{"entity": "journal", "iuid": "0372054236cc4d47a1a4f7610a6bf172", "timestamp": "2026-07-15T07:36:17.926Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Ecol%20Evol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Ecol%20Evol"}}, "title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "publications_count": 26, "publications": [{"entity": "publication", "iuid": "a7bacf7b90d34eb3aec01d340a18f9d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7bacf7b90d34eb3aec01d340a18f9d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7bacf7b90d34eb3aec01d340a18f9d9"}}, "title": "Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ephedra, Gnetales).", "authors": [{"family": "Blokzijl", "given": "Ruben", "initials": "R", "orcid": "0000-0002-5963-3537", "researcher": {"href": "https://publications.scilifelab.se/researcher/75de2e1da3244131b0cfd19ebfe0c254.json"}}, {"family": "Rydin", "given": "Catarina", "initials": "C", "orcid": "0000-0002-3347-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/70fff179e5b549c182dd7929b20f2e22.json"}}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "16", "issue": "7", "pages": "e73863", "issn-l": "2045-7758"}, "abstract": "The evolutionary history of Ephedra L. has over time proved to be a very difficult phylogenetic problem, something which probably is best reflected by the incongruent phylogenetic relationships demonstrated in and among previous studies. A low number of phylogenetically informative sites and different rooting strategies have been suggested as explanations, but the role of gene tree discordance and its underlying causes and influence on phylogenetic reconstruction in Ephedra have largely remained unexplored. In the present study, we address the phylogeny of Ephedra using information from a large set of nuclear low-copy genes obtained with a specifically designed bait set. We explore the potential effect of putative paralogy, intra-locus recombination, and chimeric sequences on phylogenetic estimation in Ephedra, while striving to minimize the risk for gene tree error. Our results indicate that recombination and putatively paralogous sequences have limited influence on phylogenetic results, although handling of putative paralogs and recombinants did improve overall species tree resolution and statistics. A robust Ephedra species phylogeny was obtained by analyzing gene trees, in which orthologous clades were inferred from data composed of orthologous and putatively paralogous sequences. The results support the division of Ephedra into three geographically defined clades, with the American clade as sister to the Mediterranean clade and the Asian clade. Relationships among species within these three clades were relatively consistent among our analytical approaches, but our results highlighted moderate to strong signals of gene tree discordance at many branches including the deepest split. Incomplete lineage sorting is a possible explanation for this discord for many branches, but hybridization/introgression is also commonly indicated.", "doi": "10.1002/ece3.73863", "pmid": "42388197", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13318514"}, {"db": "pii", "key": "ECE373863"}, {"db": "Dryad", "key": "10.5061/dryad.m63xsj4g4"}], "notes": [], "created": "2026-07-14T17:35:42.117Z", "modified": "2026-07-14T17:35:42.376Z"}, {"entity": "publication", "iuid": "4314ddab9c19449c8f14a8a5c00981fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4314ddab9c19449c8f14a8a5c00981fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4314ddab9c19449c8f14a8a5c00981fa"}}, "title": "Pan-Continental Genomic Analysis of Eurasian Perch Uncovers Global Diversity Hotspots and Postglacial Recolonization Patterns.", "authors": [{"family": "Lichman", "given": "Vitalii", "initials": "V", "orcid": "0009-0007-5955-0479", "researcher": {"href": "https://publications.scilifelab.se/researcher/379b94bfc1184a189ee57c449956ffad.json"}}, {"family": "Ozerov", "given": "Mikhail", "initials": "M"}, {"family": "L\u00f3pez", "given": "Mar\u00eda-Eugenia", "initials": "ME"}, {"family": "Noreikiene", "given": "Kristina", "initials": "K"}, {"family": "Kahar", "given": "Siim", "initials": "S"}, {"family": "Pukk", "given": "Lilian", "initials": "L"}, {"family": "Burimski", "given": "Oksana", "initials": "O"}, {"family": "Japoshvili", "given": "Bella", "initials": "B"}, {"family": "Blazhekovikj-Dimovska", "given": "Dijana", "initials": "D"}, {"family": "Lajus", "given": "Dmitry", "initials": "D"}, {"family": "Nikoli\u0107", "given": "Du\u0161an", "initials": "D"}, {"family": "Ribeiro", "given": "Filipe", "initials": "F"}, {"family": "Gebauer", "given": "Tatyana", "initials": "T"}, {"family": "Kou\u0159il", "given": "Jan", "initials": "J"}, {"family": "Peterka", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Blabolil", "given": "Petr", "initials": "P"}, {"family": "\u010cech", "given": "Martin", "initials": "M"}, {"family": "J\u016fza", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Kube\u010dka", "given": "Jan", "initials": "J"}, {"family": "Mu\u0161ka", "given": "Milan", "initials": "M"}, {"family": "\u0160mejkal", "given": "Marek", "initials": "M"}, {"family": "Va\u0161ek", "given": "Mojm\u00edr", "initials": "M"}, {"family": "Kahilainen", "given": "Kimmo", "initials": "K"}, {"family": "Lo\u017eys", "given": "Linas", "initials": "L"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Corcoran", "given": "William", "initials": "W"}, {"family": "Yilmaz", "given": "\u00d6zgen", "initials": "\u00d6"}, {"family": "Ekl\u00f6v", "given": "Peter", "initials": "P", "orcid": "0000-0002-8981-1453", "researcher": {"href": "https://publications.scilifelab.se/researcher/461265784bf643658985483277624d66.json"}}, {"family": "Tak\u00e1cs", "given": "P\u00e9ter", "initials": "P"}, {"family": "B\u00e1n\u00f3", "given": "B\u00e1lint", "initials": "B"}, {"family": "Pallos", "given": "R\u00e9ka", "initials": "R"}, {"family": "Kazakov", "given": "Stefan", "initials": "S"}, {"family": "Pehlivanov", "given": "Luchezar", "initials": "L"}, {"family": "Lecocq", "given": "Thomas", "initials": "T"}, {"family": "Lambert", "given": "Sophie", "initials": "S"}, {"family": "Lauridsen", "given": "Torben", "initials": "T"}, {"family": "Berthelsen", "given": "Andreas", "initials": "A"}, {"family": "Raposeiro", "given": "Pedro", "initials": "P"}, {"family": "Verreycken", "given": "Hugo", "initials": "H"}, {"family": "Britton", "given": "Robert", "initials": "R"}, {"family": "Borcheling", "given": "Jost", "initials": "J"}, {"family": "Kutsokon", "given": "Yuliia", "initials": "Y"}, {"family": "Didenko", "given": "Oleksandr", "initials": "O"}, {"family": "Jurajda", "given": "Pavel", "initials": "P"}, {"family": "Miranda", "given": "Rafael", "initials": "R", "orcid": "0000-0003-4798-314X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb0fd0fe7d34dc4b24af564521382bd.json"}}, {"family": "Gross", "given": "Riho", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A"}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "16", "pages": "e73502", "issn-l": "2045-7758"}, "abstract": "The contemporary distribution of genetic diversity in widespread freshwater species reflects a complex interplay between historical processes and recent demographic events. We investigated the postglacial recolonization history of the Eurasian perch (Perca fluviatilis L.) across its native range spanning Europe and Western Siberia, aiming to understand how historical and recent demographic processes have shaped contemporary genetic diversity in a widespread freshwater species. Using an integrative genomic approach, we combined whole mitochondrial genome resequencing with nuclear SNP-array genotyping (3660 SNPs) for 382 individuals from 188 locations to reconstruct patterns of lineage divergence, population structure, and admixture. We identified five highly divergent mitochondrial lineages, consistent with the existence of multiple glacial refugia across Southwestern, Southeastern, and Central Europe, as well as Siberia. Nuclear data (3660 SNPs) revealed three major genetic clusters corresponding to Western, Northern, and Southeastern Europe, along with strong regional admixture. The Baltic Sea region emerged as a contemporary hotspot of genetic diversity, likely resulting from the admixture and convergence of distinct maternal lineages during the postglacial recolonization of Northern Europe. Signals of isolation by distance were evident both within and across lineages, highlighting the role of limited dispersal in shaping current genetic patterns. The integration of mitochondrial and nuclear genomic data provided a comprehensive view of the evolutionary history of P. fluviatilis, revealing both deep historical divergence and recent admixture events. The existence of multiple glacial refugia and subsequent secondary contact underscores the complexity of postglacial recolonization processes in freshwater fauna. These findings advance our understanding of how historical and contemporary factors interact to shape biodiversity across Europe.", "doi": "10.1002/ece3.73502", "pmid": "42023045", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13099172"}, {"db": "pii", "key": "ECE373502"}], "notes": [], "created": "2026-05-11T11:47:22.623Z", "modified": "2026-05-11T11:47:22.933Z"}, {"entity": "publication", "iuid": "d07dfbb5faf14d66a0758d483af8d8b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07dfbb5faf14d66a0758d483af8d8b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07dfbb5faf14d66a0758d483af8d8b4"}}, "title": "Bite-DNA Shows Substantial Browsing on Willows (Salix spp.) by North American Bison in Yellowstone National Park.", "authors": [{"family": "Jansson", "given": "Julia L", "initials": "JL"}, {"family": "Spitzer", "given": "Robert", "initials": "R", "orcid": "0000-0003-2753-1912", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c48a231a06f41b395bd2c7d98b2b0b2.json"}}, {"family": "Brealey", "given": "Jaelle Caitlin", "initials": "JC"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1246-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccdce43407204828b73bce24fc4e6453.json"}}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "16", "issue": "4", "pages": "e73354"}, "abstract": "Riparian willows (Salix spp.) in Yellowstone National Park have long been shaped by ungulate browsing, yet the specific contribution of individual herbivore species remains unclear. We applied a bite-DNA metabarcoding approach, extracting saliva DNA from browsed willow twigs, to directly identify the browsing community across six northern range riparian sites. Mammalian DNA was successfully assigned for more than half of the collected bite samples, revealing browsing by moose (Alces alces), North American bison (Bison bison), elk (Cervus canadensis), deer (Odocoileus sp.), bighorn sheep (Ovis canadensis), and jackrabbit (Lepus townsendii). Contrary to the traditional view of bison as primarily grazers, bite-DNA showed that bison were the most frequent browsers of willows, present at all sites and contributing the majority of browsing bites. Elk, historically considered the primary browser on riparian shrubs, were detected less often, whereas mule deer browsing was consistently recorded and frequently exceeded elk. Browsing height largely overlapped among species and was significantly higher for bighorn sheep than for bison and mule deer. Diameter of browsed twigs did not differ significantly between species. Browsing composition varied locally without clear spatial patterns, suggesting that site-level factors shape where different ungulates browse willows. Our results demonstrate substantial bison browsing on riparian willows and highlight shifting herbivore impacts on Yellowstone's riparian ecosystems.", "doi": "10.1002/ece3.73354", "pmid": "42040859", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13106989"}, {"db": "pii", "key": "ECE373354"}, {"db": "Dryad", "key": "10.5061/dryad.gtht76j1w"}], "notes": [], "created": "2026-06-08T17:24:50.294Z", "modified": "2026-06-08T17:26:16.368Z"}, {"entity": "publication", "iuid": "0c35ae7c18b94e239d19318c61b04c7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c35ae7c18b94e239d19318c61b04c7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c35ae7c18b94e239d19318c61b04c7a"}}, "title": "Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.", "authors": [{"family": "L\u00f3pez Clinton", "given": "Samantha", "initials": "S", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/46b97ad0ac8541dc807e570724e58c69.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "15", "issue": "9", "pages": "e72163"}, "abstract": "Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.", "doi": "10.1002/ece3.72163", "pmid": "40964625", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440566"}, {"db": "pii", "key": "ECE372163"}], "notes": [], "created": "2025-11-19T08:12:39.732Z", "modified": "2025-11-28T10:40:00.285Z"}, {"entity": "publication", "iuid": "c245dc8469a84cbdb2c65f2c31e9c295", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c245dc8469a84cbdb2c65f2c31e9c295.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c245dc8469a84cbdb2c65f2c31e9c295"}}, "title": "Applying Deep Learning to Quantify Drivers of Long-Term Ecological Change in a Swedish Marine Protected Area.", "authors": [{"family": "Nilsson", "given": "Christian L", "initials": "CL", "orcid": "0009-0005-6356-2152", "researcher": {"href": "https://publications.scilifelab.se/researcher/692506bc15454c6c99126379028d6d6b.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S"}, {"family": "Burman", "given": "Emil", "initials": "E"}, {"family": "Germishuys", "given": "Jurie", "initials": "J"}, {"family": "Obst", "given": "Matthias", "initials": "M", "orcid": "0000-0003-0264-9631", "researcher": {"href": "https://publications.scilifelab.se/researcher/03489369c77b4208b48f006a0db3bb84.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "15", "issue": "9", "pages": "e72091", "issn-l": "2045-7758"}, "abstract": "In this study, we trained an object-detection model to classify 17 benthic invertebrate taxa in archived footage of a study site on the northern west coast of Sweden (a wall section of the Koster Fjord) within the Swedish marine protected area Kosterhavet National Park. The model displayed a mean average precision score of 0.738 and was applied to footage from 1997 to 2023, generating a dataset of 72,369 occurrence records. The dataset was used to quantify depth distributions and abundance trends of both individual taxa and functional groups over time. Depth distributions for 15 of 17 taxa occurred at depths \u2265 45 m. Distributions of 11 taxa aligned with empirical observations, and for the remaining six taxa, we propose expanded depth distributions in the area. Abundances over time significantly increased for eight taxa and decreased for five taxa, while the overall community structure throughout the study period shifted toward smaller, more heat-tolerant suspension feeders. We found that temperature preference and size were significant drivers of the observed abundance trends in individual taxa. Community structure was altered by the loss of large, heat-sensitive taxa to greater depths due to increased temperatures. We also observed a strong trend of increasing abundances in the remaining community, including six trawling-sensitive taxa, highlighting the effectiveness of the park's protective measures. To protect key cold-water species, we suggest that current fishery regulations of the national park should be expanded to deeper (colder) waters and that new marine protected areas should also be established in deep waters. Our study demonstrates the application potential of video surveillance combined with deep-learning technology, and we recommend the implementation of standardized video monitoring in marine ecosystem management.", "doi": "10.1002/ece3.72091", "pmid": "40904377", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12404701"}, {"db": "pii", "key": "ECE372091"}], "notes": [], "created": "2025-11-28T10:39:55.103Z", "modified": "2025-11-28T10:39:55.173Z"}, {"entity": "publication", "iuid": "f77da0ef90c647a0af9d18b2b04042f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f77da0ef90c647a0af9d18b2b04042f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f77da0ef90c647a0af9d18b2b04042f0"}}, "title": "Gone With the Wind: Exploring a Vanished Rock Dove, Columba livia, Hybrid Zone in the Sahara Desert.", "authors": [{"family": "Hern\u00e1ndez-Alonso", "given": "Germ\u00e1n", "initials": "G", "orcid": "0000-0001-6065-1428", "researcher": {"href": "https://publications.scilifelab.se/researcher/408d39dcc0c24431816561f71350cb0f.json"}}, {"family": "van Grouw", "given": "Hein", "initials": "H"}, {"family": "Farahani", "given": "Motahare F", "initials": "MF"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "15", "issue": "9", "pages": "e72061"}, "abstract": "Rock doves (Columba livia) are the wild ancestor of domestic and feral pigeons and had a wide distribution across Eurasia and the northern part of Africa. West African rock doves have been identified as genetically distinct from all other populations, possibly representing a distinct species. This divergence is hypothesized to have arisen through cycles of allopatry during the dry and wet Sahara periods. Based on the Refugia Theory and observed admixture patterns, it was proposed that a hybrid zone existed in the Sahara during its last green period, playing a critical role in the speciation of West African rock doves. This project aims to test the existence and location of this vanished hybrid zone by analyzing whole-genome sequences from six historical rock doves from previously unsampled populations in the Central Sahara and West Africa, along with published genomic data. By exploring population structure, genetic diversity, and admixture patterns, our results confirm the existence of the hybrid zone, likely located around the mountainous regions of northwest Africa. To explain the observed genetic differentiation of West African rock doves, we propose a four-step scenario involving speciation by reinforcement. Finally, we support a species-level taxonomic arrangement to designate the West African rock dove as C. gymnocycla.", "doi": "10.1002/ece3.72061", "pmid": "40896089", "labels": {"Ancient DNA": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12391023"}, {"db": "pii", "key": "ECE372061"}, {"db": "figshare", "key": "10.6084/m9.figshare.29267132"}], "notes": [], "created": "2025-11-05T07:40:54.780Z", "modified": "2025-11-19T07:57:17.516Z"}, {"entity": "publication", "iuid": "24d4fbfa02774c67bc52b35054cf8840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24d4fbfa02774c67bc52b35054cf8840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24d4fbfa02774c67bc52b35054cf8840"}}, "title": "Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).", "authors": [{"family": "Thureborn", "given": "Olle", "initials": "O", "orcid": "0000-0002-9609-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e3d14e6d70a454babea2bbc6e0f9fc2.json"}}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N", "orcid": "0000-0002-4276-9366", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4b4d15d30e64e2c8a1a5fc0a96b9671.json"}}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG", "orcid": "0000-0003-3618-4676", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ebbe5772ea242cab27785ab8cddcdf8.json"}}, {"family": "Rydin", "given": "Catarina", "initials": "C", "orcid": "0000-0002-3347-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/70fff179e5b549c182dd7929b20f2e22.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "14", "issue": "1", "pages": "e10868", "issn-l": "2045-7758"}, "abstract": "Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.", "doi": "10.1002/ece3.10868", "pmid": "38274863", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10809029"}, {"db": "pii", "key": "ECE310868"}, {"db": "Dryad", "key": "10.5061/dryad.80gb5mkx4"}], "notes": [], "created": "2024-03-14T11:14:28.589Z", "modified": "2025-02-28T14:09:54.820Z"}, {"entity": "publication", "iuid": "6cf92d6cc0394d27ada92112aeec7a98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cf92d6cc0394d27ada92112aeec7a98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cf92d6cc0394d27ada92112aeec7a98"}}, "title": "Retention of essential fatty acids in fish differs by species, habitat use and nutritional quality of prey.", "authors": [{"family": "Bandara", "given": "Tharindu", "initials": "T", "orcid": "0000-0002-7211-6374", "researcher": {"href": "https://publications.scilifelab.se/researcher/75c8f752dfe249199064b480bcfeebcc.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-7819-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/812b8d6654af4482a308367f052f64c7.json"}}, {"family": "Lau", "given": "Danny Chun Pong", "initials": "DCP", "orcid": "0000-0002-3246-7508", "researcher": {"href": "https://publications.scilifelab.se/researcher/28aa8ed05fc64662b9a72cf4bde0e59b.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "13", "issue": "6", "pages": "e10158", "issn-l": "2045-7758"}, "abstract": "Algae-produced long-chain polyunsaturated fatty acids (LC-PUFA; with \u226520 carbon atoms) are key biomolecules for consumer production and animal health. They are transferred to higher trophic levels and accumulated in food chains. However, LC-PUFA accumulation in consumers and their trophic transfer vary with the diet quality and the physiological demand for LC-PUFA of consumers. The goal of this study was to investigate spatial and taxonomic differences in LC-PUFA retention of coastal fish predators that potentially differ in their habitat use (benthic versus pelagic) and prey quality. We analyzed the fatty acid (FA) composition of common fish species, namely roach and European perch, as well as their potential prey from benthic and pelagic habitats in three bays of the northern Baltic Sea. We then assessed whether the fish LC-PUFA retention differed between species and among the study bays with different diet quality, that is, LC-PUFA availability. Our data indicated taxon-specific differences in the retention of LC-PUFA and their precursor FA in fish (i.e., short-chain PUFA with <20 carbon atoms). Perch did not show any spatial variation in the retention of all these FA, while roach showed spatial differences in the retention of docosahexaenoic acid (DHA) and their precursor FA, but not eicosapentaenoic acid (EPA). Data suggest that diet quality and trophic reliance on benthic prey underlay the DHA retention differences in roach. Although the PUFA supply might differ among sites, the low spatial variation in LC-PUFA content of perch and roach indicates that both fishes were able to selectively retain dietary LC-PUFA. Climate change together with other existing human-caused environmental stressors are expected to alter the algal assemblages and lower their LC-PUFA supply for aquatic food webs. Our findings imply that these stressors will pose heterogeneous impacts on different fish predators. We advocate further investigations on how environmental changes would affect the nutritional quality of the basal trophic level, and their subsequent impacts on LC-PUFA retention, trophic ecology, and performance of individual fish species.", "doi": "10.1002/ece3.10158", "pmid": "37274152", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10234757"}, {"db": "pii", "key": "ECE310158"}], "notes": [], "created": "2023-08-30T07:04:25.673Z", "modified": "2025-10-17T13:03:13.901Z"}, {"entity": "publication", "iuid": "1992fff5e6cc41f0934b9b39ee3b72f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1992fff5e6cc41f0934b9b39ee3b72f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1992fff5e6cc41f0934b9b39ee3b72f7"}}, "title": "Different spatial structure of plant-associated fungal communities above- and belowground.", "authors": [{"family": "Faticov", "given": "Maria", "initials": "M", "orcid": "0000-0001-8206-9332", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd00e5ee400e440ba76d1010f5cbe7d9.json"}}, {"family": "Abdelfattah", "given": "Ahmed", "initials": "A"}, {"family": "Hamb\u00e4ck", "given": "Peter", "initials": "P", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "13", "issue": "5", "pages": "e10065", "issn-l": "2045-7758"}, "abstract": "The distribution and community assembly of above- and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant-microbe interactions and plant health. Depending on how microbial communities are structured, we can expect different effects of the microbial community on the health of individual plants and on ecosystem processes. Importantly, the relative role of different factors will likely differ with the scale examined. Here, we address the driving factors at a landscape level, where each individual unit (oak trees) is accessible to a joint species pool. This allowed to quantify the relative effect of environmental factors and dispersal on the distribution of two types of fungal communities: those associated with the leaves and those associated with the soil of Quercus robur trees in a landscape in southwestern Finland. Within each community type, we compared the role of microclimatic, phenological, and spatial variables, and across community types, we examined the degree of association between the respective communities. Most of the variation in the foliar fungal community was found within trees, whereas soil fungal community composition showed positive spatial autocorrelation up to 50 m. Microclimate, tree phenology, and tree spatial connectivity explained little variation in the foliar and soil fungal communities. Foliar and soil fungal communities differed strongly in community structure, with no significant concordance detected between them. We provide evidence that foliar and soil fungal communities assemble independent of each other and are structured by different ecological processes.", "doi": "10.1002/ece3.10065", "pmid": "37223309", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10200691"}, {"db": "pii", "key": "ECE310065"}, {"db": "figshare", "key": "10.6084/m9.figshare.22687594"}], "notes": [], "created": "2023-10-11T09:16:14.644Z", "modified": "2024-01-16T13:48:33.507Z"}, {"entity": "publication", "iuid": "90b62e312a974e36bc3ecd5d37537c5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90b62e312a974e36bc3ecd5d37537c5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90b62e312a974e36bc3ecd5d37537c5e"}}, "title": "Species composition of shoreline wolf spider communities vary with salinity, but their diets vary with wrack inflow.", "authors": [{"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}, {"family": "Cirtwill", "given": "Alyssa R", "initials": "AR"}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Hoffmann", "given": "Alexander", "initials": "A"}, {"family": "Langbak", "given": "Marie", "initials": "M"}, {"family": "\u00c5hl\u00e9n", "given": "David", "initials": "D"}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "12", "pages": "e9701", "issn-l": "2045-7758"}, "abstract": "Wolf spiders are typically the most common group of arthropod predators on both lake and marine shorelines because of the high prey availability in these habitats. However, shores are also harsh environments due to flooding and, in proximity to marine waters, to toxic salinity levels. Here, we describe the spider community, prey availabilities, and spider diets between shoreline sites with different salinities, albeit with comparatively small differences (5\u2030 vs. 7\u2030). Despite the small environmental differences, spider communities between lower and higher saline sites showed an almost complete species turnover. At the same time, differences in prey availability or spider gut contents did not match changes in spider species composition but rather changed with habitat characteristics within a region, where spiders collected at sites with thick wrack beds had a different diet than sites with little wrack. These data suggest that shifts in spider communities are due to habitat characteristics other than prey availabilities, and the most likely candidate restricting species in high salinity would be saline sensitivity. At the same time, species absence from low-saline habitats remains unresolved.", "doi": "10.1002/ece3.9701", "pmid": "36590338", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9797640"}, {"db": "pii", "key": "ECE39701"}, {"db": "Dryad", "key": "10.5061/dryad.gxd2547qk"}], "notes": [], "created": "2023-10-04T11:56:08.364Z", "modified": "2024-01-16T13:48:34.358Z"}, {"entity": "publication", "iuid": "b5b41e59d80945f0b7a009d2dd268562", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562"}}, "title": "A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "10", "pages": "e9440", "issn-l": "2045-7758"}, "abstract": "Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome-wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate-dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean F ST = 0.23-0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's D NS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (d XY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome-wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.", "doi": "10.1002/ece3.9440", "pmid": "36311399", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9608792"}, {"db": "pii", "key": "ECE39440"}], "notes": [], "created": "2022-11-29T09:34:26.276Z", "modified": "2022-11-29T09:34:26.313Z"}, {"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": "a72cb32990a74c7e89f0d8c5a229cf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a72cb32990a74c7e89f0d8c5a229cf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a72cb32990a74c7e89f0d8c5a229cf56"}}, "title": "Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden.", "authors": [{"family": "Ellerstrand", "given": "Simon Jacobsen", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Choudhury", "given": "Shruti", "initials": "S"}, {"family": "Svensson", "given": "Kajsa", "initials": "K"}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}, {"family": "Kirkeby", "given": "Carsten", "initials": "C", "orcid": "0000-0001-9292-5526", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5e9edff945441609746525fdfc2d275.json"}}, {"family": "Powell", "given": "Daniel", "initials": "D"}, {"family": "Schlyter", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-1244-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/38df140cdd0e4a1693da808131833114.json"}}, {"family": "J\u00f6nsson", "given": "Anna Maria", "initials": "AM", "orcid": "0000-0003-2938-4725", "researcher": {"href": "https://publications.scilifelab.se/researcher/680836380a394bcdb00036fa3a6632da.json"}}, {"family": "Brydegaard", "given": "Mikkel", "initials": "M", "orcid": "0000-0003-0586-664X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b87150cf4c574f10acb2265d508dba8b.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "12", "issue": "7", "pages": "e9078"}, "abstract": "The Eurasian spruce bark beetle, Ips typographus, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few kilometers. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in I. typographus typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of I. typographus in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Str\u00f6msund (63\u00b0 46' 8\u2033 N) in the north to Nyteboda (56\u00b0 8' 50\u2033 N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (F ST) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of I. typographus in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.", "doi": "10.1002/ece3.9078", "pmid": "35822111", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9260063"}, {"db": "pii", "key": "ECE39078"}], "notes": [], "created": "2022-08-19T08:38:39.655Z", "modified": "2024-01-16T13:48:35.960Z"}, {"entity": "publication", "iuid": "436dafbcf3644397a7fb3f855f9e961a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/436dafbcf3644397a7fb3f855f9e961a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/436dafbcf3644397a7fb3f855f9e961a"}}, "title": "Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.", "authors": [{"family": "Eshghi Sahraei", "given": "Shadi", "initials": "S", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.json"}}, {"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Kluting", "given": "Kerri", "initials": "K", "orcid": "0000-0002-2328-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc941190363e475e818618f5ede34218.json"}}, {"family": "Zakieh", "given": "Mustafa", "initials": "M"}, {"family": "Rydin", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-7582-3998", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee9ea3f8490b43128a5710c693855584.json"}}, {"family": "Hytteborn", "given": "H\u00e5kan", "initials": "H"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "3", "pages": "e8676", "issn-l": "2045-7758"}, "abstract": "Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large-scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungs\u00e4ngen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.", "doi": "10.1002/ece3.8676", "pmid": "35342585", "labels": {"NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8928899"}, {"db": "pii", "key": "ECE38676"}], "notes": [], "created": "2022-03-29T04:46:34.688Z", "modified": "2024-01-16T13:48:37.364Z"}, {"entity": "publication", "iuid": "66a9893d525842b98b798790943c9b82", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66a9893d525842b98b798790943c9b82.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66a9893d525842b98b798790943c9b82"}}, "title": "Integrating omics to characterize eco-physiological adaptations: How moose diet and metabolism differ across biogeographic zones.", "authors": [{"family": "Fohringer", "given": "Christian", "initials": "C", "orcid": "0000-0003-0257-6743", "researcher": {"href": "https://publications.scilifelab.se/researcher/07a2b5abe7994953a80b2b157eb67d9c.json"}}, {"family": "Dudka", "given": "Ilona", "initials": "I"}, {"family": "Spitzer", "given": "Robert", "initials": "R"}, {"family": "Stenbacka", "given": "Fredrik", "initials": "F"}, {"family": "Rzhepishevska", "given": "Olena", "initials": "O"}, {"family": "Cromsigt", "given": "Joris P G M", "initials": "JPGM"}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G"}, {"family": "Ericsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Singh", "given": "Navinder J", "initials": "NJ"}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "11", "issue": "7", "pages": "3159-3183", "issn-l": "2045-7758"}, "abstract": "With accelerated land conversion and global heating at northern latitudes, it becomes crucial to understand, how life histories of animals in extreme environments adapt to these changes. Animals may either adapt by adjusting foraging behavior or through physiological responses, including adjusting their energy metabolism or both. Until now, it has been difficult to study such adaptations in free-ranging animals due to methodological constraints that prevent extensive spatiotemporal coverage of ecological and physiological data.Through a novel approach of combining DNA-metabarcoding and nuclear magnetic resonance (NMR)-based metabolomics, we aim to elucidate the links between diets and metabolism in Scandinavian moose Alces alces over three biogeographic zones using a unique dataset of 265 marked individuals.Based on 17 diet items, we identified four different classes of diet types that match browse species availability in respective ecoregions in northern Sweden. Individuals in the boreal zone consumed predominantly pine and had the least diverse diets, while individuals with highest diet diversity occurred in the coastal areas. Males exhibited lower average diet diversity than females.We identified several molecular markers indicating metabolic constraints linked to diet constraints in terms of food availability during winter. While animals consuming pine had higher lipid, phospocholine, and glycerophosphocholine concentrations in their serum than other diet types, birch- and willow/aspen-rich diets exhibit elevated concentrations of several amino acids. The individuals with highest diet diversity had increased levels of ketone bodies, indicating extensive periods of starvation for these individuals.Our results show how the adaptive capacity of moose at the eco-physiological level varies over a large eco-geographic scale and how it responds to land use pressures. In light of extensive ongoing climate and land use changes, these findings pave the way for future scenario building for animal adaptive capacity.", "doi": "10.1002/ece3.7265", "pmid": "33841775", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ECE37265"}, {"db": "pmc", "key": "PMC8019042"}, {"db": "Dryad", "key": "10.5061/dryad.9s4mw6mfr"}], "notes": [], "created": "2021-12-05T14:21:19.343Z", "modified": "2025-10-17T13:03:56.075Z"}, {"entity": "publication", "iuid": "2cb43ab5664d469db94c06796aaa296d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cb43ab5664d469db94c06796aaa296d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cb43ab5664d469db94c06796aaa296d"}}, "title": "Leaf shape in Populus tremula is a complex, omnigenic trait.", "authors": [{"family": "M\u00e4hler", "given": "Niklas", "initials": "N", "orcid": "0000-0003-2673-9113", "researcher": {"href": "https://publications.scilifelab.se/researcher/581734b34e9948438243f0c105e1094f.json"}}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B", "orcid": "0000-0002-9771-467X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12527c57f62e4a46b758e061ba3f80b1.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Vu\u010dak", "given": "Matej", "initials": "M", "orcid": "0000-0002-3181-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e64ed41987741f392a5c352ec92480a.json"}}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES", "orcid": "0000-0002-9788-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/3919edd84f254870a5644770152360b6.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications.scilifelab.se/researcher/987fbb5763c74f6895bee64630528d8d.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "21", "pages": "11922-11940", "issn-l": "2045-7758"}, "abstract": "Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome-wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA-Seq data that we used to perform gene co-expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.", "doi": "10.1002/ece3.6691", "pmid": "33209260", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36691"}, {"db": "pmc", "key": "PMC7663049"}, {"db": "Dryad", "key": "10.5061/dryad.3n5tb2rdt"}], "notes": [], "created": "2020-12-07T16:34:40.237Z", "modified": "2024-01-16T13:48:41.464Z"}, {"entity": "publication", "iuid": "77767504e98e44099323eb90a6f4d2c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77767504e98e44099323eb90a6f4d2c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77767504e98e44099323eb90a6f4d2c0"}}, "title": "Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient.", "authors": [{"family": "Abrego", "given": "Nerea", "initials": "N", "orcid": "0000-0001-6347-6127", "researcher": {"href": "https://publications.scilifelab.se/researcher/547484556cdb43088e953f78e97f416e.json"}}, {"family": "Huotari", "given": "Tea", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}, {"family": "Tikhonov", "given": "Gleb", "initials": "G", "orcid": "0000-0003-3040-0307", "researcher": {"href": "https://publications.scilifelab.se/researcher/83ce2dc9d0304b0bb08de20ab8354446.json"}}, {"family": "Somervuo", "given": "Panu", "initials": "P", "orcid": "0000-0003-3121-4047", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc4e5cf7203b4a2084034b7569dcd02c.json"}}, {"family": "Martin Schmidt", "given": "Niels", "initials": "N", "orcid": "0000-0002-4166-6218", "researcher": {"href": "https://publications.scilifelab.se/researcher/0248915d131f49869c9c34312664b57a.json"}}, {"family": "Ovaskainen", "given": "Otso", "initials": "O", "orcid": "0000-0001-9750-4421", "researcher": {"href": "https://publications.scilifelab.se/researcher/c754e5e5dc4244908a350074724a0418.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "16", "pages": "8989-9002", "issn-l": "2045-7758"}, "abstract": "How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.", "doi": "10.1002/ece3.6604", "pmid": "32884673", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36604"}, {"db": "pmc", "key": "PMC7452766"}, {"db": "Dryad", "key": "10.5061/dryad.9dr6j0c"}], "notes": [], "created": "2020-09-15T06:17:19.364Z", "modified": "2024-01-16T13:48:42.043Z"}, {"entity": "publication", "iuid": "5d3afacdca744fef83a8b327dedfaf5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d3afacdca744fef83a8b327dedfaf5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d3afacdca744fef83a8b327dedfaf5c"}}, "title": "Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.", "authors": [{"family": "Gonzalez", "given": "Francisco", "initials": "F"}, {"family": "Borrero-Echeverry", "given": "Felipe", "initials": "F"}, {"family": "J\u00f3svai", "given": "J\u00falia K", "initials": "JK"}, {"family": "Strandh", "given": "Maria", "initials": "M"}, {"family": "Unelius", "given": "C Rikard", "initials": "CR"}, {"family": "T\u00f3th", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Witzgall", "given": "Peter", "initials": "P", "orcid": "0000-0002-4697-3380", "researcher": {"href": "https://publications.scilifelab.se/researcher/548d4ff93a3f488e8133e5f7b1f79097.json"}}, {"family": "Bengtsson", "given": "Marie", "initials": "M"}, {"family": "Walker", "given": "William B", "initials": "WB"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "14", "pages": "7334-7348", "issn-l": "2045-7758"}, "abstract": "The search for mates and food is mediated by volatile chemicals. Insects sense food odorants and sex pheromones through odorant receptors (ORs) and pheromone receptors (PRs), which are expressed in olfactory sensory neurons. Molecular phylogenetics of ORs, informed by behavioral and functional data, generates sound hypotheses for the identification of semiochemicals driving olfactory behavior. Studying orthologous receptors and their ligands across taxa affords insights into the role of chemical communication in reproductive isolation and phylogenetic divergence. The female sex pheromone of green budworm moth Hedya nubiferana (Lepidoptera, Totricidae) is a blend of two unsaturated acetates, only a blend of both elicits male attraction. Females produce in addition codlemone, which is the sex pheromone of another tortricid, codling moth Cydia pomonella. Codlemone also attracts green budworm moth males. Concomitantly, green budworm and codling moth males are attracted to the host plant volatile pear ester. A congruent behavioral response to the same pheromone and plant volatile in two tortricid species suggests co-occurrence of dedicated olfactory channels. In codling moth, one PR is tuned to both compounds, the sex pheromone codlemone and the plant volatile pear ester. Our phylogenetic analysis finds that green budworm moth expresses an orthologous PR gene. Shared ancestry, and high levels of amino acid identity and sequence similarity, in codling and green budworm moth PRs offer an explanation for parallel attraction of both species to the same compounds. A conserved olfactory channel for a sex pheromone and a host plant volatile substantiates the alliance of social and habitat signals in insect chemical communication. Field attraction assays confirm that in silico investigations of ORs afford powerful predictions for an efficient identification of behavior-modifying semiochemicals, for an improved understanding of the mechanisms of host plant attraction in insect herbivores and for the further development of sustainable insect control.", "doi": "10.1002/ece3.6458", "pmid": "32760532", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36458"}, {"db": "pmc", "key": "PMC7391548"}], "notes": [], "created": "2020-12-07T16:29:50.620Z", "modified": "2024-01-16T13:48:42.276Z"}, {"entity": "publication", "iuid": "8cb53a7450cc4a7e80432a058a5d263d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cb53a7450cc4a7e80432a058a5d263d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cb53a7450cc4a7e80432a058a5d263d"}}, "title": "Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.", "authors": [{"family": "Zhong", "given": "Xiuqin", "initials": "X", "orcid": "0000-0002-4772-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1847f16fd2a4d1cac925c7b89b70684.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "13", "pages": "6421-6434", "issn-l": "2045-7758"}, "abstract": "Different host species often differ considerably in susceptibility to a given pathogen, but the causes of such differences are rarely known. The natural hosts of the tick-transmitted bacterium Borrelia afzelii, which is one of causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Previous studies have shown that B. afzelii-infected bank voles (Myodes glareolus) have about ten times higher bacterial load than infected yellow-necked mice (Apodemus flavicollis), indicating that these two species differ in resistance. In this study, we compared the immune response to B. afzelii infection in these host species by using RNA sequencing to quantify gene expression in spleen. Gene set enrichment analysis (GSEA) showed that several immune pathways were down-regulated in infected animals in both bank voles and yellow-necked mice. Moreover, IFN\u03b1 response was up-regulated in B. afzelii-infected yellow-necked mice, while IL6 signaling and the complement pathway were down-regulated in infected bank voles; differences in regulation of these three pathways between bank voles and yellow-necked mice could thus contribute to the difference in resistance to B. afzelii between the species. This study provides knowledge of gene expression induced by a zoonotic pathogen in its natural host, and possible species-specific regulation of immune responses associated with resistance.", "doi": "10.1002/ece3.6377", "pmid": "32724523", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36377"}, {"db": "pmc", "key": "PMC7381583"}, {"db": "Dryad", "key": "10.5061/dryad.t1g1jwt02"}], "notes": [], "created": "2020-12-07T16:29:59.033Z", "modified": "2024-01-16T13:48:42.326Z"}, {"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": "7e4ab87cd1154a83990d12f76cad4ee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e4ab87cd1154a83990d12f76cad4ee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e4ab87cd1154a83990d12f76cad4ee8"}}, "title": "Impact of demography on linked selection in two outcrossing Brassicaceae species.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Horvath", "given": "Robert", "initials": "R"}, {"family": "H\u00e4m\u00e4l\u00e4", "given": "Tuomas", "initials": "T", "orcid": "0000-0001-8306-3397", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac9fe6733a03417fbd5f6ca780c5589f.json"}}, {"family": "Savolainen", "given": "Outi", "initials": "O"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2019-09-00", "journal": {"volume": "9", "issn": "2045-7758", "issue": "17", "pages": "9532-9545", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.", "doi": "10.1002/ece3.5463", "pmid": "31534673", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE35463"}, {"db": "pmc", "key": "PMC6745670"}], "notes": [], "created": "2019-12-03T13:10:35.648Z", "modified": "2024-01-16T13:48:43.958Z"}, {"entity": "publication", "iuid": "d205bac97d41475f912f6b0f5e039ed6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d205bac97d41475f912f6b0f5e039ed6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d205bac97d41475f912f6b0f5e039ed6"}}, "title": "An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods", "authors": [{"family": "Krizsan", "given": "Sophie J", "initials": "SJ"}, {"family": "Mateos-Rivera", "given": "Alejandro", "initials": "A"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Felton", "given": "Annika", "initials": "A"}, {"family": "Anttila", "given": "Anne", "initials": "A"}, {"family": "Ramin", "given": "Mohammad", "initials": "M"}, {"family": "Vaga", "given": "Merko", "initials": "M"}, {"family": "Gidlund", "given": "Helena", "initials": "H"}, {"family": "Huhtanen", "given": "Pekka", "initials": "P"}], "type": "journal-article", "published": "2018-04-00", "journal": {"volume": "8", "issn": "2045-7758", "issue": "8", "pages": "4183-4196", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": null, "doi": "10.1002/ece3.3920", "pmid": "29721290", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:07:08.239Z", "modified": "2024-01-16T13:48:46.635Z"}, {"entity": "publication", "iuid": "16b5921c211e430d85567128299c2629", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16b5921c211e430d85567128299c2629.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16b5921c211e430d85567128299c2629"}}, "title": "Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone", "authors": [{"family": "Vowles", "given": "Tage", "initials": "T"}, {"family": "Lindwall", "given": "Frida", "initials": "F"}, {"family": "Ekblad", "given": "Alf", "initials": "A"}, {"family": "Bahram", "given": "Mohammad", "initials": "M"}, {"family": "Furneaux", "given": "Brendan R", "initials": "BR"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Bj\u00f6rk", "given": "Robert G", "initials": "RG"}], "type": "journal-article", "published": "2018-01-00", "journal": {"volume": "8", "issn": "2045-7758", "issue": "2", "pages": "1019-1030", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": null, "doi": "10.1002/ece3.3657", "pmid": "29375775", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-06-25T14:11:39.730Z", "modified": "2024-01-16T13:48:47.237Z"}, {"entity": "publication", "iuid": "d07e00d31a13460682d9cb1e01855da0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07e00d31a13460682d9cb1e01855da0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07e00d31a13460682d9cb1e01855da0"}}, "title": "Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water", "authors": [{"family": "Bailey", "given": "Allison", "initials": "A"}, {"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Thor", "given": "Peter", "initials": "P"}, {"family": "Browman", "given": "Howard I", "initials": "HI"}, {"family": "Bjelland", "given": "Reidun", "initials": "R"}, {"family": "Shema", "given": "Steven", "initials": "S"}, {"family": "Fields", "given": "David M", "initials": "DM"}, {"family": "Runge", "given": "Jeffrey A", "initials": "JA"}, {"family": "Thompson", "given": "Cameron", "initials": "C"}, {"family": "Hop", "given": "Haakon", "initials": "H"}], "type": "journal-article", "published": "2017-09-00", "journal": {"volume": "7", "issn": "2045-7758", "issue": "18", "pages": "7145-7160", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": null, "doi": "10.1002/ece3.3063", "pmid": "28944006", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Calanus glacialis Transcriptome or Gene expression", "key": "PRJNA352656"}, {"db": "SRA", "description": null, "key": "SRP092884"}], "notes": [], "created": "2018-01-09T20:49:54.365Z", "modified": "2020-01-21T13:56:14.887Z"}, {"entity": "publication", "iuid": "17d3f0529e1043fb8ddc82759f401c5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17d3f0529e1043fb8ddc82759f401c5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17d3f0529e1043fb8ddc82759f401c5f"}}, "title": "Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.", "authors": [{"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}, {"family": "Weingartner", "given": "Elisabeth", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Wirta", "given": "Helena", "initials": "H"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "6", "issn": "2045-7758", "issue": "23", "pages": "8431-8439", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "Inflow of matter and organisms may strongly affect the local density and diversity of organisms. This effect is particularly evident on shores where organisms with aquatic larval stages enter the terrestrial food web. The identities of such trophic links are not easily estimated as spiders, a dominant group of shoreline predator, have external digestion. We compared trophic links and the prey diversity of spiders on different shore types along the Baltic Sea: on open shores and on shores with a reed belt bordering the water. A priori, we hypothesized that the physical structure of the shoreline reduces the flow between ecosystem and the subsidies across the sea-land interface. To circumvent the lack of morphologically detectable remains of spider prey, we used a combination of stable isotope and molecular gut content analyses. The two tools used for diet analysis revealed complementary information on spider diets. The stable isotope analysis indicated that spiders on open shores had a marine signal of carbon isotopes, while spiders on reedy shores had a terrestrial signal. The molecular analysis revealed a diverse array of dipteran and lepidopteran prey, where spiders on open and reedy shores shared a similar diet with a comparable proportion of chironomids, the larvae of which live in the marine system. Comparing the methods suggests that differences in isotope composition of the two spider groups occurred because of differences in the chironomid diets: as larvae, chironomids of reedy shores likely fed on terrestrial detritus and acquired a terrestrial isotope signature, while chironomids of open shores utilized an algal diet and acquired a marine isotope signature. Our results illustrate how different methods of diet reconstruction may shed light on complementary aspects of nutrient transfer. Overall, they reveal that reed belts can reduce connectivity between habitats, but also function as a source of food for predators.", "doi": "10.1002/ece3.2536", "pmid": "28031795", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "ECE32536"}, {"db": "pmc", "key": "PMC5167037"}], "notes": [], "created": "2017-05-03T13:00:36.753Z", "modified": "2021-07-07T20:31:10.709Z"}, {"entity": "publication", "iuid": "62ea024c7e40454e83d316fcf1300f49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62ea024c7e40454e83d316fcf1300f49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62ea024c7e40454e83d316fcf1300f49"}}, "title": "Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?", "authors": [{"family": "Strand", "given": "Tanja M", "initials": "TM"}, {"family": "Segelbacher", "given": "Gernot", "initials": "G"}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Xiao", "given": "Lingyun", "initials": "L"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2012-02-00", "journal": {"volume": "2", "issn": "2045-7758", "issue": "2", "pages": "341-353", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here, we use both neutral and major histocompatibility complex (MHC) markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled 11 different populations; five continuous, three isolated, and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs) which both were found to be neutral, and two functional MHC genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented.", "doi": "10.1002/ece3.86", "pmid": "22423328", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3298947"}], "notes": [], "created": "2017-05-04T15:00:57.850Z", "modified": "2020-01-21T13:56:02.670Z"}], "created": "2017-05-09T09:12:27.925Z", "modified": "2020-11-27T13:14:08.805Z"}