{"entity": "researcher", "timestamp": "2026-07-15T07:57:10.373Z", "family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "affiliations": ["Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. leif.andersson@imbim.uu.se.", "Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. leif.andersson@imbim.uu.se.", "Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA. leif.andersson@imbim.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d"}}, "publications": [{"entity": "publication", "iuid": "483493d2904b4314872a2fb14d09bb93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/483493d2904b4314872a2fb14d09bb93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/483493d2904b4314872a2fb14d09bb93"}}, "title": "The population structure in the Baltic herring reflects natural selection and local adaptation.", "authors": [{"family": "Goodall", "given": "Jake", "initials": "J"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Andersson", "given": "Anastasia", "initials": "A"}, {"family": "Dahlin", "given": "Iris", "initials": "I"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "St\u00e5hl", "given": "Gunnar", "initials": "G"}, {"family": "Wennerstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L"}], "type": "journal article", "published": "2026-03-17", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "123", "issue": "11", "pages": "e2526500123", "issn-l": "0027-8424"}, "abstract": "How species time reproduction and adapt to environmental conditions are key topics in ecology and evolutionary biology. Here, we conducted a high-resolution population genetic analysis of Baltic herring, a subspecies of Atlantic herring (Clupea harengus). Genotypes at >4,500 SNPs were generated from >4,500 spawning individuals, sampled from 150 locations spanning Swedish's eastern coast. Abiotic factors-week of spawning, latitude, temperature, salinity-were used to assess how genetic variation is shaped by temporal, spatial, and environmental gradients. Our results reaffirm strong genetic differentiation between spring- and autumn-spawning ecotypes, despite hybridization suggesting ongoing gene flow between the two ecotypes. We document significant substructuring within the spring-spawning ecotype, delineating three main, previously unidentified, genetic clusters underpinned by adaptative genetic variation associated with latitude, salinity, temperature, and spawning time. Complementary linkage disequilibrium (LD) partitioning showed that adaptive loci-especially those in inversion regions-exhibit strong elevated among-population LD, consistent with divergence maintained by local selection despite ongoing gene flow. Clinal variation in allele frequencies indicated regionally distinct selection pressures, including shifts in allele frequencies at two major supergenes (inversions) and at a suite of genes correlated with abiotic factors. Importantly, rare genetic outlier populations are identified within each geographic region which further illustrates the unexpected fine-grained population structure of Baltic herring and implies a strong homing behavior in this abundant marine fish. Overall, this study demonstrates the capacity for targeted population genetic studies to detect adaptive variation in natural populations, the outcomes of which have direct implications for sustainable fisheries and biodiversity management.", "doi": "10.1073/pnas.2526500123", "pmid": "41802067", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12993978"}], "notes": [], "created": "2026-03-23T14:00:34.838Z", "modified": "2026-03-23T14:00:34.939Z"}, {"entity": "publication", "iuid": "25dfec9e03fc41aeb351f41e6acf76d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8"}}, "title": "Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr.", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Fedi", "given": "Mariano Olivera", "initials": "MO"}, {"family": "Baker", "given": "Kendall", "initials": "K"}, {"family": "Barker", "given": "Tom", "initials": "T"}, {"family": "Catchpole", "given": "Leah", "initials": "L"}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Collins", "given": "Joanna", "initials": "J"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA"}, {"family": "Durrant", "given": "Alex", "initials": "A"}, {"family": "Hindar", "given": "Kjetil", "initials": "K", "orcid": "0000-0002-2769-2284", "researcher": {"href": "https://publications.scilifelab.se/researcher/0093cfa9f60e4e7db25d898de5c194b9.json"}}, {"family": "Iannucci", "given": "Alessio", "initials": "A", "orcid": "0000-0001-7729-4412", "researcher": {"href": "https://publications.scilifelab.se/researcher/da461c1ddb4649928a998aa9802a5ea3.json"}}, {"family": "Irish", "given": "Naomi", "initials": "N"}, {"family": "Knitlhoffer", "given": "Vanda", "initials": "V"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Lucchini", "given": "Sacha", "initials": "S"}, {"family": "McTaggart", "given": "Seanna", "initials": "S"}, {"family": "P\u00e1lsson", "given": "Arnar", "initials": "A", "orcid": "0000-0002-6525-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbe0e0cea2254ede8a1149cc2b917b6a.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Snorrason", "given": "Sigur\u00f0ur S", "initials": "SS"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Swarbreck", "given": "David", "initials": "D"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Watkins", "given": "Christopher", "initials": "C"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD", "orcid": "0000-0002-7545-2162", "researcher": {"href": "https://publications.scilifelab.se/researcher/c255ed6ec2f246028326f9fece911f74.json"}}, {"family": "Xiao", "given": "Han", "initials": "H", "orcid": "0009-0000-4699-5590", "researcher": {"href": "https://publications.scilifelab.se/researcher/12a89016ae0d41788407e0b5a342d933.json"}}, {"family": "Gharbi", "given": "Karim", "initials": "K"}, {"family": "J\u00f3nsson", "given": "Zophon\u00edas O", "initials": "ZO", "orcid": "0000-0001-5798-9647", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dabaeca1ef54eb289cc48aab86ae2aa.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e70085", "volume": "34", "issue": "19", "issn-l": "0962-1083"}, "abstract": "Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.", "doi": "10.1111/mec.70085", "pmid": "40856096", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12456120"}], "notes": [], "created": "2025-09-08T06:59:34.138Z", "modified": "2025-11-28T10:51:42.317Z"}, {"entity": "publication", "iuid": "ebe4355205e54bc3b50d10a1a62fb6e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8"}}, "title": "Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.", "authors": [{"family": "Deng", "given": "Qiaoling", "initials": "Q", "orcid": "0000-0002-3776-1132", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdfda2d3f64742e8a09bbded5f322f96.json"}}, {"family": "Goodall", "given": "Jake", "initials": "J", "orcid": "0000-0003-0960-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/457d1a2733cc4a569ffeb70750999199.json"}}, {"family": "Bergenius Nord", "given": "Mikaela", "initials": "M"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Delling", "given": "Bo", "initials": "B", "orcid": "0000-0001-9148-9574", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c1c3f7ddf0945d18660ecbaa85303b0.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Palm", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9890-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebffe35bae646eb8a15163b0cb0820f.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": null, "issue": null, "pages": "e70094"}, "abstract": "How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (Coregonus albula) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring- and autumn-spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high-quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC-directed scaffolding. We generated low-coverage whole-genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring- and autumn-spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome-wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.", "doi": "10.1111/mec.70094", "pmid": "40903929", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": null, "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-09-08T14:16:37.667Z", "modified": "2025-11-21T12:48:41.202Z"}, {"entity": "publication", "iuid": "fa7febd25a2943dfb4e4ac6af99ee6cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa7febd25a2943dfb4e4ac6af99ee6cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa7febd25a2943dfb4e4ac6af99ee6cb"}}, "title": "Evolution of fast-growing piscivorous herring in the young Baltic Sea.", "authors": [{"family": "Goodall", "given": "Jake", "initials": "J", "orcid": "0000-0003-0960-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/457d1a2733cc4a569ffeb70750999199.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Bergstr\u00f6m", "given": "Ulf", "initials": "U", "orcid": "0000-0002-5478-0634", "researcher": {"href": "https://publications.scilifelab.se/researcher/d83f775f03154adfabf0a48a00cb1896.json"}}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Delling", "given": "Bo", "initials": "B", "orcid": "0000-0001-9148-9574", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c1c3f7ddf0945d18660ecbaa85303b0.json"}}, {"family": "Heimbrand", "given": "Yvette", "initials": "Y", "orcid": "0000-0002-5120-4797", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d473cd11754b15a743173ff7a23502.json"}}, {"family": "Karlsson", "given": "O Magnus", "initials": "OM", "orcid": "0000-0002-2032-6126", "researcher": {"href": "https://publications.scilifelab.se/researcher/b23affc0739a418c972c3723868c0a41.json"}}, {"family": "Larsson", "given": "Josefine", "initials": "J"}, {"family": "Waldetoft", "given": "Hannes", "initials": "H", "orcid": "0009-0006-7326-6231", "researcher": {"href": "https://publications.scilifelab.se/researcher/319b5b610a84404ba3d3d9cd51c027a3.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Wennerstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-12-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10707", "issn-l": "2041-1723"}, "abstract": "The circumstances under which species diversify to genetically distinct lineages is a fundamental question in biology. Atlantic herring (Clupea harengus) is an extremely abundant zooplanktivorous species that is subdivided into multiple ecotypes that differ regarding spawning time and genetic adaption to local environmental conditions such as temperature, salinity, and light conditions. Here we show using whole genome analysis that multiple populations of piscivorous (fish-eating) herring have evolved sympatrically after the colonization of the brackish Baltic Sea within the last 8000 years postglaciation. The piscivorous ecotype grows faster, and is much larger and less abundant than the zooplanktivorous Baltic herring. Lesions of the gill rakers in the piscivorous ecotype indicated incomplete adaptation to a fish diet. This niche expansion of herring in the young Baltic Sea, with its paucity of piscivorous species, suggests that empty niche space is more important than geographic isolation for the evolution of biodiversity.", "doi": "10.1038/s41467-024-55216-8", "pmid": "39715744", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11666761"}, {"db": "pii", "key": "10.1038/s41467-024-55216-8"}], "notes": [], "created": "2025-02-28T14:14:46.130Z", "modified": "2025-02-28T14:14:46.502Z"}, {"entity": "publication", "iuid": "a3c5e0204138422aa03a305231f99f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89"}}, "title": "An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Hodge", "given": "McKaela", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Beckman", "given": "Madeleine", "initials": "M"}, {"family": "Bellone", "given": "Rebecca R", "initials": "RR", "orcid": "0000-0001-8838-7227", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c3235fb9bc24da59f4b2685ab0924a4.json"}}, {"family": "Kallenberg", "given": "Angelica", "initials": "A", "orcid": "0000-0001-7993-6597", "researcher": {"href": "https://publications.scilifelab.se/researcher/b86eca5b3e87464ca2e00fc0f1ad44e0.json"}}, {"family": "J'Usrey", "given": "Stephanie", "initials": "S"}, {"family": "Ohmura", "given": "Hajime", "initials": "H"}, {"family": "Seki", "given": "Kazuhiro", "initials": "K"}, {"family": "Furukawa", "given": "Risako", "initials": "R", "orcid": "0009-0002-4673-0845", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5000c3c34a44dcebe85e6c8418b065e.json"}}, {"family": "Ohnuma", "given": "Aoi", "initials": "A"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Tozaki", "given": "Teruaki", "initials": "T", "orcid": "0000-0001-8797-6644", "researcher": {"href": "https://publications.scilifelab.se/researcher/8246b65d8481438885db4d4be0691aaa.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-08-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7510", "issn-l": "2041-1723"}, "abstract": "The Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two different Grey alleles, G2 carrying two tandem copies of the duplicated sequence and G3 carrying three. The latter is by far the most common allele, probably due to strong selection for the striking white phenotype. Our results reveal a remarkable dosage effect where the G3 allele is associated with fast greying and high incidence of melanoma whereas G2 is associated with slow greying and low incidence of melanoma. The copy number expansion transforms a weak enhancer to a strong melanocyte-specific enhancer that underlies hair greying (G2 and G3) and a drastically elevated risk of melanoma (G3 only). Our direct pedigree-based observation of the origin of a G2 allele from a G3 allele by copy number contraction demonstrates the dynamic evolution of this locus and provides the ultimate evidence for causality of the copy number variation of the 4.6 kb intronic sequence.", "doi": "10.1038/s41467-024-51898-2", "pmid": "39209879", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11362437"}, {"db": "pii", "key": "10.1038/s41467-024-51898-2"}], "notes": [], "created": "2024-10-21T11:17:13.688Z", "modified": "2024-11-25T10:17:52.816Z"}, {"entity": "publication", "iuid": "7cdd71fc9b3a4e96bbece5625ab29d9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7cdd71fc9b3a4e96bbece5625ab29d9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7cdd71fc9b3a4e96bbece5625ab29d9e"}}, "title": "Selection against domestication alleles in introduced rabbit populations.", "authors": [{"family": "Andrade", "given": "Pedro", "initials": "P", "orcid": "0000-0003-2540-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/beb2336f18d94c57bbf9089dd6d06ccf.json"}}, {"family": "Alves", "given": "Joel M", "initials": "JM", "orcid": "0000-0001-6138-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/118178b7f76e4b5ba3ec39914aee7b57.json"}}, {"family": "Pereira", "given": "Paulo", "initials": "P", "orcid": "0000-0001-9519-7691", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8913fec8d89466480fa55e47e47e2ce.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Silva", "given": "Eug\u00e9nio", "initials": "E", "orcid": "0000-0002-9680-3494", "researcher": {"href": "https://publications.scilifelab.se/researcher/099c8fd4d8324c5f8e39f8798d680e29.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Enbody", "given": "Erik", "initials": "E", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Afonso", "given": "Sandra", "initials": "S", "orcid": "0000-0001-7212-991X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ced62caf88e446c796ad9b022517442c.json"}}, {"family": "Faria", "given": "Rui", "initials": "R"}, {"family": "Zhang", "given": "Yexin", "initials": "Y", "orcid": "0000-0001-8253-4951", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5f20139428b4ebf93a8c478dd969264.json"}}, {"family": "Bonino", "given": "Never", "initials": "N"}, {"family": "Duckworth", "given": "Janine A", "initials": "JA"}, {"family": "Garreau", "given": "Herv\u00e9", "initials": "H", "orcid": "0000-0001-6195-1457", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9687c1ad7c04774aadaeb3f22abb034.json"}}, {"family": "Letnic", "given": "Mike", "initials": "M"}, {"family": "Strive", "given": "Tanja", "initials": "T", "orcid": "0000-0003-2971-8406", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0155b46301d490d974c8045f43ba4f6.json"}}, {"family": "Thulin", "given": "Carl-Gustaf", "initials": "CG", "orcid": "0000-0001-6543-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71a9794d2f94bdea1793abe41790d69.json"}}, {"family": "Queney", "given": "Guillaume", "initials": "G"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Jiggins", "given": "Francis M", "initials": "FM", "orcid": "0000-0001-7470-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3992869d5e249968d550b75307fdc4a.json"}}, {"family": "Ferrand", "given": "Nuno", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Carneiro", "given": "Miguel", "initials": "M", "orcid": "0000-0001-9882-7775", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1d62d41fce4469b878ea399d2d0abbf.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "8", "issue": "8", "pages": "1543-1555", "issn-l": "2397-334X"}, "abstract": "Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.", "doi": "10.1038/s41559-024-02443-3", "pmid": "38907020", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-024-02443-3"}], "notes": [], "created": "2024-11-12T10:54:12.925Z", "modified": "2024-11-25T10:19:02.495Z"}, {"entity": "publication", "iuid": "0477d212635a4177b3e68b39e3fa2f20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20"}}, "title": "Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Besnier", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Deng", "given": "Qiaoling", "initials": "Q"}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Kvamme", "given": "Cecilie", "initials": "C"}, {"family": "Bekkevold", "given": "Dorte", "initials": "D", "orcid": "0000-0002-5297-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c62afa02e94554ba1c3afcfc622555.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Lille-Lang\u00f8y", "given": "Roger", "initials": "R"}, {"family": "Leonori", "given": "Iole", "initials": "I", "orcid": "0000-0001-7673-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/abf52b64cdde43838c36347af47ea670.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Glover", "given": "Kevin A", "initials": "KA"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.", "doi": "10.1093/gbe/evae133", "pmid": "38918882", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11226789"}, {"db": "pii", "key": "7699122"}], "notes": [], "created": "2024-11-04T20:50:27.197Z", "modified": "2024-11-25T10:24:21.553Z"}, {"entity": "publication", "iuid": "ad53c190fc3143dcb083f6f54caf6c8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad53c190fc3143dcb083f6f54caf6c8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad53c190fc3143dcb083f6f54caf6c8c"}}, "title": "Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow.", "authors": [{"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Stanley", "given": "Ryan", "initials": "R", "orcid": "0000-0002-6313-0844", "researcher": {"href": "https://publications.scilifelab.se/researcher/52f69805ce8046318f7212352bc52e74.json"}}, {"family": "Bourne", "given": "Christina", "initials": "C"}, {"family": "Singh", "given": "Rabindra", "initials": "R"}, {"family": "Emond", "given": "Kim", "initials": "K"}, {"family": "Pinkham", "given": "Lisa", "initials": "L"}, {"family": "McDermid", "given": "Jenni L", "initials": "JL"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Ruzzante", "given": "Daniel E", "initials": "DE", "orcid": "0000-0002-8536-8335", "researcher": {"href": "https://publications.scilifelab.se/researcher/071429cf12c240eb92336c28ecd73be8.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "17", "issue": "3", "pages": "e13675", "issn-l": "1752-4571"}, "abstract": "Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.", "doi": "10.1111/eva.13675", "pmid": "38495946", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10940790"}, {"db": "pii", "key": "EVA13675"}, {"db": "Dryad", "key": "10.5061/dryad.0rxwdbs6k"}], "notes": [], "created": "2024-11-25T10:26:48.680Z", "modified": "2025-02-28T14:20:10.584Z"}, {"entity": "publication", "iuid": "397f0c6069f74329b30503eecca169d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2"}}, "title": "Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.", "authors": [{"family": "Sendell-Price", "given": "Ashley T", "initials": "AT", "orcid": "0000-0002-1227-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2d5fb40391442c8a62c20b1ca9a3295.json"}}, {"family": "Tulenko", "given": "Frank J", "initials": "FJ"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Kang", "given": "Du", "initials": "D", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Montandon", "given": "Margo", "initials": "M", "orcid": "0000-0002-1707-0190", "researcher": {"href": "https://publications.scilifelab.se/researcher/db6f9463614b43c1aa3d41114a8f5086.json"}}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/f292bbf542f244278bef19506b21b031.json"}}, {"family": "Kulb", "given": "Kathleen", "initials": "K"}, {"family": "Naylor", "given": "Gavin P", "initials": "GP"}, {"family": "Phillippy", "given": "Adam", "initials": "A", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Mountcastle", "given": "Jacquelyn", "initials": "J"}, {"family": "Balacco", "given": "Jennifer R", "initials": "JR"}, {"family": "Dutra", "given": "Amalia", "initials": "A"}, {"family": "Dale", "given": "Rebecca E", "initials": "RE"}, {"family": "Haase", "given": "Bettina", "initials": "B"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Myers", "given": "Gene", "initials": "G", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9e5a63cadcf4ab995f3e989bc38c024.json"}}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Currie", "given": "Peter D", "initials": "PD", "orcid": "0000-0001-8874-8862", "researcher": {"href": "https://publications.scilifelab.se/researcher/13638faa71f94e13b088922cdfa01bb3.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6628", "issn-l": "2041-1723"}, "abstract": "Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7\u00d710-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.", "doi": "10.1038/s41467-023-42238-x", "pmid": "37857613", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10587355"}, {"db": "pii", "key": "10.1038/s41467-023-42238-x"}], "notes": [], "created": "2023-12-18T15:04:16.059Z", "modified": "2024-01-16T13:48:31.927Z"}, {"entity": "publication", "iuid": "57d336fde81e4a409b232134a6c24a50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50"}}, "title": "Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Lei", "given": "Weipan", "initials": "W"}, {"family": "Chen", "given": "Juexin", "initials": "J"}, {"family": "Wei", "given": "Chentao", "initials": "C"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "12", "pages": "msad224"}, "abstract": "A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves two rare inversion haplotypes (Satellite and Faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (Independent) haplotype indicates that the inversion could be as old as 4 million years. Here we have constructed a highly contiguous genome assembly of the inversion region for both the Independent and Satellite haplotypes. Based on the new data we estimate that the recombination event(s) creating the Satellite haplotype occurred only about 70,000 years ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the Satellite and Faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N gene CENPN is disrupted by the inversion, and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.", "doi": "10.1093/molbev/msad224", "pmid": "37804117", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7296052"}], "notes": [], "created": "2023-10-10T08:45:20.886Z", "modified": "2024-01-16T13:48:31.996Z"}, {"entity": "publication", "iuid": "838e0b3db3344e009deafc5bec93347c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c"}}, "title": "Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.", "authors": [{"family": "Rancilhac", "given": "Lo\u00efs", "initials": "L", "orcid": "0000-0002-9859-1448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3a53ef0421c4c0990fbf9ef20f6bd3b.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Harris", "given": "Rebecca", "initials": "R"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": null, "issue": null, "pages": null}, "abstract": "Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the \"black-and-white wagtails\", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a \"complete evidence\" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.", "doi": "10.1093/sysbio/syad062", "pmid": "37801684", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7294611"}], "notes": [], "created": "2023-10-19T13:54:24.722Z", "modified": "2024-01-16T13:48:32.004Z"}, {"entity": "publication", "iuid": "0e6c5f5e44e3406b9d3f38f57c040da5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e6c5f5e44e3406b9d3f38f57c040da5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e6c5f5e44e3406b9d3f38f57c040da5"}}, "title": "Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.", "authors": [{"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Sendell-Price", "given": "Ashley T", "initials": "AT"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Visscher", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-2143-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdb41d4720b436494304f74e33206ae.json"}}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR", "orcid": "0000-0002-7347-5758", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a184c706054257a130b2ae0694d858.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-09-29", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "381", "issue": "6665", "pages": "eadf6218"}, "abstract": "A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Gal\u00e1pagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.", "doi": "10.1126/science.adf6218", "pmid": "37769091", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-12T11:14:44.927Z", "modified": "2024-01-16T13:48:32.043Z"}, {"entity": "publication", "iuid": "4ab0b7f2d3b44dedbf4230ac6274f925", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ab0b7f2d3b44dedbf4230ac6274f925.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ab0b7f2d3b44dedbf4230ac6274f925"}}, "title": "Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes.", "authors": [{"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Jouneau", "given": "Alice", "initials": "A"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Oudin", "given": "Jean-Francois", "initials": "JF"}, {"family": "Adenot", "given": "Pierre", "initials": "P"}, {"family": "Omar", "given": "Jihad", "initials": "J"}, {"family": "Brochard", "given": "Vincent", "initials": "V"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-06-06", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "23", "pages": "e2216799120", "issn-l": "0027-8424"}, "abstract": "ZC3H11A (zinc finger CCCH domain-containing protein 11A) is a stress-induced mRNA-binding protein required for efficient growth of nuclear-replicating viruses. The cellular functions of ZC3H11A during embryonic development are unknown. Here, we report the generation and phenotypic characterization of Zc3h11a knockout (KO) mice. Heterozygous null Zc3h11a mice were born at the expected frequency without distinguishable phenotypic differences compared with wild-type mice. In contrast, homozygous null Zc3h11a mice were missing, indicating that Zc3h11a is crucial for embryonic viability and survival. Zc3h11a -/- embryos were detected at the expected Mendelian ratios up to late preimplantation stage (E4.5). However, phenotypic characterization at E6.5 revealed degeneration of Zc3h11a -/- embryos, indicating developmental defects around the time of implantation. Transcriptomic analyses documented a dysregulation of glycolysis and fatty acid metabolic pathways in Zc3h11a-/- embryos at E4.5. Proteomic analysis indicated a tight interaction between ZC3H11A and mRNA-export proteins in embryonic stem cells. CLIP-seq analysis demonstrated that ZC3H11A binds a subset of mRNA transcripts that are critical for metabolic regulation of embryonic cells. Furthermore, embryonic stem cells with an induced deletion of Zc3h11a display an impaired differentiation toward epiblast-like cells and impaired mitochondrial membrane potential. Altogether, the results show that ZC3H11A is participating in export and posttranscriptional regulation of selected mRNA transcripts required to maintain metabolic processes in embryonic cells. While ZC3H11A is essential for the viability of the early mouse embryo, inactivation of Zc3h11a expression in adult tissues using a conditional KO did not lead to obvious phenotypic defects.", "doi": "10.1073/pnas.2216799120", "pmid": "37252988", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10266022"}], "notes": [], "created": "2023-11-29T11:18:46.020Z", "modified": "2023-11-29T11:18:46.029Z"}, {"entity": "publication", "iuid": "8d34b82577f64f6b877c9b79fd1ede24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d34b82577f64f6b877c9b79fd1ede24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d34b82577f64f6b877c9b79fd1ede24"}}, "title": "The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus).", "authors": [{"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Farrell", "given": "Edward D", "initials": "ED", "orcid": "0000-0002-0070-9154", "researcher": {"href": "https://publications.scilifelab.se/researcher/941224a45e9242398fbcd4dacbe812c1.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "6", "pages": "1201-1219", "issn-l": "1752-4571"}, "abstract": "Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.", "doi": "10.1111/eva.13559", "pmid": "37360028", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10286234"}, {"db": "pii", "key": "EVA13559"}], "notes": [], "created": "2023-08-14T06:20:40.908Z", "modified": "2024-01-16T13:48:33.272Z"}, {"entity": "publication", "iuid": "4deb700f9a5d4e66bb1ede6b222c2a2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4deb700f9a5d4e66bb1ede6b222c2a2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4deb700f9a5d4e66bb1ede6b222c2a2d"}}, "title": "A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP"}, {"family": "Rochus", "given": "Christina M", "initials": "CM"}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "V\u00e4in\u00f6l\u00e4", "given": "Risto", "initials": "R"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-05-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "5", "pages": null}, "abstract": "Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25-26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (FST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years.", "doi": "10.1093/gbe/evad069", "pmid": "37120751", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10182735"}, {"db": "pii", "key": "7147330"}], "notes": [], "created": "2023-10-30T09:48:24.059Z", "modified": "2024-01-16T13:48:33.434Z"}, {"entity": "publication", "iuid": "c27764ed4c514f2592c156cc59d23608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608"}}, "title": "Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6033"}, "abstract": "Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.", "doi": "10.1038/s41467-022-33723-w", "pmid": "36229469", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-33723-w"}, {"db": "pmc", "key": "PMC9562234"}], "notes": [], "created": "2022-11-09T16:00:11.231Z", "modified": "2024-01-16T13:48:34.742Z"}, {"entity": "publication", "iuid": "7f08b122459149d9ac2a582fcc398431", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f08b122459149d9ac2a582fcc398431.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f08b122459149d9ac2a582fcc398431"}}, "title": "Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Dobreva", "given": "Mariya P", "initials": "MP", "orcid": "0000-0002-7152-1044", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7264631debb4687be22a07e768c4a07.json"}}, {"family": "Abzhanov", "given": "Arhat", "initials": "A"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S", "orcid": "0000-0003-4826-0349", "researcher": {"href": "https://publications.scilifelab.se/researcher/602a2f371eae45e4b9d8f9748f285ef4.json"}}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sendell-Price", "given": "Ashley T", "initials": "AT"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG"}, {"family": "Valle", "given": "Carlos A", "initials": "CA", "orcid": "0000-0002-5523-634X", "researcher": {"href": "https://publications.scilifelab.se/researcher/69b5e00396c5482786b9eeeea2316cfb.json"}}, {"family": "Vasco", "given": "Karla", "initials": "K", "orcid": "0000-0002-4617-5864", "researcher": {"href": "https://publications.scilifelab.se/researcher/e080c032415840ca864356927ac7fda9.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR", "orcid": "0000-0002-7347-5758", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a184c706054257a130b2ae0694d858.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2022-07-08", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "27", "pages": "eabm5982", "issn-l": "2375-2548"}, "abstract": "Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.", "doi": "10.1126/sciadv.abm5982", "pmid": "35857449", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9269886"}], "notes": [], "created": "2022-11-09T15:47:58.882Z", "modified": "2024-01-16T13:48:35.858Z"}, {"entity": "publication", "iuid": "a51b73263a6d4b939a0085b5f33e1f97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a51b73263a6d4b939a0085b5f33e1f97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a51b73263a6d4b939a0085b5f33e1f97"}}, "title": "Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.", "authors": [{"family": "Li", "given": "Jingyi", "initials": "J"}, {"family": "Lee", "given": "Mi-Ok", "initials": "MO"}, {"family": "Chen", "given": "Junfeng", "initials": "J"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Dorshorst", "given": "Benjamin J", "initials": "BJ"}, {"family": "Siegel", "given": "Paul B", "initials": "PB", "orcid": "0000-0003-1415-7781", "researcher": {"href": "https://publications.scilifelab.se/researcher/7945724419eb443c84341086cca382cf.json"}}, {"family": "Inaba", "given": "Masafumi", "initials": "M"}, {"family": "Jiang", "given": "Ting-Xin", "initials": "TX", "orcid": "0000-0003-1972-8985", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dacf1a76c35436fa36cc75b0dbe28d7.json"}}, {"family": "Chuong", "given": "Cheng-Ming", "initials": "CM", "orcid": "0000-0001-9673-3994", "researcher": {"href": "https://publications.scilifelab.se/researcher/4396f32b3ded4decb329859b5d14f420.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-10-12", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "41", "issn-l": "0027-8424"}, "abstract": "Melanotic (Ml) is a mutation in chickens that extends black (eumelanin) pigmentation in normally brown or red (pheomelanin) areas, thus affecting multiple within-feather patterns [J. W. Moore, J. R. Smyth Jr, J. Hered. 62, 215-219 (1971)]. In the present study, linkage mapping using a back-cross between Dark Cornish (Ml/Ml) and Partridge Plymouth Rock (ml +/ml ) chickens assigned +Ml to an 820-kb region on chromosome 1. Identity-by-descent mapping, via whole-genome sequencing and diagnostic tests using a diverse set of chickens, refined the localization to the genomic region harboring GJA5 encoding gap-junction protein 5 (alias connexin 40) previously associated with pigmentation patterns in zebrafish. An insertion/deletion polymorphism located in the vicinity of the GJA5 promoter region was identified as the candidate causal mutation. Four different GJA5 transcripts were found to be expressed in feather follicles and at least two showed differential expression between genotypes. The results showed that Melanotic constitutes a cis-acting regulatory mutation affecting GJA5 expression. A recent study established the melanocortin-1 receptor (MC1R) locus and the interaction between the MC1R receptor and its antagonist agouti-signaling protein as the primary mechanism underlying variation in within-feather pigmentation patterns in chickens. The present study advances understanding the mechanisms underlying variation in plumage color in birds because it demonstrates that the activity of connexin 40/GJA5 can modulate the periodic pigmentation patterns within individual feathers.", "doi": "10.1073/pnas.2109363118", "pmid": "34607956", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2109363118"}, {"db": "pmc", "key": "PMC8521658"}], "notes": [], "created": "2021-12-10T11:08:58.593Z", "modified": "2024-01-16T13:48:38.245Z"}, {"entity": "publication", "iuid": "e2c7e0df97dc45de9a909aafc53e6ff6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2c7e0df97dc45de9a909aafc53e6ff6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2c7e0df97dc45de9a909aafc53e6ff6"}}, "title": "ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression.", "authors": [{"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Younis", "given": "Shady", "initials": "S"}], "type": "journal article", "published": "2021-09-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "19484", "issn-l": "2045-2322"}, "abstract": "The expression of Igf2 in mammals shows a complex regulation involving multiple promoters and epigenetic mechanisms. We previously identified a novel regulatory mechanism based on the interaction between the transcriptional factor ZBED6 and Igf2 intron. Disruption of the ZBED6-Igf2 interaction leads to a dramatic up-regulation of IGF2 expression postnatally. In the current study we characterize an additional layer of regulation involving miR483 encoded by another Igf2 intron. We found a highly significant up-regulation of miR483 expression when the ZBED6-Igf2 axis is disrupted in transgenic mice. Furthermore, CRISPR/Cas9 mediated knock-out of miR483 in C2C12 myoblast cells, both wild-type and cells with disrupted ZBED6-Igf2 axis (Igf2dGGCT), resulted in down-regulation of Igf2 expression and a reduced proliferation rate. This was further validated using miR483 mimics and inhibitors. RNA-seq analysis revealed a significant enrichment of genes involved in the PI3K-Akt signaling pathway among genes down-regulated in miR483-/- cells, including Igf2 down-regulation. The opposite pattern was observed in Igf2dGGCT cells, where Igf2 is up-regulated. Our data suggest a positive feedback between miR483 and Igf2 promoter activity, strongly affecting how ZBED6 controls Igf2 expression in various cell types.", "doi": "10.1038/s41598-021-98777-0", "pmid": "34593874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-98777-0"}, {"db": "pmc", "key": "PMC8484269"}], "notes": [], "created": "2022-01-16T20:56:35.213Z", "modified": "2022-01-16T20:56:35.229Z"}, {"entity": "publication", "iuid": "47e2059a8c6d4ea5aefb39c53bc5c234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234"}}, "title": "Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.", "authors": [{"family": "Chen", "given": "Junfeng", "initials": "J", "orcid": "0000-0001-6155-411X", "researcher": {"href": "https://publications.scilifelab.se/researcher/270488419b56484993472f518ba1d286.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Mo", "given": "Chunheng", "initials": "C"}, {"family": "Younis", "given": "Shady", "initials": "S", "orcid": "0000-0002-4319-1738", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b77c6e3ed14b9ba2e10132f89ef781.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Mol\u00e9s", "given": "Gregorio", "initials": "G", "orcid": "0000-0001-5762-6993", "researcher": {"href": "https://publications.scilifelab.se/researcher/26c43e28a3fa49ccad6c77ae61f87777.json"}}, {"family": "G\u00f3mez", "given": "Ana", "initials": "A"}, {"family": "Kleinau", "given": "Gunnar", "initials": "G"}, {"family": "Scheerer", "given": "Patrick", "initials": "P", "orcid": "0000-0001-5028-2075", "researcher": {"href": "https://publications.scilifelab.se/researcher/50350a6ed93442f38ea62edb86eaa99b.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "795", "issn-l": "2399-3642"}, "abstract": "The underlying molecular mechanisms that determine long day versus short day breeders remain unknown in any organism. Atlantic herring provides a unique opportunity to examine the molecular mechanisms involved in reproduction timing, because both spring and autumn spawners exist within the same species. Although our previous whole genome comparisons revealed a strong association of TSHR alleles with spawning seasons, the functional consequences of these variants remain unknown. Here we examined the functional significance of six candidate TSHR mutations strongly associated with herring reproductive seasonality. We show that the L471M missense mutation in the spring-allele causes enhanced cAMP signaling. The best candidate non-coding mutation is a 5.2 kb retrotransposon insertion upstream of the TSHR transcription start site, near an open chromatin region, which is likely to affect TSHR expression. The insertion occurred prior to the split between Pacific and Atlantic herring and was lost in the autumn-allele. Our study shows that strongly associated coding and non-coding variants at the TSHR locus may both contribute to the regulation of seasonal reproduction in herring.", "doi": "10.1038/s42003-021-02307-7", "pmid": "34172814", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02307-7"}, {"db": "pmc", "key": "PMC8233318"}, {"db": "Dryad", "key": "10.5061/dryad.pnvx0k6kr"}], "notes": [], "created": "2021-12-07T21:41:02.372Z", "modified": "2024-01-16T13:48:39.437Z"}, {"entity": "publication", "iuid": "1ca0729f557a4cd3b8cb790b4a9d5961", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ca0729f557a4cd3b8cb790b4a9d5961.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ca0729f557a4cd3b8cb790b4a9d5961"}}, "title": "Asymmetric introgression reveals the genetic architecture of a plumage trait.", "authors": [{"family": "Semenov", "given": "Georgy A", "initials": "GA", "orcid": "0000-0002-7218-7885", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bb787f3be449299a263dcab28021b9.json"}}, {"family": "Linck", "given": "Ethan", "initials": "E"}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Harris", "given": "Rebecca B", "initials": "RB"}, {"family": "Khaydarov", "given": "David R", "initials": "DR"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Taylor", "given": "Scott A", "initials": "SA", "orcid": "0000-0001-9580-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c6baa1b23242e0bfd586d7e42c0cb9.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1019", "issn-l": "2041-1723"}, "abstract": "Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.", "doi": "10.1038/s41467-021-21340-y", "pmid": "33589637", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21340-y"}, {"db": "pmc", "key": "PMC7884433"}, {"db": "Dryad", "key": "10.5061/dryad.dv41ns1wv"}], "notes": [], "created": "2021-06-09T12:16:14.581Z", "modified": "2024-01-16T13:48:40.705Z"}, {"entity": "publication", "iuid": "1f5e1b21a6a5486793d238251900e16e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f5e1b21a6a5486793d238251900e16e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f5e1b21a6a5486793d238251900e16e"}}, "title": "Ecological adaptation in European eels is based on phenotypic plasticity.", "authors": [{"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG"}, {"family": "Palm", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9890-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebffe35bae646eb8a15163b0cb0820f.json"}}, {"family": "Wickstr\u00f6m", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6335-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce9d80227974a21be858a2925338f93.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-01-26", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "4", "pages": "e2022620118", "issn-l": "0027-8424"}, "abstract": "The relative role of genetic adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.", "doi": "10.1073/pnas.2022620118", "pmid": "33479174", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2022620118"}, {"db": "pmc", "key": "PMC7848574"}], "notes": [], "created": "2021-06-09T12:16:45.953Z", "modified": "2024-01-16T13:48:40.922Z"}, {"entity": "publication", "iuid": "0e0f91643ac84e9e82be060080efcbe8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e0f91643ac84e9e82be060080efcbe8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e0f91643ac84e9e82be060080efcbe8"}}, "title": "Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding.", "authors": [{"family": "Gustafsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-4854-5531", "researcher": {"href": "https://publications.scilifelab.se/researcher/16dd7e73adad4f85972d1d546bfa6d2a.json"}}, {"family": "Eckhard", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-5863-4514", "researcher": {"href": "https://publications.scilifelab.se/researcher/78dae054a57d43c89852aac77a2ad6da.json"}}, {"family": "Ye", "given": "Weihua", "initials": "W"}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Jemth", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Selmer", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2020-12-03", "journal": {"title": "Biomolecules", "issn": "2218-273X", "volume": "10", "issue": "12", "issn-l": null}, "abstract": "Phosphoglucomutase 5 (PGM5) in humans is known as a structural muscle protein without enzymatic activity, but detailed understanding of its function is lacking. PGM5 belongs to the alpha-D-phosphohexomutase family and is closely related to the enzymatically active metabolic enzyme PGM1. In the Atlantic herring, Clupea harengus, PGM5 is one of the genes strongly associated with ecological adaptation to the brackish Baltic Sea. We here present the first crystal structures of PGM5, from the Atlantic and Baltic herring, differing by a single substitution Ala330Val. The structure of PGM5 is overall highly similar to structures of PGM1. The structure of the Baltic herring PGM5 in complex with the substrate glucose-1-phosphate shows conserved substrate binding and active site compared to human PGM1, but both PGM5 variants lack phosphoglucomutase activity under the tested conditions. Structure comparison and sequence analysis of PGM5 and PGM1 from fish and mammals suggest that the lacking enzymatic activity of PGM5 is related to differences in active-site loops that are important for flipping of the reaction intermediate. The Ala330Val substitution does not alter structure or biophysical properties of PGM5 but, due to its surface-exposed location, could affect interactions with protein-binding partners.", "doi": "10.3390/biom10121631", "pmid": "33287293", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7761743"}, {"db": "pii", "key": "biom10121631"}], "notes": [], "created": "2024-04-03T14:12:52.445Z", "modified": "2024-04-03T14:12:52.932Z"}, {"entity": "publication", "iuid": "154532dd2cc14c359aedcbc68f77a29c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/154532dd2cc14c359aedcbc68f77a29c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/154532dd2cc14c359aedcbc68f77a29c"}}, "title": "Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.", "authors": [{"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Ring", "given": "Henrik", "initials": "H"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Blanco-Aguiar", "given": "Jos\u00e9 A", "initials": "JA"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F", "orcid": "0000-0001-7552-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6bad55b67431c82e2e54e5b007917.json"}}, {"family": "Carneiro", "given": "Miguel", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "comparative study", "published": "2020-10-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "10", "pages": "1918-1928", "issn-l": "1759-6653"}, "abstract": "Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.", "doi": "10.1093/gbe/evaa158", "pmid": "32835359", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5896528"}, {"db": "pmc", "key": "PMC7594241"}], "notes": [], "created": "2020-09-15T07:00:59.512Z", "modified": "2024-01-16T13:48:41.617Z"}, {"entity": "publication", "iuid": "35f57851b81546e785433040d1f08581", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35f57851b81546e785433040d1f08581.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35f57851b81546e785433040d1f08581"}}, "title": "Reconstruction of the birth of a male sex chromosome present in Atlantic herring.", "authors": [{"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Chen", "given": "Junfeng", "initials": "J"}, {"family": "Herpin", "given": "Amaury", "initials": "A"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "P\u00e9ron", "given": "Sandrine", "initials": "S"}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Tr\u00f6tschel", "given": "Christian", "initials": "C"}, {"family": "Poetsch", "given": "Ansgar", "initials": "A", "orcid": "0000-0002-7540-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/24924a964a1e4e9abd93d50ca404a680.json"}}, {"family": "Korsching", "given": "Kai", "initials": "K"}, {"family": "B\u00f6nigk", "given": "Wolfgang", "initials": "W"}, {"family": "K\u00f6rschen", "given": "Heinz G", "initials": "HG"}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Folkvord", "given": "Arild", "initials": "A", "orcid": "0000-0002-4763-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e48870c7654bf0898cb9ff2a064b99.json"}}, {"family": "Kaupp", "given": "U Benjamin", "initials": "UB", "orcid": "0000-0002-0696-6397", "researcher": {"href": "https://publications.scilifelab.se/researcher/e94d12b7c4624985b0f6f7c8b798c969.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2020-09-29", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "117", "issue": "39", "pages": "24359-24368", "issn-l": "0027-8424"}, "abstract": "The mechanisms underlying sex determination are astonishingly plastic. Particularly the triggers for the molecular machinery, which recalls either the male or female developmental program, are highly variable and have evolved independently and repeatedly. Fish show a huge variety of sex determination systems, including both genetic and environmental triggers. The advent of sex chromosomes is assumed to stabilize genetic sex determination. However, because sex chromosomes are notoriously cluttered with repetitive DNA and pseudogenes, the study of their evolution is hampered. Here we reconstruct the birth of a Y chromosome present in the Atlantic herring. The region is tiny (230 kb) and contains only three intact genes. The candidate male-determining gene BMPR1BBY encodes a truncated form of a BMP1B receptor, which originated by gene duplication and translocation and underwent rapid protein evolution. BMPR1BBY phosphorylates SMADs in the absence of ligand and thus has the potential to induce testis formation. The Y region also contains two genes encoding subunits of the sperm-specific Ca2+ channel CatSper required for male fertility. The herring Y chromosome conforms with a characteristic feature of many sex chromosomes, namely, suppressed recombination between a sex-determining factor and genes that are beneficial for the given sex. However, the herring Y differs from other sex chromosomes in that suppression of recombination is restricted to an \u223c500-kb region harboring the male-specific and sex-associated regions. As a consequence, any degeneration on the herring Y chromosome is restricted to those genes located in the small region affected by suppressed recombination.", "doi": "10.1073/pnas.2009925117", "pmid": "32938798", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "2009925117"}, {"db": "pmc", "key": "PMC7533707"}], "notes": [], "created": "2020-09-24T13:52:16.130Z", "modified": "2024-01-16T13:48:41.694Z"}, {"entity": "publication", "iuid": "9d7fcd3fe5d84966ab5d1e2cf5d5137b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d7fcd3fe5d84966ab5d1e2cf5d5137b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d7fcd3fe5d84966ab5d1e2cf5d5137b"}}, "title": "Female-biased gene flow between two species of Darwin's finches.", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S", "orcid": "0000-0003-4826-0349", "researcher": {"href": "https://publications.scilifelab.se/researcher/602a2f371eae45e4b9d8f9748f285ef4.json"}}, {"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "7", "pages": "979-986", "issn-l": "2397-334X"}, "abstract": "The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Gal\u00e1pagos island of Daphne Major, two species of Darwin's finches, Geospiza fortis and G. scandens, hybridize rarely and back-cross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole-genome sequences to compare genomes from periods before and after successful interbreeding followed by back-crossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci primarily reflects female-biased gene flow, arising from a hybrid-male disadvantage in competition for high-quality territories and mates, rather than from genetic incompatibilities at Z-linked loci.", "doi": "10.1038/s41559-020-1183-9", "pmid": "32367030", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-1183-9"}], "notes": [], "created": "2020-07-03T05:28:11.615Z", "modified": "2024-01-16T13:48:42.318Z"}, {"entity": "publication", "iuid": "885ef893417d418db138a1903108bcd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/885ef893417d418db138a1903108bcd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/885ef893417d418db138a1903108bcd8"}}, "title": "Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "de la Paz Celorio Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Andersson", "given": "Anastasia", "initials": "A"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.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": "2019-10-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "9", "issue": "19", "pages": "11448-11463"}, "abstract": "Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( \u2248 0.002 and \u03c0 \u00af \u2248 0.001 when mapping to \u03c0 \u00afS. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.", "doi": "10.1002/ece3.5646", "pmid": "31641485", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6802065"}, {"db": "pii", "key": "ECE35646"}, {"db": "Dryad", "key": "10.5061/dryad.q1h4k0n"}], "notes": [], "created": "2019-11-20T09:43:21.469Z", "modified": "2024-01-16T13:48:43.776Z"}, {"entity": "publication", "iuid": "c99b8ca4a3ec485baadfc7ac77ad0ee5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c99b8ca4a3ec485baadfc7ac77ad0ee5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c99b8ca4a3ec485baadfc7ac77ad0ee5"}}, "title": "Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG"}, {"family": "Bekkevold", "given": "Dorte", "initials": "D", "orcid": "0000-0002-5297-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c62afa02e94554ba1c3afcfc622555.json"}}, {"family": "Folkvord", "given": "Arild", "initials": "A", "orcid": "0000-0002-4763-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e48870c7654bf0898cb9ff2a064b99.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Kleinau", "given": "Gunnar", "initials": "G"}, {"family": "Scheerer", "given": "Patrick", "initials": "P"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2019-09-10", "journal": {"volume": "116", "issn": "1091-6490", "issue": "37", "pages": "18473-18478", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The evolutionary process that occurs when a species colonizes a new environment provides an opportunity to explore the mechanisms underlying genetic adaptation, which is essential knowledge for understanding evolution and the maintenance of biodiversity. Atlantic herring has an estimated total breeding stock of about 1 trillion (10 12) and has colonized the brackish Baltic Sea within the last 10,000 y. Minute genetic differentiation between Atlantic and Baltic herring populations at selectively neutral loci combined with this rapid adaptation to a new environment facilitated the identification of hundreds of loci underlying ecological adaptation. A major question in the field of evolutionary biology is to what extent such an adaptive process involves selection of novel mutations with large effects or genetic changes at many loci, each with a small effect on phenotype (i.e., selection on standing genetic variation). Here we show that a missense mutation in rhodopsin (Phe261Tyr) is an adaptation to the red-shifted Baltic Sea light environment. The transition from phenylalanine to tyrosine differs only by the presence of a hydroxyl moiety in the latter, but this results in an up to 10-nm red-shifted light absorbance of the receptor. Remarkably, an examination of the rhodopsin sequences from 2,056 species of fish revealed that the same missense mutation has occurred independently and been selected for during at least 20 transitions between light environments across all fish. Our results provide a spectacular example of convergent evolution and how a single amino acid change can have a major effect on ecological adaptation.", "doi": "10.1073/pnas.1908332116", "pmid": "31451650", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1908332116"}, {"db": "pmc", "key": "PMC6744887"}], "notes": [], "created": "2019-11-25T14:59:20.457Z", "modified": "2024-01-16T13:48:43.886Z"}]}