{"entity": "researcher", "timestamp": "2026-08-11T08:09:58.272Z", "family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "affiliations": ["Centre for Palaeogenetics, Stockholm, Sweden.", "Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.", "Department of Zoology, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68"}}, "publications": [{"entity": "publication", "iuid": "999289be0c1e406bb30bd4b40e7a2f00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00"}}, "title": "Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost", "authors": [{"family": "Selvatici", "given": "Sofia", "initials": "S"}, {"family": "Jin", "given": "Chenyu", "initials": "C"}, {"family": "Zazula", "given": "Grant", "initials": "G", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Moots", "given": "Hannah M", "initials": "HM", "orcid": "0000-0002-6637-6321", "researcher": {"href": "https://publications.scilifelab.se/researcher/5105354f578c480ba144061ffbb49bf5.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Parducci", "given": "Laura", "initials": "L", "orcid": "0000-0003-1956-4757", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4c737e2c7c4266b598a89aa2116a91.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}], "type": "journal-article", "published": "2026-03-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ond\u00ebk Hw\u00ebch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as \"Ts'ey\" in the H\u00e4n language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.", "doi": "10.1038/s41598-026-44540-2", "pmid": "41845022", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996357"}, {"db": "pii", "key": "10.1038/s41598-026-44540-2"}], "notes": [], "created": "2026-03-23T13:18:35.892Z", "modified": "2026-03-24T09:12:30.461Z"}, {"entity": "publication", "iuid": "19a4115c6ad14acaaf738a62c51e4f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69"}}, "title": "Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Feinauer", "given": "Isabelle S", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Kuzmina", "given": "Elena A", "initials": "EA"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Stewart", "given": "John R", "initials": "JR", "orcid": "0000-0002-3506-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e8f2e54f1a4f1d96d8f4ae1de97a93.json"}}, {"family": "Knul", "given": "Monika V", "initials": "MV", "orcid": "0000-0002-0650-0992", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff550d1088bb4857a28277ae1db41452.json"}}, {"family": "Noiret", "given": "Pierre", "initials": "P"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Ehrich", "given": "Dorothee", "initials": "D"}, {"family": "Pokrovsky", "given": "Ivan", "initials": "I"}, {"family": "Fedorov", "given": "Vadim B", "initials": "VB", "orcid": "0000-0003-3938-4200", "researcher": {"href": "https://publications.scilifelab.se/researcher/017b3cc7d41e46feb13e4e919b0c2dd5.json"}}, {"family": "Goropashnaya", "given": "Anna V", "initials": "AV", "orcid": "0009-0005-4712-6297", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e89f839e5c24f0dbef8deadb3a17f8d.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "122", "issue": "28", "pages": "e2424333122"}, "abstract": "The Norwegian lemming (Lemmus lemmus) is a small rodent distributed across the Fennoscandian mountain tundra and the Kola Peninsula. The Norwegian lemming likely evolved during the Late Pleistocene and inhabited Fennoscandia shortly prior to the Last Glacial Maximum. However, the exact timing and origins of the species, and its phylogenetic position relative to the closely related Siberian lemming (Lemmus sibiricus) remain disputed. Moreover, the presence of ancient or contemporary gene flow between both species is largely untested. The Norwegian lemming displays characteristic phenotypic and behavioral adaptations (e.g., coat color, aggression) that are not present in other Lemmus species. We generated a de novo genome assembly for the Norwegian lemming and resequenced nine modern and two ancient Lemmus spp. genomes. We show that all Lemmus species form distinct monophyletic clades, with concordant topology between the mitochondrial and nuclear genome phylogenies. The Siberian lemming is divided into two distinct but paraphyletic clades, one in the east and one in the west, where the western clade represents a sister taxon to the Norwegian lemming. We estimate that the Norwegian and western Siberian lemming diverged shortly before the Last Glacial Maximum, making the Norwegian lemming one of the youngest known mammalian species. We did not find any indication of gene flow between L. lemmus and L. sibiricus, suggesting postglacial isolation of L. lemmus. Furthermore, we identify species-specific genomic differences in genes related to coat color and fat transport, which are likely associated with the distinctive coloration and overwintering behavior observed in the Norwegian lemming.", "doi": "10.1073/pnas.2424333122", "pmid": "40587810", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12280882"}], "notes": [], "created": "2025-07-01T06:45:31.166Z", "modified": "2025-11-14T11:07:37.863Z"}, {"entity": "publication", "iuid": "a609fcce04e94ce4a51830b45ac8941d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d"}}, "title": "A Million Years of Mammoth Mitogenome Evolution.", "authors": [{"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Thomas Thorpe", "given": "Jessica A", "initials": "JA", "orcid": "0000-0003-2302-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7ce837837546e48d5debf6d6aa9b41.json"}}, {"family": "Li", "given": "Wenxi", "initials": "W", "orcid": "0009-0001-5130-9521", "researcher": {"href": "https://publications.scilifelab.se/researcher/f001ea19092e433b9abc9431fe45b63e.json"}}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patricia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Barlow", "given": "Axel", "initials": "A", "orcid": "0000-0002-5532-9458", "researcher": {"href": "https://publications.scilifelab.se/researcher/293d4982ed124c75896e1838bab18b8f.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Henneberger", "given": "Kirstin", "initials": "K"}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Moreland", "given": "Kelsey N", "initials": "KN", "orcid": "0000-0002-3571-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44fb07639f84500b325ea44d7faf08d.json"}}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA", "orcid": "0000-0002-1938-7052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bac46fda6c98402aa8743eeacef7a962.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/06418b4f9e90443d94452c87fb0b0588.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Mol", "given": "Dick", "initials": "D", "orcid": "0009-0005-4772-4625", "researcher": {"href": "https://publications.scilifelab.se/researcher/9baa2917aafa4ab59b27c7be2a2f246a.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P", "orcid": "0000-0001-6547-9890", "researcher": {"href": "https://publications.scilifelab.se/researcher/14e81a9e6a164940a46a57249be26006.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Vartanyan", "given": "Sergey", "initials": "S", "orcid": "0000-0001-7806-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c472e06d8fa43a0b8a5575d5aec48e8.json"}}, {"family": "Zazula", "given": "Grant D", "initials": "GD", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-04-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "42", "issue": "4", "pages": null}, "abstract": "The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.", "doi": "10.1093/molbev/msaf065", "pmid": "40202893", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11980863"}, {"db": "pii", "key": "8107989"}], "notes": [], "created": "2025-05-05T12:32:34.796Z", "modified": "2025-11-28T10:49:58.497Z"}, {"entity": "publication", "iuid": "708018decd8e4d788c4ddf8b8c1b2630", "links": {"self": {"href": "https://publications.scilifelab.se/publication/708018decd8e4d788c4ddf8b8c1b2630.json"}, "display": {"href": "https://publications.scilifelab.se/publication/708018decd8e4d788c4ddf8b8c1b2630"}}, "title": "Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations", "authors": [{"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal-article", "published": "2024-04-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "25", "issue": "2", "pages": "513-531", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-023-01586-3", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-08T13:27:59.260Z", "modified": "2024-11-25T10:10:59.738Z"}, {"entity": "publication", "iuid": "d63a8f09078149d8bf45ad1611ae68e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d63a8f09078149d8bf45ad1611ae68e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d63a8f09078149d8bf45ad1611ae68e1"}}, "title": "New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Keehnen", "given": "Naomi", "initials": "N"}, {"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "2", "pages": "e17213", "issn-l": "0962-1083"}, "abstract": "International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's \u03f4 and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.", "doi": "10.1111/mec.17213", "pmid": "38014725", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-02T13:26:58.174Z", "modified": "2024-11-25T10:27:09.260Z"}, {"entity": "publication", "iuid": "6a3ba31b04c54d138e7e1e4e193684e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a3ba31b04c54d138e7e1e4e193684e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a3ba31b04c54d138e7e1e4e193684e0"}}, "title": "GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.", "authors": [{"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2022-06-13", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "23", "issue": "1", "pages": "228", "issn-l": "1471-2105"}, "abstract": "Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.\n\nHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub ( https://github.com/NBISweden/GenErode ).\n\nGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.", "doi": "10.1186/s12859-022-04757-0", "pmid": "35698034", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC9195343"}, {"db": "pii", "key": "10.1186/s12859-022-04757-0"}], "notes": [], "created": "2022-08-01T12:22:30.120Z", "modified": "2024-01-16T13:48:36.134Z"}, {"entity": "publication", "iuid": "ee30e00b2af443009f454bd2fc3b373a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee30e00b2af443009f454bd2fc3b373a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee30e00b2af443009f454bd2fc3b373a"}}, "title": "Population genomics of the critically endangered k\u0101k\u0101p\u014d", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Foster", "given": "Yasmin", "initials": "Y"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Rhie", "given": "Arang", "initials": "A", "orcid": "0000-0002-9809-8127", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dfb02e5b09465ea5b24d4a45652799.json"}}, {"family": "Phillippy", "given": "Adam M", "initials": "AM", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Korlach", "given": "Jonas", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-2237-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1dac1c74d3497aa987c5a615f2d6c4.json"}}, {"family": "Chow", "given": "William", "initials": "W"}, {"family": "Pelan", "given": "Sarah", "initials": "S"}, {"family": "Mendes Damas", "given": "Joanna D", "initials": "JD"}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Hastie", "given": "Alex R", "initials": "AR"}, {"family": "Formenti", "given": "Giulio", "initials": "G", "orcid": "0000-0002-7554-5991", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdf78195993a481483d7cbbf1a6d64ed.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O", "orcid": "0000-0002-6450-7551", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae69dfab7d841d4850da7349714cd9c.json"}}, {"family": "Guhlin", "given": "Joseph", "initials": "J"}, {"family": "Harrop", "given": "Thomas W R", "initials": "TWR"}, {"family": "Le Lec", "given": "Marissa F", "initials": "MF"}, {"family": "Dearden", "given": "Peter K", "initials": "PK"}, {"family": "Haggerty", "given": "Leanne", "initials": "L"}, {"family": "Martin", "given": "Fergal J", "initials": "FJ"}, {"family": "Kodali", "given": "Vamsi", "initials": "V"}, {"family": "Thibaud-Nissen", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Iorns", "given": "David", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Gemmell", "given": "Neil J", "initials": "NJ", "orcid": "0000-0003-0671-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca2b0a676d84b878b3f9faa8748e148.json"}}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Moorhouse", "given": "Ron", "initials": "R"}, {"family": "Digby", "given": "Andrew", "initials": "A"}, {"family": "Eason", "given": "Daryl", "initials": "D"}, {"family": "Vercoe", "given": "Deidre", "initials": "D"}, {"family": "Howard", "given": "Jason", "initials": "J"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Robertson", "given": "Bruce C", "initials": "BC", "orcid": "0000-0002-5348-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/765ee347a5f04b29b28a17f14f707231.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal-article", "published": "2021-10-00", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "1", "issue": "1", "pages": "100002", "issn-l": null}, "abstract": null, "doi": "10.1016/j.xgen.2021.100002", "pmid": "36777713", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-04-28T06:50:35.104Z", "modified": "2023-06-19T12:48:03.795Z"}, {"entity": "publication", "iuid": "735c9b9d0c6245a788a78a937efb44eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb"}}, "title": "Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Steiner", "given": "Cynthia C", "initials": "CC", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Brace", "given": "Selina", "initials": "S", "orcid": "0000-0003-2126-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/476fbd04aaaf453f943f5eea976c3cff.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "historical article", "published": "2021-04-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2393", "issn-l": "2041-1723"}, "abstract": "Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.", "doi": "10.1038/s41467-021-22386-8", "pmid": "33896938", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-22386-8"}, {"db": "pmc", "key": "PMC8071806"}], "notes": [], "created": "2021-04-30T07:55:37.656Z", "modified": "2024-01-16T13:48:39.991Z"}, {"entity": "publication", "iuid": "a28f46bafc084df78efa91e2f3f049c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a28f46bafc084df78efa91e2f3f049c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a28f46bafc084df78efa91e2f3f049c7"}}, "title": "Million-year-old DNA sheds light on the genomic history of mammoths.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J"}, {"family": "Hartmann", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3476-0169", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ae4f0b70c4c33a7070830804670f8.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Thomas", "given": "Jessica A", "initials": "JA"}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b98a6e55a69644cda1e305da05c6838d.json"}}, {"family": "Fidan", "given": "Fatma Rabia", "initials": "FR", "orcid": "0000-0001-5877-7945", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d1cb5fb5754f25b1adbad44e9f4adf.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "591", "issue": "7849", "pages": "265-269"}, "abstract": "Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.", "doi": "10.1038/s41586-021-03224-9", "pmid": "33597750", "labels": {"NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03224-9"}, {"db": "pmc", "key": "PMC7116897"}, {"db": "mid", "key": "EMS114570"}], "notes": [], "created": "2021-02-22T13:16:35.556Z", "modified": "2024-01-16T13:48:40.588Z"}, {"entity": "publication", "iuid": "3e21cc6163c14d55a5a03727b870e2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1"}}, "title": "Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.", "authors": [{"family": "Feuerborn", "given": "Tatiana R", "initials": "TR"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2020-11-30", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "844", "issn-l": "1471-2164"}, "abstract": "After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.\n\nHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.\n\nWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.", "doi": "10.1186/s12864-020-07229-y", "pmid": "33256612", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07229-y"}, {"db": "pmc", "key": "PMC7708127"}], "notes": [], "created": "2020-12-07T16:36:42.754Z", "modified": "2024-01-16T13:48:41.282Z"}]}