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  • 1.
    Abalde, Samuel
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Crocetta, Fabio
    Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Tenorio, Manuel J.
    Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
    D'Aniello, Salvatore
    Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Fassio, Giulia
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Rodríguez-Flores, Paula C.
    Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
    Uribe, Juan E.
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Afonso, Carlos M.L.
    Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal.
    Oliverio, Marco
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Zardoya, Rafael
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus2023In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 186, p. 107838-107838, article id 107838Article in journal (Refereed)
    Abstract [en]

    The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.

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  • 2. 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.

  • 3. 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)
  • 4. 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.

  • 5. Brealey, Jaelle C.
    et al.
    Leitao, Henrique G.
    Department of Ecology and Genetics/Animal Ecology, Uppsala University.
    Hofstede, Thijs
    Department of Ecology and Genetics/Animal Ecology, Uppsala University.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Guschanski, Katerina
    Department of Ecology and Genetics/Animal Ecology, Uppsala University.
    The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans2021In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 31, no 20, p. 4650-4658.e6Article in journal (Refereed)
    Abstract [en]

    Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.4 However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.

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  • 6. Broushaki, Farnaz
    et al.
    Thomas, Mark G
    Link, Vivian
    López, Saioa
    van Dorp, Lucy
    Kirsanow, Karola
    Hofmanová, Zuzana
    Diekmann, Yoan
    Cassidy, Lara M
    Díez-del-Molino, David
    Kousathanas, Athanasios
    Sell, Christian
    Robson, Harry K
    Martiniano, Rui
    Blöcher, Jens
    Scheu, Amelie
    Kreutzer, Susanne
    Bollongino, Ruth
    Bobo, Dean
    Davoudi, Hossein
    Munoz, Olivia
    Currat, Mathias
    Abdi, Kamyar
    Biglari, Fereidoun
    Craig, Oliver E
    Bradley, Daniel G
    Shennan, Stephen
    Veeramah, Krishna R
    Mashkour, Marjan
    Wegmann, Daniel
    Hellenthal, Garrett
    Burger, Joachim
    Early Neolithic genomes from the eastern Fertile Crescent.2016In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 353, no 6298Article in journal (Refereed)
    Abstract [en]

    We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.

  • 7. 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.

  • 8. 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)
  • 9. Diez-del-Molino, David
    et al.
    Sanchez-Barreiro, Fatima
    Barnes, Ian
    Gilbert, M. Thomas P.
    Dalen, Love
    Quantifying Temporal Genomic Erosion in Endangered Species2018In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 33, no 3, p. 176-185Article in journal (Refereed)
  • 10. Doan, Karolina
    et al.
    Mackiewicz, Pawel
    Sandoval-Castellanos, Edson
    Stefaniak, Krzysztof
    Ridush, Bogdan
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Weglenski, Piotr
    Stankovic, Ana
    The history of Crimean red deer population and Cervus phylogeography in Eurasia2018In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 183, no 1, p. 208-225Article in journal (Refereed)
  • 11. Dussex, Nicolas
    et al.
    Tørresen, Ole K.
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Le Moullec, Mathilde
    Veiberg, Vebjørn
    Tooming-Klunderud, Ave
    Skage, Morten
    Garmann-Aarhus, Benedicte
    Wood, Jonathan
    Rasmussen, Jacob A.
    Pedersen, Åshild Ø.
    Martin, Sarah L.F.
    Røed, Knut H.
    Jakobsen, Kjetill S.
    Dalén, Love
    Hansen, Brage B.
    Martin, Michael D.
    Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer2023In: iScience, ISSN 2589-0042, Vol. 26, no 10, p. 107811-107811, article id 107811Article in journal (Refereed)
  • 12. Díez-del-Molino, David
    et al.
    Dehasque, Marianne
    Chacón-Duque, J. Camilo
    Pečnerová, Patrícia
    Tikhonov, Alexei
    Protopopov, Albert
    Plotnikov, Valeri
    Kanellidou, Foteini
    Nikolskiy, Pavel
    Mortensen, Peter
    Swedish Museum of Natural History, Department of Zoology.
    Danilov, Gleb K.
    Vartanyan, Sergey
    Gilbert, M. Thomas P.
    Lister, Adrian M.
    Heintzman, Peter D.
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dalén, Love
    Genomics of adaptive evolution in the woolly mammoth2023In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 33, no 9, p. 1753-1764.e4Article in journal (Refereed)
  • 13. Granquist, Sandra M
    et al.
    Esparza-Salas, Rodrigo
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Hauksson, Erlingur
    Karlsson, Olle
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Angerbjörn, Anders
    Fish consumption of harbour seals (Phoca vitulina) in north western Iceland assessed by DNA metabarcoding and morphological analysis2018In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056Article in journal (Refereed)
  • 14. Haussler, David
    et al.
    O'Brien, Stephen J.
    Ryder, Oliver A.
    Barker, F. Keith
    Clamp, Michele
    Crawford, Andrew J.
    Hanner, Robert
    Hanotte, Olivier
    Johnson, Warren E.
    McGuire, Jimmy A.
    Miller, Webb
    Murphy, Robert W.
    Murphy, William J.
    Sheldon, Frederick H.
    Sinervo, Barry
    Venkatesh, Byrappa
    Wiley, Edward O.
    Allendorf, Fred W.
    Amato, George
    Baker, C. Scott
    Bauer, Aaron
    Beja-Pereira, Albano
    Bermingham, Eldredge
    Bernardi, Giacomo
    Bonvicino, Cibele R.
    Brenner, Sydney
    Burke, Terry
    Cracraft, Joel
    Diekhans, Mark
    Edwards, Scott
    Ericson, Per G. P.
    Estes, James
    Fjelsda, Jon
    Flesness, Nate
    Gamble, Tony
    Gaubert, Philippe
    Graphodatsky, Alexander S.
    Graves, Jennifer A. Marshall
    Green, Eric D.
    Green, Richard E.
    Hackett, Shannon
    Hebert, Paul
    Helgen, Kristofer M.
    Joseph, Leo
    Kessing, Bailey
    Kingsley, David M.
    Lewin, Harris A.
    Luikart, Gordon
    Martelli, Paolo
    Moreira, Miguel A. M.
    Nguyen, Ngan
    Orti, Guillermo
    Pike, Brian L.
    Rawson, David Michael
    Schuster, Stephan C.
    Seuanez, Hector N.
    Shaffer, H. Bradley
    Springer, Mark S.
    Stuart, Joshua Michael
    Sumner, Joanna
    Teeling, Emma
    Vrijenhoek, Robert C.
    Ward, Robert D.
    Warren, Wesley C.
    Wayne, Robert
    Williams, Terrie M.
    Wolfe, Nathan D.
    Zhang, Ya-Ping
    Graph-Odatsky, Alexander
    Johnson, Warren E.
    Felsenfeld, Adam
    Turner, Steve
    Genome, K. Community Scientists
    Mammals, Grp
    Birds, Grp
    Amphibians Reptiles, Grp
    Fishes, Grp
    General Policy, Grp
    Anal, Grp
    Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species2009In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 100, no 6, p. 659-674Article in journal (Other academic)
  • 15.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Tortella rigens (Bryophyta, Pottiaceae): relationships, regional variation, and conservation aspects2015In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110Article in journal (Refereed)
  • 16.
    Hedenäs, Lars
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Bisang, Irene
    Swedish Museum of Natural History, Department of Botany.
    Infraspecific diversity in a spore-dispersed species with limited distribution range2015In: Systematics and Biodiversity, ISSN 1477-2000, E-ISSN 1478-0933, Vol. 13, p. 17-27Article in journal (Refereed)
  • 17.
    Kalthoff, Daniela
    Swedish Museum of Natural History, Department of Zoology.
    Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)2017In: Scientific Reports, E-ISSN 2045-2322, article id 41417Article in journal (Refereed)
    Abstract [en]

    The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its nativerange. Despite a wide historic distribution, the black rhinoceros was traditionally thought of asdepauperate in genetic variation, and with very little known about its evolutionary history. Thisknowledge gap has hampered conservation efforts because hunting has dramatically reduced thespecies' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity.Here we examined the range-wide genetic structure of historic and modern populations using thelargest and most geographically representative sample of black rhinoceroses ever assembled. Usingboth mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species'mitochondrial genetic variation, including the most ancestral lineages that are now absent frommodern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad,Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historicrange of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southernKenya, where a handful of individuals survive in the Masai Mara. We also identify conservation unitsthat will help maintain evolutionary potential. Our results suggest a complete re-evaluation of currentconservation management paradigms for the black rhinoceros.

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  • 18. Koren, Lee
    et al.
    Matas, Devorah
    Pecnerova, Patricia
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Tikhonov, Alexei
    Gilbert, M. Thomas P.
    Wynne-Edwards, Katherine E.
    Geffen, Eli
    Testosterone in ancient hair from an extinct species2018In: Palaeontology, ISSN 0031-0239, E-ISSN 1475-4983, Vol. 61, no 6, p. 797-802Article in journal (Refereed)
  • 19. Krzewinska, Maja
    et al.
    Kilinc, Gulsah Merve
    Juras, Anna
    Koptekin, Dilek
    Chylenski, Maciej
    Nikitin, Alexey G.
    Shcherbakov, Nikolai
    Shuteleva, Iia
    Leonova, Tatiana
    Kraeva, Liudmila
    Sungatov, Flarit A.
    Sultanova, Alfija N.
    Potekhina, Inna
    Lukasik, Sylwia
    Krenz-Niedbala, Marta
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sinika, Vitaly
    Jakobsson, Mattias
    Stora, Jan
    Gotherstrom, Anders
    Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads2018In: Science Advances, E-ISSN 2375-2548, Vol. 4, no 10, article id eaat4457Article in journal (Refereed)
  • 20. Lado, Sara
    et al.
    Farelo, Liliana
    Forest, Vianney
    Acevedo, Pelayo
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Melo-Ferreira, Jose
    Post-glacial range revolutions in South European hares (Lepus spp.): Insights from ancient DNA and ecological niche modelling2018In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 45, no 12, p. 2609-2618Article in journal (Refereed)
  • 21.
    Lagerholm, Vendela
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sandoval-Castellanos, E.
    Ehrich, D.
    Abramson, N.
    Nadachowski, A.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Germonpré, M.
    Angerbjörn, A.
    Stewart, J.
    Dalén, L.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    On the Origin of the Norwegian Lemming2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2060-2071Article in journal (Refereed)
  • 22.
    Lah, Ljerka
    et al.
    University of Potsdam, Germany.
    Trense, Daronja
    University of Potsdam, Germany.
    Benke, Harald
    Deutches Meeremuseum, Stralsund, Germany.
    Berggren, Per
    Dove Marine Laboratory, School of Marine Science and Technology, Newcastle University, UK.
    Gunnlaugsson, Þorvaldur
    Marine Research Institute, Reykjavik, Iceland.
    Christina, Lockyer
    North Atlantic Marine Mammal Commission, Tromsö, Norway.
    Özturk, Ayaka
    Marine Biology Department, Istanbul University, Turkey.
    Pawliczka, Iwona
    Hel Marine Station, University of Gdansk, Poland.
    Roos, Anna
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Siebert, Ursula
    ITAW, Univ of Veterinary Medicine, Hannover Foundation, Busum, Germany.
    Skora, Krzysztof
    Hel Marine Station, Univ of Gansk, Poland.
    Vikingsson, Gisli
    Marine Research Institute, Reykjavik, Iceland.
    Ralph, Tiedemann
    Unit of Evolutionary Biology/Zooology, University of Potsdam, Germany.
    Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise2016In: PLOS ONE, E-ISSN 1932-6203, Plos, Vol. 11, no 10, p. e0162792-Article in journal (Refereed)
    Abstract [en]

    The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-bydistance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.

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  • 23.
    Lilja, Tobias
    et al.
    SVA, National Veterinary Institute.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Troell, Karin
    SVA, National Veterinary Institute.
    Lindström, Anders
    SVA, National Veterinary Institute.
    Species identification of Swedish mosquitoes through DNA metabarcoding2017In: Journal of the European Mosquito Control Association, Vol. 35, p. 1-9Article in journal (Refereed)
    Abstract [en]

    DNA-barcoding utilises a fragment of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify most animal species. Using next generation sequencing (NGS), this method can be further developed into metabarcoding processes that allow the simultaneous identification of several species from a mixed sample. We created a database of COI sequences of 27 mosquito species collected in Sweden, and combined our data with 27 additional sequences from GenBank to cover the taxa recently documented in Sweden and to include possible invasive taxa. Comparisons show that COI metabarcoding reliably identifies 41 of 54 species and the remainder to species group. Using three independent primer pairs along the COI gene, we further developed this barcoding approach to simultaneously identify Swedish mosquitoes in communities using NGS and quantify relative abundance of each mosquito species in the sample, using bioinformatics methods. We tested the accuracy of the metabarcoding method using communities assembled from morphologically identified mosquitoes, revealing 80% positive identification rate and the estimates of population structure which reflects the input sample. We conclude that metabarcoding is useful as a high throughput identification technique and for the quantification of species.

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    JEMCA 35 p 1-9 Supplementary Material_p1-8.pdf
  • 24.
    Malm, Tobias
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Rota, Jadranka
    Department of Biology, Lund University, Lund, Sweden.
    Chazot, Nicolas
    Department of Biology, Lund University, Lund, Sweden.
    Peña, Carlos
    HipLead, San Francisco, CA, United States of America.
    Wahlberg, Niklas
    Department of Biology, Lund University, Lund, Sweden.
    A simple method for data partitioning based on relative evolutionary rates2018In: PeerJ, E-ISSN 2167-8359, p. 1-21, article id 6:e5498Article in journal (Refereed)
    Abstract [en]

    Background. Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns.

    Methods. We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as kmeans. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

    Results. Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset.

    Discussion. We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

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  • 25.
    Mattupalli, Chakradhar
    et al.
    Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A.;Department of Plant Pathology, Washington State University, Mount Vernon NWREC, Mount Vernon, WA 98273, U.S.A..
    Cuenca, Fernanda Proaño
    Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, U.S.A.;Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A..
    Shiller, Jason B.
    Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A.;Scion, Rotorua 3046, New Zealand.
    Watkins, Tara
    Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A.;Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, U.S.A..
    Hansen, Karen
    Swedish Museum of Natural History, Department of Botany.
    Garzon, Carla D.
    Department of Plant Science and Landscape Architecture, Delaware Valley University, Doylestown, PA 18901, U.S.A..
    Marek, Stephen M.
    Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A..
    Young, Carolyn A.
    Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A.;Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A..
    Genetic Diversity of Phymatotrichopsis omnivora Based on Mating Type and Microsatellite Markers Reveals Heterothallic Mating System2022In: Plant Disease, ISSN 0191-2917, E-ISSN 1943-7692, Vol. 106, no 8, p. 2105-2116Article in journal (Refereed)
    Abstract [en]

    Phymatotrichopsis omnivora is a member of Pezizomycetes and causes root rot disease on a broad range of dicotyledonous plants. Using recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n = 43) and spore mats (n = 29) collected from four locations (Oklahoma, Texas, Arizona, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Furthermore, the developed SSR markers did not show cross-transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the United States in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny, providing impetus for future studies that focus on identifying sexual morphs in nature.

  • 26. Meadows, Jennifer R. S.
    et al.
    Kidd, Jeffrey M.
    Wang, Guo-Dong
    Parker, Heidi G.
    Schall, Peter Z.
    Bianchi, Matteo
    Christmas, Matthew J.
    Bougiouri, Katia
    Buckley, Reuben M.
    Hitte, Christophe
    Nguyen, Anthony K.
    Wang, Chao
    Jagannathan, Vidhya
    Niskanen, Julia E.
    Frantz, Laurent A. F.
    Arumilli, Meharji
    Hundi, Sruthi
    Lindblad-Toh, Kerstin
    Ginja, Catarina
    Agustina, Kadek Karang
    André, Catherine
    Boyko, Adam R.
    Davis, Brian W.
    Drögemüller, Michaela
    Feng, Xin-Yao
    Gkagkavouzis, Konstantinos
    Iliopoulos, Giorgos
    Harris, Alexander C.
    Hytönen, Marjo K.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Liu, Yan-Hu
    Lymberakis, Petros
    Poulakakis, Nikolaos
    Pires, Ana Elisabete
    Racimo, Fernando
    Ramos-Almodovar, Fabian
    Savolainen, Peter
    Venetsani, Semina
    Tammen, Imke
    Triantafyllidis, Alexandros
    vonHoldt, Bridgett
    Wayne, Robert K.
    Larson, Greger
    Nicholas, Frank W.
    Lohi, Hannes
    Leeb, Tosso
    Zhang, Ya-Ping
    Ostrander, Elaine A.
    Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture2023In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, no 1, article id 187Article in journal (Refereed)
    Abstract [en]

    Background

    The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

    Results

    We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

    Conclusions

    We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

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  • 27. Palkopoulou, Eleftheria
    et al.
    Lipson, Mark
    Mallick, Swapan
    Nielsen, Svend
    Rohland, Nadin
    Baleka, Sina
    Karpinski, Emil
    Ivancevici, Atma M.
    To, Thu-Hien
    Kortschak, Daniel
    Raison, Joy M.
    Qu, Zhipeng
    Chin, Tat-Jun
    Alt, Kurt W.
    Claesson, Stefan
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    MacPhee, Ross D. E.
    Meller, Harald
    Rocar, Alfred L.
    Ryder, Oliver A.
    Heiman, David
    Young, Sarah
    Breen, Matthew
    Williams, Christina
    Aken, Bronwen L.
    Ruffier, Magali
    Karlsson, Elinor
    Johnson, Jeremy
    Di Palma, Federica
    Alfoldi, Jessica
    Adelsoni, David L.
    Mailund, Thomas
    Munch, Kasper
    Lindblad-Toh, Kerstin
    Hofreiter, Michael
    Poinar, Hendrik
    Reich, David
    A comprehensive genomic history of extinct and living elephants2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 11, p. E2566-E2574Article in journal (Refereed)
  • 28. Palkopoulou, Eleftheria
    et al.
    Mallick, Swapan
    Skoglund, Pontus
    Enk, Jacob
    Rohland, Nadin
    Li, Heng
    Omrak, Ayca
    Vartanyan, Sergey
    Poinar, Hendrik
    Gotherstrom, Anders
    Reich, David
    Dalen, Love
    Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth2015In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 10, p. 1395-1400Article in journal (Refereed)
  • 29. Pawar, Harvinder
    et al.
    Rymbekova, Aigerim
    Cuadros-Espinoza, Sebastian
    Huang, Xin
    de Manuel, Marc
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lobon, Irene
    Alvarez-Estape, Marina
    Haber, Marc
    Dolgova, Olga
    Han, Sojung
    Esteller-Cucala, Paula
    Juan, David
    Ayub, Qasim
    Bautista, Ruben
    Kelley, Joanna L.
    Cornejo, Omar E.
    Lao, Oscar
    Andrés, Aida M.
    Guschanski, Katerina
    Ssebide, Benard
    Cranfield, Mike
    Tyler-Smith, Chris
    Xue, Yali
    Prado-Martinez, Javier
    Marques-Bonet, Tomas
    Kuhlwilm, Martin
    Ghost admixture in eastern gorillas2023In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 7, no 9, p. 1503-1514Article in journal (Refereed)
  • 30.
    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.

  • 31.
    Peona, Valentina
    et al.
    Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden.
    Palacios-Gimenez, Octavio M.
    Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden.
    Blommaert, Julie
    Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden.
    Liu, Jing
    MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China;Department of Neuroscience and Development, University of Vienna, Vienna, Austria.
    Haryoko, Tri
    Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia.
    Jønsson, Knud A.
    Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
    Zhou, Qi
    MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China;Department of Neuroscience and Development, University of Vienna, Vienna, Austria;Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China.
    Jern, Patric
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Suh, Alexander
    Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden;School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK.
    The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities2021In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 376, no 1833, p. 20200186-20200186Article in journal (Refereed)
    Abstract [en]

    It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.

  • 32. Pečnerová, Patrícia
    et al.
    Díez-Del-Molino, David
    Vartanyan, Sergey
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.2016In: Scientific Reports, E-ISSN 2045-2322, Vol. 6Article in journal (Refereed)
    Abstract [en]

    According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

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  • 33. Pujolar, J. M.
    et al.
    Dalén, L.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Olsen, R. A.
    Hansen, M. M.
    Madsen, J.
    First de novo whole genome sequencing and assembly of the pink-footed goose2018In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 110, no 2, p. 75-79Article in journal (Refereed)
  • 34. Resl, P.
    et al.
    Bujold, A.R.
    Tagirdzhanova, G.
    Meidl, P
    Freire Rallo, S.
    Kono, M.
    Fernández-Brime, Samantha
    Swedish Museum of Natural History, Department of Botany.
    Gudmundsson, H.
    Sigmar Andresson, O.
    Muggia, Lucia
    Mayrhofer, H
    McCutcheon, J.P.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Werth, S.
    Willis, L.M.
    Spribille, T.
    Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 2634Article in journal (Refereed)
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  • 35.
    Sandoval-Castellanos, Edson
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Palkopoulou, Eleftheria
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Back to BaySICS: A User-Friendly Program for Bayesian Statistical Inference from Coalescent Simulations2014In: PLOS ONE, E-ISSN 1932-6203, Vol. 9, no 5Article in journal (Refereed)
    Abstract [en]

    Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.

  • 36. Sawangproh, Weerachon
    et al.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Lang, A. S.
    Hansson, B.
    Cronberg, Nils
    Genetransfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum2020In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 125, p. 565-579Article in journal (Refereed)
  • 37. Shafer, Aaron B. A.
    et al.
    Wolf, Jochen B. W.
    Alves, Paulo C.
    Bergstrom, Linnea
    Bruford, Michael W.
    Brannstrom, Ioana
    Colling, Guy
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    De Meester, Luc
    Ekblom, Robert
    Fawcett, Katie D.
    Fior, Simone
    Hajibabaei, Mehrdad
    Hill, Jason A.
    Hoezel, A. Rus
    Hoglund, Jacob
    Jensen, Evelyn L.
    Krause, Johannes
    Kristensen, Torsten N.
    Kruetzen, Michael
    McKay, John K.
    Norman, Anita J.
    Ogden, Rob
    Osterling, E. Martin
    Ouborg, N. Joop
    Piccolo, John
    Popovic, Danijela
    Primmer, Craig R.
    Reed, Floyd A.
    Roumet, Marie
    Salmona, Jordi
    Schenekar, Tamara
    Schwartz, Michael K.
    Segelbacher, Gernot
    Senn, Helen
    Thaulow, Jens
    Valtonen, Mia
    Veale, Andrew
    Vergeer, Philippine
    Vijay, Nagarjun
    Vila, Caries
    Weissensteiner, Matthias
    Wennerstrom, Lovisa
    Wheat, Christopher W.
    Zielinski, Piotr
    Genomics and the challenging translation into conservation practice2015In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 30, no 2, p. 78-87Article in journal (Refereed)
  • 38. Shafer, Aaron B. A.
    et al.
    Wolf, Jochen B. W.
    Alves, Paulo C.
    Bergstrom, Linnea
    Colling, Guy
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    De Meester, Luc
    Ekblom, Robert
    Fior, Simone
    Hajibabaei, Mehrdad
    Hoezel, A. Rus
    Hoglund, Jacob
    Jensen, Evelyn L.
    Kruetzen, Michael
    Norman, Anita J.
    Osterling, E. Martin
    Ouborg, N. Joop
    Piccolo, John
    Primmer, Craig R.
    Reed, Floyd A.
    Roumet, Marie
    Salmona, Jordi
    Schwartz, Michael K.
    Segelbacher, Gernot
    Thaulow, Jens
    Valtonen, Mia
    Vergeer, Philippine
    Weissensteiner, Matthias
    Wheat, Christopher W.
    Vila, Carlese
    Zielinski, Piotr
    Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply2016In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal (Refereed)
  • 39. Skoglund, Pontus
    et al.
    Ersmark, Erik
    Palkopoulou, Eleftheria
    Dalen, Love
    Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds2015In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 11, p. 1515-1519Article in journal (Refereed)
  • 40.
    Stanton, David William Graham
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    More grist for the mill? Species delimitation in the genomic era and its implications for conservation2019In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 20, no 1, p. 101-113Article in journal (Refereed)
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  • 41.
    Sánchez-Barreiro, Fátima
    et al.
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    De Cahsan, Binia
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Westbury, Michael V
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Sun, Xin
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Margaryan, Ashot
    Globe Institute, University of Copenhagen , Copenhagen , Denmark.
    Fontsere, Claudia
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park , Barcelona, Catalonia , Spain.
    Bruford, Michael W
    Cardiff School of Biosciences, Cardiff University , Cardiff , UK.
    Russo, Isa-Rita M
    Cardiff School of Biosciences, Cardiff University , Cardiff , UK.
    Kalthoff, Daniela C
    Swedish Museum of Natural History, Department of Zoology. Swedish Museum of Natural History.
    Sicheritz-Pontén, Thomas
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University , Kedah , Malaysia.
    Petersen, Bent
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University , Kedah , Malaysia.
    Dalén, Love
    Department of Zoology, Centre for Palaeogenetics , Stockholm University, Stockholm , Sweden;Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm , Sweden.
    Zhang, Guojie
    Section for Ecology and Evolution, Department of Biology, University of Copenhagen , Copenhagen , Denmark;State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , People's Republic of China;Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , People's Republic of China;BGI Research, BGI-Shenzhen , Shenzhen , People's Republic of China.
    Marquès-Bonet, Tomás
    Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park , Barcelona, Catalonia , Spain;National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology , Barcelona , Spain;Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona, Catalonia , Spain.
    Gilbert, M Thomas P
    Globe Institute, University of Copenhagen , Copenhagen , Denmark;Department of Natural History, NTNU University Museum , Trondheim , Norway.
    Moodley, Yoshan
    Department of Biological Sciences, University of Venda , Thohoyandou , Republic of South Africa.
    Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros2023In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, no 9, article id msad180Article in journal (Refereed)
    Abstract [en]

    The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

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  • 42.
    Sánchez‐Barreiro, Fátima
    et al.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Gopalakrishnan, Shyam
    GLOBE Institute University of Copenhagen Copenhagen Denmark;DTU Bioinformatics Kongens Lyngby Hovedstaden Denmark;Center for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark.
    Ramos‐Madrigal, Jazmín
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Westbury, Michael V.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Manuel, Marc
    Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra) Barcelona Biomedical Research Park Barcelona Spain.
    Margaryan, Ashot
    GLOBE Institute University of Copenhagen Copenhagen Denmark;Center for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark.
    Ciucani, Marta M.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Vieira, Filipe G.
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Patramanis, Yannis
    GLOBE Institute University of Copenhagen Copenhagen Denmark.
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Timmons, Zena
    Department of Natural Sciences National Museums Scotland Edinburgh UK.
    Sicheritz‐Pontén, Thomas
    GLOBE Institute University of Copenhagen Copenhagen Denmark;Centre of Excellence for Omics‐Driven Computational Biodiscovery (COMBio) Faculty of Applied Sciences AIMST University Kedah Malaysia.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Centre for Palaeogenetics Stockholm Sweden;Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.
    Ryder, Oliver A.
    San Diego Zoo Institute for Conservation Research Escondido CA USA.
    Zhang, Guojie
    Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark;State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China;Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China;BGI‐Shenzhen Shenzhen China.
    Marquès‐Bonet, Tomás
    Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra) Barcelona Biomedical Research Park Barcelona Spain;National Centre for Genomic Analysis–Centre for Genomic Regulation Barcelona Institute of Science and Technology Barcelona Spain;Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain.
    Moodley, Yoshan
    Department of Zoology University of Venda Thohoyandou South Africa.
    Gilbert, M. Thomas P.
    GLOBE Institute University of Copenhagen Copenhagen Denmark;Center for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark;Norwegian University of Science and Technology University Museum Trondheim Norway.
    Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 23, p. 6355-6369Article in journal (Refereed)
    Abstract [en]

    Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.

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  • 43.
    Tison, J-L.
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Blennow, Viktor
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Palkopoulou, E
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gustavsson, Petra
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Roos, Anna
    Swedish Museum of Natural History, Department of Environmental research and monitoring. Department of Environmental Toxicology, Uppsala Universitet.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden.2015In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, no 371, article id 384Article in journal (Refereed)
  • 44. Tverin, Malin
    et al.
    Esparza-Salas, Rodrigo
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Strömberg, Annika
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Tang, Patrik
    Kokkonen, Iiris
    Herrero, Annika
    Kauhala, Kaarina
    Karlsson, Olle
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Tiilikainen, Raisa
    Vetemaa, Markus
    Sinisalo, Tuula
    Käkela, Reijo
    Lundström, Karl
    Complementary methods assessing short and long-term prey of a marine top predator ‒ Application to the grey seal-fishery conflict in the Baltic Sea2019In: PLOS ONE, E-ISSN 1932-6203, Vol. 14, no 1, article id e0208694Article in journal (Refereed)
    Abstract [en]

    The growing grey seal (Halichoerus grypus) population in the Baltic Sea has created conflicts with local fisheries, comparable to similar emerging problems worldwide. Adequate information on the foraging habits is a requirement for responsible management of the seal population. We investigated the applicability of available dietary assessment methods by comparing morphological analysis and DNA metabarcoding of gut contents (short-term diet; n = 129/125 seals, respectively), and tissue chemical markers i.e. fatty acid (FA) profiles of blubber and stable isotopes (SIs) of liver and muscle (mid- or long-term diet; n = 108 seals for the FA and SI markers). The methods provided complementary information. Short-term methods indicated prey species and revealed dietary differences between age groups and areas but for limited time period. In the central Baltic, herring was the main prey, while in the Gulf of Finland percid and cyprinid species together comprised the largest part of the diet. Perch was also an important prey in the western Baltic Proper. The DNA analysis provided firm identification of many prey species, which were neglected or identified only at species group level by morphological analysis. Liver SIs distinguished spatial foraging patterns and identified potentially migrated individuals, whereas blubber FAs distinguished individuals frequently utilizing certain types of prey. Tissue chemical markers of adult males suggested specialized feeding to certain areas and prey, which suggest that these individuals are especially prone to cause economic losses for fisheries. We recommend combined analyses of gut contents and tissue chemical markers as dietary monitoring methodology of aquatic top predators to support an optimal ecosystem-based management.

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  • 45. Urena, I.
    et al.
    Ersmark, E.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Samaniego, J. A.
    Galindo-Pellicena, M. A.
    Cregut-Bonnoure, E.
    Bolivar, H.
    Gomez-Olivencia, A.
    Rios-Garaizar, J.
    Garate, D.
    Dalén, L.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Arsuaga, J. L.
    Valdiosera, C. E.
    Unraveling the genetic history of the European wild goats2018In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 185, p. 189-198Article in journal (Refereed)
  • 46. van der Valk, Tom
    et al.
    Sandoval-Castellanos, Edson
    Caillaud, Damien
    Ngobobo, Urbain
    Binyinyi, Escobar
    Nishuli, Radar
    Stoinski, Tara
    Gilissen, Emmanuel
    Sonet, Gontran
    Semal, Patrick
    Kalthoff, Daniela C.
    Swedish Museum of Natural History, Department of Zoology.
    Dalén, Love
    Guschanski, Katerina
    Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas2018In: Scientific Reports, E-ISSN 2045-2322, Vol. 8, article id 6551Article in journal (Refereed)
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  • 47. Verschut, Vasiliki
    et al.
    Strandmark, Alma
    Esparza-Salas, Rodrigo
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Hambäck, Peter
    Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
  • 48. Wennerstrom, Lovisa
    et al.
    Ryman, Nils
    Tison, Jean-Luc
    Hasslow, Anna
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Laikre, Linda
    Genetic landscape with sharp discontinuities shaped by complex demographic history in moose (Alces alces)2016In: Journal of Mammalogy, ISSN 0022-2372, E-ISSN 1545-1542, Vol. 97, no 1, p. 1-13Article in journal (Refereed)
    Abstract [en]

    The moose (Alces alces) is the most intensely managed game species in Fennoscandia; approximately one-third of the population, ca. 160,000 animals, is harvested annually. Despite the species' biological and socioeconomic importance, there are knowledge gaps with respect to its intraspecific diversity and genetic structure. Recent studies of moose in neighboring countries report 2 genetic groups in Finland, 3 in Norway with one of them suggested to be of ancient origin, and no indications of bottlenecks. To delineate the spatial genetic landscape of the Swedish moose, we used allozyme variability from over 20,000 georeferenced moose collected all over Sweden in combination with 12 microsatellites (n = 1,200) and mitochondrial DNA (mtDNA) sequences (n = 44). We combined individual-based and traditional statistical approaches with coalescence-based simulations. The results indicate a complex history with bottlenecks and recent expansions that is consistent with historical records. Swedish moose are separated into 2 major genetic groups, a northern and a southern one, where the southern group is further divided into 3 subgroups. The 2 main subpopulations are moderately differentiated (F-ST = 0.1; R-ST = 0.07) and separated by sharp genetic discontinuities occurring over a relatively narrow transition zone in central Sweden that coincides with a similar, previously reported transition zone in Norway. This differentiation is not reflected in mtDNA variation, where no significant divergence was observed. Together with the F-ST andR(ST) similarities, this suggests that the 2 major subpopulations in Sweden reflect divergence shaped after the postglacial recolonization of Scandinavia. Neighborhood size assessments indicate that gene flow is relatively restricted with an estimated average dispersal distance of 3.5-11.1 km, and spatial autocorrelograms suggest that genetic similarity decreases almost linearly over space resulting in continuous genetic clines within major subgroups. Management areas largely coincide with genetic clusters, simplifying the integration of genetic information into management.

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  • 49. Westbury, Michael, V
    et al.
    Hartmann, Stefanie
    Barlow, Axel
    Wiesel, Ingrid
    Leo, Viyanna
    Welch, Rebecca
    Parker, Daniel M.
    Sicks, Florian
    Ludwig, Arne
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Hofreiter, Michael
    Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena2018In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 5, p. 1225-1237Article in journal (Refereed)
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  • 50. Xenikoudakis, G.
    et al.
    Ersmark, E.
    Tison, J. -L
    Waits, L.
    Kindberg, J.
    Swenson, J. E.
    Dalen, L.
    Consequences of a demographic bottleneck on geneticstructure and variation in the Scandinavian brown bear2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 13, p. 3441-3454Article in journal (Refereed)
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