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  • 1. Angerbjorn, Anders
    et al.
    Eide, Nina E.
    Dalen, Love
    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)
  • 2. 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)
  • 3. Brace, Selina
    et al.
    Palkopoulou, Eleftheria
    Dalen, Love
    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)
  • 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. 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)
  • 6. 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, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44585Article in journal (Refereed)
  • 7. 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)
  • 8. Dalen, L
    et al.
    Elmhagen, B
    Angerbjorn, A
    DNA analysis on fox faeces and competition induced niche shifts2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 8, p. 2389-2392Article in journal (Refereed)
  • 9. Dalen, L
    et al.
    Fuglei, E
    Hersteinsson, P
    Kapel, C M O
    Roth, J D
    Samelius, G
    Tannerfeldt, M
    Angerbjorn, A
    Population history and genetic structure of a circumpolar species: the arctic fox2005In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 84, no 1, p. 79-89Article in journal (Refereed)
  • 10. Dalen, L
    et al.
    Gotherstrom, A
    Angerbjorn, A
    Identifying species from pieces of faeces2004In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 5, no 1, p. 109-111Article in journal (Refereed)
  • 11. Dalen, L
    et al.
    Gotherstrom, A
    Tannerfeldt, M
    Angerbjorn, A
    Is the endangered Fennoscandian arctic fox (Alopex lagopus) population genetically isolated?2002In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 105, no 2, p. 171-178, article id PII S0006-3207(01)00180-XArticle in journal (Refereed)
  • 12. Dalen, L.
    et al.
    Kvaloy, K.
    Linnell, J. D. C.
    Elmhagen, B.
    Strand, O.
    Tannerfeldt, M.
    Henttonen, H.
    Fuglei, E.
    Landa, A.
    Angerbjorn, A.
    Population structure in a critically endangered arctic fox population: does genetics matter?2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 10, p. 2809-2819Article in journal (Refereed)
  • 13. Dalen, Love
    et al.
    Gotherstrom, Anders
    Meijer, Tomas
    Shapiro, Beth
    Recovery of DNA from Footprints in the Snow2007In: Canadian field-naturalist, ISSN 0008-3550, Vol. 121, no 3, p. 321-324Article in journal (Refereed)
  • 14.
    Dalen, Love
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lagerholm, Vendela K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 6, article id 169Article in journal (Refereed)
  • 15. Dalen, Love
    et al.
    Nystrom, Veronica
    Valdiosera, Cristina
    Germonpre, Mietje
    Sablin, Mikhail
    Turner, Elaine
    Angerbjorn, Anders
    Arsuaga, Juan Luis
    Gotherstrom, Anders
    Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox2007In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, no 16, p. 6726-6729Article in journal (Refereed)
  • 16. Dalen, Love
    et al.
    Orlando, Ludovic
    Shapiro, Beth
    Brandstrom-Durling, Mikael
    Quam, Rolf
    Gilbert, M. Thomas P.
    Diez Fernandez-Lomana, J. Carlos
    Willerslev, Eske
    Luis Arsuaga, Juan
    Goetherstrom, Anders
    Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West2012In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 8, p. 1893-1897Article in journal (Refereed)
  • 17. Dalerum, F.
    et al.
    Freire, S.
    Angerbjorn, A.
    Lecomte, N.
    Lindgren, A.
    Meijer, T.
    Pecnerova, P.
    Dalen, L.
    Exploring the diet of arctic wolves (Canis lupus arctos) at their northern range limit2018In: Canadian Journal of Zoology, ISSN 0008-4301, E-ISSN 1480-3283, Vol. 96, no 3, p. 277-281Article in journal (Refereed)
  • 18. Dalerum, Fredrik
    et al.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Frojd, Christina
    Lecomte, Nicolas
    Lindgren, Asa
    Meijer, Tomas
    Pecnerova, Patricia
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Angerbjorn, Anders
    Spatial variation in Arctic hare (Lepus arcticus) populations around the Hall Basin2017In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, no 10, p. 2113-2118Article in journal (Refereed)
  • 19. 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)
  • 20. 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)
  • 21. Elmhagen, Bodil
    et al.
    Destouni, Georgia
    Angerbjorn, Anders
    Borgstrom, Sara
    Boyd, Emily
    Cousins, Sara A. O.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ehrlen, Johan
    Ermold, Matti
    Hamback, Peter A.
    Hedlund, Johanna
    Hylander, Kristoffer
    Jaramillo, Fernando
    Lagerholm, Vendela K.
    Lyon, Steve W.
    Moor, Helen
    Nykvist, Bjorn
    Pasanen-Mortensen, Marianne
    Plue, Jan
    Prieto, Carmen
    van der Velde, Ype
    Lindborg, Regina
    Interacting effects of change in climate, human population, land use, and water use on biodiversity and ecosystem services2015In: Ecology & society, ISSN 1708-3087, E-ISSN 1708-3087, Vol. 20, no 1, article id UNSP 23Article in journal (Refereed)
  • 22.
    Ersmark, Erik
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Orlando, Ludovic
    Sandoval-Castellanos, Edson
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barnes, Ian
    Barnett, Ross
    Stuart, Anthony
    Lister, Adrian
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Population Demography and Genetic Diversity in the Pleistocene Cave Lion2015In: Open Quaternary, Vol. 1, no 4, p. 1-14Article in journal (Refereed)
  • 23. Geffen, Eli
    et al.
    Kam, Michael
    Hefner, Reuven
    Hersteinsson, Pall
    Angerbjorn, Anders
    Dalen, Love
    Fuglei, Eva
    Noren, Karin
    Adams, Jennifer R.
    Vucetich, John
    Meier, Thomas J.
    Mech, L. D.
    vonHoldt, Bridgett M.
    Stahler, Daniel R.
    Wayne, Robert K.
    Kin encounter rate and inbreeding avoidance in canids2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 24, p. 5348-5358Article in journal (Refereed)
  • 24. Geffen, Eli
    et al.
    Waidyaratne, Sitara
    Dalen, Love
    Angerbjoern, Anders
    Vila, Carles
    Hersteinsson, Pall
    Fuglei, Eva
    White, Paula A.
    Goltsman, Michael
    Kapel, Christian M. O.
    Wayne, Robert K.
    Sea ice occurrence predicts genetic isolation in the Arctic fox2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 20, p. 4241-4255Article in journal (Refereed)
  • 25. Gilbert, M Thomas P
    et al.
    Drautz, Daniela I
    Lesk, Arthur M
    Ho, Simon Y W
    Qi, Ji
    Ratan, Aakrosh
    Hsu, Chih-Hao
    Sher, Andrei
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Götherström, Anders
    Tomsho, Lynn P
    Rendulic, Snjezana
    Packard, Michael
    Campos, Paula F
    Kuznetsova, Tatyana V
    Shidlovskiy, Fyodor
    Tikhonov, Alexei
    Willerslev, Eske
    Iacumin, Paola
    Buigues, Bernard
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Germonpré, Mietje
    Kosintsev, Pavel
    Nikolaev, Vladimir
    Nowak-Kemp, Malgosia
    Knight, James R
    Irzyk, Gerard P
    Perbost, Clotilde S
    Fredrikson, Karin M
    Harkins, Timothy T
    Sheridan, Sharon
    Miller, Webb
    Schuster, Stephan C
    Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 24, p. 8327-32Article in journal (Refereed)
    Abstract [en]

    We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

  • 26. Gilbert, M Thomas P
    et al.
    Tomsho, Lynn P
    Rendulic, Snjezana
    Packard, Michael
    Drautz, Daniela I
    Sher, Andrei
    Tikhonov, Alexei
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Kuznetsova, Tatyana
    Kosintsev, Pavel
    Campos, Paula F
    Higham, Thomas
    Collins, Matthew J
    Wilson, Andrew S
    Shidlovskiy, Fyodor
    Buigues, Bernard
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Germonpré, Mietje
    Götherström, Anders
    Iacumin, Paola
    Nikolaev, Vladimir
    Nowak-Kemp, Malgosia
    Willerslev, Eske
    Knight, James R
    Irzyk, Gerard P
    Perbost, Clotilde S
    Fredrikson, Karin M
    Harkins, Timothy T
    Sheridan, Sharon
    Miller, Webb
    Schuster, Stephan C
    Whole-genome shotgun sequencing of mitochondria from ancient hair shafts.2007In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 317, no 5846, p. 1927-30Article in journal (Refereed)
    Abstract [en]

    Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

  • 27.
    Gopalakrishnan, Shyam
    et al.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Samaniego Castruita, Jose A.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Sinding, Mikkel-Holger S.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Kuderna, Lukas F. K.
    Institute of Evolutionary Biology (UPF-CSIC), PRBB Dr. CNAG-CRG, Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST) .
    Räikkönen, Jannikke
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Petersen, Bent
    Department of Bio and Health Informatics Technical University of Denmark .
    Sicheritz-Ponten, Thomas
    Department of Bio and Health Informatics Technical University of Denmark .
    Larson, Greger
    Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art University of Oxford .
    Orlando, Ludovic
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Marques-Bonet, Tomas
    Institute of Evolutionary Biology (UPF-CSIC), PRBB Dr. CNAG-CRG, Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST) Catalan Institution of Research and Advanced Studies (ICREA).
    Hansen, Anders J.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Centre for GeoGenetics, Natural History Museum of Denmark University of CopenhagenTrace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University, NTNU University Museum, Norwegian University of Science and Technology.
    The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, no 495, p. 1-11Article in journal (Refereed)
  • 28. Haddad, Nizar Jamal
    et al.
    Al-Nakeeb, Kosai
    Petersen, Bent
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Blom, Nikolaj
    Sicheritz-Ponten, Thomas
    Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)2017In: MITOCHONDRIAL DNA PART B-RESOURCES, ISSN 2380-2359, Vol. 2, p. 139-140Article in journal (Refereed)
  • 29. Hambäck, Peter A.
    et al.
    Weingartner, Elisabeth
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Wirta, Helena
    Roslin, Tomas
    Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes2016In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 23, p. 8431-8439Article in journal (Refereed)
  • 30. Herfindal, Ivar
    et al.
    Linnell, John D. C.
    Elmhagen, Bodil
    Andersen, Roy
    Eide, Nina E.
    Frafjord, Karl
    Henttonen, Heikki
    Kaikusalo, Asko
    Mela, Matti
    Tannerfeldt, Magnus
    Dalen, Love
    Strand, Olav
    Landa, Arild
    Angerbjorn, Anders
    Population persistence in a landscape context: the case of endangered arctic fox populations in Fennoscandia2010In: Ecography, ISSN 0906-7590, E-ISSN 1600-0587, Vol. 33, no 5, p. 932-941Article in journal (Refereed)
  • 31.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Convergent evolution, habitat shifts and variable diversification rates in the ovenbird-woodcreeper family (Furnariidae).2009In: BMC evolutionary biology, ISSN 1471-2148, Vol. 9, p. 268-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The Neotropical ovenbird-woodcreeper family (Furnariidae) is an avian group characterized by exceptionally diverse ecomorphological adaptations. For instance, members of the family are known to construct nests of a remarkable variety. This offers a unique opportunity to examine whether changes in nest design, accompanied by expansions into new habitats, facilitates diversification. We present a multi-gene phylogeny and age estimates for the ovenbird-woodcreeper family and use these results to estimate the degree of convergent evolution in both phenotype and habitat utilisation. Furthermore, we discuss whether variation in species richness among ovenbird clades could be explained by differences in clade-specific diversification rates, and whether these rates differ among lineages with different nesting habits. In addition, the systematic positions of some enigmatic ovenbird taxa and the postulated monophyly of some species-rich genera are evaluated.

    RESULTS: The phylogenetic results reveal new examples of convergent evolution and show that ovenbirds have independently colonized open habitats at least six times. The calculated age estimates suggest that the ovenbird-woodcreeper family started to diverge at ca 33 Mya, and that the timing of habitat shifts into open environments may be correlated with the aridification of South America during the last 15 My. The results also show that observed large differences in species richness among clades can be explained by a substantial variation in net diversification rates. The synallaxines, which generally are adapted to dry habitats and build exposed vegetative nests, had the highest diversification rate of all major furnariid clades.

    CONCLUSION: Several key features may have played an important role for the radiation and evolution of convergent phenotypes in the ovenbird-woodcreeper family. Our results suggest that changes in nest building strategy and adaptation to novel habitats may have played an important role in a diversification that included multiple radiations into more open and bushy environments. The synallaxines were found to have had a particularly high diversification rate, which may be explained by their ability to build exposed vegetative nests and thus to expand into a variety of novel habitats that emerged during a period of cooling and aridification in South America.

  • 32. Kodandaramaiah, U.
    et al.
    Weingartner, E.
    Janz, N.
    Dalen, L.
    Nylin, S.
    Population structure in relation to host-plant ecology and Wolbachia infestation in the comma butterfly2011In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, no 10, p. 2173-2185Article in journal (Refereed)
  • 33. 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)
  • 34. 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)
  • 35. 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)
  • 36.
    Lagerholm, Vendela K.
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Noren, Karin
    Ehrich, Dorothee
    Ims, Rolf A.
    Killengreen, Siw T.
    Abramson, Natalia I.
    Niemimaa, Jukka
    Angerbjorn, Anders
    Henttonen, Heikki
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Run to the hills: gene flow among mountain areas leads to low genetic differentiation in the Norwegian lemming2017In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 121, no 1, p. 1-14Article in journal (Refereed)
  • 37.
    Lagerholm, Vendela K.
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sandoval-Castellanos, Edson
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Vaniscotte, Amelie
    Potapova, Olga R.
    Tomek, Teresa
    Bochenski, Zbigniew M.
    Shepherd, Paul
    Barton, Nick
    Van Dyck, Marie-Claire
    Miller, Rebecca
    Hoglund, Jacob
    Yoccoz, Nigel G.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stewart, John R.
    Range shifts or extinction?: Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds2017In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 23, no 4, p. 1425-1435Article in journal (Refereed)
  • 38.
    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)
  • 39. Lindenfors, P
    et al.
    Dalen, L
    Angerbjorn, A
    The monophyletic origin of delayed implantation in carnivores and its implications2003In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 57, no 8, p. 1952-1956Article in journal (Refereed)
  • 40. Liu, Shiping
    et al.
    Lorenzen, Eline D.
    Fumagalli, Matteo
    Li, Bo
    Harris, Kelley
    Xiong, Zijun
    Zhou, Long
    Korneliussen, Thorfinn Sand
    Somel, Mehmet
    Babbitt, Courtney
    Wray, Greg
    Li, Jianwen
    He, Weiming
    Wang, Zhuo
    Fu, Wenjing
    Xiang, Xueyan
    Morgan, Claire C.
    Doherty, Aoife
    O’Connell, Mary J.
    McInerney, James O.
    Born, Erik W.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dietz, Rune
    Orlando, Ludovic
    Sonne, Christian
    Zhang, Guojie
    Nielsen, Rasmus
    Willerslev, Eske
    Wang, Jun
    Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears2014In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 157, no 4, p. 785-794Article in journal (Refereed)
    Abstract [en]

    Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.

  • 41. Malmstrom, H
    et al.
    Stora, J
    Dalen, L
    Holmlund, G
    Gotherstrom, A
    Extensive human DNA contamination in extracts from ancient dog bones and teeth2005In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 22, no 10, p. 2040-2047Article in journal (Refereed)
  • 42. Meijer, T.
    et al.
    Noren, K.
    Hellstrom, P.
    Dalen, L.
    Angerbjorn, A.
    Estimating population parameters in a threatened arctic fox population using molecular tracking and traditional field methods2008In: Animal Conservation, ISSN 1367-9430, E-ISSN 1469-1795, Vol. 11, no 4, p. 330-338Article in journal (Refereed)
  • 43. Mellows, Andrew
    et al.
    Barnett, Ross
    Dalen, Love
    Sandoval-Castellanos, Edson
    Linderholm, Anna
    McGovern, Thomas H.
    Church, Mike J.
    Larson, Greger
    The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox2012In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 279, no 1747, p. 4568-4573Article in journal (Refereed)
  • 44. Miller, Webb
    et al.
    Drautz, Daniela I
    Janecka, Jan E
    Lesk, Arthur M
    Ratan, Aakrosh
    Tomsho, Lynn P
    Packard, Mike
    Zhang, Yeting
    McClellan, Lindsay R
    Qi, Ji
    Zhao, Fangqing
    Gilbert, M Thomas P
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Arsuaga, Juan Luis
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Huson, Daniel H
    Helgen, Kristofer M
    Murphy, William J
    Götherström, Anders
    Schuster, Stephan C
    The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).2009In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 19, no 2, p. 213-20Article in journal (Refereed)
    Abstract [en]

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

  • 45. Noren, K
    et al.
    Dalen, L
    Kvaloy, K
    Angerbjorn, A
    Detection of farm fox and hybrid genotypes among wild arctic foxes in Scandinavia2005In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 6, no 6, p. 885-894Article in journal (Refereed)
  • 46. Noren, K.
    et al.
    Hersteinsson, P.
    Samelius, G.
    Eide, N. E.
    Fuglei, E.
    Elmhagen, B.
    Dalen, L.
    Meijer, T.
    Angerbjorn, A.
    From monogamy to complexity: social organization of arctic foxes (Vulpes lagopus) in contrasting ecosystems2012In: Canadian Journal of Zoology, ISSN 0008-4301, E-ISSN 1480-3283, Vol. 90, no 9, p. 1102-1116Article in journal (Refereed)
  • 47. Noren, K.
    et al.
    Kvaloy, K.
    Nystrom, V.
    Landa, A.
    Dalen, L.
    Eide, N. E.
    Ostbye, E.
    Henttonen, H.
    Angerbjorn, A.
    Farmed arctic foxes on the Fennoscandian mountain tundra: implications for conservation2009In: Animal Conservation, ISSN 1367-9430, E-ISSN 1469-1795, Vol. 12, no 5, p. 434-444Article in journal (Refereed)
  • 48. Noren, Karin
    et al.
    Carmichael, Lindsey
    Dalen, Love
    Hersteinsson, Pall
    Samelius, Gustaf
    Fuglei, Eva
    Kapel, Christian M. O.
    Menyushina, Irina
    Strobeck, Curtis
    Angerbjorn, Anders
    Arctic fox Vulpes lagopus population structure: circumpolar patterns and processes2011In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 120, no 6, p. 873-885Article in journal (Refereed)
  • 49. Noren, Karin
    et al.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Flagstad, Oystein
    Berteaux, Dominique
    Wallen, Johan
    Angerbjorn, Anders
    Evolution, ecology and conservation-revisiting three decades of Arctic fox population genetic research2017In: Polar Research, ISSN 0800-0395, E-ISSN 1751-8369, Vol. 36, article id 4Article in journal (Refereed)
  • 50. Noren, Karin
    et al.
    Godoy, Erika
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Meijer, Tomas
    Angerbjorn, Anders
    Inbreeding depression in a critically endangered carnivore2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 14, p. 3309-3318Article in journal (Refereed)
    Abstract [en]

    Harmful effects arising from matings between relatives (inbreeding) is a long-standing observation that is well founded in theory. Empirical evidence for inbreeding depression in natural populations is however rare because of the challenges of assembling pedigrees supplemented with fitness traits. We examined the occurrence of inbreeding and subsequent inbreeding depression using a unique data set containing a genetically verified pedigree with individual fitness traits for a critically endangered arctic fox (Vulpes lagopus) population. The study covered nine years and was comprised of 33 litters with a total of 205 individuals. We recorded that the present population was founded by only five individuals. Over the study period, the population exhibited a tenfold increase in average inbreeding coefficient with a final level corresponding to half-sib matings. Inbreeding mainly occurred between cousins, but we also observed two cases of full-sib matings. The pedigree data demonstrated clear evidence of inbreeding depression on traditional fitness traits where inbred individuals displayed reduced survival and reproduction. Fitness traits were however differently affected by the fluctuating resource abundande. Inbred individuals born at low-quality years displayed reduced first-year survival, while inbred individuals born at high-quality years were less likely to reproduce. The documentation of inbreeding depression in fundamental fitness traits suggests that inbreeding depression can limit population recovery. Introducing new genetic material to promote a genetic rescue effect may thus be necessary for population long-term persistence.

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