{"entity": "researcher", "timestamp": "2026-06-09T03:01:58.640Z", "family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "affiliations": ["Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.", "Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 18C, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17"}}, "publications": [{"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": "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": "345d335f75d34a9c989df5d83cc38c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93"}}, "title": "Historical RNA expression profiles from the extinct Tasmanian tiger.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6717-5011", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9e4e4366bb94239b2635da3f2a510de.json"}}, {"family": "Eriksson", "given": "Eli", "initials": "E", "orcid": "0000-0002-0340-3062", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb10331c72f24f2291455003f81a7a98.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V", "orcid": "0000-0002-6810-1591", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8bb2f06511f4c3695c1e84dac62e6bb.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2975-9400", "researcher": {"href": "https://publications.scilifelab.se/researcher/db755021d4474a7c836bdb418b5d12ca.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "33", "issue": "8", "pages": "1299-1316"}, "abstract": "Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a \u223c130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.", "doi": "10.1101/gr.277663.123", "pmid": "37463752", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10552650"}, {"db": "pii", "key": "gr.277663.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-09-20T16:48:10.289Z", "modified": "2024-01-16T13:48:32.754Z"}, {"entity": "publication", "iuid": "ffa17d5833774c64ae24d57daf592ed5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffa17d5833774c64ae24d57daf592ed5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffa17d5833774c64ae24d57daf592ed5"}}, "title": "Origins and genetic legacy of prehistoric dogs.", "authors": [{"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0002-4096-9268", "researcher": {"href": "https://publications.scilifelab.se/researcher/77429e0da9574e9ab3d1a14ae5dbb803.json"}}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Schmidt", "given": "Ryan", "initials": "R"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Lebrasseur", "given": "Ophelie", "initials": "O", "orcid": "0000-0003-0687-8538", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f100bd635446739f54bcabbf1840bc.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}, {"family": "Lin", "given": "Audrey T", "initials": "AT", "orcid": "0000-0003-2505-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1f6e691ce04fd396757c4918535cc2.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG", "orcid": "0000-0003-1791-3175", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe55ca79f7a438dbbda3e97e3780223.json"}}, {"family": "Anthony", "given": "David", "initials": "D", "orcid": "0000-0001-9122-0313", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe0401df8e44a82a3c69a7a0478007d.json"}}, {"family": "Antipina", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-3003-942X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c0ad9634824dabbef732e81a68ec60.json"}}, {"family": "Amiri", "given": "Sarieh", "initials": "S", "orcid": "0000-0002-6835-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae40113ed34f4ed1a173637c864e1c38.json"}}, {"family": "Bar-Oz", "given": "Guy", "initials": "G"}, {"family": "Bazaliiskii", "given": "Vladimir I", "initials": "VI"}, {"family": "Bulatovi\u0107", "given": "Jelena", "initials": "J", "orcid": "0000-0002-0672-067X", "researcher": {"href": "https://publications.scilifelab.se/researcher/977f7acdf2e94256bc664d52f8b99922.json"}}, {"family": "Brown", "given": "Dorcas", "initials": "D"}, {"family": "Carmagnini", "given": "Alberto", "initials": "A"}, {"family": "Davy", "given": "Tom", "initials": "T", "orcid": "0000-0002-9466-5497", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9e9bebf8ad41d2a53d4c475f719b88.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Fiore", "given": "Ivana", "initials": "I", "orcid": "0000-0001-5721-0760", "researcher": {"href": "https://publications.scilifelab.se/researcher/48a313be55974f488d3804f980eb0dd0.json"}}, {"family": "Fulton", "given": "Deirdre", "initials": "D"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Haile", "given": "James", "initials": "J", "orcid": "0000-0002-8521-8337", "researcher": {"href": 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"Orton", "given": "David", "initials": "D", "orcid": "0000-0003-4069-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b0e6ccfd34e49a1878181fa931114de.json"}}, {"family": "Pasari\u0107", "given": "Maja", "initials": "M"}, {"family": "Radivojevi\u0107", "given": "Miljana", "initials": "M", "orcid": "0000-0001-7329-305X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19d71e76741c4d7eacc555b9328291c7.json"}}, {"family": "Rajkovi\u0107", "given": "Dragana", "initials": "D"}, {"family": "Roberts", "given": "Benjamin", "initials": "B"}, {"family": "Ryan", "given": "Hannah", "initials": "H", "orcid": "0000-0002-4320-4594", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a07befb801c478692e3508b663d1a97.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": 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"Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Pinhasi", "given": "Ron", "initials": "R", "orcid": "0000-0003-1629-8131", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8eedf480ae494d9e6249ec58dd1867.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}], "type": "journal article", "published": "2020-10-30", "journal": {"title": "Science", "issn": "1095-9203", "volume": "370", "issue": "6516", "pages": "557-564", "issn-l": "0036-8075"}, "abstract": "Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.", "doi": "10.1126/science.aba9572", "pmid": "33122379", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "370/6516/557"}, {"db": "pmc", "key": "PMC7116352"}, {"db": "mid", "key": "EMS103415"}], "notes": [], "created": "2021-01-08T16:29:50.956Z", "modified": "2021-11-10T12:45:57.753Z"}]}