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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. 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)
  • 3. 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.

  • 4. 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)
  • 5. 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)
  • 6. 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)
  • 7. 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)
  • 8. 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)
  • 9. 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)
  • 10. 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)
  • 11. 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)
  • 12. 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)
  • 13. 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)
  • 14.
    Dussex, Nicolas
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    von Seth, Johanna
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Knapp, Michael
    Kardailsky, Olga
    Robertson, Bruce C.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction2019In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 15, no 9, article id 20190491Article in journal (Refereed)
    Abstract [en]

    Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia (Heteralocha acutirostris) and South Island kokako (Callaeas cinereus). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island kokako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Maori may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island kokako.

  • 15. 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)
  • 16.
    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)
  • 17. 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)
  • 18. 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)
  • 19. 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.

  • 20. 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.

  • 21. 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)
  • 22. 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)
  • 23.
    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.

  • 24. 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)
  • 25.
    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)
  • 26. 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)
  • 27. 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.

  • 28. 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)
  • 29. 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)
  • 30. 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)
  • 31. 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.

  • 32. 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)
  • 33. 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)
  • 34. 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)
  • 35. 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)
  • 36. 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.

  • 37. Nystrom, J
    et al.
    Dalen, L
    Hellstrom, P
    Ekenstedt, J
    Angleby, H
    Angerbjorn, A
    Effect of local prey availability on gyrfalcon diet: DNA analysis on ptarmigan remains at nest sites2006In: Journal of Zoology, ISSN 0952-8369, E-ISSN 1469-7998, Vol. 269, no 1, p. 57-64Article in journal (Refereed)
  • 38. Nystrom, Jesper
    et al.
    Ekenstedt, Johan
    Angerbjorn, Anders
    Thulin, Linda
    Hellstrom, Peter
    Dalen, Love
    Golden Eagles on the Swedish mountain tundra - diet and breeding success in relation to prey fluctuations2006In: Ornis Fennica, ISSN 0030-5685, Vol. 83, no 4, p. 145-152Article in journal (Refereed)
  • 39. Nystrom, V.
    et al.
    Angerbjorn, A.
    Dalen, L.
    Genetic consequences of a demographic bottleneck in the Scandinavian arctic fox2006In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 114, no 1, p. 84-94Article in journal (Refereed)
  • 40. Nystrom, Veronica
    et al.
    Dalen, Love
    Vartanyan, Sergey
    Liden, Kerstin
    Ryman, Nils
    Angerbjorn, Anders
    Temporal genetic change in the last remaining population of woolly mammoth2010In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 277, no 1692, p. 2331-2337Article in journal (Refereed)
  • 41. Nystrom, Veronica
    et al.
    Humphrey, Joanne
    Skoglund, Pontus
    McKeown, Niall J.
    Vartanyan, Sergey
    Shaw, Paul W.
    Liden, Kerstin
    Jakobsson, Mattias
    Barnes, Ian
    Angerbjorn, Anders
    Lister, Adrian
    Dalen, Love
    Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 14, p. 3391-3402Article in journal (Refereed)
  • 42. Nyström, V.
    et al.
    Humphrey, J.
    Skoglund, P.
    McKeown, N. J.
    Vartanyan, S.
    Shaw, P. W.
    Liden, K.
    Jakobsson, M.
    Barnes, I.
    Angerbjorn, A.
    Lister, A.
    Dalén, L.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 14, p. 3391-3402Article in journal (Refereed)
  • 43. Orr, Teri J.
    et al.
    Lindenfors, Patrick
    Dalen, Love
    Angerbjorn, Anders
    Garland, Theodore, Jr.
    Delayed implantation in carnivores, causes and consequences and reproductive effort.2009In: Integrative and Comparative Biology, ISSN 1540-7063, E-ISSN 1557-7023, Vol. 49, p. E127-E127Article in journal (Refereed)
  • 44. Palkopoulou, Eleftheria
    et al.
    Baca, Mateusz
    Abramson, Natalia I.
    Sablin, Mikhail
    Socha, Pawel
    Nadachowski, Adam
    Prost, Stefan
    Germonpre, Mietje
    Kosintsev, Pavel
    Smirnov, Nickolay G.
    Vartanyan, Sergey
    Ponomarev, Dmitry
    Nystroem, Johanna
    Nikolskiy, Pavel
    Jass, Christopher N.
    Litvinov, Yuriy N.
    Kalthoff, Daniela C.
    Grigoriev, Semyon
    Fadeeva, Tatyana
    Douka, Aikaterini
    Higham, Thomas F. G.
    Ersmark, Erik
    Pitulko, Vladimir
    Pavlova, Elena
    Stewart, John R.
    Weglenski, Piotr
    Stankovic, Anna
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings2016In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 22, no 5, p. 1710-1721Article in journal (Refereed)
    Abstract [en]

    Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.

  • 45. Palkopoulou, Eleftheria
    et al.
    Dalen, Love
    Lister, Adrian M.
    Vartanyan, Sergey
    Sablin, Mikhail
    Sher, Andrei
    Edmark, Veronica Nystrom
    Brandstrom, Mikael D.
    Germonpre, Mietje
    Barnes, Ian
    Thomas, Jessica A.
    Holarctic genetic structure and range dynamics in the woolly mammoth2013In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1770, article id 20131910Article in journal (Refereed)
  • 46. 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)
  • 47. 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, ISSN 2045-2322, 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.

  • 48. Rodriguez, Ricardo
    et al.
    Ramirez, Oscar
    Valdiosera, Cristina E.
    Garcia, Nuria
    Alda, Fernando
    Madurell-Malapeira, Joan
    Marmi, Josep
    Doadrio, Ignacio
    Willerslev, Eske
    Gotherstrom, Anders
    Luis Arsuaga, Juan
    Thomas, Mark G.
    Lalueza-Fox, Carles
    Dalen, Love
    50,000 years of genetic uniformity in the critically endangered Iberian lynx2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 18, p. 3785-3795Article in journal (Refereed)
  • 49.
    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, ISSN 1932-6203, 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.

  • 50. Sarnblad, Anna
    et al.
    Danbolt, Magnus
    Dalen, Love
    Amir, Omar A.
    Berggren, Per
    Phylogenetic placement and population structure of Indo-Pacific bottlenose dolphins (Tursiops aduncus) off Zanzibar, Tanzania, based on mtDNA sequences2011In: Marine mammal science, ISSN 0824-0469, E-ISSN 1748-7692, Vol. 27, no 2, p. 431-448Article in journal (Refereed)
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