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  • 1.
    Broman, Elias
    et al.
    Stockholm University.
    Bonaglia, Stefano
    Stockholm University.
    Holovachov, Oleksandr
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Marzocchi, Ugo
    Aarhus University.
    Hall, Per O.J.
    University of Gothenburg.
    Nascimento, Francisco J.A.
    Stockholm University.
    Uncovering diversity and metabolic spectrum of animals in dead zone sediments2020Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 3, s. 1-12, artikel-id 106Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ocean deoxygenation driven by global warming and eutrophication is a primary concern for marine life. Resistant animals may be present in dead zone sediments, however there is lack of information on their diversity and metabolism. Here we combined geochemistry, microscopy, and RNA-seq for estimating taxonomy and functionality of micrometazoans along an oxygen gradient in the largest dead zone in the world. Nematodes are metabolically active at oxygen concentrations below 1.8μmolL−1, and their diversity and community structure are different between low oxygen areas. This is likely due to toxic hydrogen sulfide and its potential to be oxidized by oxygen or nitrate. Zooplankton resting stages dominate the metazoan community, and these populations possibly use cytochrome c oxidase as an oxygen sensor to exit dormancy. Our study sheds light on mechanisms of animal adaptation to extreme environments. These biological resources can be essential for recolonization of dead zones when oxygen conditions improve.

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  • 2. de Raad, Jordi
    et al.
    Päckert, Martin
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Janke, Axel
    Kryukov, Alexey P.
    Martens, Jochen
    Red’kin, Yaroslav A.
    Sun, Yuehua
    Töpfer, Till
    Schleuning, Matthias
    Neuschulz, Eike Lena
    Nilsson, Maria A.
    Speciation and population divergence in a mutualistic seed dispersing bird2022Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 5, nr 1, artikel-id 429Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds.

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  • 3.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Zuccon, Dario
    Larsson, Petter
    Tison, Jean-Luc
    Emslie, Steven D.
    Götherström, Anders
    Hume, Julian P.
    Werdelin, Lars
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Qu, Yanhua
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture2022Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 5, nr 1, artikel-id 857Artikel i tidskrift (Refereegranskat)
  • 4. Kersten, Oliver
    et al.
    Star, Bastiaan
    Leigh, Deborah M.
    Anker-Nilssen, Tycho
    Strøm, Hallvard
    Danielsen, Jóhannis
    Descamps, Sébastien
    Erikstad, Kjell E.
    Fitzsimmons, Michelle G.
    Fort, Jérôme
    Hansen, Erpur S.
    Harris, Mike P.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Kleven, Oddmund
    Mallory, Mark L.
    Jakobsen, Kjetill S.
    Boessenkool, Sanne
    Complex population structure of the Atlantic puffin revealed by whole genome analyses2021Ingår i: Communications Biology, E-ISSN 2399-3642Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The factors underlying gene flow and genomic population structure in vagile seabirds arenotoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate thepopulation structure of the Atlantic puffin (Fratercula arctica) by assembling its referencegenome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies.We identify four large, genetically distinct clusters, observe isolation-by-distance betweencolonies within these clusters, and obtain evidence for a secondary contact zone. Theseobservations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlightthe power of whole genome data to reveal unexpected population structure in vagile marineseabirds and its value for seabird taxonomy, evolution and conservation

  • 5.
    Leasi, Francesca
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi. Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga,.
    Sevigny, Joseph
    Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire.
    Laflamme, Eric
    Department of Mathematics, Plymouth State University.
    Artois, Tom
    Centre for Environmental Sciences, Hasselt University.
    Curini-Galletti, Marco
    Dipartimento di Medicina Veterinaria, University of Sassari,.
    Navarrete, Alberto
    Departmento de Sistemática y Ecología Acuática, El Colegio de la Frontera Sur, Unidad Chetumal.
    Di Domenico, Maikon
    Centro de Estudos do Mar, Universidade Federal do Paraná.
    Goetz, Freya
    Department of Invertebrate Zoology, Smithsonian National Museum of Natural History.
    Hall, Jeffrey
    Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire.
    Hochberg, Rick
    Department of Biological Science, University of Massachusetts Lowell.
    Jörger, Katharina
    Department of Biology, Ludwig-Maximilians–University of Munich.
    Jondelius, Ulf
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Todaro, Antonio
    Department of Life Sciences, University of Modena & Reggio Emilia.
    Wirshing, Herman
    Department of Invertebrate Zoology, Smithsonian National Museum of Natural History.
    Norenburg, Jonathan
    Department of Invertebrate Zoology, Smithsonian National Museum of Natural History.
    Thomas, Kelley
    Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire.
    Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach2018Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 112Artikel i tidskrift (Refereegranskat)
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  • 6. Lyras, George A.
    et al.
    Werdelin, Lars
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    van der Geer, Bartholomeus G. M.
    van der Geer, Alexandra A. E.
    Fossil brains provide evidence of underwater feeding in early seals2023Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 6, nr 1, artikel-id 747Artikel i tidskrift (Refereegranskat)
  • 7. Martinez, Alejandro
    et al.
    Eckert, Ester
    Artois, Tom
    Careddu, Giovanni
    Casu, Marco
    Curini-Galletti, Marco
    Gazale, Vittorio
    Gobert, Stefan
    Ivanenko, Viatcheslav
    Jondelius, Ulf
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Marzano, Marinella
    Pesole, Graziano
    Zanello, Aldo
    Todaro, Antonio
    Fontaneto, Diego
    Human access impacts biodiversity of microscopic animals in sandy beaches2020Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 3, artikel-id 175Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow “swash” zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity.

  • 8.
    Owen, Kylie
    et al.
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning. Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution.
    Saeki, Kentaro
    Department of Chemistry, Kumamoto University, Kumamoto.
    Warren, Joseph
    School of Marine and Atmospheric Sciences, Stony Brook University.
    Bocconcelli, Alessandro
    Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution.
    Wiley, David
    Stellwagen Bank National Marine Sanctuary, NOAA National Ocean Service.
    Ohira, Shin-Ichi
    Department of Chemistry, Kumamoto University.
    Bombosch, Annette
    Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution.
    Toda, Kei
    Department of Chemistry, Kumamoto University.
    Zitterbart, Daniel
    Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution.
    Natural dimethyl sulfide gradients would lead marine predators to higher prey biomass2021Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 4, artikel-id 149Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Finding prey is essential to survival, with marine predators hypothesised to track chemicals such as dimethyl sulfide (DMS) while foraging. Many predators are attracted to artificially released DMS, and laboratory experiments have shown that zooplankton grazing on phytoplankton accelerates DMS release. However, whether natural DMS concentrations are useful for predators and correlated to areas of high prey biomass remains a fundamental knowledge gap. Here, we used concurrent hydroacoustic surveys and in situ DMS measurements to present evidence that zooplankton biomass is spatially correlated to natural DMS concentration in air and seawater. Using agent simulations, we also show that following gradients of DMS would lead zooplankton predators to areas of higher prey biomass than swimming randomly. Further understanding of the conditions and scales over which these gradients occur, and how they are used by predators, is essential to predicting the impact of future changes in the ocean on predator foraging success.

  • 9.
    Ronquist, Fredrik
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Kudlicka, Jan
    Senderov, Viktor
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Borgström, Johannes
    Lartillot, Nicolas
    Lundén, Daniel
    Murray, Lawrence
    Schön, Thomas B.
    Broman, David
    Universal probabilistic programming offers a powerful approach to statistical phylogenetics2021Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 4, nr 1, artikel-id 244Artikel i tidskrift (Refereegranskat)
1 - 9 av 9
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