{"entity": "researcher", "timestamp": "2026-09-23T15:25:58.788Z", "family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "affiliations": ["Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, \u00d8ster Voldgade 5-7, 1350, Copenhagen, Denmark."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea20be00d9a149568c27a0e5d0f66c9f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea20be00d9a149568c27a0e5d0f66c9f"}}, "publications": [{"entity": "publication", "iuid": "56c46e1b963a4bf48b7a7a5f53c487ee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/56c46e1b963a4bf48b7a7a5f53c487ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/56c46e1b963a4bf48b7a7a5f53c487ee"}}, "title": "The spatiotemporal distribution of human pathogens in ancient Eurasia.", "authors": [{"family": "Sikora", "given": "Martin", "initials": "M", "orcid": "0000-0003-2818-8319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beafb6d9130f44499a10c6c87c564780.json"}}, {"family": "Canteri", "given": "Elisabetta", "initials": "E", "orcid": "0000-0001-9867-8247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5fc0ee79aef4ec095d06cccd2a4b71a.json"}}, {"family": "Fernandez-Guerra", "given": "Antonio", "initials": "A", "orcid": "0000-0002-8679-490X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3563b7c6e5ec4118930b990e840168f5.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "\u00c5gren", "given": "Rasmus", "initials": "R"}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Irving-Pease", "given": "Evan K", "initials": "EK", "orcid": "0000-0003-1940-2192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f80a5f9f8b454ce88efb11e74c3912fe.json"}}, {"family": "M\u00fchlemann", "given": "Barbara", "initials": "B", "orcid": "0000-0002-5314-8530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35f3e699eaf84986847937ac13c8a360.json"}}, {"family": "Holtsmark Nielsen", "given": "Sofie", "initials": "S", "orcid": "0000-0001-7463-360X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13719f1e05304d1fba41d9baf6b0f9a0.json"}}, {"family": "Scorrano", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-0887-4023", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/935eb6f68c864debbde934525e1f51b4.json"}}, {"family": "Allentoft", "given": "Morten E", "initials": "ME", "orcid": "0000-0003-4424-3568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cfd5fe5a5dc495692f8ad64fab493fa.json"}}, {"family": "Valeur Seersholm", "given": "Frederik", "initials": "F"}, {"family": "Schroeder", "given": "Hannes", "initials": "H", "orcid": "0000-0002-6743-0270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/623076c82c834c71b5891c8fd946699a.json"}}, {"family": "Gaunitz", "given": "Charleen", "initials": "C"}, {"family": "Stenderup", "given": "Jesper", "initials": "J", "orcid": "0000-0002-6916-106X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71debf22da9c4acab17b8a23114e3b28.json"}}, {"family": "Vinner", "given": "Lasse", "initials": "L"}, {"family": "Jones", "given": "Terry C", "initials": "TC", "orcid": "0000-0003-1120-9531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/651eb5c468d94ce9bc0aaaba84a742dc.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG"}, {"family": "Parkhill", "given": "Julian", "initials": "J", "orcid": "0000-0002-7069-5958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b580193f0e8d402aa87005842bc05567.json"}}, {"family": "Fugger", "given": "Lars", "initials": "L", "orcid": "0000-0003-2883-3226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6dda4131ea4846a8ad356e98bb35754a.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea20be00d9a149568c27a0e5d0f66c9f.json"}}, {"family": "Kristiansen", "given": "Kristian", "initials": "K", "orcid": "0000-0003-2423-308X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/626861a01f554f3fbef631a704f30078.json"}}, {"family": "Iversen", "given": "Astrid K N", "initials": "AKN", "orcid": "0000-0002-3507-5956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7cc90874c69434d8e821e1bb10abdf3.json"}}, {"family": "Willerslev", "given": "Eske", "initials": "E", "orcid": "0000-0002-7081-6748", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2588e4ee35c14ceba39e54327b47b244.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "643", "issue": "8073", "pages": "1011-1019", "issn-l": "0028-0836"}, "abstract": "Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain1. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens2, many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock3. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe4,5.", "doi": "10.1038/s41586-025-09192-8", "pmid": "40634616", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12286840"}, {"db": "pii", "key": "10.1038/s41586-025-09192-8"}], "notes": [], "created": "2026-09-23T08:54:32.105Z", "modified": "2026-09-23T08:54:32.874Z"}, {"entity": "publication", "iuid": "919b592edda54099a0b4b37338ab2000", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/919b592edda54099a0b4b37338ab2000.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/919b592edda54099a0b4b37338ab2000"}}, "title": "Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.", "authors": [{"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f363e8d74594ffeb0d68aa6d774b242.json"}}, {"family": "Kidd", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-9631-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87d00735bd48420896025e5e52aa7298.json"}}, {"family": "Wang", "given": "Guo-Dong", "initials": "GD", "orcid": "0000-0002-9407-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61a7c21f358b4feea0ec783219f7ac42.json"}}, {"family": "Parker", "given": "Heidi G", "initials": "HG", "orcid": "0000-0002-9707-6380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bbe68238e524a85bdf7f2556b61301f.json"}}, {"family": "Schall", "given": "Peter Z", "initials": "PZ", "orcid": "0000-0003-1016-6998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81d0ab278ec44c4b83e1180740fa9a26.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/997ea196d4ae4c9790a715246dbfac82.json"}}, {"family": "Bougiouri", "given": "Katia", "initials": "K", "orcid": "0000-0002-7890-2755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14fbc8f63c084c1f948d7f819c7e4be8.json"}}, {"family": "Buckley", "given": "Reuben M", "initials": "RM", "orcid": "0000-0001-6334-3906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52f6dd32f4b9457b82e1f381b36657f8.json"}}, {"family": "Hitte", "given": "Christophe", "initials": "C", "orcid": "0000-0003-1714-437X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2aec5eba577458badfa5f3e9da2c7e2.json"}}, {"family": "Nguyen", "given": "Anthony K", "initials": "AK", "orcid": "0000-0002-9634-1904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19d1cf1c2d5f4529b41628766ccb2cd8.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cfac9dfcdfc04a88b002ffe4ee8a5bb4.json"}}, {"family": "Jagannathan", "given": "Vidhya", "initials": "V", "orcid": "0000-0002-8155-0041", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61e55b7d7ff44bfa8c602463aff78927.json"}}, {"family": "Niskanen", "given": "Julia E", "initials": "JE", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fe654ab4f7443a69dd17a6b43c79f47.json"}}, {"family": "Frantz", "given": "Laurent A F", "initials": "LAF", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/268c91b6ad33496da684e340f543862c.json"}}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Hundi", "given": "Sruthi", "initials": "S", "orcid": "0000-0002-5803-1841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5637e79b33854d3eb24d9cb1e16786bd.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Ginja", "given": "Catarina", "initials": "C", "orcid": "0000-0003-2278-7089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb9e7853817d4232b6bf2c81f2d1f4a9.json"}}, {"family": "Agustina", "given": "Kadek Karang", "initials": "KK", "orcid": "0000-0002-7128-0914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82ae61c2ab1e4aa1af4eedae1c5c9fbb.json"}}, {"family": "Andr\u00e9", "given": "Catherine", "initials": "C"}, {"family": "Boyko", "given": "Adam R", "initials": "AR", "orcid": "0000-0002-9125-6874", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93514d8cc7b945619ed50443e7ca6030.json"}}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/860474a0b2384119b8c9da985ca7ea93.json"}}, {"family": "Dr\u00f6gem\u00fcller", "given": "Michaela", "initials": "M", "orcid": "0000-0001-9378-7903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4872d6278d63408a89dbc598d2e60d49.json"}}, {"family": "Feng", "given": "Xin-Yao", "initials": "XY", "orcid": "0000-0002-2603-3105", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b78583f4ca5e422fb11ee6039575dae5.json"}}, {"family": "Gkagkavouzis", "given": "Konstantinos", "initials": "K"}, {"family": "Iliopoulos", "given": "Giorgos", "initials": "G"}, {"family": "Harris", "given": "Alexander C", "initials": "AC", "orcid": "0000-0002-6868-5363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b30f17aba31406f9f269364f4cc7507.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1389bbb3ba141598a0a896b056dea89.json"}}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC", "orcid": "0000-0003-2439-5484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbf95ba94cfa41ef8a2ad3e8e34d23cf.json"}}, {"family": "Liu", "given": "Yan-Hu", "initials": "YH", "orcid": "0000-0001-9991-4571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fb30cae56ae46528587c81431298e7f.json"}}, {"family": "Lymberakis", "given": "Petros", "initials": "P"}, {"family": "Poulakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Pires", "given": "Ana Elisabete", "initials": "AE", "orcid": "0000-0002-1118-8569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f6a7202e66442a882c5ff8760dc761e.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea20be00d9a149568c27a0e5d0f66c9f.json"}}, {"family": "Ramos-Almodovar", "given": "Fabian", "initials": "F", "orcid": "0000-0001-9094-7895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b43257be391040d8a140a60258987f9c.json"}}, {"family": "Savolainen", "given": "Peter", "initials": "P", "orcid": "0000-0002-1495-8338", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06353af3236049c4988c0bb038443a96.json"}}, {"family": "Venetsani", "given": "Semina", "initials": "S"}, {"family": "Tammen", "given": "Imke", "initials": "I", "orcid": "0000-0002-5520-6597", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f46ec5759b447068f4ffbe2731ad9d0.json"}}, {"family": "Triantafyllidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0003-0469-011X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25f2df58b8044a2cbc9d3f2c451c95bf.json"}}, {"family": "vonHoldt", "given": "Bridgett", "initials": "B", "orcid": "0000-0001-6908-1687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea3f2e1adc0e429782a368580bae269c.json"}}, {"family": "Wayne", "given": "Robert K", "initials": "RK", "orcid": "0000-0003-3537-2245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41d2b28a69849bc8be3c905c36e01d6.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbcb4bf5ac644e2b9dd19083c9a90b9d.json"}}, {"family": "Nicholas", "given": "Frank W", "initials": "FW", "orcid": "0000-0002-9178-3965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/230edbe08715408993169026dcd90fcd.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eab428714c9f4f5eb0de63ffc7500f25.json"}}, {"family": "Leeb", "given": "Tosso", "initials": "T", "orcid": "0000-0003-0553-4880", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b9a5b55628740d99bdb37372a1c37b3.json"}}, {"family": "Zhang", "given": "Ya-Ping", "initials": "YP", "orcid": "0000-0002-5401-1114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08315abecebf43c0adc5874c44e3cf11.json"}}, {"family": "Ostrander", "given": "Elaine A", "initials": "EA", "orcid": "0000-0001-6075-9738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb08ca2565ce45c9adfa484cf60b2909.json"}}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "24", "issue": "1", "pages": "187", "issn-l": "1474-7596"}, "abstract": "The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 \u00d7 data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.\n\nWe report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.\n\nWe have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.", "doi": "10.1186/s13059-023-03023-7", "pmid": "37582787", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10426128"}, {"db": "pii", "key": "10.1186/s13059-023-03023-7"}], "notes": [], "created": "2026-09-23T07:32:42.444Z", "modified": "2026-09-23T07:32:43.598Z"}]}