{"entity": "researcher", "timestamp": "2026-07-18T02:55:47.899Z", "family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "affiliations": ["Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058"}}, "publications": [{"entity": "publication", "iuid": "a1a66eb9378f48bcbb9c32923b5503e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3"}}, "title": "Genome Variation in Three Anthophora Bee Species Reflects Divergent Demographic Histories", "authors": [{"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/2270d42b20f6456a8db81f41503b0063.json"}}, {"family": "Dias", "given": "Guilherme", "initials": "G", "orcid": "0000-0002-1459-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/73778a1096e04b5d94f8d5c6f3584d99.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A", "orcid": "0000-0002-5438-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/57ec91022afd4c1390433d6383a06fc0.json"}}, {"family": "Mosbech", "given": "Mai\u2010Britt", "initials": "M", "orcid": "0000-0002-6068-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/efde81e53e6e48cba694e82e6fa8d38c.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Lager", "given": "Nina", "initials": "N"}, {"family": "Strand", "given": "Anna\u2010Sofi", "initials": "A"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lindblad\u2010Toh", "given": "Kerstin", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Mol Ecol", "issn": "0962-1083", "pages": "e70204", "volume": "34", "issue": "24", "issn-l": "0962-1083"}, "abstract": "Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.", "doi": "10.1111/mec.70204", "pmid": "41387163", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-17T11:40:16.625Z", "modified": "2025-12-21T19:08:10.173Z"}, {"entity": "publication", "iuid": "4454335dc4504444ac7197bda2a143ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4454335dc4504444ac7197bda2a143ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4454335dc4504444ac7197bda2a143ad"}}, "title": "Genetic mapping in the red mason bee implicates ANTSR as an ancient sex-determining locus in bees and ants.", "authors": [{"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Magnusson", "given": "Sara", "initials": "S"}, {"family": "Huser", "given": "Linn", "initials": "L"}, {"family": "Nor Fuad", "given": "Muhammad Nafiz Ikhwan Bin", "initials": "MNIB"}, {"family": "Everitt", "given": "Turid", "initials": "T"}, {"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC"}, {"family": "Theodorou", "given": "Panagiotis", "initials": "P"}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Paxton", "given": "Robert J", "initials": "RJ"}, {"family": "Seidelmann", "given": "Karsten", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "23", "issue": "11", "pages": "e3003458", "issn-l": "1544-9173"}, "abstract": "Haplodiploid inheritance, in which females are diploid and males are haploid, is found in all species of Hymenoptera. Sex in haplodiploids is commonly determined by the alleles present at a complementary sex determination (CSD) locus, with heterozygosity triggering the female developmental pathway. The identity of this locus differs among taxa and is only known in a few species. Here, we map a single CSD locus to a 2 kbp region in the genome of the red mason bee Osmia bicornis. It overlaps the long noncoding RNA ANTSR, which has been identified as the sex-determining gene in the invasive ant Linepithema humile. This locus is homozygous in diploid males and exhibits extremely high levels of haplotype diversity, consistent with the action of frequency-dependent selection. The elevated levels of heterozygosity in the CSD locus enable us to fine-map potentially functional genetic variation within it. We also identify elevated levels of genetic diversity in the ortholog of the CSD locus in five other bee and ant genera, suggesting that it may govern sex determination widely in Hymenoptera. Our data are consistent with the hypothesis that ANTSR evolved a role in sex determination over 150 million years ago and is the ancestral sex-determination locus of bees and ants.", "doi": "10.1371/journal.pbio.3003458", "pmid": "41183133", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12594375"}, {"db": "pii", "key": "PBIOLOGY-D-25-02082"}], "notes": [], "created": "2025-11-21T13:19:56.177Z", "modified": "2025-11-21T13:19:56.233Z"}, {"entity": "publication", "iuid": "20bf7f8602df4703bfd5057606fcaa7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20bf7f8602df4703bfd5057606fcaa7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20bf7f8602df4703bfd5057606fcaa7b"}}, "title": "A Novel Supergene Controls Queen Size and Colony Social Organization in the Ant Myrmica ruginodis.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Sepp\u00e4", "given": "Perttu", "initials": "P", "orcid": "0000-0001-5393-6943", "researcher": {"href": "https://publications.scilifelab.se/researcher/700fa3a2724f442884d886463b1cf95c.json"}}, {"family": "Downing", "given": "Philip A", "initials": "PA", "orcid": "0000-0002-5286-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e004ff0660ee411cb310ab108f29c171.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Helanter\u00e4", "given": "Heikki", "initials": "H", "orcid": "0000-0002-6468-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/3947ff78ae914e6785fb081458619533.json"}}, {"family": "Viljakainen", "given": "Lumi", "initials": "L", "orcid": "0000-0002-6587-6156", "researcher": {"href": "https://publications.scilifelab.se/researcher/462f8aece21843458fa4e3f99a5c5449.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "11", "issn-l": "0737-4038"}, "abstract": "Large independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Their independent origins, as well as the similarities of the associated phenotypes, make ant supergenes a promising system for studying the parallel evolution of genome organization and adaptability. However, the genetic basis of differences in social organization and queen phenotypes remains unknown in many ant species, limiting the potential power of this system for comparative studies. We investigated the genetic basis of colony social organization in the queen-size dimorphic ant Myrmica ruginodis by sampling 95 queens from 31 colonies in southern Finland. Whole-genome sequencing revealed a novel 9 Mb supergene associated with both queen size and social organization. Queens homozygous for the AA haplotype were larger and found only in single-queen colonies, while queens in multiple-queen colonies were smaller and carried only AB and BB genotypes. This supergene is not homologous to previously identified supergenes in ants, suggesting it arose through a distinct evolutionary pathway.", "doi": "10.1093/molbev/msaf255", "pmid": "41077914", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12572780"}, {"db": "pii", "key": "8284624"}], "notes": [], "created": "2025-11-21T14:49:16.789Z", "modified": "2025-11-21T14:49:17.100Z"}, {"entity": "publication", "iuid": "63a842231cd742ccb297c01941f01486", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a842231cd742ccb297c01941f01486.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a842231cd742ccb297c01941f01486"}}, "title": "Unexpectedly low recombination rates and presence of hotspots in termite genomes.", "authors": [{"family": "Everitt", "given": "Turid", "initials": "T", "orcid": "0000-0002-6273-4507", "researcher": {"href": "https://publications.scilifelab.se/researcher/403d4411d0a748eaad9d5810f68e1875.json"}}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T", "orcid": "0000-0003-2929-0585", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ecda02e06b04ead95eefe4e4ee9eed8.json"}}, {"family": "Elsner", "given": "Daniel", "initials": "D"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Liu", "given": "Yuanzhen", "initials": "Y"}, {"family": "Larva", "given": "Tuuli", "initials": "T"}, {"family": "Korb", "given": "Judith", "initials": "J", "orcid": "0000-0001-9577-9376", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95a4169232b4fba987bf584d68d41a6.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2025-05-02", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "35", "issue": "5", "pages": "1124-1137", "issn-l": "1088-9051"}, "abstract": "Meiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates among metazoans, whereas high recombination rates have not been found among nonsocial species from this insect order. It is unknown whether elevated recombination rates are a ubiquitous feature of all social insects. In many metazoan taxa, recombination is mainly restricted to hotspots a few kilobases in length. However, little is known about the prevalence of recombination hotspots in insect genomes. Here we infer recombination rate and its fine-scale variation across the genomes of two social species from the insect order Blattodea: the termites Macrotermes bellicosus and Cryptotermes secundus We used linkage disequilibrium-based methods to infer recombination rate. We infer that recombination rates are close to 1 cM/Mb in both species, similar to the average metazoan rate. We also observe a highly punctate distribution of recombination in both termite genomes, indicative of the presence of recombination hotspots. We infer the presence of full-length PRDM9 genes in the genomes of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low recombination rates in termites indicates that eusociality is not universally connected to elevated recombination rate. We speculate that the elevated recombination rates in social Hymenoptera are instead promoted by intense selection among haploid males.", "doi": "10.1101/gr.279180.124", "pmid": "40113265", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12047536"}, {"db": "pii", "key": "gr.279180.124"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2025-11-21T15:54:31.653Z", "modified": "2025-11-21T15:54:32.018Z"}, {"entity": "publication", "iuid": "c7627b55efd14033b6996b8c5aab3b0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7627b55efd14033b6996b8c5aab3b0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7627b55efd14033b6996b8c5aab3b0d"}}, "title": "Large Inversions Shape Diversification and Genome Evolution in Common Quails.", "authors": [{"family": "Ravagni", "given": "Sara", "initials": "S", "orcid": "0000-0003-0320-3447", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb16a7faa1a4952b3247d440d2cdf5f.json"}}, {"family": "Montero-Mendieta", "given": "Santiago", "initials": "S", "orcid": "0000-0002-8350-4655", "researcher": {"href": "https://publications.scilifelab.se/researcher/c23cf6e0a3d84637b564cd4ece502dfa.json"}}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0003-0291-7819", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7aebc9371db4bbcb03eaef58473fc3e.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Rodr\u00edguez-Teijeiro", "given": "Jos\u00e9 Domingo", "initials": "JD"}, {"family": "Sanchez-Donoso", "given": "Ines", "initials": "I"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "9", "pages": "e17740"}, "abstract": "Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (Coturnix coturnix), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new de novo genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.", "doi": "10.1111/mec.17740", "pmid": "40183764", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "NGI Other": null}, "xrefs": [], "notes": [], "created": "2025-08-19T13:25:18.999Z", "modified": "2025-11-19T08:38:35.719Z"}, {"entity": "publication", "iuid": "f10b8ed3023044179d906f560e975bb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f10b8ed3023044179d906f560e975bb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f10b8ed3023044179d906f560e975bb4"}}, "title": "Genomic variation in montane bumblebees in Scandinavia: High levels of intraspecific diversity despite population vulnerability.", "authors": [{"family": "Liu", "given": "Yuanzhen", "initials": "Y", "orcid": "0000-0003-0212-0674", "researcher": {"href": "https://publications.scilifelab.se/researcher/3182284868704c84b8f00064b1540312.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Larva", "given": "Tuuli", "initials": "T"}, {"family": "Cantwell-Jones", "given": "Aoife", "initials": "A"}, {"family": "Gill", "given": "Richard J", "initials": "RJ"}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "4", "pages": "e17251", "issn-l": "0962-1083"}, "abstract": "Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole-genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (NE ) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high NE and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in NE indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.", "doi": "10.1111/mec.17251", "pmid": "38112228", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-25T10:27:14.456Z", "modified": "2024-11-25T10:27:14.515Z"}, {"entity": "publication", "iuid": "27e5410cdd1f47228b9aa1c4b75dea54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27e5410cdd1f47228b9aa1c4b75dea54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27e5410cdd1f47228b9aa1c4b75dea54"}}, "title": "The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees.", "authors": [{"family": "Everitt", "given": "Turid", "initials": "T"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Hoffmann", "given": "Wolfgang", "initials": "W"}, {"family": "Neumann", "given": "Peter", "initials": "P"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2023-09-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "9", "issn-l": "1759-6653"}, "abstract": "A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.", "doi": "10.1093/gbe/evad157", "pmid": "37625795", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10484329"}, {"db": "pii", "key": "7251443"}], "notes": [], "created": "2023-10-11T09:08:46.279Z", "modified": "2024-01-16T13:48:32.323Z"}, {"entity": "publication", "iuid": "52b6011191b94c74b6f4baaea4ff448c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52b6011191b94c74b6f4baaea4ff448c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52b6011191b94c74b6f4baaea4ff448c"}}, "title": "Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.", "authors": [{"family": "Dyrhage", "given": "Karl", "initials": "K"}, {"family": "Garcia-Montaner", "given": "Andrea", "initials": "A"}, {"family": "Tamarit", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4940-719X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b6e6e8715ff4f76985f2e09972e1013.json"}}, {"family": "Seeger", "given": "Christian", "initials": "C"}, {"family": "N\u00e4slund", "given": "Kristina", "initials": "K"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Vasquez", "given": "Alejandra", "initials": "A"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE"}], "type": "journal article", "published": "2022-11-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "14", "issue": "11", "issn-l": "1759-6653"}, "abstract": "The honeybee gut microbiome is thought to be important for bee health, but the role of the individual members is poorly understood. Here, we present closed genomes and associated mobilomes of 102 Apilactobacillus kunkeei isolates obtained from the honey crop (foregut) of honeybees sampled from beehives in Helsingborg in the south of Sweden and from the islands Gotland and \u00c5land in the Baltic Sea. Each beehive contained a unique composition of isolates and repeated sampling of similar isolates from two beehives in Helsingborg suggests that the bacterial community is stably maintained across bee generations during the summer months. The sampled bacterial population contained an open pan-genome structure with a high genomic density of transposons. A subset of strains affiliated with phylogroup A inhibited growth of the bee pathogen Melissococcus plutonius, all of which contained a 19.5 kb plasmid for the synthesis of the antimicrobial compound kunkecin A, while a subset of phylogroups B and C strains contained a 32.9 kb plasmid for the synthesis of a putative polyketide antibiotic. This study suggests that the mobile gene pool of A. kunkeei plays a key role in pathogen defense in honeybees, providing new insights into the evolutionary dynamics of defensive symbiont populations.", "doi": "10.1093/gbe/evac153", "pmid": "36263788", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9648514"}, {"db": "pii", "key": "6764223"}], "notes": [], "created": "2022-11-21T10:10:14.246Z", "modified": "2024-01-16T13:48:34.499Z"}, {"entity": "publication", "iuid": "bac07fae3c0e4214bca1d4ff1a326f39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39"}}, "title": "A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Whitley", "given": "Kaitlyn M", "initials": "KM"}, {"family": "Sullivan", "given": "Isabel", "initials": "I"}, {"family": "Geib", "given": "Jennifer C", "initials": "JC"}, {"family": "Miller-Struttmann", "given": "Nicole E", "initials": "NE"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "31", "issue": "4", "pages": "1111-1127"}, "abstract": "Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species (\"incognitus\"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.", "doi": "10.1111/mec.16291", "pmid": "34837435", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Long read": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-11-30T12:41:55.744Z", "modified": "2024-01-16T13:48:37.663Z"}, {"entity": "publication", "iuid": "00097c342d474f85a1fe229a74798c7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00097c342d474f85a1fe229a74798c7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00097c342d474f85a1fe229a74798c7b"}}, "title": "Massive genome inversion drives coexistence of divergent morphs in common quails.", "authors": [{"family": "Sanchez-Donoso", "given": "Ines", "initials": "I", "orcid": "0000-0003-2773-9844", "researcher": {"href": "https://publications.scilifelab.se/researcher/917f54b110bd4aca8efbcf3cd9aef4e7.json"}}, {"family": "Ravagni", "given": "Sara", "initials": "S", "orcid": "0000-0003-0320-3447", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb16a7faa1a4952b3247d440d2cdf5f.json"}}, {"family": "Rodr\u00edguez-Teijeiro", "given": "J Domingo", "initials": "JD"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Huang", "given": "Yan", "initials": "Y"}, {"family": "Maldonado-Linares", "given": "Andros", "initials": "A"}, {"family": "Puigcerver", "given": "Manel", "initials": "M"}, {"family": "Jim\u00e9nez-Blasco", "given": "Irene", "initials": "I"}, {"family": "Andrade", "given": "Pedro", "initials": "P"}, {"family": "Gon\u00e7alves", "given": "David", "initials": "D"}, {"family": "Friis", "given": "Guillermo", "initials": "G", "orcid": "0000-0002-0731-6468", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa844934c3544b37ba2c9874ed8f9b8d.json"}}, {"family": "Roig", "given": "Ignasi", "initials": "I", "orcid": "0000-0003-0313-3581", "researcher": {"href": "https://publications.scilifelab.se/researcher/138805893cb940d39e98c8347f909260.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2022-01-24", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "2", "pages": "462-469.e6"}, "abstract": "The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats,1,2 and whose females may lay successive clutches at different locations while migrating.3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jim\u00e9nez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.", "doi": "10.1016/j.cub.2021.11.019", "pmid": "34847353", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)01543-8"}], "notes": [], "created": "2021-11-30T12:50:56.211Z", "modified": "2022-08-19T08:57:48.552Z"}, {"entity": "publication", "iuid": "b7eea19211a243ea8425fff9af2dc589", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7eea19211a243ea8425fff9af2dc589.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7eea19211a243ea8425fff9af2dc589"}}, "title": "Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Whitley", "given": "Kaitlyn M", "initials": "KM"}, {"family": "Larva", "given": "Tuuli", "initials": "T"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Miller-Struttmann", "given": "Nicole E", "initials": "NE"}, {"family": "Geib", "given": "Jennifer C", "initials": "JC"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "comparative study", "published": "2021-07-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "8", "pages": "3126-3143"}, "abstract": "Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (dXY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.", "doi": "10.1093/molbev/msab086", "pmid": "33823537", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6199435"}, {"db": "pmc", "key": "PMC8321533"}], "notes": [], "created": "2021-04-12T09:33:02.825Z", "modified": "2024-01-16T13:48:39.049Z"}, {"entity": "publication", "iuid": "9d7fcd3fe5d84966ab5d1e2cf5d5137b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d7fcd3fe5d84966ab5d1e2cf5d5137b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d7fcd3fe5d84966ab5d1e2cf5d5137b"}}, "title": "Female-biased gene flow between two species of Darwin's finches.", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S", "orcid": "0000-0003-4826-0349", "researcher": {"href": "https://publications.scilifelab.se/researcher/602a2f371eae45e4b9d8f9748f285ef4.json"}}, {"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "7", "pages": "979-986", "issn-l": "2397-334X"}, "abstract": "The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Gal\u00e1pagos island of Daphne Major, two species of Darwin's finches, Geospiza fortis and G. scandens, hybridize rarely and back-cross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole-genome sequences to compare genomes from periods before and after successful interbreeding followed by back-crossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci primarily reflects female-biased gene flow, arising from a hybrid-male disadvantage in competition for high-quality territories and mates, rather than from genetic incompatibilities at Z-linked loci.", "doi": "10.1038/s41559-020-1183-9", "pmid": "32367030", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-1183-9"}], "notes": [], "created": "2020-07-03T05:28:11.615Z", "modified": "2024-01-16T13:48:42.318Z"}, {"entity": "publication", "iuid": "682ced28421b4e41a56a47cbb2c7ab77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/682ced28421b4e41a56a47cbb2c7ab77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/682ced28421b4e41a56a47cbb2c7ab77"}}, "title": "Chromosomal inversions associated with environmental adaptation in honeybees.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "28", "issn": "1365-294X", "issue": "6", "pages": "1358-1374", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Chromosomal inversions can facilitate local adaptation in the presence of gene flow by suppressing recombination between well-adapted native haplotypes and poorly adapted migrant haplotypes. East African mountain populations of the honeybee Apis mellifera are highly divergent from neighbouring lowland populations at two extended regions in the genome, despite high similarity in the rest of the genome, suggesting that these genomic regions harbour inversions governing local adaptation. Here, we utilize a new highly contiguous assembly of the honeybee genome to characterize these regions. Using whole-genome sequencing data from 55 highland and lowland bees, we find that the highland haplotypes at both regions are present at high frequencies in three independent highland populations but extremely rare elsewhere. The boundaries of both divergent regions are characterized by regions of high homology with each other positioned in opposite orientations and contain highly repetitive, long inverted repeats with homology to transposable elements. These regions are likely to represent inversion breakpoints that participate in nonallelic homologous recombination. Using long-read data, we confirm that the lowland samples are contiguous across breakpoint regions. We do not find evidence for disruption of functional sequence by these breakpoints, which suggests that the inversions are likely maintained due to their allelic content conferring local adaptation in highland environments. Finally, we identify a third divergent genomic region, which contains highly divergent segregating haplotypes that also may contain inversion variants under selection. The results add to a growing body of evidence indicating the importance of chromosomal inversions in local adaptation.", "doi": "10.1111/mec.14944", "pmid": "30431193", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T12:54:04.519Z", "modified": "2024-01-16T13:48:44.639Z"}]}