{"entity": "researcher", "timestamp": "2026-06-09T03:20:17.923Z", "family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "affiliations": ["Division of Population Genetics Department of Zoology Stockholm University Stockholm Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132"}}, "publications": [{"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": "708018decd8e4d788c4ddf8b8c1b2630", "links": {"self": {"href": "https://publications.scilifelab.se/publication/708018decd8e4d788c4ddf8b8c1b2630.json"}, "display": {"href": "https://publications.scilifelab.se/publication/708018decd8e4d788c4ddf8b8c1b2630"}}, "title": "Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations", "authors": [{"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"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": "2024-04-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "25", "issue": "2", "pages": "513-531", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-023-01586-3", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-08T13:27:59.260Z", "modified": "2024-11-25T10:10:59.738Z"}, {"entity": "publication", "iuid": "d63a8f09078149d8bf45ad1611ae68e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d63a8f09078149d8bf45ad1611ae68e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d63a8f09078149d8bf45ad1611ae68e1"}}, "title": "New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Keehnen", "given": "Naomi", "initials": "N"}, {"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.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": "2024-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "2", "pages": "e17213", "issn-l": "0962-1083"}, "abstract": "International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's \u03f4 and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.", "doi": "10.1111/mec.17213", "pmid": "38014725", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-02T13:26:58.174Z", "modified": "2024-11-25T10:27:09.260Z"}, {"entity": "publication", "iuid": "28a8e085d9004e98b312750d425227bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28a8e085d9004e98b312750d425227bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28a8e085d9004e98b312750d425227bb"}}, "title": "Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ericsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ekblom", "given": "Robert", "initials": "R", "orcid": "0000-0003-2222-1966", "researcher": {"href": "https://publications.scilifelab.se/researcher/e326451a036042b89707ea3d68af0c5c.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2023-10-17", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "1035", "issn-l": "2399-3642"}, "abstract": "Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.", "doi": "10.1038/s42003-023-05385-x", "pmid": "37848497", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582009"}, {"db": "pii", "key": "10.1038/s42003-023-05385-x"}], "notes": [], "created": "2023-11-25T05:31:13.184Z", "modified": "2024-01-16T13:48:31.935Z"}, {"entity": "publication", "iuid": "52d17bcd67b34305a5fe00573dccf416", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52d17bcd67b34305a5fe00573dccf416.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52d17bcd67b34305a5fe00573dccf416"}}, "title": "Genomic dynamics of brown trout populations released to a novel environment.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.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": "2022-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "12", "issue": "7", "pages": "e9050"}, "abstract": "Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.", "doi": "10.1002/ece3.9050", "pmid": "35813906", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9251865"}, {"db": "pii", "key": "ECE39050"}], "notes": [], "created": "2022-08-01T12:29:56.905Z", "modified": "2024-01-16T13:48:36.012Z"}, {"entity": "publication", "iuid": "9acb1bb14347433d9f52a2ccf0633011", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9acb1bb14347433d9f52a2ccf0633011.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9acb1bb14347433d9f52a2ccf0633011"}}, "title": "Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.", "authors": [{"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Andersson", "given": "Anastasia", "initials": "A", "orcid": "0000-0002-5698-4948", "researcher": {"href": "https://publications.scilifelab.se/researcher/53b4f2c97b3d4261874f12f7142e3630.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Keehnen", "given": "Naomi L P", "initials": "NLP", "orcid": "0000-0002-8782-3477", "researcher": {"href": "https://publications.scilifelab.se/researcher/524a74275ed848a8a6ccbdf5509e90e0.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "H\u00f6ssjer", "given": "Ola", "initials": "O", "orcid": "0000-0003-2767-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/09226c21334345f086f157d9e7f3136a.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Karlsson", "given": "Sten", "initials": "S"}, {"family": "Kardos", "given": "Marty", "initials": "M"}, {"family": "St\u00e5hl", "given": "Gunnar", "initials": "G"}, {"family": "Allendorf", "given": "Fred W", "initials": "FW", "orcid": "0000-0003-3663-6425", "researcher": {"href": "https://publications.scilifelab.se/researcher/a877524fe9d343f0a7b92711dbf8f608.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": "2022-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "31", "issue": "2", "pages": "498-511", "issn-l": "0962-1083"}, "abstract": "The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersj\u00f6arna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST \u2248 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.", "doi": "10.1111/mec.16252", "pmid": "34699656", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "RefSeq", "key": "GCA_901001165.1"}], "notes": [], "created": "2021-11-10T08:24:51.845Z", "modified": "2024-01-16T13:48:37.867Z"}, {"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"}]}