{"entity": "journal", "iuid": "33fcb6c4a8c043859680e54f4216e5c7", "timestamp": "2026-04-20T21:21:10.889Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/BMC%20Ecol%20Evol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/BMC%20Ecol%20Evol"}}, "title": "BMC Ecol Evol", "issn": "2730-7182", "issn-l": null, "publications_count": 5, "publications": [{"entity": "publication", "iuid": "c050833f0c82481bb5fca4a4262261f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c050833f0c82481bb5fca4a4262261f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c050833f0c82481bb5fca4a4262261f2"}}, "title": "Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.", "authors": [{"family": "Yildirim", "given": "Y", "initials": "Y"}, {"family": "Kristensson", "given": "D", "initials": "D"}, {"family": "Outomuro", "given": "D", "initials": "D"}, {"family": "Mikolajewski", "given": "D", "initials": "D"}, {"family": "R\u00f6din M\u00f6rch", "given": "P", "initials": "P"}, {"family": "Sniegula", "given": "S", "initials": "S"}, {"family": "Johansson", "given": "F", "initials": "F"}], "type": "journal article", "published": "2024-02-03", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "24", "issue": "1", "pages": "19", "issn-l": null}, "abstract": "Describing geographical variation in morphology of organisms in combination with data on genetic differentiation and biogeography can provide important information on how natural selection shapes such variation. Here we study genetic structure using ddRAD seq and wing shape variation using geometric morphometrics in 14 populations of the damselfly Lestes sponsa along its latitudinal range in Europe.\n\nThe genetic analysis showed a significant, yet relatively weak population structure with high genetic heterozygosity and low inbreeding coefficients, indicating that neutral processes contributed very little to the observed wing shape differences. The genetic analysis also showed that some regions of the genome (about 10%) are putatively shaped by selection. The phylogenetic analysis showed that the Spanish and French populations were the ancestral ones with northern Swedish and Finnish populations being the most derived ones. We found that wing shape differed significantly among populations and showed a significant quadratic (but weak) relationship with latitude. This latitudinal relationship was largely attributed to allometric effects of wing size, but non-allometric variation also explained a portion of this relationship. However, wing shape showed no phylogenetic signal suggesting that lineage-specific variation did not contribute to the variation along the latitudinal gradient. In contrast, wing size, which is correlated with body size in L. sponsa, had a strong negative correlation with latitude.\n\nOur results suggest a relatively weak population structure among the sampled populations across Europe, but a clear differentiation between south and north populations. The observed geographic phenotypic variation in wing shape may have been affected by different local selection pressures or environmental effects.", "doi": "10.1186/s12862-024-02207-4", "pmid": "38308224", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10838002"}, {"db": "pii", "key": "10.1186/s12862-024-02207-4"}], "notes": [], "created": "2024-03-21T09:24:09.188Z", "modified": "2024-11-25T10:29:31.490Z"}, {"entity": "publication", "iuid": "4b75ebd89eb8484b9e4587ef0e570612", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b75ebd89eb8484b9e4587ef0e570612.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b75ebd89eb8484b9e4587ef0e570612"}}, "title": "Balancing selection on the complement system of a wild rodent.", "authors": [{"family": "Nandakumar", "given": "Mridula", "initials": "M"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2023-05-25", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "23", "issue": "1", "pages": "21", "issn-l": null}, "abstract": "Selection pressure exerted by pathogens can influence patterns of genetic diversity in the host. In the immune system especially, numerous genes encode proteins involved in antagonistic interactions with pathogens, paving the way for coevolution that results in increased genetic diversity as a consequence of balancing selection. The complement system is a key component of innate immunity. Many complement proteins interact directly with pathogens, either by recognising pathogen molecules for complement activation, or by serving as targets of pathogen immune evasion mechanisms. Complement genes can therefore be expected to be important targets of pathogen-mediated balancing selection, but analyses of such selection on this part of the immune system have been limited.\n\nUsing a population sample of whole-genome resequencing data from wild bank voles (n = 31), we estimated the extent of genetic diversity and tested for signatures of balancing selection in multiple complement genes (n = 44). Complement genes showed higher values of standardised \u03b2 (a statistic expected to be high under balancing selection) than the genome-wide average of protein coding genes. One complement gene, FCNA, a pattern recognition molecule that interacts directly with pathogens, was found to have a signature of balancing selection, as indicated by the Hudson-Kreitman-Aguad\u00e9 test (HKA) test. Scans for localised signatures of balancing selection in this gene indicated that the target of balancing selection was found in exonic regions involved in ligand binding.\n\nThe present study adds to the growing evidence that balancing selection may be an important evolutionary force on components of the innate immune system. The identified target in the complement system typifies the expectation that balancing selection acts on genes encoding proteins involved in direct interactions with pathogens.", "doi": "10.1186/s12862-023-02122-0", "pmid": "37231383", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10214634"}, {"db": "pii", "key": "10.1186/s12862-023-02122-0"}], "notes": [], "created": "2023-10-11T08:50:27.738Z", "modified": "2024-01-16T13:48:33.370Z"}, {"entity": "publication", "iuid": "8d88408f966c47f889a1837ae4c1b936", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d88408f966c47f889a1837ae4c1b936.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d88408f966c47f889a1837ae4c1b936"}}, "title": "Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex.", "authors": [{"family": "Ottenburghs", "given": "Jente", "initials": "J"}, {"family": "Honka", "given": "Johanna", "initials": "J"}, {"family": "Heikkinen", "given": "Marja E", "initials": "ME"}, {"family": "Madsen", "given": "Jesper", "initials": "J"}, {"family": "M\u00fcskens", "given": "Gerhard J D M", "initials": "GJDM"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2023-01-19", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "23", "issue": "1", "pages": "2", "issn-l": null}, "abstract": "Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus).\n\nFirst, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree.\n\nThe evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.", "doi": "10.1186/s12862-023-02103-3", "pmid": "36658479", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9854053"}, {"db": "pii", "key": "10.1186/s12862-023-02103-3"}], "notes": [], "created": "2023-11-30T13:15:16.114Z", "modified": "2024-01-16T13:48:34.115Z"}, {"entity": "publication", "iuid": "aeb500e0ef0b45969b3c981d10c0624f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb500e0ef0b45969b3c981d10c0624f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb500e0ef0b45969b3c981d10c0624f"}}, "title": "Population dynamics and demographic history of Eurasian collared lemmings.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Marangoni", "given": "Aurelio", "initials": "A"}, {"family": "Baca", "given": "Mateusz", "initials": "M"}, {"family": "Popovi\u0107", "given": "Danijela", "initials": "D"}, {"family": "Goropashnaya", "given": "Anna V", "initials": "AV"}, {"family": "Stewart", "given": "John R", "initials": "JR"}, {"family": "Knul", "given": "Monika V", "initials": "MV"}, {"family": "Noiret", "given": "Pierre", "initials": "P"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Jimenez", "given": "Elodie-Laure", "initials": "EL"}, {"family": "Abramson", "given": "Natalia I", "initials": "NI"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Kuzmina", "given": "Elena A", "initials": "EA"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Fedorov", "given": "Vadim B", "initials": "VB"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2022-11-03", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "issn-l": null, "volume": "22", "issue": "1", "pages": "126"}, "abstract": "Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.\n\nHere, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.\n\nThis study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.", "doi": "10.1186/s12862-022-02081-y", "pmid": "36329382", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9632076"}, {"db": "pii", "key": "10.1186/s12862-022-02081-y"}], "notes": [], "created": "2022-12-19T10:39:31.539Z", "modified": "2024-01-16T13:48:34.525Z"}, {"entity": "publication", "iuid": "2561d68da0bd4709abff07531e1c6b60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2561d68da0bd4709abff07531e1c6b60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2561d68da0bd4709abff07531e1c6b60"}}, "title": "Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).", "authors": [{"family": "Eriksson", "given": "J S", "initials": "JS", "orcid": "0000-0002-1303-730X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0df5892d479444caadecbc155894ad2.json"}}, {"family": "Bacon", "given": "C D", "initials": "CD"}, {"family": "Bennett", "given": "D J", "initials": "DJ"}, {"family": "Pfeil", "given": "B E", "initials": "BE"}, {"family": "Oxelman", "given": "B", "initials": "B"}, {"family": "Antonelli", "given": "A", "initials": "A"}], "type": "journal article", "published": "2021-06-02", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "21", "issue": "1", "pages": "107", "issn-l": null}, "abstract": "The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events.\n\nUsing target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus.\n\nHere, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.", "doi": "10.1186/s12862-021-01751-7", "pmid": "34078291", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-021-01751-7"}, {"db": "pmc", "key": "PMC8170824"}, {"db": "Dryad", "key": "10.5061/dryad.hqbzkh1fc"}], "notes": [], "created": "2021-10-01T09:00:24.434Z", "modified": "2021-12-06T13:46:16.831Z"}], "created": "2021-10-01T09:00:24.477Z", "modified": "2021-10-01T09:00:24.477Z"}