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  • 1. Autenrieth, Marijke
    et al.
    Hartmann, Stefanie
    Lah, Ljerka
    Roos, Anna
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Dennis, Alice B.
    Tiedemann, Ralph
    High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)2018In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 1, p. 1469-1481Article in journal (Refereed)
    Abstract [en]

    The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.

  • 2.
    Celemín, Enrique
    et al.
    University of Potsdam, Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology Potsdam Germany.
    Autenrieth, Marijke
    University of Potsdam, Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology Potsdam Germany.
    Roos, Anna
    Swedish Museum of Natural History, Department of Environmental research and monitoring. Swedish Museum of Natural History Stockholm Sweden.
    Pawliczka, Iwona
    Prof. Krzysztof Skóra Hel Marine Station, Faculty of Oceanography and Geography University of Gdansk Hel Poland.
    Quintela, María
    Institute of Marine Research Bergen Norway.
    Lindstrøm, Ulf
    Institute of Marine Research Tromsø Norway;UiT The Arctic University of Norway Tromsø Norway.
    Benke, Harald
    Deutsches Meeresmuseum Stralsund Germany.
    Siebert, Ursula
    Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation Büsum Germany.
    Lockyer, Christina
    Age Dynamics Kongens Lyngby Denmark.
    Berggren, Per
    School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK.
    Özturk, A. Amaha
    Marine Biology Department, Faculty of Fisheries Istanbul University Istanbul Turkey.
    Özturk, Bayram
    Marine Biology Department, Faculty of Fisheries Istanbul University Istanbul Turkey.
    Lesage, Véronique
    Fisheries and Oceans Canada Maurice Lamontagne Institute Mont‐Joli Quebec Canada.
    Tiedemann, Ralph
    University of Potsdam, Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology Potsdam Germany.
    Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters2023In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998Article in journal (Refereed)
    Abstract [en]

    The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here, we produced 74 whole genomes at intermediate coverage to study Harbour porpoise's evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high quality SNPs sampled at eight localities across the North Atlantic and adjacent waters, which we used for population structure, demographic and genotype–environment association analyses. Our results suggest a genetic differentiation between three subspecies (P.p. relicta, P.p. phocoena and P.p. meridionalis), and three distinct populations within P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima's D suggest population contraction in Black Sea and Iberian porpoises, but expansion in the P.p. phocoena populations. Phylogenetic trees indicate post-glacial colonization from a southern refugium. Genotype–environment association analysis identified salinity as major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species, shows how strong environmental gradients and local adaptation may lead to population differentiation, and how neutral and adaptive markers can give different perspectives on population subdivision. The results have great conservation implications as we found inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

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  • 3.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.
    Thörn, Filip
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden;Department of Zoology Stockholm University Stockholm Sweden.
    Müller, Ingo A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden;Department of Zoology Stockholm University Stockholm Sweden.
    Jønsson, Knud A.
    Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark.
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.
    Blom, Mozes P. K.
    Museum für Naturkunde Leibniz Institut für Evolutions‐ und Biodiversitätsforschung Berlin Germany.
    A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins2022In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 22, no 7, p. 2672-2684Article in journal (Refereed)
    Abstract [en]

    Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present-day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high-throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.

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  • 4.
    Marquina, Daniel
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Andersson, Anders
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods2018In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998Article in journal (Refereed)
  • 5.
    Marquina, Daniel
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Esparza-Salas, Rodrigo
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Roslin, Tomas
    Swedish University of Agricultural Sciences.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches2019In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, p. 1516-1530Article in journal (Refereed)
  • 6. Peona, Valentina
    et al.
    Blom, Mozes P. K.
    Xu, Luohao
    Burri, Reto
    Sullivan, Shawn
    Bunikis, Ignas
    Liachko, Ivan
    Haryoko, Tri
    Jønsson, Knud A.
    Zhou, Qi
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Suh, Alexander
    Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise2021In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, ISSN - 1755-098X, Vol. 21, no 1, p. 263-286Article in journal (Refereed)
  • 7.
    Peona, Valentina
    et al.
    Department of Ecology and Genetics—Evolutionary Biology Science for Life Laboratories Uppsala University Uppsala Sweden;Department of Organismal Biology—Systematic Biology Science for Life Laboratories Uppsala University Uppsala Sweden.
    Blom, Mozes P. K.
    Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden;Museum für Naturkunde Leibniz Institut für Evolutions‐ und Biodiversitätsforschung Berlin Germany.
    Xu, Luohao
    Department of Neurosciences and Developmental Biology University of Vienna Vienna Austria.
    Burri, Reto
    Department of Population Ecology Institute of Ecology and Evolution Friedrich‐Schiller‐University Jena Jena Germany.
    Sullivan, Shawn
    Phase Genomics Seattle WA USA.
    Bunikis, Ignas
    Department of Immunology, Genetics and Pathology Science for Life Laboratory Uppsala Genome CenterUppsala University Uppsala Sweden.
    Liachko, Ivan
    Phase Genomics Seattle WA USA.
    Haryoko, Tri
    Research Centre for Biology Museum Zoologicum BogorienseIndonesian Institute of Sciences (LIPI) Cibinong Indonesia.
    Jønsson, Knud A.
    Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark.
    Zhou, Qi
    Department of Neurosciences and Developmental Biology University of Vienna Vienna Austria;MOE Laboratory of Biosystems Homeostasis & Protection Life Sciences Institute Zhejiang University Hangzhou China;Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.
    Suh, Alexander
    Department of Ecology and Genetics—Evolutionary Biology Science for Life Laboratories Uppsala University Uppsala Sweden;Department of Organismal Biology—Systematic Biology Science for Life Laboratories Uppsala University Uppsala Sweden;School of Biological Sciences—Organisms and the Environment University of East Anglia Norwich UK.
    Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise2020In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 21, no 1, p. 263-286Article in journal (Refereed)
    Abstract [en]

    Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.

  • 8. Piredda, Roberta
    et al.
    Grimm, Guido W.
    Schulze, Ernst-Detlef
    Denk, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    Simeone, Marco C.
    High-throughput sequencing of 5S-IGS in oaks – exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples2021In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 21, p. 495-510Article in journal (Refereed)
    Abstract [en]

    Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.

  • 9.
    Schmidt, Stefan
    et al.
    SNSB-Zoologische Staatssammlung München, Munich, Germany.
    Taeger, Andreas
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Morinière, Jérôme
    SNSB-Zoologische Staatssammlung München, Munich, Germany.
    Liston, Andrew
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Blank, Stephan
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Kramp, Katja
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Kraus, Manfred
    Nürnberg, Germany.
    Schmidt, Olga
    SNSB-Zoologische Staatssammlung München, Munich, Germany.
    Heibo, Erik
    Lierskogen, Norway.
    Prous, Marko
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Nyman, Tommi
    Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
    Malm, Tobias
    Swedish Museum of Natural History, Department of Zoology.
    Stahlhut, Julie
    Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.
    Identification of sawflies and horntails (Hymenoptera, ‘Symphyta’) through DNA barcodes: successes and caveats2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, p. 670-685Article in journal (Refereed)
    Abstract [en]

    The ‘Symphyta’ is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of ‘Symphyta’, mainly adults, and 4362 sequences covering 1037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non-European origin. The utility of barcoding for species identification and taxonomy of ‘Symphyta’ is discussed on the basis of examples from each of the included families. A significant level of cryptic species diversity was apparent in many groups. Other attractive applications include the identification of immature stages without the need to rear them, community analyses based on metabarcoding of bulk samples and association of the sexes of adults.

  • 10. van der Valk, Tom
    et al.
    Durazo, Frida Lona
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Guschanski, Katerina
    Whole mitochondrial genome capture from faecal samples and museum-preserved specimens2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed)
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  • 11. van der Valk, Tom
    et al.
    Vezzi, Francesco
    Ormestad, Mattias
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Guschanski, Katerina
    Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies2020In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 20, no 5, SI, p. 1171-1181Article in journal (Refereed)
    Abstract [en]

    The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.

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