{"entity": "researcher", "timestamp": "2026-08-13T19:09:08.293Z", "family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "affiliations": ["Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, 17893, Sweden.", "Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, 51014, Estonia."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8"}}, "publications": [{"entity": "publication", "iuid": "fecec34336824e84b6c3dd0f90675ef4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fecec34336824e84b6c3dd0f90675ef4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fecec34336824e84b6c3dd0f90675ef4"}}, "title": "Contrasting population genomic structuring of northern pike ( Esox lucius L.) in fresh\u2010 and brackish water environments: Implications for management and conservation", "authors": [{"family": "Diaz\u2010Suarez", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-1726-2563", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f3f9866fe543b78c91c9c62c362cdd.json"}}, {"family": "L\u00f3pez", "given": "Mar\u00eda\u2010Eugenia", "initials": "M"}, {"family": "Sundblad", "given": "G\u00f6ran", "initials": "G"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}], "type": "journal-article", "published": "2026-03-30", "journal": {"title": "J. Fish Biol.", "issn": "0022-1112", "issn-l": null}, "abstract": "Understanding the factors that shape population genetic structure is crucial for advancing evolutionary studies and developing effective management and conservation strategies. The northern pike (Esox lucius L.) is a top teleost predator that inhabits fresh and brackish water environments in the northern hemisphere. Pike populations in the brackish Baltic Sea typically display strong genetic structuring, with coastal sympatric populations that separate during spring for spawning in either shallow, sheltered brackish bays or in freshwater tributaries and wetlands. In contrast to the Baltic Sea, genomic structuring in freshwater environments, particularly in large lacustrine systems, remains poorly understood. To address this gap, we used restriction site-associated DNA-sequencing to assess the genetic structure and diversity of northern pike in two ecologically contrasting habitats: freshwater V\u00e4nern Lake, Sweden (8932 single nucleotide polimorphisms [SNPs]), and the brackish Baltic Sea around Saaremaa, Estonia (6899 SNPs). The results show strong genetic structuring and lower genetic diversity in brackish environment compared to the higher genetic diversity and extremely low genetic structuring observed in freshwater habitat. We found no evidence of divergent selection within environments. However, we identified 187 outlier SNPs and 62 outlier genes distinguishing the brackish and freshwater environments, potentially reflecting adaptation to salinity. Notably, several of these genes are associated with key biological processes, including osmotic stress regulation (akap13), early development (tfap2a) and pathogens response (tlr18). From a fisheries management perspective, our results indicate that the freshwater system can be managed as a single stock, while strong population structuring among Baltic coastal pike likely requires either large-scale solutions and/or population-specific fine-scale management efforts to maintain the genetic and life-history diversity among brackish coastal pike populations.", "doi": "10.1111/jfb.70417", "pmid": "41912439", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-04-10T13:09:47.227Z", "modified": "2026-04-16T09:42:58.777Z"}, {"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": "dfd9f82be43c4473bdafe52ed31479ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd9f82be43c4473bdafe52ed31479ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd9f82be43c4473bdafe52ed31479ca"}}, "title": "Parasite spillover rather than niche expansion explains infection of host brain by diplostomid eye flukes.", "authors": [{"family": "Diaz-Suarez", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-1726-2563", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f3f9866fe543b78c91c9c62c362cdd.json"}}, {"family": "Kisand", "given": "Veljo", "initials": "V", "orcid": "0000-0002-5535-1639", "researcher": {"href": "https://publications.scilifelab.se/researcher/f34359c7f74a409f98dca6688e368332.json"}}, {"family": "Kahar", "given": "Siim", "initials": "S"}, {"family": "Gross", "given": "Riho", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Noreikiene", "given": "Kristina", "initials": "K", "orcid": "0000-0001-7529-4902", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ac9138a3a55468e99283202735f7489.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "292", "issue": "2040", "pages": "20242648", "issn-l": "0962-8452"}, "abstract": "Parasites often occupy specific sites within their host, which has important implications for host performance and parasite transmission. Nonetheless, parasitic infections can occur beyond their typical location within a host, significantly altering host-parasite interactions. Yet, the causes behind the atypical tissue tropism are poorly understood. Here, we focus on a ubiquitous group of diplostomid parasites that form diverse communities in fish eyes. We used targeted DNA metabarcoding (cytochrome c oxydase subunit 1, COX1, 250 bp) to evaluate potential mechanisms underlying eye parasite atypical tissue tropism to the brain of two widespread fish species (Eurasian perch and common roach). We found that the most common eye-infecting species (Tylodelphys clavata, Diplostomum baeri) are present in the brains of perch but not in roach. The bipartite network comprising 5 species and 24 mitochondrial haplotypes revealed no brain-specific haplotypes, indicating an apparent lack of genetic divergence between brain- and eye-infecting parasites. Instead, the prevalence, intensity and diversity of eye infections were positively correlated with brain infections. Thus, our results suggest that the most parsimonious mechanism underlying brain infection is density-dependent spillover rather than parasite divergence-driven niche expansion. We anticipate that 'off-target' infections are likely to be severely underestimated in nature with important ecological, evolutionary and medical implications.", "doi": "10.1098/rspb.2024.2648", "pmid": "39904393", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11793966"}], "notes": [], "created": "2025-11-28T10:50:19.633Z", "modified": "2025-11-28T10:50:19.824Z"}, {"entity": "publication", "iuid": "e572bce7ac984e7ea1ff903fed9a1293", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e572bce7ac984e7ea1ff903fed9a1293.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e572bce7ac984e7ea1ff903fed9a1293"}}, "title": "Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing.", "authors": [{"family": "Ozerov", "given": "Mikhail Yu", "initials": "MY", "orcid": "0000-0002-1817-7707", "researcher": {"href": "https://publications.scilifelab.se/researcher/952f3c17dea44942be07ff8d52cf59c0.json"}}, {"family": "Flaj\u0161hans", "given": "Martin", "initials": "M", "orcid": "0000-0002-0357-5788", "researcher": {"href": "https://publications.scilifelab.se/researcher/d53be81465624a1cb6d3f47d3b1b9b40.json"}}, {"family": "Noreikiene", "given": "Kristina", "initials": "K", "orcid": "0000-0001-7529-4902", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ac9138a3a55468e99283202735f7489.json"}}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Gross", "given": "Riho", "initials": "R", "orcid": "0000-0003-0311-3003", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d4530137e284124a79fd721f567703f.json"}}], "type": "journal article", "published": "2020-11-05", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "10", "issue": "11", "pages": "3897-3906", "issn-l": "2160-1836"}, "abstract": "The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: \u223c0.8Gb assembly (scaffold N 50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.", "doi": "10.1534/g3.120.401711", "pmid": "32917720", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "g3.120.401711"}, {"db": "pmc", "key": "PMC7642921"}], "notes": [], "created": "2020-11-16T09:14:08.125Z", "modified": "2024-01-16T13:48:41.407Z"}]}