{"entity": "researcher", "timestamp": "2026-07-17T07:57:53.276Z", "family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "affiliations": ["Centre for Palaeogenetics, Stockholm, Sweden.", "Department of Zoology, Stockholm University, Stockholm, Sweden.", "Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e"}}, "publications": [{"entity": "publication", "iuid": "c115bbb0dfbc4b998a5920a0fb8492e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c115bbb0dfbc4b998a5920a0fb8492e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c115bbb0dfbc4b998a5920a0fb8492e8"}}, "title": "Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia.", "authors": [{"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/891a915ffd054c57b7c0d107c4e1b7e1.json"}}, {"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Regn\u00e9ll", "given": "Carl", "initials": "C", "orcid": "0000-0002-5662-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/65820ac7ae1c4b6a87dd1334087e677d.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Gyllencreutz", "given": "Richard", "initials": "R", "orcid": "0000-0003-3193-8598", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c1d90a4e134dceb7f816725596aa6f.json"}}, {"family": "Greenwood", "given": "Sarah L", "initials": "SL", "orcid": "0000-0003-3048-7916", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4036ea604943ca9e8d0e2d7ae48d23.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2026-04-21", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "123", "issue": "16", "pages": "e2527944123", "issn-l": "0027-8424"}, "abstract": "After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two directions-from the south and the northeast-resulting in a nonoverlapping distribution of two distinct mitochondrial clades. A contact zone in central Sweden separates populations with mitochondrial clade 1a in the south from those with clade 3a in the north. However, a paucity of brown bear subfossils in Scandinavia has limited testing of this prevailing model using ancient DNA. Here, we present a high-coverage brown bear mitogenome (231\u00d7) and nuclear genome-wide data (0.05\u00d7) extracted from lake sediment dated to 9.6 cal. ka BP from northern Sweden, representing the oldest known record of brown bear in the region. At this point in the Early Holocene, the Fennoscandian Ice Sheet was in its final stages of recession. Surprisingly, our analyses suggest that this environmental genome represents one male individual carrying clade 1a and with southern brown bear nuclear ancestry, despite being found far north of the contact zone. This suggests the individual was a migratory bear and had dispersed northward from its birthplace. Our finding adds to the scarce genomic record of Early Holocene brown bears and highlights the use of sedimentary ancient DNA as a powerful source of genomic information.", "doi": "10.1073/pnas.2527944123", "pmid": "41973920", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13099568"}], "notes": [], "created": "2026-05-11T11:39:29.980Z", "modified": "2026-05-11T11:39:30.533Z"}, {"entity": "publication", "iuid": "af8e8e9ebf9c485889bde183fd55210f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af8e8e9ebf9c485889bde183fd55210f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af8e8e9ebf9c485889bde183fd55210f"}}, "title": "Temporal genomics reveals widespread but unexpected consequences of a bottleneck in the Scandinavian brown bear", "authors": [{"family": "Lindahl", "given": "Amanda", "initials": "A"}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Ravasini", "given": "Francesco", "initials": "F"}, {"family": "Meleg", "given": "Ioana N", "initials": "IN", "orcid": "0000-0002-0836-4971", "researcher": {"href": "https://publications.scilifelab.se/researcher/01e901f9e2924bee8e3de6bfbcd8fe62.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}], "type": "journal-article", "published": "2026-03-25", "journal": {"title": "R. Soc. open sci.", "issn": "2054-5703", "issn-l": "2054-5703", "volume": "13", "issue": "3", "pages": null}, "abstract": null, "doi": "10.1098/rsos.251947", "pmid": null, "labels": {"Ancient DNA": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-26T13:53:56.827Z", "modified": "2026-04-16T09:43:31.467Z"}, {"entity": "publication", "iuid": "053ef45f515a4c6d94ba0ee3a1b5a74a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a"}}, "title": "Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.", "authors": [{"family": "Gu\u00f0j\u00f3nsd\u00f3ttir", "given": "S\u00f3lveig M", "initials": "SM", "orcid": "0009-0002-6435-4409", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d580e28f1f4e9ea90b46b330b6dcff.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Leme\u017e", "given": "\u0160pela", "initials": "\u0160", "orcid": "0000-0002-0387-1421", "researcher": {"href": "https://publications.scilifelab.se/researcher/381dee4d331a43369d747adc51275fea.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "18", "issue": "1", "issn-l": "1759-6653"}, "abstract": "Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced a high-coverage genome from muscle tissue of a 14,400-year-old woolly rhinoceros (Coelodonta antiquitatis)-a cold-adapted herbivore that went extinct \u223c14,000-years ago-found inside a permafrost-preserved wolf's stomach. We compared genome-wide diversity, inbreeding, genetic load, and population size changes in this sample with two other Late Pleistocene Siberian woolly rhinoceros. We found no evidence of population size decline, nor any genomic erosion, shortly prior to the species' demise. Given the few long homozygous segments, typically indicative of recent inbreeding, we infer a stable population size only a few centuries before extinction. Thus, the woolly rhinoceros' extinction likely happened rapidly, during the B\u00f8lling-Aller\u00f8d interstadial. This study demonstrates the ability to recover high-quality DNA from unlikely sources to elucidate species' extinction dynamics.", "doi": "10.1093/gbe/evaf239", "pmid": "41530912", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12799484"}, {"db": "pii", "key": "8414728"}], "notes": [], "created": "2026-01-22T13:27:26.594Z", "modified": "2026-01-22T13:27:27.263Z"}, {"entity": "publication", "iuid": "ea181adcfb564b289434e673fccd07a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3"}}, "title": "Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years.", "authors": [{"family": "Gilardet", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4851-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f507b07ed934c73988dfd0537254485.json"}}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-7973-6173", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b1165126184cb980f8bc7e9b9c0fdd.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Southon", "given": "John", "initials": "J"}, {"family": "Vasiliev", "given": "Sergey K", "initials": "SK"}, {"family": "Shunkov", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-1388-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/c43a1135a5804441b6ab9680f7cbd2b3.json"}}, {"family": "Kozlikin", "given": "Maxim B", "initials": "MB", "orcid": "0000-0001-5082-3345", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2a8523fc1c42178159bbd3e8b64ecc.json"}}, {"family": "Douka", "given": "Katerina", "initials": "K", "orcid": "0000-0002-0558-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a6efe4f6db44f6b85ed2653d2a3342f.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.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": "2025-10-29", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby paleontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or paleoproteomics. In this study, we screened these bovine bones for ancient DNA and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harbored diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.", "doi": "10.1093/gbe/evaf206", "pmid": "41206445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12628791"}, {"db": "pii", "key": "8315343"}], "notes": [], "created": "2025-11-21T17:51:54.435Z", "modified": "2025-11-21T17:51:56.168Z"}, {"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"}]}