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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 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 Cedex 33615, France
| | - Harmony De Belvalet
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Marie-Hélène Pemonge
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Pauline Garberi
- Université Côte d'Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264) , Nice 06300, France
| | - Didier Binder
- Université Côte d'Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264) , Nice 06300, France
| | - Henri Duday
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Marie-France Deguilloux
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Mélanie Pruvost
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
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Bergström A. Improving data archiving practices in ancient genomics. Sci Data 2024; 11:754. [PMID: 38987254 PMCID: PMC11236975 DOI: 10.1038/s41597-024-03563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.
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Affiliation(s)
- Anders Bergström
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Vincenti G, Molinaro L, Sajjadi SMS, Moradi H, Pagani L, Fabbri PF. Female biased adult sex ratio in the Bronze Age cemetery of Shahr-i Sokhta (Iran) as an indicator of long distance trade and matrilocality. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24911. [PMID: 38348756 DOI: 10.1002/ajpa.24911] [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: 06/11/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVES This paper starts from the unusual observation of the overrepresentation of females among adults in the cemetery of Bronze Age Shahr-i Sokhta (Seistan, Iran) and explores the post marital residence pattern. By integrating taphonomical (skeletal preservation), anthropological (sex ratio [SR], sexual dimorphism, stress indicators, age at death), archeological (long distance trade indicators, habitation floor area, social role of women), and ancient DNA (heterozygosity levels in X chromosomes) data we test the hypothesis of post marital matrilocality in the site. METHODS We computed the SR (pelvis-based sex determination) in a random unpublished adult sample from the cemetery of Shahr-i Sokhta and in two samples previously published by other authors. We used comparative data on SR from: a large Supra Regional multi-chronological sample of sites, n = 47, with 8808 adult sexed individuals, from Southern Europe, Egypt, Middle East, Southern Russia; a Regional Bronze Age sample of sites (n = 10) from Bactria Margiana and Indus Valley with 1324 adult sexed individuals. We estimated the heterozygosity levels in X chromosomes compared with the rest of the autosomes on the assumption that in a matrilocal society females should show lower variability than men. RESULTS Adult SR in a sample (n = 549) from Shahr-i Sokhta is 70.5, the overrepresentation of females is shared with Regional Bronze Age sites from Bactria Margiana (SR = 72.09) and Indus Valley (SR = 67.54). On the contrary, in a larger Supra Regional multi-chronological sample of sites, mean SR ranges between 112.7 (Bronze Age) and 163.1 (Middle Ages). Taphonomical and anthropological indicators do not explain the overrepresentation of female skeletons. Archeological indicators suggest a high social status of women and that the society was devoted to long range trade activities. heterozygosity levels in X chromosomes are in agreement with a matrilocal society. CONCLUSIONS Indicators suggest that Bronze Age Shahr-ì Sokhta was a matrilocal society and that long distance trade was an important economic factor producing an overrepresentation of adult female skeletons in the cemetery.
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Affiliation(s)
- Giorgia Vincenti
- MAIPS, Multidisciplinary Archaeological Italian Project at Shahr-i Sokhta - Dipartimento Beni Culturali, Laboratorio di Antropologia Fisica, Università del Salento, Lecce, Italy
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | - Pier Francesco Fabbri
- MAIPS, Multidisciplinary Archaeological Italian Project at Shahr-i Sokhta, Università del Salento, Lecce, Italy
- Museo Fiorentino di Preistoria, Firenze, Italy
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Granja R, Araújo AC, Lugli F, Silvestrini S, Silva AM, Gonçalves D. Unbalanced sex-ratio in the Neolithic individuals from the Escoural Cave (Montemor-o-Novo, Portugal) revealed by peptide analysis. Sci Rep 2023; 13:19902. [PMID: 37964077 PMCID: PMC10646114 DOI: 10.1038/s41598-023-47037-4] [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: 08/11/2023] [Accepted: 11/08/2023] [Indexed: 11/16/2023] Open
Abstract
The sex profile estimation of pre-historic communities is often complicated by the commingled and scattered nature of skeletal assemblages. Demographic profiles are usually lacking and provide very truncated representations of these populations but proteomic analysis of sex-specific amelogenin peptides in tooth enamel brings new promise to these studies. The main objective was to obtain the sex profile of the human assemblage recovered from the Neolithic cave-necropolis of Escoural (Montemor-o-Novo, southern Portugal) through liquid chromatography-mass spectrometry. The secondary objective was to analyse sex-specific linear enamel hypoplasias (LEH), and to test the reliability of canine odontometric sex estimation. Sex estimation through peptide analysis was carried out in 36 left permanent canines which were macroscopically examined for the presence of LEH. The canine buccolingual diameter was used for odontometric sex estimation. The obtained sex ratio (0.5:1, M:F) is biased to female individuals, probably due to cultural factors since the natural sex ratio of the human population falls between 0.95:1 and 1.02:1 (M:F). A high frequency of LEH was observed, but with no significant sexual differences (p = 0.554). The mean LEH age of onset occurred at 3 years of age, with no significant differences between the sexes (p = 0.116), and was possibly related to the weaning process. Odontometric sex estimation revealed a correct classification of 80%, with a high number of males mistakenly attributed to females. This study is one of the largest samples subjected to peptide analysis, and thus demonstrates its usefulness on the research of commingled and scattered skeletal assemblages.
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Affiliation(s)
- Raquel Granja
- Laboratory of Archaeosciences (LARC/CIBIO/InBIO), Direção-Geral do Património Cultural, Calçada do Mirante à Ajuda n.º 10, 1300-418, Lisbon, Portugal.
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
- Centre for Archaeology, University of Lisbon (UNIARQ), Faculty of Humanities, University of Lisbon, Alameda da Universidade, 1600-214, Lisbon, Portugal.
| | - Ana Cristina Araújo
- Laboratory of Archaeosciences (LARC/CIBIO/InBIO), Direção-Geral do Património Cultural, Calçada do Mirante à Ajuda n.º 10, 1300-418, Lisbon, Portugal
- Centre for Archaeology, University of Lisbon (UNIARQ), Faculty of Humanities, University of Lisbon, Alameda da Universidade, 1600-214, Lisbon, Portugal
| | - Federico Lugli
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Institut für Geowissenschaften, Goethe-Universität Frankfurt, Frankfurt Am Main, Germany
- BONES Lab, Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Sara Silvestrini
- BONES Lab, Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Ana Maria Silva
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- Centre for Archaeology, University of Lisbon (UNIARQ), Faculty of Humanities, University of Lisbon, Alameda da Universidade, 1600-214, Lisbon, Portugal
- Laboratory of Forensic Anthropology, Centre for Functional Ecology-Science for People & the Planet (CFE), Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - David Gonçalves
- Laboratory of Archaeosciences (LARC/CIBIO/InBIO), Direção-Geral do Património Cultural, Calçada do Mirante à Ajuda n.º 10, 1300-418, Lisbon, Portugal
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- Laboratory of Forensic Anthropology, Centre for Functional Ecology-Science for People & the Planet (CFE), Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
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