{"entity": "researcher", "timestamp": "2026-07-19T06:05:27.805Z", "family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "affiliations": ["Centre for Palaeogenetics, Stockholm, Sweden. johanna.n.vonseth@gmail.com.", "Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden. johanna.n.vonseth@gmail.com.", "Department of Zoology, Stockholm University, Stockholm, Sweden. johanna.n.vonseth@gmail.com."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341"}}, "publications": [{"entity": "publication", "iuid": "d92378d3b8974814af478f714c0337fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d92378d3b8974814af478f714c0337fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d92378d3b8974814af478f714c0337fb"}}, "title": "Temporal genomic change in the Scandinavian Arctic fox (Vulpes lagopus)", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Hasselgren", "given": "Malin", "initials": "M"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Farelo", "given": "Liliana", "initials": "L"}, {"family": "Wall\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Landa", "given": "Arild", "initials": "A"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Melo-Ferreira", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0003-4473-1908", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2343a14dc6f4ca4910c45d551a6908b.json"}}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal-article", "published": "2025-08-01", "journal": {"issn": "0024-4082", "volume": "204", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1093/zoolinnean/zlaf078", "pmid": null, "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-10-30T13:23:09.560Z", "modified": "2025-11-14T11:08:09.295Z"}, {"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": 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{"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": "4e382676e4e14ad396c85b058fdd2640", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e382676e4e14ad396c85b058fdd2640.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e382676e4e14ad396c85b058fdd2640"}}, "title": "Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.", "authors": [{"family": "Liu", "given": "Shanlin", "initials": "S", "orcid": "0000-0001-8118-8313", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8eebb29461c4496a1b4e1b033f1afec.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Mitchell", "given": "Kieren J", "initials": "KJ", "orcid": "0000-0002-3921-0262", "researcher": {"href": "https://publications.scilifelab.se/researcher/10db4b20d5a7487899186d6c65fa5f0c.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Duch\u00eane", "given": "David A", "initials": "DA"}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Heiniger", "given": "Holly", "initials": "H"}, {"family": "S\u00e1nchez-Barreiro", "given": "F\u00e1tima", "initials": "F"}, {"family": "Margaryan", "given": "Ashot", "initials": "A"}, {"family": "Andr\u00e9-Olsen", "given": "Remi", "initials": "R"}, {"family": "De Cahsan", "given": "Binia", "initials": "B", "orcid": "0000-0002-6978-6633", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a80844d21584199ab3acdd49cef8b37.json"}}, {"family": "Meng", "given": "Guanliang", "initials": "G", "orcid": "0000-0002-6488-1527", "researcher": {"href": "https://publications.scilifelab.se/researcher/7191d467d9b3497f80212ff402c8f9cd.json"}}, {"family": "Yang", "given": "Chentao", "initials": "C", "orcid": "0000-0003-3447-2316", "researcher": {"href": "https://publications.scilifelab.se/researcher/62ca43a2664c43c3a3e5e6377399ca50.json"}}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Moodley", "given": "Yoshan", "initials": "Y", "orcid": "0000-0003-4216-2924", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de66994605d4a809f28b04c8dcf91c6.json"}}, {"family": "Rookmaaker", "given": "Kees", "initials": "K", "orcid": "0000-0003-3121-5197", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc8b2d6563f84ad9bf8118836b5e470b.json"}}, {"family": "Bruford", "given": "Michael W", "initials": "MW"}, {"family": "Ryder", "given": "Oliver", "initials": "O"}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Bruins-van Sonsbeek", "given": "Linda G R", "initials": "LGR"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Cooper", "given": "Alan", "initials": "A"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Dunn", "given": "Robert R", "initials": "RR"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Antoine", "given": "Pierre-Olivier", "initials": "PO"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2021-09-16", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "184", "issue": "19", "pages": "4874-4885.e16", "issn-l": "0092-8674"}, "abstract": "Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (\u223c16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.", "doi": "10.1016/j.cell.2021.07.032", "pmid": "34433011", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(21)00891-6"}], "notes": [], "created": "2021-10-01T09:03:51.039Z", "modified": "2024-01-16T13:48:38.478Z"}, {"entity": "publication", "iuid": "9efe05ebc70c4c4693210baba690ef94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9efe05ebc70c4c4693210baba690ef94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9efe05ebc70c4c4693210baba690ef94"}}, "title": "Genomic and fitness consequences of inbreeding in an endangered carnivore.", "authors": [{"family": "Hasselgren", "given": "Malin", "initials": "M", "orcid": "0000-0002-4875-4413", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e7f1368a98040f4a683c3d082483079.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9707-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/40450a7e8cda45ba8292b9a677b3fb29.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "12", "pages": "2790-2799", "issn-l": "0962-1083"}, "abstract": "Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.", "doi": "10.1111/mec.15943", "pmid": "33955096", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.gmsbcc2mn"}], "notes": [], "created": "2021-06-09T12:16:53.553Z", "modified": "2024-01-16T13:48:39.611Z"}, {"entity": "publication", "iuid": "503a270c509f483ba14d05ddc08c1626", "links": {"self": {"href": "https://publications.scilifelab.se/publication/503a270c509f483ba14d05ddc08c1626.json"}, "display": {"href": "https://publications.scilifelab.se/publication/503a270c509f483ba14d05ddc08c1626"}}, "title": "African and Asian leopards are highly differentiated at the genomic level.", "authors": [{"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Becker", "given": "Matthew S", "initials": "MS"}, {"family": "Cahill", "given": "James A", "initials": "JA"}, {"family": "Fickel", "given": "Joerns", "initials": "J", "orcid": "0000-0002-0593-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/40018134351a481ab2d00b4113404c47.json"}}, {"family": "F\u00f6rster", "given": "Daniel W G", "initials": "DWG", "orcid": "0000-0002-6934-0404", "researcher": {"href": "https://publications.scilifelab.se/researcher/71cd2161c82547d7a0bb7d4049a41473.json"}}, {"family": "Gries", "given": "Katrin", "initials": "K", "orcid": "0000-0001-9441-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95bd682636c4becb3e977da6b5f221e.json"}}, {"family": "Hartmann", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3476-0169", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ae4f0b70c4c33a7070830804670f8.json"}}, {"family": "Havm\u00f8ller", "given": "Rasmus Wors\u00f8e", "initials": "RW"}, {"family": "Henneberger", "given": "Kirstin", "initials": "K"}, {"family": "Kern", "given": "Christian", "initials": "C", "orcid": "0000-0003-0298-064X", "researcher": {"href": "https://publications.scilifelab.se/researcher/268334dc599142d0929293626d4d35c3.json"}}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Mayer", "given": "Frieder", "initials": "F"}, {"family": "OBrien", "given": "Stephen J", "initials": "SJ", "orcid": "0000-0001-7857-0757", "researcher": {"href": "https://publications.scilifelab.se/researcher/261799ba7d5b4989b5f0f7b0388e3f32.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Sinding", "given": "Mikkel-Holder S", "initials": "MS"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Uphyrkina", "given": "Olga", "initials": "O", "orcid": "0000-0002-4436-1647", "researcher": {"href": "https://publications.scilifelab.se/researcher/649667810d2849a4957d5d9f475eb225.json"}}, {"family": "Wachter", "given": "Bettina", "initials": "B", "orcid": "0000-0002-0414-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a28e4139fcf84006a6b132d49edddbce.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bhak", "given": "Jong", "initials": "J"}, {"family": "Manica", "given": "Andrea", "initials": "A", "orcid": "0000-0003-1895-450X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9332f04a6854ba18fad50c5fca8891c.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2021-05-10", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "9", "pages": "1872-1882.e5", "issn-l": "0960-9822"}, "abstract": "Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.", "doi": "10.1016/j.cub.2021.03.084", "pmid": "33848458", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00457-7"}], "notes": [], "created": "2021-06-09T12:14:28.866Z", "modified": "2021-11-10T12:24:57.977Z"}, {"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": "364977e412bd4a06b3b41e15769ebbf7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/364977e412bd4a06b3b41e15769ebbf7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/364977e412bd4a06b3b41e15769ebbf7"}}, "title": "Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Knapp", "given": "Michael", "initials": "M", "orcid": "0000-0002-0937-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b51a33edaea4bcf965b51daf13749c2.json"}}, {"family": "Kardailsky", "given": "Olga", "initials": "O"}, {"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": "2019-09-27", "journal": {"volume": "15", "issn": "1744-957X", "issue": "9", "pages": "20190491", "title": "Biol. Lett.", "issn-l": "1744-9561"}, "abstract": "Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia (Heteralocha acutirostris) and South Island k\u014dkako (Callaeas cinereus). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island k\u014dkako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Ma\u014dri may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island k\u014dkako.", "doi": "10.1098/rsbl.2019.0491", "pmid": "31480938", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6769136"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4638131"}], "notes": [], "created": "2019-12-02T16:53:10.262Z", "modified": "2024-01-16T13:48:43.814Z"}, {"entity": "publication", "iuid": "58825a68ec3c48ff88d9c006248ff996", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58825a68ec3c48ff88d9c006248ff996.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58825a68ec3c48ff88d9c006248ff996"}}, "title": "Full Mitogenomes in the Critically Endangered K\u0101k\u0101p\u014d Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.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": "2018-04-19", "journal": {"volume": "9", "issn": "2073-4425", "issue": "4", "title": "Genes", "pages": "220", "issn-l": "2073-4425"}, "abstract": "Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered k\u0101k\u0101p\u014d (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of k\u0101k\u0101p\u014d contributed to a rapid loss of genetic diversity following severe population declines.", "doi": "10.3390/genes9040220", "pmid": "29671759", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5924562"}, {"db": "pii", "key": "genes9040220"}], "notes": [], "created": "2018-10-31T19:46:53.308Z", "modified": "2023-06-19T12:48:48.519Z"}]}