbereich Paläobiologie - Biogeologie Senckenberg, Centre for Human Evolution and Palaeoenvironment (SHEP), Universität Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
| | - Pascale Yvorra
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, BP 647, 5 rue du Château de l'Horloge, 13094 Aix-en-Provence Cedex 2, France
| | - Christophe Tenailleau
- Centre Inter-Universitaire de Recherche et d'Ingénierie des Matériaux, UMR 5085 CNRS-Université de Toulouse (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Benjamin Duployer
- Centre Inter-Universitaire de Recherche et d'Ingénierie des Matériaux, UMR 5085 CNRS-Université de Toulouse (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Hélène Coqueugniot
- École Pratique des Hautes Études - Paris Sciences et Lettres University, 4-14 rue Ferrus, 75014 Paris, France; University of Bordeaux-Montaigne, CNRS, EPHE, Archéosciences, UMR 6034, 33607 Pessac, France
| | - Olivier Dutour
- École Pratique des Hautes Études - Paris Sciences et Lettres University, 4-14 rue Ferrus, 75014 Paris, France; University of Bordeaux-Montaigne, CNRS, EPHE, Archéosciences, UMR 6034, 33607 Pessac, France
| | - Thomas Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna 1090, Austria
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
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28
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Scheib CL, Hui R, Rose AK, D’Atanasio E, Inskip SA, Dittmar J, Cessford C, Griffith SJ, Solnik A, Wiseman R, Neil B, Biers T, Harknett SJ, Sasso S, Biagini SA, Runfeldt G, Duhig C, Evans C, Metspalu M, Millett MJ, O’Connell TC, Robb JE, Kivisild T. Low Genetic Impact of the Roman Occupation of Britain in Rural Communities. Mol Biol Evol 2024; 41:msae168. [PMID: 39268685 PMCID: PMC11393495 DOI: 10.1093/molbev/msae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 07/25/2024] [Accepted: 08/07/2024] [Indexed: 09/17/2024] Open
Abstract
The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.
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Affiliation(s)
- Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu Tartu 51010, Estonia
- St John's College, University of Cambridge, Cambridge CB2 1TP, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
- Alan Turing Institute, British Library, London NW1 2DB, UK
| | - Alice K Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology, IBPM CNR, Rome 00185, Italy
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jenna Dittmar
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| | - Craig Cessford
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Samuel J Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu Tartu 51010, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Rob Wiseman
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Benjamin Neil
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Trish Biers
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | | | - Stefania Sasso
- Estonian Biocentre, Institute of Genomics, University of Tartu Tartu 51010, Estonia
| | - Simone A Biagini
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | | | - Corinne Duhig
- Wolfson College, University of Cambridge, Cambridge CB3 9BB, UK
| | - Christopher Evans
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu Tartu 51010, Estonia
| | - Martin J Millett
- Faculty of Classics, University of Cambridge, Cambridge CB3 9DA, UK
| | - Tamsin C O’Connell
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - John E Robb
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu Tartu 51010, Estonia
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
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29
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Tian Y, Koncz I, Defant S, Giostra C, Vyas DN, Sołtysiak A, Pejrani Baricco L, Fetner R, Posth C, Brandt G, Bedini E, Modi A, Lari M, Vai S, Francalacci P, Fernandes R, Steinhof A, Pohl W, Caramelli D, Krause J, Izdebski A, Geary PJ, Veeramah KR. The role of emerging elites in the formation and development of communities after the fall of the Roman Empire. Proc Natl Acad Sci U S A 2024; 121:e2317868121. [PMID: 39159385 PMCID: PMC11388374 DOI: 10.1073/pnas.2317868121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 06/26/2024] [Indexed: 08/21/2024] Open
Abstract
Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups.
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Affiliation(s)
- Yijie Tian
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - István Koncz
- Department of Humanities, Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary
| | - Sarah Defant
- Department of History and Cultural Studies, Institute of Prehistoric Archaeology, Freie Universität Berlin, Berlin 14195, Germany
- Max Planck Institute of Geoanthropology, Jena 07743, Germany
- Department of Philosophy and Humanities, Institute of Greek and Latin Languages and Literatures, Freie Universität Berlin, Berlin 14195, Germany
| | - Caterina Giostra
- Department of History, Archaeology and Art History, Catholic University Milan, Milan 20103, Italy
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Arkadiusz Sołtysiak
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Warszawa 00-927, Poland
| | - Luisella Pejrani Baricco
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Torino, Torino TO 10122, Italy
| | - Rafał Fetner
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Warszawa 00-927, Poland
| | - Cosimo Posth
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen 72074, Germany
| | - Guido Brandt
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Elena Bedini
- Department of History, Archaeology and Art History, Catholic University Milan, Milan 20103, Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari 09126, Italy
| | - Ricardo Fernandes
- Max Planck Institute of Geoanthropology, Jena 07743, Germany
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Warszawa 00-927, Poland
- Arne Faculty of Arts, Masaryk University, Brno-střed 602 00, Czech Republic
- Climate Change and History Research Initiative, Princeton University, Princeton, NJ 08542
| | - Axel Steinhof
- Max Planck Institute for Biogeochemistry, Jena 07745, Germany
| | - Walter Pohl
- Institute for Medieval Research, Austrian Academy of Sciences; Institute for Austrian Historical Research, University of Vienna, Vienna 1020, Austria
| | - David Caramelli
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Adam Izdebski
- Max Planck Institute of Geoanthropology, Jena 07743, Germany
- Institute of History, Jagiellonian University in Krakow, Kraków 31-007, Poland
| | - Patrick J Geary
- School of Historical Studies, Institute for Advanced Study, Princeton, NJ 08540
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
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30
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de la Fuente Castro C, Cortés C, Raghavan M, Castillo D, Castro M, Verdugo RA, Moraga M. The Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina. Genome Biol Evol 2024; 16:evae196. [PMID: 39235046 PMCID: PMC11411372 DOI: 10.1093/gbe/evae196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/06/2024] Open
Abstract
The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.
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Affiliation(s)
- Constanza de la Fuente Castro
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, 8380453, Región Metropolitana, Chile
- Department of Human Genetics, University of Chicago, Chicago, 60637, IL, USA
| | - Constanza Cortés
- Escuela de Arqueología, Universidad Austral, Puerto Montt, 5504327, Región de Los Lagos, Chile
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, 60637, IL, USA
| | - Daniela Castillo
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, 8380453, Región Metropolitana, Chile
| | - Mario Castro
- Museo Nacional de Historia Natural, Parque Quinta Normal, Santiago, 8500000, Región Metropolitana, Chile
- Departamento de Morfología, Facultad de Medicina, Clínica Alemana-Universidad del Desarrollo, Santiago, 7610615, Región Metropolitana, Chile
| | - Ricardo A Verdugo
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, 8380453, Región Metropolitana, Chile
- Departamento de Oncología Básico-Clínica, Universidad de Chile, Santiago, 8380453, Región Metropolitana, Chile
- Instituto de Investigación Interdisciplinaria, Universidad de Talca, Talca 3465548, Región del Maule, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, 8380453, Región Metropolitana, Chile
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, 7800284, Región Metropolitana, Chile
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31
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Zagorc B, Blanz M, Gelabert P, Sawyer S, Oberreiter V, Cheronet O, Chen HS, Carić M, Visković E, Olalde I, Ivanova-Bieg M, Novak M, Reich D, Pinhasi R. Bioarchaeological Perspectives on Late Antiquity in Dalmatia: Paleogenetic, Dietary, and Population Studies of the Hvar - Radošević burial site. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2024; 16:150. [PMID: 39606698 PMCID: PMC11600397 DOI: 10.1007/s12520-024-02050-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/19/2024] [Indexed: 11/29/2024]
Abstract
Late Antiquity Dalmatia was a time and place of political unrest in the Roman Empire that influenced the lives of those in that region. The Late Antique burial site of Hvar - Radošević, spanning the 3rd to 5th centuries CE, is located on the Croatian Dalmatian island of Hvar. Given the time frame and location on a busy marine trade route, the study of this burial site offers us a glimpse into the lives of the Late Antique population living on this island. It comprises 33 individuals, with 17 buried within a confined grave tomb and the remaining individuals buried in separate locations in the tomb's proximity. The study aims to provide a new perspective on the lives of people on the island during those times by studying ancestry, population structure, possible differences within the buried population, dietary habits, and general health. The genetic analysis of the ancestral origins of the individuals buried at Hvar - Radošević revealed a diverse population reflective of the era's genetic variability. The identification of genetic outliers suggests a range of ancestries from distinct regions of the Roman Empire, possibly linked to trade routes associated with the Late Antique port in ancient Hvar. Stable isotope ratio analysis (δ13C and δ15N) indicated a diet mainly consisting of C3 plants, with minimal consumption of marine foods. High childhood mortality rates, physiological stress markers, and dental diseases suggest a low quality of life in the population. Assessment of kinship and dietary patterns revealed no discernible distinctions between individuals buried within the tomb and those buried outside, indicative of an absence of differential burial practices based on social status and familial ties among this specific buried population.
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Affiliation(s)
- Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Magdalena Blanz
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Vienna Institute of Archaeological Sciences (VIAS), University of Vienna, Vienna, Austria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Hao Shan Chen
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Zagreb, Croatia
| | | | - Iňigo Olalde
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Ikerbasque—Basque Foundation of Science, Bilbao, Spain
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Maria Ivanova-Bieg
- Vor- und Frühgeschichtliche Archäologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Zagreb, Croatia
- Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, Koper, Slovenia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
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32
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Moreno-Mayar JV, Sousa da Mota B, Higham T, Klemm S, Gorman Edmunds M, Stenderup J, Iraeta-Orbegozo M, Laborde V, Heyer E, Torres Hochstetter F, Friess M, Allentoft ME, Schroeder H, Delaneau O, Malaspinas AS. Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas. Nature 2024; 633:389-397. [PMID: 39261618 PMCID: PMC11390480 DOI: 10.1038/s41586-024-07881-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/26/2024] [Indexed: 09/13/2024]
Abstract
Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse-the 'ecocide' theory2-4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5-7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670-1950 CE) and whole-genome sequenced (0.4-25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250-1430 CE.
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Affiliation(s)
- J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tom Higham
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS) Network, University of Vienna, Vienna, Austria
| | - Signe Klemm
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper Stenderup
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Miren Iraeta-Orbegozo
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Véronique Laborde
- Direction Générale Déléguée aux Collections, Muséum national d'Histoire naturelle, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | | | - Martin Friess
- Eco-anthropologie (EA), Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Rodríguez-Varela R, Yaka R, Pochon Z, Sanchez-Pinto I, Solaun JL, Naidoo T, Guinet B, Pérez-Ramallo P, Lagerholm VK, de Anca Prado V, Valdiosera C, Krzewińska M, Herrasti L, Azkarate A, Götherström A. Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis. SCIENCE ADVANCES 2024; 10:eadp8625. [PMID: 39196943 PMCID: PMC11352919 DOI: 10.1126/sciadv.adp8625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/30/2024]
Abstract
Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Iban Sanchez-Pinto
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - José Luis Solaun
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
| | - Benjamin Guinet
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Lourdes Herrasti
- Departamento de Antropología, Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | - Agustín Azkarate
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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34
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Arzelier A, De Belvalet H, Pemonge MH, Garberi P, Binder D, Duday H, Deguilloux MF, Pruvost M. Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France. Proc Biol Sci 2024; 291:rspb20241215. [PMID: 39191285 PMCID: PMC11349438 DOI: 10.1098/rspb.2024.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/26/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.
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Affiliation(s)
- Ana Arzelier
- Université de Bordeaux, CNRS, De la Préhistoire à l’Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199), Pessac Cedex33615, France
| | - Harmony De Belvalet
- Université de Bordeaux, CNRS, De la Préhistoire à l’Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199), Pessac Cedex33615, France
| | - Marie-Hélène Pemonge
- Université de Bordeaux, CNRS, De la Préhistoire à l’Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199), Pessac Cedex33615, France
| | - Pauline Garberi
- Université Côte d’Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264), Nice06300, France
| | - Didier Binder
- Université Côte d’Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264), Nice06300, France
| | - Henri Duday
- Université de Bordeaux, CNRS, De la Préhistoire à l’Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199), Pessac Cedex33615, France
| | - Marie-France Deguilloux
- Université de Bordeaux, CNRS, De la Préhistoire à l’Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199), Pessac Cedex33615, France
| | - Mélanie Pruvost
- Université de Bordeaux, CNRS, De la Préhistoire à l’Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199), Pessac Cedex33615, France
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35
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Gretzinger J, Schmitt F, Mötsch A, Carlhoff S, Lamnidis TC, Huang Y, Ringbauer H, Knipper C, Francken M, Mandt F, Hansen L, Freund C, Posth C, Rathmann H, Harvati K, Wieland G, Granehäll L, Maixner F, Zink A, Schier W, Krausse D, Krause J, Schiffels S. Evidence for dynastic succession among early Celtic elites in Central Europe. Nat Hum Behav 2024; 8:1467-1480. [PMID: 38831077 PMCID: PMC11343710 DOI: 10.1038/s41562-024-01888-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
The early Iron Age (800 to 450 BCE) in France, Germany and Switzerland, known as the 'West-Hallstattkreis', stands out as featuring the earliest evidence for supra-regional organization north of the Alps. Often referred to as 'early Celtic', suggesting tentative connections to later cultural phenomena, its societal and population structure remain enigmatic. Here we present genomic and isotope data from 31 individuals from this context in southern Germany, dating between 616 and 200 BCE. We identify multiple biologically related groups spanning three elite burials as far as 100 km apart, supported by trans-regional individual mobility inferred from isotope data. These include a close biological relationship between two of the richest burial mounds of the Hallstatt culture. Bayesian modelling points to an avuncular relationship between the two individuals, which may suggest a practice of matrilineal dynastic succession in early Celtic elites. We show that their ancestry is shared on a broad geographic scale from Iberia throughout Central-Eastern Europe, undergoing a decline after the late Iron Age (450 BCE to ~50 CE).
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felicitas Schmitt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Angela Mötsch
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Selina Carlhoff
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Yilei Huang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Corina Knipper
- Curt Engelhorn Zentrum Archäometrie gGmbH, Mannheim, Germany
| | - Michael Francken
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Franziska Mandt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Leif Hansen
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Hannes Rathmann
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Katerina Harvati
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
- DFG Center for Advanced Studies in the Humanities 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Günther Wieland
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Lena Granehäll
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Wolfram Schier
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Dirk Krausse
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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36
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Sedig J, Snow M, Searcy M, Diaz JLP, LeBlanc S, Ramos F, Eccles L, Reich D. High levels of consanguinity in a child from Paquimé, Chihuahua, Mexico. ANTIQUITY 2024; 98:1023-1039. [PMID: 39493412 PMCID: PMC11529752 DOI: 10.15184/aqy.2024.94] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2024]
Abstract
This study reports results from the ancient DNA analysis of a unique child burial at Paquimé, northern Chihuahua, Mexico. Located between Mesoamerican and Ancestral Puebloan groups, Paquimé (also known as Casas Grandes) was a vibrant multicultural centre during the 13th-14th centuries AD. Archaeologists have long debated Paquimé's social organization. Our analysis of Burial 23-8 has revealed that this child, placed under the centre post of an important room, had parents who were close genetic relatives. We argue that this child's consanguinity and special depositional context resulted from an elite family's practice of aggrandizing social status.
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Affiliation(s)
- Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Michael Searcy
- Department of Anthropology, Brigham Young University, Provo, UT, USA
| | - José Luis Punzo Diaz
- Centro Instituto Nacional de Antropología e Historía-Michoacán, Instituto Nacional de Antropología e Historia, Mexico
| | - Steven LeBlanc
- Peabody Museum of Anthropology and Ethnology, Harvard University, Cambridge, MA, USA
| | - Frank Ramos
- Department of Geological Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Laurie Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, PA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
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37
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Gyuris B, Vyazov L, Türk A, Flegontov P, Szeifert B, Langó P, Mende BG, Csáky V, Chizhevskiy AA, Gazimzyanov IR, Khokhlov AA, Kolonskikh AG, Matveeva NP, Ruslanova RR, Rykun MP, Sitdikov A, Volkova EV, Botalov SG, Bugrov DG, Grudochko IV, Komar O, Krasnoperov AA, Poshekhonova OE, Chikunova I, Sungatov F, Stashenkov DA, Zubov S, Zelenkov AS, Ringbauer H, Cheronet O, Pinhasi R, Akbari A, Rohland N, Mallick S, Reich D, Szécsényi-Nagy A. Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.21.599526. [PMID: 39091721 PMCID: PMC11291037 DOI: 10.1101/2024.07.21.599526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.
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Affiliation(s)
- Balázs Gyuris
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University; Budapest, Hungary
| | - Leonid Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Attila Türk
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
- Hungarian Prehistory Research group, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Bea Szeifert
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Péter Langó
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Hungarian Research Network (HUN-REN); Budapest, Hungary
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Andrey A Chizhevskiy
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | | | | | - Aleksandr G Kolonskikh
- R.G. Kuzeev Institute of Ethnological Studies, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | | | - Rida R Ruslanova
- National Museum of the Republic of Bashkortostan; Ufa, Republic of Bashkortostan, Russia
| | | | - Ayrat Sitdikov
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
- Department of Archaeology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia
| | - Elizaveta V Volkova
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | - Sergei G Botalov
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Dmitriy G Bugrov
- National Museum of Tatarstan Republic; Kazan, Republic of Tatarstan, Russia
| | - Ivan V Grudochko
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Oleksii Komar
- Institute of Archaeology, National Academy of Sciences of Ukraine; Kyiv, Ukraine
| | - Alexander A Krasnoperov
- Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch of the Russian Academy of Sciences; Izhevsk, Udmurt Republic, Russia
| | - Olga E Poshekhonova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Irina Chikunova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Flarit Sungatov
- Institute of History, Language and Literature, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | - Dmitrii A Stashenkov
- Samara Regional Museum of History and Local Lore named after P. V. Alabin; Samara, Russia
| | - Sergei Zubov
- Research Laboratory of Archeology, Samara National Research University; Samara, Russia
| | | | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology; Leipzig, Germany
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ali Akbari
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
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Sasso S, Saag L, Spros R, Beneker O, Molinaro L, Biagini SA, Lehouck A, Van De Vijver K, Hui R, D’Atanasio E, Kushniarevich A, Kabral H, Metspalu E, Guellil M, Ali MQA, Geypen J, Hoebreckx M, Berk B, De Winter N, Driesen P, Pijpelink A, Van Damme P, Scheib CL, Deschepper E, Deckers P, Snoeck C, Dewilde M, Ervynck A, Tambets K, Larmuseau MHD, Kivisild T. Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders. Proc Natl Acad Sci U S A 2024; 121:e2406734121. [PMID: 38913897 PMCID: PMC11228521 DOI: 10.1073/pnas.2406734121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.
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Affiliation(s)
- Stefania Sasso
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Rachèl Spros
- Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050Brussels, Belgium
- Research Unit: Social History of Capitalism, Vrije Universiteit Brussel, 1050Brussels, Belgium
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
| | | | - Simone A. Biagini
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003Barcelona, Spain
| | | | | | - Ruoyun Hui
- Alan Turing Institute, NW1 2DBLondon, United Kingdom
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology, Italian National Research Council, Rome, Italy
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Helja Kabral
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Evolutionary Anthropology, University of Vienna, 1030Vienna, Austria
| | | | | | | | - Birgit Berk
- Birgit Berk Fysische Anthropologie, 6231ECMeerssen, Netherlands
| | | | | | - April Pijpelink
- Crematie en Inhumatie Analyse (CRINA) Fysische Antropologie, 5237JG 's-Hertogenbosch, Netherlands
| | - Philip Van Damme
- Department of Neurology, KU Leuven and Center for Brain & Disease Research Vlaamse Instituut voor Biotechnologie, 3000Leuven, Belgium
- Department of Neurosciences, KU Leuven and Center for Brain & Disease Research VIB, 3000Leuven, Belgium
| | - Christiana L. Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Zoology, University of Cambridge, CB2 3EJCambridge, United Kingdom
- Department of Archaeology, University of Cambridge, CB2 3DZCambridge, United Kingdom
- St John’s College, University of Cambridge, CB2 1TPCambridge, United Kingdom
| | - Ewoud Deschepper
- Historical Archaeology Research Group, Department of Archaeology, Ghent University, 9000Ghent, Belgium
| | | | - Christophe Snoeck
- Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050Brussels, Belgium
| | | | | | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | | | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
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Xia ZY, Chen X, Wang CC, Deng Q. Tracing the fine-scale demographic history and recent admixture in Hmong-Mien speakers. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24945. [PMID: 38708925 DOI: 10.1002/ajpa.24945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 05/07/2024]
Abstract
The linguistic, historical, and subsistent uniqueness of Hmong-Mien (HM) speakers offers a wonderful opportunity to investigate how these factors impact the genetic structure. The genetic differentiation among HM speakers and their population history are not well characterized. Here, we generate genome-wide data from 65 Yao ethnicity samples and analyze them with published data, particularly by leveraging haplotype-based methods. We determined that the fine-scale genetic substructure of HM speakers corresponds better with linguistic classification than with geography. Particularly, parallels between serial founder events and language differentiations can be observed in West Hmongic speakers. Multiple lines of evidence indicate that ~500-year-old GaoHuaHua individuals are most closely related to West Hmongic-speaking Bunu. The strong genetic bottleneck of some HM-speaking groups, especially Bunu, could potentially be associated with their long-term practice of swidden agriculture to some degree. The inferred admixture dates for most of the HM speakers overlap with the reign of the Ming dynasty (1368-1644 CE). Besides a common genetic origin for HM speakers, their genetic ancestry is shared primarily with neighboring Han Chinese and Tai-Kadai speakers in south China. In conclusion, our analyses reveal that recent isolation and admixture events have contributed to the genetic population history of present-day HM speakers.
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Affiliation(s)
- Zi-Yang Xia
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xingcai Chen
- Department of Human Anatomy, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Qiongying Deng
- Department of Human Anatomy, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, Nanning, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Key Laboratory of Human Development and Disease Research, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning, Guangxi, China
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40
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Parasayan O, Laurelut C, Bôle C, Bonnabel L, Corona A, Domenech-Jaulneau C, Paresys C, Richard I, Grange T, Geigl EM. Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome. SCIENCE ADVANCES 2024; 10:eadl2468. [PMID: 38896620 PMCID: PMC11186501 DOI: 10.1126/sciadv.adl2468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives' genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes.
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Affiliation(s)
- Oğuzhan Parasayan
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Christophe Laurelut
- INRAP Grand Est, Châlons-en-Champagne, France
- UMR 8215 Trajectoires (CNRS-University Paris I), Paris, France
| | - Christine Bôle
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UAR3633, Paris Descartes Sorbonne Université Paris Cité, Paris, France
| | | | - Alois Corona
- Service archéologique interdépartemental, 78180 Montigny-le-Bretonneux, France
| | - Cynthia Domenech-Jaulneau
- Service Régional, Direction Régionale des Affaires culturelles d’Île-de-France, UMR 8215 Trajectoires (CNRS-University Paris I), Paris, France
| | - Cécile Paresys
- INRAP Grand Est, Châlons-en-Champagne, France
- UMR 6472 CEPAM (CNRS-Nice University), Nice, France
| | - Isabelle Richard
- INRAP Grand Est, Châlons-en-Champagne, France
- UMR 6472 CEPAM (CNRS-Nice University), Nice, France
| | - Thierry Grange
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Eva-Maria Geigl
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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41
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Bai F, Liu Y, Wangdue S, Wang T, He W, Xi L, Tsho Y, Tsering T, Cao P, Dai Q, Liu F, Feng X, Zhang M, Ran J, Ping W, Payon D, Mao X, Tong Y, Tsring T, Chen Z, Fu Q. Ancient genomes revealed the complex human interactions of the ancient western Tibetans. Curr Biol 2024; 34:2594-2605.e7. [PMID: 38781957 DOI: 10.1016/j.cub.2024.04.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/21/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.
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Affiliation(s)
- Fan Bai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi'an 710054, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Jingkun Ran
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Danzin Payon
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Zehui Chen
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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42
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Childebayeva A, Fricke F, Rohrlach AB, Huang L, Schiffels S, Vesakoski O, Mannermaa K, Semerau L, Aron F, Solodovnikov K, Rykun M, Moiseyev V, Khartanovich V, Kovtun I, Krause J, Kuzminykh S, Haak W. Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry. Commun Biol 2024; 7:723. [PMID: 38862782 PMCID: PMC11166947 DOI: 10.1038/s42003-024-06343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.
- Department of Anthropology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Anthropology, University of Kansas, Lawrence, KS, 66044, USA.
| | - Fabian Fricke
- German Archaeological Institute, Eurasia Department, Berlin, 14195, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Outi Vesakoski
- Department of Finnish and Finno-Ugric Languages, University of Turku, Turku, 20014, Finland
| | - Kristiina Mannermaa
- Department of Cultures, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Konstantin Solodovnikov
- Institute of Problems of Northern Development, Tyumen Scientific Center of the Siberian Branch of Russian Academy of Sciences, Tyumen, 625008, Russia
| | - Marina Rykun
- Department of Anthropology and Ethnology, National Research Tomsk State University, Tomsk, 634050, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Igor Kovtun
- Igor V. Kovtun, Independent Researcher, Kemerovo, 650000, Russia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Sergey Kuzminykh
- Russian Academy of Sciences, Institute of Archaeology, Laboratory of Natural Scientific Methods, Moscow, 117292, Russia
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.
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43
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Gnecchi-Ruscone GA, Rácz Z, Samu L, Szeniczey T, Faragó N, Knipper C, Friedrich R, Zlámalová D, Traverso L, Liccardo S, Wabnitz S, Popli D, Wang K, Radzeviciute R, Gulyás B, Koncz I, Balogh C, Lezsák GM, Mácsai V, Bunbury MME, Spekker O, le Roux P, Szécsényi-Nagy A, Mende BG, Colleran H, Hajdu T, Geary P, Pohl W, Vida T, Krause J, Hofmanová Z. Network of large pedigrees reveals social practices of Avar communities. Nature 2024; 629:376-383. [PMID: 38658749 PMCID: PMC11078744 DOI: 10.1038/s41586-024-07312-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies2. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.
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Affiliation(s)
| | - Zsófia Rácz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Levente Samu
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Norbert Faragó
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Corina Knipper
- Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany
| | - Ronny Friedrich
- Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany
| | - Denisa Zlámalová
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia
| | - Luca Traverso
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Salvatore Liccardo
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Sandra Wabnitz
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Divyaratan Popli
- Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rita Radzeviciute
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - István Koncz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Csilla Balogh
- Department of Art History, Istanbul Medeniyet University, Istanbul, Turkey
| | - Gabriella M Lezsák
- Institute of History, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Viktor Mácsai
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Magdalena M E Bunbury
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| | - Olga Spekker
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Petrus le Roux
- Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Heidi Colleran
- BirthRites Lise Meitner Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tamás Hajdu
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary
| | | | - Walter Pohl
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary.
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia.
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44
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Sirak K, Jansen Van Rensburg J, Brielle E, Chen B, Lazaridis I, Ringbauer H, Mah M, Mallick S, Micco A, Rohland N, Callan K, Curtis E, Kearns A, Lawson AM, Workman JN, Zalzala F, Ahmed Al-Orqbi AS, Ahmed Salem EM, Salem Hasan AM, Britton DC, Reich D. Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia. Nat Ecol Evol 2024; 8:817-829. [PMID: 38332026 PMCID: PMC11009077 DOI: 10.1038/s41559-024-02322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024]
Abstract
Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 CE at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter-gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.
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Affiliation(s)
- Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | | | - Esther Brielle
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bowen Chen
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew Mah
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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45
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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. CELL GENOMICS 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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46
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Simões LG, Peyroteo-Stjerna R, Marchand G, Bernhardsson C, Vialet A, Chetty D, Alaçamlı E, Edlund H, Bouquin D, Dina C, Garmond N, Günther T, Jakobsson M. Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France. Proc Natl Acad Sci U S A 2024; 121:e2310545121. [PMID: 38408241 DOI: 10.1073/pnas.2310545121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/13/2023] [Indexed: 02/28/2024] Open
Abstract
Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.
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Affiliation(s)
- Luciana G Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Rita Peyroteo-Stjerna
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
- Department of Cultural Sciences, Linnaeus University, 351 95 Växjö, Sweden
- Centre for Archaeology, School of Arts and Humanities, University of Lisbon, 1600-214 Lisbon, Portugal
| | - Grégor Marchand
- Centre de Recherche en Archéologie, Archéosciences, Histoire, Université de Rennes, Rennes, CNRS 35065, France
| | - Carolina Bernhardsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Amélie Vialet
- Muséum national d'Histoire naturelle, UMR7194, Université Perpignan Via Domitia, Department "Homme et Environnement", Paris 75013, France
| | - Darshan Chetty
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Department of Entomology, Texas A&M University, College Station, TX 77843
| | - Erkin Alaçamlı
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Forensic Section, Regional Investigation Unit, Swedish Police Authority, 753 32 Uppsala, Sweden
| | - Denis Bouquin
- UMR 6298, ARTEHIS, Université de Bourgogne-CNRS, Bâtiment Sciences Gabriel, 21000 Dijon, France
- Service Archéologique du Grand Reims, 51100 Reims, France
| | - Christian Dina
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | | | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
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47
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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48
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Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
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Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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49
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Ringbauer H, Huang Y, Akbari A, Mallick S, Olalde I, Patterson N, Reich D. Accurate detection of identity-by-descent segments in human ancient DNA. Nat Genet 2024; 56:143-151. [PMID: 38123640 PMCID: PMC10786714 DOI: 10.1038/s41588-023-01582-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 12/23/2023]
Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.
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Affiliation(s)
- Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, University of the Basque Country, Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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50
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White LC, Städele V, Ramirez Amaya S, Langergraber K, Vigilant L. Female chimpanzees avoid inbreeding even in the presence of substantial bisexual philopatry. ROYAL SOCIETY OPEN SCIENCE 2024; 11:230967. [PMID: 38234436 PMCID: PMC10791533 DOI: 10.1098/rsos.230967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
Inbreeding (reproduction between relatives) often decreases the fitness of offspring and is thus expected to lead to the evolution of inbreeding avoidance strategies. Chimpanzees (Pan troglodytes) are expected to avoid inbreeding as they are long-lived, invest heavily in offspring and may encounter adult, opposite sex kin frequently, especially in populations where both males and females commonly remain in the group in which they were born (bisexual philopatry). However, it is unclear whether substantial bisexual philopatry has been a feature of chimpanzees' evolutionary history or whether it is a result of recent anthropogenic interference, as the only groups for which it has been documented are significantly impacted by human encroachment and experience notable rates of potentially unsustainable inbreeding. Here we use 14 years of observational data and a large genomic dataset of 256 481 loci sequenced from 459 individuals to document dispersal and inbreeding dynamics in an eastern chimpanzee (P. t. schweinfurthii) community with low levels of anthropogenic disturbance. We document the first case of substantial bisexual philopatry in a relatively undisturbed chimpanzee community and show that, despite an increased inbreeding risk incurred by females who do not disperse before reaching reproductive age, natal females were still able to avoid producing inbred offspring.
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Affiliation(s)
- Lauren C. White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, Melbourne, Australia
| | - Veronika Städele
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Sebastian Ramirez Amaya
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Kevin Langergraber
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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