{"doi":"10.1038/s41586-024-07651-2","title":"Repeated plague infections across six generations of Neolithic Farmers","abstract":"<jats:title>Abstract</jats:title><jats:p>In the period between 5,300 and 4,900 calibrated years before present (cal.<jats:sc>bp</jats:sc>), populations across large parts of Europe underwent a period of demographic decline<jats:sup>1,2</jats:sup>. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline<jats:sup>3</jats:sup>, others for the spread of an early form of plague<jats:sup>4</jats:sup>. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in<jats:italic>Yersinia pseudotuberculosis</jats:italic>, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.</jats:p>","journal":"Nature","year":2024,"id":653209,"datarank":0.5837730447165941,"base_score":3.8918202981106265,"endowment":3.8918202981106265,"self_citation_contribution":0.5837730447165941,"citation_network_contribution":0.0,"self_endowment_contribution":0.5837730447165941,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":48,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":983051,"name":"Karl-Göran Sjögren","orcid":"0000-0003-1791-3175","position":1,"is_corresponding":false},{"id":1704330,"name":"Julia Koelman","orcid":null,"position":2,"is_corresponding":false},{"id":983094,"name":"Malou Blank","orcid":"0000-0002-0057-8756","position":3,"is_corresponding":false},{"id":1704331,"name":"Emma M. 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However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline<jats:sup>3</jats:sup>, others for the spread of an early form of plague<jats:sup>4</jats:sup>. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in<jats:italic>Yersinia pseudotuberculosis</jats:italic>, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.</jats:p>","is_dataset_classified":null,"base_score":3.8918202981106265,"endowment":3.8918202981106265,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"38987589","pmcid":"PMC11291285","openalex_id":"https://openalex.org/W4400491896","authors":[],"funders":[{"funder_name":"Lundbeck Foundation","grant_id":"R155-2013-16338","title":null},{"funder_name":"Lundbeck Foundation","grant_id":"R302-2018-2155","title":null},{"funder_name":"Lundbeck Foundation","grant_id":"R322-2019-2610","title":null},{"funder_name":"Wellcome Trust","grant_id":"unidentified","title":"unidentified"},{"funder_name":"Wellcome Trust","grant_id":"","title":null},{"funder_name":"Wellcome Trust","grant_id":"","title":null}],"total_grants":6,"fwci":18.4345,"citation_percentile":0.99554625,"influential_citations":0,"citation_trend":[{"year":2024,"count":1},{"year":2025,"count":29},{"year":2026,"count":18}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1038/s41586-024-07651-2","host_type":"journal"},{"url":"https://doi.org/10.1038/s41586-024-07651-2","host_type":"publisher"},{"url":"https://www.nature.com/articles/s41586-024-07651-2.pdf","host_type":"publisher"},{"url":"https://www.nature.com/articles/s41586-024-07651-2","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/38987589","host_type":"repository"},{"url":"https://ora.ox.ac.uk/objects/uuid:5c97e732-1769-4174-97d9-9bd4d9098dd6","host_type":"repository"},{"url":"https://www.repository.cam.ac.uk/handle/1810/372066","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11291285","host_type":"repository"},{"url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-547870","host_type":"repository"},{"url":"https://lup.lub.lu.se/record/296c3ecd-1805-4ec4-b696-9aa152bebcb3","host_type":"repository"},{"url":"https://researchprofiles.ku.dk/da/publications/f01ff38c-6a53-4e3b-bc1e-519ab9184bf3","host_type":"repository"},{"url":"https://bia.unibz.it/esploro/outputs/journalArticle/Repeated-plague-infections-across-six-generations/991006838897201241","host_type":"journal"},{"url":"https://europepmc.org/articles/PMC11291285","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11291285?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1038/s41586-024-07651-2","host_type":""},{"url":"https://curis.ku.dk/ws/files/413743806/s41586_024_07651_2.pdf","host_type":""},{"url":"https://doi.org/https://doi.org/10.1038/s41586-024-07651-2","host_type":""}],"fields_of_study":["Yersinia bacterium, plague, ectoparasites research","Zoonotic diseases and public health","Paleopathology and ancient diseases","06 humanities and the arts","0601 history and archaeology","Female","Humans","Male","Cemeteries","Farmers","Genome, Bacterial","Genomics","History, Ancient","Pedigree","Phylogeny","Plague","Population Dynamics","Scandinavian and Nordic Countries","Time Factors","Virulence Factors","Yersinia pestis"],"mesh_terms":["Farmers","Female","Humans","Male","Pedigree","Phylogeny","Plague","Population Dynamics","Scandinavian and Nordic Countries","Time Factors","Yersinia pestis","Genome, Bacterial","Genomics","Virulence Factors","History, Ancient","Cemeteries"],"keywords":["Plague (disease)","Biology","Geography","Archaeology","Male","Plague","Farmers","Time Factors","Virulence Factors","Yersinia pestis","Population Dynamics","Genetics and Genomics","Genetik och genomik","Genomics","Scandinavian and Nordic Countries","Article","Pedigree","Humans","Female","Cemeteries","Genome, Bacterial","History, Ancient","Phylogeny"],"sdg_mappings":[{"sdg_number":2,"sdg_label":"2. 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