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  • 1. Aberer, André
    et al.
    Stamatakis, Alexis
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 161-176Article in journal (Refereed)
  • 2. Alstrom, Per
    et al.
    Rasmussen, Pamela C.
    Sangster, George
    Dalvi, Shashank
    Round, Philip D.
    Zhang, Ruiying
    Yao, Cheng-Te
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Le Manh, Hung
    Lei, Fumin
    Olsson, Urban
    Multiple species within the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex revealed through an integrative taxonomic approach2019In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, p. 1-32Article in journal (Refereed)
    Abstract [en]

    We re-evaluated the taxonomy of the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age-related, geographical and taxon-specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non-sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan’s Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.

  • 3. Alström, Per
    et al.
    Cibois, Alice
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Zuccon, Dario
    Gelang, Magnus
    Fjeldså, Jon
    Andersen, Michael J.
    Moyle, Robert G.
    Pasquet, Eric
    Olsson, Urban
    Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 127, p. 367-375Article in journal (Refereed)
    Abstract [en]

    The widespread Old World avian family Locustellidae (‘grassbirds and allies’) comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a clade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.

  • 4. Alström, Per
    et al.
    Jønsson, Knud A.
    Fjeldså, Jon
    Ödeen, Anders
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dramatic niche shifts and morphological change in two insular bird species2015In: Royal Society Open Science, ISSN 2054-5703, Vol. 2, article id 140364Article in journal (Refereed)
    Abstract [en]

    Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.

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  • 5.
    Alström, Per
    et al.
    Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University , Norbyvägen 18D, 752 36 Uppsala , Sweden;Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 , Chinaa.
    Mohammadi, Zeinolabedin
    Department of Biology, Faculty of Sciences, Golestan University , Gorgan , Iran.
    Donald, Paul F
    BirdLife International, The David Attenborough Building , Pembroke Street, Cambridge CB2 3QZ , UK;Department of Zoology, University of Cambridge , Downing Street, Cambridge CB2 3EJ , UK.
    Nymark, Marianne
    Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University , Norbyvägen 18D, 752 36 Uppsala , Sweden.
    Enbody, Erik D
    Department of Medical Biochemistry and Microbiology, Uppsala University , 751 23 Uppsala , Sweden;Department of Biomolecular Engineering, University of California, Santa Cruz , Santa Cruz, CA 95060 , USA.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Naturhistoriska riksmuseet.
    Elisha, Emmanuel Barde
    Nigerian Montane Forest Project (NMPF), Ngel Nyaki Forest Reserve , Mambilla Plateau, Taraba State , Nigeria;A.P. Leventis Ornithological Research Institute (APLORI), Biological Conservatory , Jos-East, Plateau State , Nigeria.
    Ndithia, Henry K
    Department of Zoology, Ornithology Section, National Museums of Kenya , PO Box 40658-00100 GPO, Nairobi , Kenya.
    Tieleman, B Irene
    Groningen Institute for Evolutionary Life Sciences, University of Groningen , Nijenborgh 7, 9747 AG Groningen , The Netherlands.
    Engelbrecht, Derek
    Department of Biodiversity, University of Limpopo , Private Bag X1106, Sovenga, 0727 , South Africa.
    Olsson, Urban
    Department of Biological and Environmental Sciences, University of Gothenburg , PO Box 463, 405 30 Göteborg , Sweden;Gothenburg Global Biodiversity Centre , PO Box 461, 405 30 Göteborg , Sweden.
    Rancilhac, Loïs
    Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University , Norbyvägen 18D, 752 36 Uppsala , Sweden.
    Stervander, Martin
    Bird Group, Natural History Museum , Akeman Street, Tring, Hertfordshire HP23 6AP , UK.
    Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)2023In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642Article in journal (Refereed)
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  • 6. Alström, Per
    et al.
    Mohammadi, Zeinolabedin
    Enbody, Erik D.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Naturhistoriska riksmuseet.
    Engelbrecht, Derek
    Crochet, Pierre-André
    Guillaumet, Alban
    Rancilhac, Loïs
    Tieleman, B. Irene
    Olsson, Urban
    Donald, Paul F.
    Stervander, Martin
    Systematics of the avian family Alaudidae using multilocus and genomic data2023In: Avian Research, ISSN 2053-7166, Vol. 14, p. 100095-100095, article id 100095Article in journal (Refereed)
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    fulltext
  • 7. Alström, Per
    et al.
    Rasmussen, Pamela C.
    Sangster, George
    Dalvi, Shashank
    Round, Philip D.
    Zhang, Ruiying
    Yao, Cheng-Te
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Le Manh, Hung
    Lei, Fumin
    Olsson, Urban
    Multiple species within the Striated Prinia Prinia crinigera–Brown Prinia P. polychroa complex revealed through an integrative taxonomic approach2020In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 162, no 3, p. 936-967Article in journal (Refereed)
    Abstract [en]

    We re‐evaluated the taxonomy of the Striated Prinia Prinia crinigera–Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age‐related, geographical and taxon‐specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non‐sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.

  • 8. Alström, Per
    et al.
    Zhang, R
    Zhao, M
    Wang, J
    Zhu, X
    Gwee, C.H.
    Hao, Y
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jia, C
    Prawiradilaga, D M
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lei, Fumin
    Olsson, Urban
    Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 141-152Article in journal (Refereed)
  • 9. Ameen, Carly
    et al.
    Feuerborn, Tatiana R.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Brown, Sarah K.
    Linderholm, Anna
    Hulme-Beaman, Ardern
    Lebrasseur, Ophelie
    Sinding, Mikkel-Holger S.
    Lounsberry, Zachary T.
    Lin, Audrey T.
    Appelt, Martin
    Bachmann, Lutz
    Betts, Matthew
    Britton, Kate
    Darwent, John
    Dietz, Rune
    Fredholm, Merete
    Gopalakrishnan, Shyam
    Goriunova, Olga I.
    Gronnow, Bjarne
    Haile, James
    Hallsson, Jon Hallsteinn
    Harrison, Ramona
    Heide-Jorgensen, Mads Peter
    Knecht, Rick
    Losey, Robert J.
    Masson-MacLean, Edouard
    McGovern, Thomas H.
    McManus-Fry, Ellen
    Meldgaard, Morten
    Midtdal, Aslaug
    Moss, Madonna L.
    Nikitin, Iurii G.
    Nomokonova, Tatiana
    Palsdottir, Albina Hulda
    Perri, Angela
    Popov, Aleksandr N.
    Rankin, Lisa
    Reuther, Joshua D.
    Sablin, Mikhail
    Schmidt, Anne Lisbeth
    Shirar, Scott
    Smiarowski, Konrad
    Sonne, Christian
    Stiner, Mary C.
    Vasyukov, Mitya
    West, Catherine F.
    Ween, Gro Birgit
    Wennerberg, Sanne Eline
    Wiig, Oystein
    Woollett, James
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Hansen, Anders J.
    Gilbert, M. Thomas P.
    Sacks, Benjamin N.
    Frantz, Laurent
    Larson, Greger
    Dobney, Keith
    Darwent, Christyann M.
    Evin, Allowen
    Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1916, article id 20191929Article in journal (Refereed)
    Abstract [en]

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

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  • 10. Angerbjorn, Anders
    et al.
    Eide, Nina E.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Elmhagen, Bodil
    Hellstrom, Peter
    Ims, Rolf A.
    Killengreen, Siw
    Landa, Arild
    Meijer, Tomas
    Mela, Matti
    Niemimaa, Jukka
    Noren, Karin
    Tannerfeldt, Magnus
    Yoccoz, Nigel G.
    Henttonen, Heikki
    Carnivore conservation in practice: replicated management actions on a large spatial scale2013In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 50, no 1, p. 59-67Article in journal (Refereed)
  • 11.
    Arribas, Paula
    et al.
    Island Ecology and Evolution Research Group Instituto de Productos Naturales y Agrobiología (IPNA‐CSIC) San Cristóbal de la Laguna Spain.
    Andújar, Carmelo
    Island Ecology and Evolution Research Group Instituto de Productos Naturales y Agrobiología (IPNA‐CSIC) San Cristóbal de la Laguna Spain.
    Bidartondo, Martin I.
    Department of Life Sciences Imperial College London London UK;Comparative Plant and Fungal Biology Royal Botanic Gardens London UK.
    Bohmann, Kristine
    Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe Institute University of Copenhagen Copenhagen Denmark.
    Coissac, Éric
    Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc LECA, Laboratoire d’Ecologie Alpine Grenoble France.
    Creer, Simon
    School of Natural Sciences Bangor University Gwynedd UK.
    deWaard, Jeremy R.
    Centre for Biodiversity Genomics University of Guelph Guelph Canada;School of Environmental Sciences University of Guelph Guelph Canada.
    Elbrecht, Vasco
    Centre for Biodiversity Monitoring (ZBM) Zoological Research Museum Alexander Koenig Bonn Germany.
    Ficetola, Gentile F.
    Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc LECA, Laboratoire d’Ecologie Alpine Grenoble France;Department of Environmental Sciences and Policy University of Milano Milano Italy.
    Goberna, Marta
    Department of Environment and Agronomy INIA Madrid Spain.
    Kennedy, Susan
    Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University Onna‐son Japan;Department of Biogeography Trier University Trier Germany.
    Krehenwinkel, Henrik
    Department of Biogeography Trier University Trier Germany.
    Leese, Florian
    Aquatic Ecosystem Research, Faculty of Biology University of Duisburg‐Essen Essen Germany;Centre for Water and Environmental Research (ZWU) Essen University of Duisburg‐Essen Essen Germany.
    Novotny, Vojtech
    Biology Centre, Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic;Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Yu, Douglas W.
    State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China;Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China;School of Biological Sciences University of East Anglia Norwich UK.
    Zinger, Lucie
    Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM Université PSL Paris France.
    Creedy, Thomas J.
    Department of Life Sciences Natural History Museum London UK.
    Meramveliotakis, Emmanouil
    Department of Biological Sciences University of Cyprus Nicosia Cyprus.
    Noguerales, Víctor
    Department of Biological Sciences University of Cyprus Nicosia Cyprus.
    Overcast, Isaac
    Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM Université PSL Paris France;Division of Vertebrate Zoology American Museum of Natural History New York USA.
    Morlon, Hélène
    Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM Université PSL Paris France.
    Vogler, Alfried P.
    Department of Life Sciences Imperial College London London UK;Department of Life Sciences Natural History Museum London UK.
    Papadopoulou, Anna
    Department of Biological Sciences University of Cyprus Nicosia Cyprus.
    Emerson, Brent C.
    Island Ecology and Evolution Research Group Instituto de Productos Naturales y Agrobiología (IPNA‐CSIC) San Cristóbal de la Laguna Spain.
    Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 5, p. 1120-1135Article in journal (Refereed)
  • 12.
    Bachmann, Lutz
    et al.
    Natural History Museum University of Oslo Oslo Norway.
    Beermann, Jan
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany;Helmholtz Institute for Functional Marine Biodiversity at Oldenburg University Oldenburg Germany.
    Brey, Thomas
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany;Helmholtz Institute for Functional Marine Biodiversity at Oldenburg University Oldenburg Germany;University of Bremen Bremen Germany.
    de Boer, Hugo J.
    Natural History Museum University of Oslo Oslo Norway.
    Dannheim, Jennifer
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany.
    Edvardsen, Bente
    Department of Biosciences, Section for Aquatic Biology and Toxicology University of Oslo Oslo Norway.
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Holston, Kevin C.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics The Swedish Museum of Natural History Stockholm Sweden.
    Johansson, Veronika A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics The Swedish Museum of Natural History Stockholm Sweden.
    Kloss, Paul
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany;Helmholtz Institute for Functional Marine Biodiversity at Oldenburg University Oldenburg Germany.
    Konijnenberg, Rebecca
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany.
    Osborn, Karen J.
    Department of Invertebrate Zoology Smithsonian National Museum of Natural History Washington DC USA.
    Pappalardo, Paula
    Department of Invertebrate Zoology Smithsonian National Museum of Natural History Washington DC USA.
    Pehlke, Hendrik
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany.
    Piepenburg, Dieter
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany;Helmholtz Institute for Functional Marine Biodiversity at Oldenburg University Oldenburg Germany;Institute for Ecosystem Research, Kiel University Kiel Germany.
    Struck, Torsten H.
    Natural History Museum University of Oslo Oslo Norway.
    Sundberg, Per
    Department of Marine Sciences Gothenburg University Gothenburg Sweden.
    Markussen, Stine Svalheim
    Norwegian Biodiversity Information Centre Trondheim Norway.
    Teschke, Katharina
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Functional Ecology Bremerhaven Germany;Helmholtz Institute for Functional Marine Biodiversity at Oldenburg University Oldenburg Germany.
    Vanhove, Maarten P. M.
    Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology Hasselt University Diepenbeek Belgium.
    The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 20222023In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 52, no 3, p. 187-214Article in journal (Refereed)
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  • 13.
    Bachmann, Lutz
    et al.
    University of Oslo Natural History Museum P.O. Box 1172 Blindern NO 0318 Oslo Norway.
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sundberg, Per
    University of Gothenburg Department of Marine Sciences P.O. Box 463 SE 40530 Gothenburg Sweden.
    Systematics and biodiversity research in the era of genomics2016In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 45, no S1, p. 3-4Article in journal (Other academic)
  • 14. Bakker, Freek T
    et al.
    Antonelli, Alexandre
    Clarke, Julia A
    Cook, Joseph A
    Edwards, Scott V
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Faurby, Søren
    Ferrand, Nuno
    Gelang, Magnus
    Gillespie, Rosemary G
    Irestedt, Martin
    Lundin, Kennet
    Larsson, Ellen
    Matos-Maravi­, Pavel
    Muller, Johannes
    von Proschwitz, Ted
    Roderick, George K
    Schliep, Alexander
    Wahlberg, Niklas
    Wiedenhoeft, John
    Källersjö, Mari
    The Global Museum: natural history collections and the future of evolutionary science and public education2020In: PeerJ, E-ISSN 2167-8359, ISSN 2167-8359, Vol. 8, article id e8225Article in journal (Refereed)
    Abstract [en]

    Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.

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  • 15. Bannikova, Anna A.
    et al.
    Jenkins, Paulina D.
    Solovyeva, Evgeniya N.
    Pavlova, Svetlana, V
    Demidova, Tatiana B.
    Simanovsky, Sergey A.
    Sheftel, Boris, I
    Lebedev, Vladimir S.
    Fang, Yun
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Abramov, Alexei, V
    Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae): molecular and morphological analyses with the discussion of tribal affinities2019In: ZooKeys, ISSN 1313-2989, E-ISSN 1313-2970, no 888, p. 133-158Article in journal (Refereed)
    Abstract [en]

    The first genetic study of the holotype of the Gansu short-tailed shrew, Blarinella griselda Thomas, 1912, is presented. The mitochondrial analysis demonstrated that the type specimen of B. griselda is close to several recently collected specimens from southern Gansu, northern Sichuan and Shaanxi, which are highly distinct from the two species of Asiatic short-tailed shrews of southern Sichuan, Yunnan, and Vietnam, B. quadraticauda and B. wardi. Our analysis of four nuclear genes supported the placement of B. griselda as sister to B. quadraticauda / B. wardi, with the level of divergence between these two clades corresponding to that among genera of Soricinae. A new generic name, Parablarinella, is proposed for the Gansu short-tailed shrew. Karyotypes of Parablarinella griselda (2n = 49, NFa = 50) and B. quadraticauda (2n = 49, NFa = 62) from southern Gansu are described. The tribal affinities of Blarinellini and Blarinini are discussed.

  • 16.
    Barani-Beiranvand, Hossein
    et al.
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, Khorasan E Razavi, Mashhad, Iran..
    Aliabadian, Mansour
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, Khorasan E Razavi, Mashhad, Iran.;Ferdowsi Univ Mashhad, Inst Appl Zool, RDZI, Mashhad, Iran..
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Qu, Yanhua
    Chinese Acad Sci, Inst Zool, Beijing, Peoples R China..
    Darvish, Jamshid
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, Khorasan E Razavi, Mashhad, Iran.;Ferdowsi Univ Mashhad, Inst Appl Zool, Res Dept Rodentol, Mashhad, Iran..
    Szekely, Tamas
    Univ Bath, Dept Biol & Biochem, Bath, Avon, England..
    van Dijk, Rene E.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England..
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden..
    Phylogeny of penduline tits inferred from mitochondrial and microsatellite genotyping2017In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 48, no 7, p. 932-940Article in journal (Refereed)
    Abstract [en]

    Penduline tits (Remiz spp.) are renowned for their diverse mating and parenting strategies, and are a well-studied system by behavioural ecologists. However, the phylogenetic relationships and species delimitations within this genus are poorly understood. Here, we investigate phylogenetic relationships within the genus Remiz by examining the genetic variation in the mitochondrial cytochrome-b gene of 64 individuals and in ten autosomal microsatellite markers from 44 individuals. The taxon sampling includes individuals from all currently recognized species (R. pendulinus, R. macronyx, R. coronatus, and R. consobrinus) and most subspecies in the Palearctic region. We showed that R. coronatus and R. consobrinus are genetically well differentiated and constitute independent evolutionary lineages, separated from each other and from R. pendulinus/macronyx. However, we found no evidence for significant differentiation among R. pendulinus/macronyx individuals in mtDNA haplotypes and only marginal differences between R. pendulinus and R. macronyx in microsatellite markers. Hence, based on present data our recommendation is to treat R. pendulinus and R. macronyx as conspecific and R. coronatus and R. consobrinus as separate species.

  • 17.
    Barani-Beiranvand, Hossein
    et al.
    Dept of Biology, Faculty of Science, Ferdowsi Univ. of Mashhad, Iran Mashhad, Khorasan-e Razavi; Mashhad Iran.
    Aliabadian, Mansour
    Dept of Biology, Faculty of Science, Ferdowsi Univ. of Mashhad, Iran Mashhad, Khorasan-e Razavi; Mashhad Iran;Research Dept of Zoological Innovation (RDZI), Inst. of Applied Zoology, Ferdowsi Univ. of Mashhad; Mashhad Iran.
    Irestedt, Martin
    Dept of Bioinformatics and Genetics, Swedish Museum of Natural History; Stockholm Sweden.
    Qu, Yanhua
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Darvish, Jamshid
    Research Dept of Rodentology, Inst. of Applied Zoology, Ferdowsi Univ. of Mashhad; Mashhad Iran.
    Székely, Tamás
    Dept of Biology and Biochemistry, Univ. of Bath; Bath UK.
    Van Dijk, René E.
    Dept of Animal and Plant Sciences, Univ. of Sheffield; Sheffield UK.
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Phylogeny of penduline tits inferred from mitochondrial and microsatellite genotyping2017In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 48, no 7, p. 932-940Article in journal (Refereed)
  • 18. Barlow, A
    et al.
    Paijmans, J L A
    Alberti, F
    Gasparyan, B
    Bar-Oz, G
    Pinhasi, R
    Foronova, I
    Puzachenko, A Y
    Pacher, M
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Baryshnikov, G
    Hofreiter, M
    Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears2021In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 31, no 8, p. 1771-+Article in journal (Refereed)
  • 19. Barlow, Axel
    et al.
    Cahill, James A.
    Hartmann, Stefanie
    Theunert, Christoph
    Xenikoudakis, Georgios
    Fortes, Gloria G.
    Paijmans, Johanna L. A.
    Rabeder, Gernot
    Frischauf, Christine
    Grandal-d'Anglade, Aurora
    Garcia-Vazquez, Ana
    Murtskhvaladze, Marine
    Saarma, Urmas
    Anijalg, Peeter
    Skrbinsek, Tomaz
    Bertorelle, Giorgio
    Gasparian, Boris
    Bar-Oz, Guy
    Pinhasi, Ron
    Slatkin, Montgomery
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Shapiro, Beth
    Hofreiter, Michael
    Partial genomic survival of cave bears in living brown bears2018In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, no 10, p. 1563-1570Article in journal (Refereed)
  • 20. Barnett, Ross
    et al.
    Westbury, Michael V.
    Sandoval-Velasco, Marcela
    Vieira, Filipe Garrett
    Jeon, Sungwon
    Zazula, Grant
    Martin, Michael D.
    Ho, Simon Y.W.
    Mather, Niklas
    Gopalakrishnan, Shyam
    Ramos-Madrigal, Jazmín
    de Manuel, Marc
    Zepeda-Mendoza, M. Lisandra
    Antunes, Agostinho
    Baez, Aldo Carmona
    De Cahsan, Binia
    Larson, Greger
    O’Brien, Stephen J.
    Eizirik, Eduardo
    Johnson, Warren E.
    Koepfli, Klaus-Peter
    Wilting, Andreas
    Fickel, Jörns
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lorenzen, Eline D.
    Marques-Bonet, Tomas
    Hansen, Anders J.
    Zhang, Guojie
    Bhak, Jong
    Yamaguchi, Nobuyuki
    Gilbert, M. Thomas P.
    Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens2020In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445Article in journal (Refereed)
    Abstract [en]

    Summary Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.

  • 21. Batalha-Filho, Henrique
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Silveira, Luis F
    Miyaki, Cristina Y
    Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest.2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, no 1, p. 86-94Article in journal (Refereed)
    Abstract [en]

    The Neotropical Synallaxis ruficapilla complex is endemic to the Atlantic Forest and is comprised of three species: S. ruficapilla, S. whitneyi, and S. infuscata. This group is closely related to the Synallaxis moesta complex that occurs in the Andes, Tepuis, and Guianan shield. Here we used mitochondrial and nuclear gene sequences to infer the phylogeny and the time of diversification of the S. ruficapilla and S. moesta complexes. We also included samples of an undescribed population of Synallaxis that resembles other populations of the S. ruficapilla complex. Our results showed that different geographical lineages within the S. ruficapilla complex are reciprocally monophyletic, but the northern form (S. infuscata) grouped with an Andean taxon. This suggests that at least two lineages of this group independently colonized the Atlantic Forest. Specimens of the undescribed population formed a monophyletic clade with deep divergence. Estimated diversification dates were within the late Pliocene to Pleistocene (2.75-0.16 million of years ago). This suggests that at this time there was a higher connectivity between habitats in the rugged landscapes of the circum-Amazonian bioregions. The observed Pleistocene diversification within the Atlantic Forest is congruent in space and time with studies of other co-distributed organisms, and may be associated with climate changes and tectonic activity during this period.

  • 22. Batalha-Filho, Henrique
    et al.
    Pessoa, Rodrigo O
    Fabre, Pierre-Henri
    Fjeldså, Jon
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Silveira, Luís F
    Miyaki, Cristina Y
    Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests.2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 79, p. 422-432Article in journal (Refereed)
    Abstract [en]

    We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

  • 23.
    Bengtson, Annika
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Englund, Markus
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pruski, John F.
    Anderberg, Arne Alfred
    Swedish Museum of Natural History, Department of Botany.
    Phylogeny of the Athroismeae (Asteraceae), with a new circumscription of the tribe2017In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 66, no 2, p. 408-420Article in journal (Refereed)
    Abstract [en]

    Athroismeae is a small tribe of the Asteraceae-Asteroideae, the members of which show considerable variation in morphology. A molecular phylogenetic study of the tribe is presented for the first time, based on plastid (ndhF, trnH-psbA, trnL-trnF) and nuclear data (ETS, ITS). The phylogenetic relationships between the different genera within Athroismeae are discussed, and in addition, three unispecific genera: Anisochaeta, Artemisiopsis and Symphyllocarpus as well as Duhaldea (Inula) stuhlmannii, all earlier placed in other tribes, are here shown to belong within Athroismeae. Symphyllocarpus is sister to Centipeda and the earlier Symphyllocarpinae includes Centipedinae in synonymy. Furthermore, Cardosoa and Philyrophyllum are found to be integrated within Anisopappus and their generic status cannot be maintained. An outline of an amended circumscription of the Athroismeae is presented, with three new combinations and a description of the new subtribe Lowryanthinae.

  • 24. Bergh, Stefan
    et al.
    Blidmo, Roger
    Carlsson, Anders
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Olsson, Eva
    Åkerlund, Agneta
    Sörmländsk stenåldersforskning1987Report (Other academic)
  • 25. Bergstrom, Anders
    et al.
    Frantz, Laurent
    Schmidt, Ryan
    Ersmark, Erik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lebrasseur, Ophelie
    Girdland-Flink, Linus
    Lin, Audrey T.
    Stora, Jan
    Sjogren, Karl-Goran
    Anthony, David
    Antipina, Ekaterina
    Amiri, Sarieh
    Bar-Oz, Guy
    Bazaliiskii, Vladimir I.
    Bulatovic, Jelena
    Brown, Dorcas
    Carmagnini, Alberto
    Davy, Tom
    Fedorov, Sergey
    Fiore, Ivana
    Fulton, Deirdre
    Germonpre, Mietje
    Haile, James
    Irving-Pease, Evan K.
    Jamieson, Alexandra
    Janssens, Luc
    Kirillova, Irina
    Horwitz, Liora Kolska
    Kuzmanovic-Cvetkovic, Julka
    Kuzmin, Yaroslav
    Losey, Robert J.
    Dizdar, Daria Loznjak
    Mashkour, Marjan
    Novak, Mario
    Onar, Vedat
    Orton, David
    Pasaric, Maja
    Radivojevic, Miljana
    Rajkovic, Dragana
    Roberts, Benjamin
    Ryan, Hannah
    Sablin, Mikhail
    Shidlovskiy, Fedor
    Stojanovic, Ivana
    Tagliacozzo, Antonio
    Trantalidou, Katerina
    Ullen, Inga
    Villaluenga, Aritza
    Wapnish, Paula
    Dobney, Keith
    Gotherstrom, Anders
    Linderholm, Anna
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pinhasi, Ron
    Larson, Greger
    Skoglund, Pontus
    Origins and genetic legacy of prehistoric dogs2020In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 370, no 6516, p. 557-563Article in journal (Refereed)
    Abstract [en]

    Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

  • 26. Bergstrom, Anders
    et al.
    Stanton, David WG
    Taron, Ulrike H
    Frantz, Laurent
    Sinding, Mikkel-Holger S
    Ersmark, Erik
    Pfrengle, Saskia
    Cassatt-Johnstone, Molly
    Lebrasseur, Ophelie
    Girdland-Flink, Linus
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Grey wolf genomic history reveals a dual ancestry of dogs2022In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 607, p. 313-320Article in journal (Refereed)
    Download full text (pdf)
    fulltext
  • 27. Bieker, Vanessa C
    et al.
    Battlay, Paul
    Petersen, Bent
    Sun, Xin
    Wilson, Jonathan
    Brealey, Jaelle C
    Bretagnolle, François
    Nurkowski, Kristin
    Lee, Chris
    Barreiro, Fátima Sánchez
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Uncovering the genomic basis of an extraordinary plant invasion2022In: Science Advances, E-ISSN 2375-2548, Vol. 8, no 34Article in journal (Refereed)
  • 28. Boeskorov, G G
    et al.
    Plotnikov, V V
    Protopopov, A V
    Baryshnikov, G F
    Fosse, P
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stanton, D W G
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pavlov, I S
    Suzuki, N
    Tikhonov, A N
    The Preliminary Analysis of Cave Lion Cubs Panthera spelaea (Goldfuss, 1810) from the Permafrost of Siberia2021In: Quaternary, E-ISSN 2571-550X, Vol. 4, no 3Article in journal (Refereed)
    Download full text (pdf)
    fulltext
  • 29. Brace, Selina
    et al.
    Palkopoulou, Eleftheria
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lister, Adrian M.
    Miller, Rebecca
    Otte, Marcel
    Germonpre, Mietje
    Blockley, Simon P. E.
    Stewart, John R.
    Barnes, Ian
    Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 50, p. 20532-20536Article in journal (Refereed)
  • 30. Brace, Selina
    et al.
    Thomas, Jessica A.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Burger, Joachim
    MacPhee, Ross D. E.
    Barnes, Ian
    Turvey, Samuel T.
    Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 12, p. 3095-3103Article in journal (Refereed)
    Abstract [en]

    The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a similar to 750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.

  • 31. Braga, Mariana P.
    et al.
    Janz, Niklas
    Department of Zoology Stockholm University Stockholm Sweden.
    Nylin, Sören
    Department of Zoology Stockholm University Stockholm Sweden.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Landis, Michael J.
    Department of Biology Washington University in St. Louis St. Louis MO USA.
    Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants2021In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 24, no 10, p. 2134-2145Article in journal (Refereed)
  • 32. Braga, Mariana P.
    et al.
    Landis, Michael J.
    Nylin, Sören
    Janz, Niklas
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Bayesian Inference of Ancestral Host–Parasite Interactions under a Phylogenetic Model of Host Repertoire Evolution2020In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 69, p. 1149-1162Article in journal (Refereed)
  • 33. Brealey, Jaelle C
    et al.
    Leitão, Henrique G
    van der Valk, Tom
    Xu, Wenbo
    Bougiouri, Katia
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Guschanski, Katerina
    Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 10, p. 3003-3022Article in journal (Refereed)
    Abstract [en]

    Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

  • 34. Cahill, James A
    et al.
    Stirling, Ian
    Kistler, Logan
    Salamzade, Rauf
    Ersmark, Erik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Stockholms Universitet.
    Fulton, Tara L
    Stiller, Mathias
    Green, Richard E
    Shapiro, Beth
    Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof, and Chichagof Islands (ABC Islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC Islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC Islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. This article is protected by copyright. All rights reserved.

  • 35. Cai, T L
    et al.
    Cibois, Alice
    Alström, Per
    Moyle, R G
    Kennedy, J D
    Shao, S M
    Zhang, R Y
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gelang, Magnus
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Lei, Fumin
    Fjeldså, Jon
    Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes)2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 346-356Article in journal (Refereed)
  • 36.
    Cannon, Johanna
    et al.
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Vellutini, Bruno
    Sars International Centre for Marine Molecular Biology.
    Smith, Julian
    Winthrop University.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jondelius, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Hejnol, Andreas
    Sars International Centre for Marine Molecular Biology.
    Xenacoelomorpha is the sister group to Nephrozoa2016In: Nature, ISSN ISSN: 0028-0836, Vol. 530, p. 89-93Article in journal (Refereed)
    Abstract [en]

    The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships1. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (= Nephrozoa, namely protostomes and deuterostomes)2,3 or is a clade inside Deuterostomia4. Thus, determining the phylogenetic position of this clade is pivotal for understanding the early evolution of bilaterian features, or as a case of drastic secondary loss of complexity. Here we show robust phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa. Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes and using different models of evolution under maximum likelihood and Bayesian inference analyses, strongly corroborate this result. Rigorous testing of 25 experimental data sets designed to exclude data partitions and taxa potentially prone to reconstruction biases indicates that long- branch attraction, saturation, and missing data do not influence these results. The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa. 

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  • 37. Cappellini, Enrico
    et al.
    Gentry, Anthea
    Palkopoulou, Eleftheria
    Ishida, Yasuko
    Cram, David
    Roos, Anna-Marie
    Watson, Mick
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Fernholm, Bo
    Swedish Museum of Natural History, Department of Zoology.
    Agnelli, Paolo
    Barbagli, Fausto
    Littlewood, D. Tim. J.
    Kelstrup, Christian D.
    Olsen, Jesper V.
    Lister, Adrian M.
    Roca, Alfred L.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)2014In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 170, p. 222-232Article in journal (Refereed)
  • 38. Cappellini, Enrico
    et al.
    Welker, Frido
    Pandolfi, Luca
    Ramos-Madrigal, Jazmin
    Samodova, Diana
    Ruther, Patrick L.
    Fotakis, Anna K.
    Lyon, David
    Moreno-Mayar, J. Victor
    Bukhsianidze, Maia
    Jersie-Christensen, Rosa Rakownikow
    Mackie, Meaghan
    Ginolhac, Aurelien
    Ferring, Reid
    Tappen, Martha
    Palkopoulou, Eleftheria
    Dickinson, Marc R.
    Stafford, Thomas W., Jr.
    Chan, Yvonne L.
    Gotherstrom, Anders
    Nathan, Senthilvel K. S. S.
    Heintzman, Peter D.
    Kapp, Joshua D.
    Kirillova, Irina
    Moodley, Yoshan
    Agusti, Jordi
    Kahlke, Ralf-Dietrich
    Kiladze, Gocha
    Martinez-Navarro, Bienvenido
    Liu, Shanlin
    Velasco, Marcela Sandoval
    Sinding, Mikkel-Holger S.
    Kelstrup, Christian D.
    Allentoft, Morten E.
    Orlando, Ludovic
    Penkman, Kirsty
    Shapiro, Beth
    Rook, Lorenzo
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Olsen, Jesper V.
    Lordkipanidze, David
    Willerslev, Eske
    Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 574, no 7776, p. 103-+Article in journal (Refereed)
    Abstract [en]

    The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa(1). However, the irreversible post-mortem degradation(2) of ancient DNA has so far limited its recovery-outside permafrost areasto specimens that are not older than approximately 0.5 million years (Myr)(3). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I-4. and suggested the presence of protein residues in fossils of the Cretaceous period(5)-although with limited phylogenetic use(6). In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch(7-9), using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)(10). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the Glade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates(11), and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

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  • 39.
    Caputo, A
    et al.
    Stockholm University.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Foster, R A
    Stockholm University.
    The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration2019In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 366, no 2, article id fny297Article in journal (Refereed)
  • 40. Chang, Dan
    et al.
    Knapp, Michael
    Enk, Jacob
    Lippold, Sebastian
    Kircher, Martin
    Lister, Adrian
    MacPhee, Ross D. E.
    Widga, Christopher
    Czechowski, Paul
    Sommer, Robert
    Hodges, Emily
    Stuempel, Nikolaus
    Barnes, Ian
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Derevianko, Anatoly
    Germonpre, Mietje
    Hillebrand-Voiculescu, Alexandra
    Constantin, Silviu
    Kuznetsova, Tatyana
    Mol, Dick
    Rathgeber, Thomas
    Rosendahl, Wilfried
    Tikhonov, Alexey N.
    Willerslev, Eske
    Hannon, Greg
    Lalueza-Fox, Carles
    Joger, Ulrich
    Poinar, Hendrik
    Hofreiter, Michael
    Shapiro, Beth
    The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis2017In: Scientific Reports, E-ISSN 2045-2322, Vol. 7, article id 44585Article in journal (Refereed)
  • 41. Chattopadhyay, Balaji
    et al.
    Forcina, Giovanni
    Garg, Kritika M.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Guerrini, Monica
    Barbanera, Filippo
    Rheindt, Frank E.
    Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change2021In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646Article in journal (Refereed)
    Abstract [en]

    We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

  • 42. Chen, Yilin
    et al.
    Ge, Deyan
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Song, Gang
    Wen, Zhixin
    Luo, Xu
    Yang, Qisen
    Lei, Fumin
    Qu, Yanhua
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Alpine burrow-sharing mammals and birds show similar population-level climate change risks2023In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 13, no 9, p. 990-996Article in journal (Refereed)
  • 43. Chen, Yilin
    et al.
    Jiang, Zhiyong
    Fan, Ping
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Song, Gang
    Luo, Xu
    Lei, Fumin
    Qu, Yanhua
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4821Article in journal (Refereed)
  • 44. Christidis, Les
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ohlson, Jan I
    The suboscine passerines2020In: The Largest Avian Radiation / [ed] Fjeldså, J., Christidis, L. & Ericson, P.G.P, Barcelona: Lynx Edicions , 2020, p. 65-65Chapter in book (Other academic)
  • 45. Cibois, Alice
    et al.
    Gelang, Magnus
    Alström, Per
    Pasquet, Eric
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Olsson, Urban
    Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae), and a proposal for a revised taxonomy2018In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 47, p. 428-440Article in journal (Refereed)
  • 46. Cibois, Alice
    et al.
    Vallotton, L
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Blom, Mozes P.K.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Genetic and radiographic insights into the only known mounted specimen of Kangaroo Island Emu2020In: Revue suisse de zoologie, ISSN 0035-418X, Vol. 126, p. 209-217Article in journal (Refereed)
  • 47. Cockerill, Christopher A
    et al.
    Hasselgren, Malin
    Dussex, Nicolas
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    von Seth, Johanna
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Angerbjörn, Anders
    Wallén, Johan F
    Landa, Arild
    Eide, Nina E
    Flagstad, Øystein
    Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus)2022In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 13, no 11Article in journal (Refereed)
  • 48. Cole, Theresa
    et al.
    Rawlence, Nic
    Dussex, Nicolas
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Elleberg, Ursulla
    Houston, Dave
    Mattern, Thomas
    Miskelly, Colin
    Morrisson, Kyle
    Scofield, Paul
    Tennyson, Alan
    Tompson, David
    Wood, Jamie
    Waters, Jonathan
    Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 131, p. 72-79Article in journal (Refereed)
    Abstract [en]

    Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as ‘Eudyptes spp.’, we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.

  • 49. Collinson, J M
    et al.
    McGowan, R Y
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    First British records of ‘Eastern’ and ‘Western’ Subalpine Warblers2014In: British birds, Vol. 107, p. 282-285Article, book review (Other (popular science, discussion, etc.))
  • 50. Cotton, James A.
    et al.
    Berriman, Matthew
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barnes, Ian
    Eradication genomics-lessons for parasite control2018In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 361, no 6398, p. 130-131Article in journal (Refereed)
1234567 1 - 50 of 432
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