{"entity": "journal", "iuid": "2727726e61db469c8e51a2424ef81b95", "timestamp": "2026-10-11T05:30:09.441Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/BMC%20Evol.%20Biol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/BMC%20Evol.%20Biol."}}, "title": "BMC Evol. Biol.", "issn": "1471-2148", "issn-l": "1471-2148", "publications_count": 12, "publications": [{"entity": "publication", "iuid": "8b85fb5237c649c98d5e35c07b496e3c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b85fb5237c649c98d5e35c07b496e3c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b85fb5237c649c98d5e35c07b496e3c"}}, "title": "Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean \"island-shrews\".", "authors": [{"family": "Woods", "given": "Roseina", "initials": "R"}, {"family": "Turvey", "given": "Samuel T", "initials": "ST", "orcid": "0000-0002-3717-4800", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f9849b335e4e74b810b08cabe6759a.json"}}, {"family": "Brace", "given": "Selina", "initials": "S"}, {"family": "McCabe", "given": "Christopher V", "initials": "CV"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Rayfield", "given": "Emily J", "initials": "EJ"}, {"family": "Brown", "given": "Mark J F", "initials": "MJF"}, {"family": "Barnes", "given": "Ian", "initials": "I"}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "BMC Evol. Biol.", "issn": "1471-2148", "volume": "20", "issue": "1", "pages": "106", "issn-l": "1471-2148"}, "abstract": "The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae (\"island-shrews\") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island.\n\nPrincipal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.\n\nOur combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.", "doi": "10.1186/s12862-020-01668-7", "pmid": "32811443", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-020-01668-7"}, {"db": "pmc", "key": "PMC7437022"}], "notes": [], "created": "2020-12-07T16:29:53.095Z", "modified": "2021-11-10T12:48:12.533Z"}, {"entity": "publication", "iuid": "0b0d84d71da8411a974593d2c45402ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b0d84d71da8411a974593d2c45402ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b0d84d71da8411a974593d2c45402ca"}}, "title": "Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Qu", "given": "Yanhua", "initials": "Y"}, {"family": "Rasmussen", "given": "Pamela C", "initials": "PC"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-07-24", "journal": {"volume": "19", "issn": "1471-2148", "issue": "1", "pages": "151", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex.\n\nWe generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade.\n\nWe found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, \"stepping-stone\" dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea.", "doi": "10.1186/s12862-019-1481-5", "pmid": "31340765", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-019-1481-5"}, {"db": "pmc", "key": "PMC6657069"}], "notes": [], "created": "2019-12-02T17:20:03.644Z", "modified": "2020-01-21T13:56:15.644Z"}, {"entity": "publication", "iuid": "6b812784022e4f1e8c0e5f4d03e6ab5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b812784022e4f1e8c0e5f4d03e6ab5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b812784022e4f1e8c0e5f4d03e6ab5a"}}, "title": "Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2019-06-18", "journal": {"volume": "19", "issn": "1471-2148", "issue": "1", "pages": "124", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clade members.\n\nGenome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete Mmuc T (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNAIleTAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales-derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc-clade members.\n\nPhages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc- and Mneo-clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes.", "doi": "10.1186/s12862-019-1447-7", "pmid": "31215393", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-019-1447-7"}, {"db": "pmc", "key": "PMC6582537"}], "notes": [], "created": "2019-11-25T14:08:36.735Z", "modified": "2024-01-16T13:48:44.244Z"}, {"entity": "publication", "iuid": "59b8dae6dc8d41c6885ed37cf0f856a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b8dae6dc8d41c6885ed37cf0f856a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b8dae6dc8d41c6885ed37cf0f856a3"}}, "title": "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.", "authors": [{"family": "Smythe", "given": "Ashleigh B", "initials": "AB"}, {"family": "Holovachov", "given": "Oleksandr", "initials": "O"}, {"family": "Kocot", "given": "Kevin M", "initials": "KM"}], "type": "journal article", "published": "2019-06-13", "journal": {"volume": "19", "issn": "1471-2148", "issue": "1", "pages": "121", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum.\n\nWe supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with a high proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA.\n\nExpanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment.", "doi": "10.1186/s12862-019-1444-x", "pmid": "31195978", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-019-1444-x"}, {"db": "pmc", "key": "PMC6567515"}], "notes": [], "created": "2019-12-02T17:20:53.416Z", "modified": "2020-01-21T13:56:15.752Z"}, {"entity": "publication", "iuid": "8b7c4d75fc1a4d75ab4c9519a85a6c35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b7c4d75fc1a4d75ab4c9519a85a6c35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b7c4d75fc1a4d75ab4c9519a85a6c35"}}, "title": "Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.", "authors": [{"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Lattenkamp", "given": "Ella Z", "initials": "EZ"}, {"family": "Meyer-Lucht", "given": "Yvonne", "initials": "Y"}, {"family": "Luquet", "given": "Emilien", "initials": "E"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2017-08-14", "journal": {"volume": "17", "issn": "1471-2148", "issue": "1", "pages": "189", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites.\n\nUsing outlier analyses, we identified the MHC II exon 2 (corresponding to the \u03b2-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations.\n\nOur results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.", "doi": "10.1186/s12862-017-1022-z", "pmid": "28806900", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-017-1022-z"}, {"db": "pmc", "key": "PMC5557520"}], "notes": [], "created": "2018-01-09T20:49:55.495Z", "modified": "2021-06-21T14:58:37.712Z"}, {"entity": "publication", "iuid": "f4dc3cf02d2449a18177221e5fc4126e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4dc3cf02d2449a18177221e5fc4126e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4dc3cf02d2449a18177221e5fc4126e"}}, "title": "Paternal personality and social status influence offspring activity in zebrafish.", "authors": [{"family": "Zajitschek", "given": "Susanne", "initials": "S"}, {"family": "Herbert-Read", "given": "James E", "initials": "JE"}, {"family": "Abbasi", "given": "Nasir M", "initials": "NM"}, {"family": "Zajitschek", "given": "Felix", "initials": "F"}, {"family": "Immler", "given": "Simone", "initials": "S"}], "type": "journal article", "published": "2017-07-03", "journal": {"title": "BMC Evol. Biol.", "issn": "1471-2148", "volume": "17", "issue": "1", "pages": "157", "issn-l": "1471-2148"}, "abstract": "Evidence for the transmission of non-genetic information from father to offspring is rapidly accumulating. While the impact of chemical and physical factors such as toxins or diet on the fitness of the parents and their offspring have been studied extensively, the importance of behavioural and social circumstances has only recently been recognised. Behavioural traits such as personality characteristics can be relatively stable, and partly comprise a genetic component but we know little about the non-genetic transmission of plastic behavioural traits from parents to offspring. We investigated the relative effect of personality and of social dominance as indicators at the opposite ends of the plasticity range on offspring behaviour in the zebrafish (Danio rerio). We assessed male boldness, a behavioural trait that has previously been shown previously to possess genetic underpinnings, and experimentally manipulated male social status to assess the association between the two types of behaviour and their correlation with offspring activity.\n\nWe found a clear interaction between the relatively stable and putative genetic effects based on inherited differences in personality and the experimentally induced epigenetic effects from changes in the social status of the father on offspring activity.\n\nOur study shows that offspring behaviour is determined by a combination of paternal personality traits and on-genetic effects derived from the social status of the father.", "doi": "10.1186/s12862-017-1005-0", "pmid": "28673261", "labels": {"Genome Engineering Zebrafish": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-017-1005-0"}, {"db": "pmc", "key": "PMC5496241"}], "notes": [], "created": "2017-10-26T09:24:43.057Z", "modified": "2017-10-26T09:24:43.060Z"}, {"entity": "publication", "iuid": "f4aa030b75a846cd8d77fe2e15cb90b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4aa030b75a846cd8d77fe2e15cb90b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4aa030b75a846cd8d77fe2e15cb90b1"}}, "title": "Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity.", "authors": [{"family": "Lagman", "given": "David", "initials": "D"}, {"family": "Franz\u00e9n", "given": "Ilkin E", "initials": "IE"}, {"family": "Eggert", "given": "Joel", "initials": "J"}, {"family": "Larhammar", "given": "Dan", "initials": "D"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM"}], "type": "journal article", "published": "2016-06-13", "journal": {"volume": "16", "issn": "1471-2148", "issue": "1", "pages": "124", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Phosphodiesterase 6 (PDE6) is a protein complex that hydrolyses cGMP and acts as the effector of the vertebrate phototransduction cascade. The PDE6 holoenzyme consists of catalytic and inhibitory subunits belonging to two unrelated gene families. Rods and cones express distinct genes from both families: PDE6A and PDE6B code for the catalytic and PDE6G the inhibitory subunits in rods while PDE6C codes for the catalytic and PDE6H the inhibitory subunits in cones. We performed phylogenetic and comparative synteny analyses for both gene families in genomes from a broad range of animals. Furthermore, gene expression was investigated in zebrafish.\n\nWe found that both gene families expanded from one to three members in the two rounds of genome doubling (2R) that occurred at the base of vertebrate evolution. The PDE6 inhibitory subunit gene family appears to be unique to vertebrates and expanded further after the teleost-specific genome doubling (3R). We also describe a new family member that originated in 2R and has been lost in amniotes, which we have named pde6i. Zebrafish has retained two additional copies of the PDE6 inhibitory subunit genes after 3R that are highly conserved, have high amino acid sequence identity, are coexpressed in the same photoreceptor type as their amniote orthologs and, interestingly, show strikingly different daily oscillation in gene expression levels.\n\nTogether, these data suggest specialisation related to the adaptation to different light intensities during the day-night cycle, most likely maintaining the regulatory function of the PDE inhibitory subunits in the phototransduction cascade.", "doi": "10.1186/s12862-016-0695-z", "pmid": "27296292", "labels": {"Genome Engineering Zebrafish": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-016-0695-z"}, {"db": "pmc", "key": "PMC4906994"}], "notes": [], "created": "2017-05-03T13:02:38.939Z", "modified": "2017-09-06T11:49:55.048Z"}, {"entity": "publication", "iuid": "c76b9b8a177c4cd4addd6e1f5eb0e960", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c76b9b8a177c4cd4addd6e1f5eb0e960.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c76b9b8a177c4cd4addd6e1f5eb0e960"}}, "title": "Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.", "authors": [{"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "Mde L"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}, {"family": "Janz", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2016-03-08", "journal": {"volume": "16", "issn": "1471-2148", "issue": null, "pages": "59", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to feed on a wide repertoire of plants is crucial for the control of pest species and for the elucidation of the macroevolutionary mechanisms of speciation and diversification of insect herbivores. Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were reared on different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness.\n\nUsing both unsupervised and supervised methods of data analysis, we found that the tissue-specific patterns of caterpillar gene expression are better explained by the evolutionary history of adaptation of the insects to the plants than by plant phylogeny.\n\nOur findings suggest that V. cardui may use two sets of expressed genes to achieve polyphagy, one associated with the ancestral capability to consume Rosids and Asterids, and another allowing the caterpillar to incorporate a wide range of novel host-plants.", "doi": "10.1186/s12862-016-0627-y", "pmid": "26956800", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-016-0627-y"}, {"db": "pmc", "key": "PMC4782335"}, {"db": "ArrayExpress", "description": "RNA-seq data", "key": "E-MTAB-3861"}], "notes": [], "created": "2017-05-08T07:58:17.816Z", "modified": "2024-01-16T13:48:50.357Z"}, {"entity": "publication", "iuid": "0a7b6b2abd4a4e889ce668f557369942", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a7b6b2abd4a4e889ce668f557369942.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a7b6b2abd4a4e889ce668f557369942"}}, "title": "Population structure and genetic diversity in the nannandrous moss Homalothecium lutescens: does the dwarf male system facilitate gene flow?", "authors": [{"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Hansson", "given": "Bengt", "initials": "B"}, {"family": "Cronberg", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2015-12-03", "journal": {"volume": "15", "issn": "1471-2148", "issue": null, "pages": "270", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Nannandry is a sexual system where males (\"dwarf males\") are much smaller than the conspecific females. Dwarf males occur in a wide range of unrelated organisms but the evolutionary advantages of this condition are poorly understood. The dwarf male sexual system results in differences in the mode of dispersal and establishment as well as the life span between males and females. Such differences must have profound effects on the population dynamics and genetic structures. We have studied four populations of the nannandrous moss Homalothecium lutescens in southern Sweden. We genotyped dwarf males and female shoots with the aim of describing the genetic diversity and structure of the populations.\n\nDwarf males were most related to their host shoot, then their colony (within 0.5 m(2)) and then the rest of the population, which suggests restricted spore dispersal. However, a few dwarf males in each population appeared to originate from other colonies and sometimes even other populations. Genetic diversity of dwarf males was generally high but showed no tendency to be consistently higher or lower than female genetic diversity within the four populations.\n\nAlthough most dwarf males have local origin, sporadic dispersal events occur. The ability of the dwarf males to establish in high numbers in mature colonies facilitates gene flow between populations as well as increases the potential to accumulate genetic diversity within populations.", "doi": "10.1186/s12862-015-0545-4", "pmid": "26634921", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-015-0545-4"}, {"db": "pmc", "key": "PMC4669626"}, {"db": "Dryad", "key": "10.5061/dryad.1860S"}], "notes": [], "created": "2017-10-30T13:24:27.426Z", "modified": "2020-01-21T13:56:08.227Z"}, {"entity": "publication", "iuid": "7c889d7ff9734652b7df10a2192898a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c889d7ff9734652b7df10a2192898a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c889d7ff9734652b7df10a2192898a9"}}, "title": "Within-species divergence in the seminal fluid proteome and its effect on male and female reproduction in a beetle.", "authors": [{"family": "Goenaga", "given": "Julieta", "initials": "J"}, {"family": "Yamane", "given": "Takashi", "initials": "T"}, {"family": "R\u00f6nn", "given": "Johanna", "initials": "J"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2015-12-02", "journal": {"volume": "15", "issn": "1471-2148", "issue": null, "pages": "266", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Male seminal fluid proteins (SFPs), transferred to females during mating, are important reproductive proteins that have multifarious effects on female reproductive physiology and that often show remarkably rapid and divergent evolution. Inferences regarding natural selection on SFPs are based primarily on interspecific comparative studies, and our understanding of natural within-species variation in SFPs and whether this relates to reproductive phenotypes is very limited. Here, we introduce an empirical strategy to study intraspecific variation in and selection upon the seminal fluid proteome. We then apply this in a study of 15 distinct populations of the seed beetle Callosobruchus maculatus.\n\nPhenotypic assays of these populations showed significant differences in reproductive phenotypes (male success in sperm competition and male ability to stimulate female fecundity). A quantitative proteomic study of replicated samples of male accessory glands revealed a large number of potential SFPs, of which \u2265127 were found to be transferred to females at mating. Moreover, population divergence in relative SFP abundance across populations was large and remarkably multidimensional. Most importantly, variation in male SFP abundance across populations was associated with male sperm competition success and male ability to stimulate female egg production.\n\nOur study provides the first direct evidence for postmating sexual selection on standing intraspecific variation in SFP abundance and the pattern of divergence across populations in the seminal fluid proteome match the pattern predicted by the postmating sexual selection paradigm for SFP evolution. Our findings provide novel support for the hypothesis that sexual selection on SFPs is an important engine of incipient speciation.", "doi": "10.1186/s12862-015-0547-2", "pmid": "26627998", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-015-0547-2"}, {"db": "pmc", "key": "PMC4667481"}], "notes": [], "created": "2017-05-02T12:57:32.035Z", "modified": "2017-05-30T15:06:00.521Z"}, {"entity": "publication", "iuid": "f6d9330dc7e94358a4219441a106771d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6d9330dc7e94358a4219441a106771d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6d9330dc7e94358a4219441a106771d"}}, "title": "Genetic and morphological evidence for introgression between three species of willows.", "authors": [{"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Verkhozina", "given": "Alla V", "initials": "AV"}, {"family": "Katyshev", "given": "Alexander I", "initials": "AI"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann Christin", "initials": "AC"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Berlin", "given": "Sofia", "initials": "S"}], "type": "journal article", "published": "2015-09-16", "journal": {"volume": "15", "issn": "1471-2148", "issue": null, "pages": "193", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Hybridization and introgression are said to occur relatively frequently in plants, and in particular among different species of willows. However, data on the actual frequency of natural hybridization and introgression is rare. Here, we report the first fine-scale genetic analysis of a contact zone shared between the three basket willow species, Salix dasyclados, S. schwerinii and S. viminalis in the vicinity of the Lake Baikal in Southern Siberia. Individuals were sampled in fourteen populations and classified as pure species or hybrids based on a set of morphological characters. They were then genotyped at 384 nuclear SNP and four chloroplast SSR loci. The STRUCTURE and NewHybrids softwares were used to estimate the frequency and direction of hybridization using genotypic data at the nuclear SNP loci.\n\nAs many as 19 % of the genotyped individuals were classified as introgressed individuals and these were mainly encountered in the centre of the contact zone. All introgressed individuals were backcrosses to S. viminalis or S. schwerinii and no F1 or F2 hybrids were found. The rest of the genotyped individuals were classified as pure species and formed two clusters, one with S. schwerinii individuals and the other with S. viminalis and S. dasyclados individuals. The two clusters were significantly genetically differentiated, with F ST = 0.333 (0.282-0.382, p < 0.001). In contrast, for the chloroplast haplotypes, no genetic differentiation was observed as they were completely shared between the species. Based on morphological classification only 5 % of the individuals were classified as introgressed individuals, which was much less than what was detected using genotypic data.\n\nWe have discovered a new willow hybrid zone with relatively high frequency of introgressed individuals. The low frequency of F1 hybrids indicates that ongoing hybridization is limited, which could be because of the presence of reproductive barriers or simply because the conditions are not favorable for hybridization. We further conclude that in order to get a complete picture of the species composition of a hybrid zone it is necessary to use a combination of morphological characters and genetic data from both nuclear and chloroplast markers.", "doi": "10.1186/s12862-015-0461-7", "pmid": "26376815", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-015-0461-7"}, {"db": "pmc", "key": "PMC4574262"}], "notes": [], "created": "2017-05-02T12:57:00.819Z", "modified": "2020-01-21T13:56:06.363Z"}, {"entity": "publication", "iuid": "42302ed840ee429b92fda660d9ee7bea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42302ed840ee429b92fda660d9ee7bea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42302ed840ee429b92fda660d9ee7bea"}}, "title": "Dating the diversification of the major lineages of Passeriformes (Aves).", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PG"}, {"family": "Klopfstein", "given": "Seraina", "initials": "S"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Nguyen", "given": "Jacqueline M T", "initials": "JM"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}], "type": "journal article", "published": "2014-01-15", "journal": {"volume": "14", "issn": "1471-2148", "issue": null, "pages": "8", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% of all living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the late Cretaceous. However, previous molecular dating studies have relied heavily on the geological split between New Zealand and Antarctica, assumed to have occurred 85-82 Mya, for calibrating the molecular clock and might thus be circular in their argument.\n\nThis study provides a time-scale for the evolution of the major clades of passerines using seven nuclear markers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealand split from Antarctica 85-52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretations of the New Zealand-Antarctica vicariance event influence our age estimates. Our results suggest that the diversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration for the New Zealand-Antarctica vicariance event (85-52 Mya) dramatically increases the 95% credibility intervals and leads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genes analyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines, which can be used as secondary calibration points in future molecular studies.\n\nOur analysis takes recent paleontological and geological findings into account and provides the best estimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporal framework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, and adds to the growing support for a Cretaceous origin of Passeriformes.", "doi": "10.1186/1471-2148-14-8", "pmid": "24422673", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2148-14-8"}, {"db": "pmc", "key": "PMC3917694"}], "notes": [], "created": "2017-05-04T14:56:29.498Z", "modified": "2020-01-21T13:53:20.488Z"}], "created": "2017-05-09T09:12:15.465Z", "modified": "2020-11-27T13:14:03.623Z"}