{"entity": "researcher", "timestamp": "2026-04-16T18:01:48.155Z", "family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "affiliations": ["Department of Ecology and Genetics Uppsala University Uppsala Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b"}}, "publications": [{"entity": "publication", "iuid": "1b64b2e873f440098c5413b843a1c9cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf"}}, "title": "From high masked to high realized genetic load in inbred Scandinavian wolves.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "7", "pages": "1567-1580"}, "abstract": "When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.", "doi": "10.1111/mec.16802", "pmid": "36458895", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.7m0cfxpzj"}], "notes": [], "created": "2023-11-29T09:02:42.251Z", "modified": "2024-01-16T13:48:33.734Z"}, {"entity": "publication", "iuid": "84cea954e35f463d9145c008e1921ca1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84cea954e35f463d9145c008e1921ca1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84cea954e35f463d9145c008e1921ca1"}}, "title": "Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).", "authors": [{"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K", "orcid": "0000-0002-8457-310X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc84301b6f3943058c16d3f644713078.json"}}, {"family": "Dutoit", "given": "Ludovic", "initials": "L", "orcid": "0000-0002-0164-9878", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e987a37c504d9eb3069525bbca54ad.json"}}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Kardos", "given": "Martin", "initials": "M"}, {"family": "Gustafsson", "given": "Lars", "initials": "L", "orcid": "0000-0001-6566-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04fef54f3f5431f86062e52aaf00748.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "16", "pages": "3965-3973", "issn-l": "0962-1083"}, "abstract": "Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne ) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often unknown. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary Ne of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate Ne at a few thousand (4000-7000). The approach based on LD provided higher estimates of Ne (20,000-32,000) and was associated with high variance, often resulting in infinite Ne . We conclude that whole-genome sequencing data offers new possibilities to estimate high (>1000) contemporary Ne , but also note that such estimates remain challenging, in particular for LD-based methods for contemporary Ne estimation.", "doi": "10.1111/mec.16025", "pmid": "34145933", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCA_000247815.2"}], "notes": [], "created": "2021-12-07T21:36:36.159Z", "modified": "2024-01-16T13:48:38.980Z"}, {"entity": "publication", "iuid": "623279ebcab34ac7abee4d1296a1fd72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/623279ebcab34ac7abee4d1296a1fd72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/623279ebcab34ac7abee4d1296a1fd72"}}, "title": "Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Aspi", "given": "Jouni", "initials": "J"}, {"family": "Berglund", "given": "Jonas", "initials": "J"}, {"family": "Kojola", "given": "Ilpo", "initials": "I"}, {"family": "Tirronen", "given": "Konstantin", "initials": "K"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "3", "pages": "721-734", "issn-l": "1752-4571"}, "abstract": "Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridization between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and admixture showed that wolves and dogs were well-separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.", "doi": "10.1111/eva.13151", "pmid": "33767747", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13151"}, {"db": "pmc", "key": "PMC7980305"}, {"db": "Dryad", "key": "10.5061/dryad.8gtht76n6"}], "notes": [], "created": "2021-06-01T20:53:12.887Z", "modified": "2024-01-16T13:48:40.561Z"}]}