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  • 1. Ameen, Carly
    et al.
    Feuerborn, Tatiana R.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Brown, Sarah K.
    Linderholm, Anna
    Hulme-Beaman, Ardern
    Lebrasseur, Ophelie
    Sinding, Mikkel-Holger S.
    Lounsberry, Zachary T.
    Lin, Audrey T.
    Appelt, Martin
    Bachmann, Lutz
    Betts, Matthew
    Britton, Kate
    Darwent, John
    Dietz, Rune
    Fredholm, Merete
    Gopalakrishnan, Shyam
    Goriunova, Olga I.
    Gronnow, Bjarne
    Haile, James
    Hallsson, Jon Hallsteinn
    Harrison, Ramona
    Heide-Jorgensen, Mads Peter
    Knecht, Rick
    Losey, Robert J.
    Masson-MacLean, Edouard
    McGovern, Thomas H.
    McManus-Fry, Ellen
    Meldgaard, Morten
    Midtdal, Aslaug
    Moss, Madonna L.
    Nikitin, Iurii G.
    Nomokonova, Tatiana
    Palsdottir, Albina Hulda
    Perri, Angela
    Popov, Aleksandr N.
    Rankin, Lisa
    Reuther, Joshua D.
    Sablin, Mikhail
    Schmidt, Anne Lisbeth
    Shirar, Scott
    Smiarowski, Konrad
    Sonne, Christian
    Stiner, Mary C.
    Vasyukov, Mitya
    West, Catherine F.
    Ween, Gro Birgit
    Wennerberg, Sanne Eline
    Wiig, Oystein
    Woollett, James
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Hansen, Anders J.
    Gilbert, M. Thomas P.
    Sacks, Benjamin N.
    Frantz, Laurent
    Larson, Greger
    Dobney, Keith
    Darwent, Christyann M.
    Evin, Allowen
    Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic2019Ingår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, nr 1916, artikel-id 20191929Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

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  • 2. Angerbjorn, Anders
    et al.
    Eide, Nina E.
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 scale2013Ingår i: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 50, nr 1, s. 59-67Artikel i tidskrift (Refereegranskat)
  • 3. Bannikova, Anna A.
    et al.
    Jenkins, Paulina D.
    Solovyeva, Evgeniya N.
    Pavlova, Svetlana, V
    Demidova, Tatiana B.
    Simanovsky, Sergey A.
    Sheftel, Boris, I
    Lebedev, Vladimir S.
    Fang, Yun
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Abramov, Alexei, V
    Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae): molecular and morphological analyses with the discussion of tribal affinities2019Ingår i: ZooKeys, ISSN 1313-2989, E-ISSN 1313-2970, nr 888, s. 133-158Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 4. Barlow, A
    et al.
    Paijmans, J L A
    Alberti, F
    Gasparyan, B
    Bar-Oz, G
    Pinhasi, R
    Foronova, I
    Puzachenko, A Y
    Pacher, M
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Baryshnikov, G
    Hofreiter, M
    Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears2021Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 31, nr 8, s. 1771-+Artikel i tidskrift (Refereegranskat)
  • 5. 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
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Shapiro, Beth
    Hofreiter, Michael
    Partial genomic survival of cave bears in living brown bears2018Ingår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 10, s. 1563-1570Artikel i tidskrift (Refereegranskat)
  • 6. Barnett, Ross
    et al.
    Westbury, Michael V.
    Sandoval-Velasco, Marcela
    Vieira, Filipe Garrett
    Jeon, Sungwon
    Zazula, Grant
    Martin, Michael D.
    Ho, Simon Y.W.
    Mather, Niklas
    Gopalakrishnan, Shyam
    Ramos-Madrigal, Jazmín
    de Manuel, Marc
    Zepeda-Mendoza, M. Lisandra
    Antunes, Agostinho
    Baez, Aldo Carmona
    De Cahsan, Binia
    Larson, Greger
    O’Brien, Stephen J.
    Eizirik, Eduardo
    Johnson, Warren E.
    Koepfli, Klaus-Peter
    Wilting, Andreas
    Fickel, Jörns
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lorenzen, Eline D.
    Marques-Bonet, Tomas
    Hansen, Anders J.
    Zhang, Guojie
    Bhak, Jong
    Yamaguchi, Nobuyuki
    Gilbert, M. Thomas P.
    Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens2020Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 7. Bergstrom, Anders
    et al.
    Frantz, Laurent
    Schmidt, Ryan
    Ersmark, Erik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lebrasseur, Ophelie
    Girdland-Flink, Linus
    Lin, Audrey T.
    Stora, Jan
    Sjogren, Karl-Goran
    Anthony, David
    Antipina, Ekaterina
    Amiri, Sarieh
    Bar-Oz, Guy
    Bazaliiskii, Vladimir I.
    Bulatovic, Jelena
    Brown, Dorcas
    Carmagnini, Alberto
    Davy, Tom
    Fedorov, Sergey
    Fiore, Ivana
    Fulton, Deirdre
    Germonpre, Mietje
    Haile, James
    Irving-Pease, Evan K.
    Jamieson, Alexandra
    Janssens, Luc
    Kirillova, Irina
    Horwitz, Liora Kolska
    Kuzmanovic-Cvetkovic, Julka
    Kuzmin, Yaroslav
    Losey, Robert J.
    Dizdar, Daria Loznjak
    Mashkour, Marjan
    Novak, Mario
    Onar, Vedat
    Orton, David
    Pasaric, Maja
    Radivojevic, Miljana
    Rajkovic, Dragana
    Roberts, Benjamin
    Ryan, Hannah
    Sablin, Mikhail
    Shidlovskiy, Fedor
    Stojanovic, Ivana
    Tagliacozzo, Antonio
    Trantalidou, Katerina
    Ullen, Inga
    Villaluenga, Aritza
    Wapnish, Paula
    Dobney, Keith
    Gotherstrom, Anders
    Linderholm, Anna
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Pinhasi, Ron
    Larson, Greger
    Skoglund, Pontus
    Origins and genetic legacy of prehistoric dogs2020Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 370, nr 6516, s. 557-563Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 8. Bergstrom, Anders
    et al.
    Stanton, David WG
    Taron, Ulrike H
    Frantz, Laurent
    Sinding, Mikkel-Holger S
    Ersmark, Erik
    Pfrengle, Saskia
    Cassatt-Johnstone, Molly
    Lebrasseur, Ophelie
    Girdland-Flink, Linus
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Grey wolf genomic history reveals a dual ancestry of dogs2022Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 607, s. 313-320Artikel i tidskrift (Refereegranskat)
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  • 9. Boeskorov, G G
    et al.
    Plotnikov, V V
    Protopopov, A V
    Baryshnikov, G F
    Fosse, P
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Stanton, D W G
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Pavlov, I S
    Suzuki, N
    Tikhonov, A N
    The Preliminary Analysis of Cave Lion Cubs Panthera spelaea (Goldfuss, 1810) from the Permafrost of Siberia2021Ingår i: Quaternary, E-ISSN 2571-550X, Vol. 4, nr 3Artikel i tidskrift (Refereegranskat)
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  • 10. Brace, Selina
    et al.
    Palkopoulou, Eleftheria
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 instability2012Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, nr 50, s. 20532-20536Artikel i tidskrift (Refereegranskat)
  • 11. Brace, Selina
    et al.
    Thomas, Jessica A.
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Burger, Joachim
    MacPhee, Ross D. E.
    Barnes, Ian
    Turvey, Samuel T.
    Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family2016Ingår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, nr 12, s. 3095-3103Artikel i tidskrift (Refereegranskat)
    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.

  • 12. Brealey, Jaelle C
    et al.
    Leitão, Henrique G
    van der Valk, Tom
    Xu, Wenbo
    Bougiouri, Katia
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Guschanski, Katerina
    Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome2020Ingår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, nr 10, s. 3003-3022Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 13. Cappellini, Enrico
    et al.
    Gentry, Anthea
    Palkopoulou, Eleftheria
    Ishida, Yasuko
    Cram, David
    Roos, Anna-Marie
    Watson, Mick
    Johansson, Ulf S.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Fernholm, Bo
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Agnelli, Paolo
    Barbagli, Fausto
    Littlewood, D. Tim. J.
    Kelstrup, Christian D.
    Olsen, Jesper V.
    Lister, Adrian M.
    Roca, Alfred L.
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gilbert, M. Thomas P.
    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)2014Ingår i: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 170, s. 222-232Artikel i tidskrift (Refereegranskat)
  • 14. Cappellini, Enrico
    et al.
    Welker, Frido
    Pandolfi, Luca
    Ramos-Madrigal, Jazmin
    Samodova, Diana
    Ruther, Patrick L.
    Fotakis, Anna K.
    Lyon, David
    Moreno-Mayar, J. Victor
    Bukhsianidze, Maia
    Jersie-Christensen, Rosa Rakownikow
    Mackie, Meaghan
    Ginolhac, Aurelien
    Ferring, Reid
    Tappen, Martha
    Palkopoulou, Eleftheria
    Dickinson, Marc R.
    Stafford, Thomas W., Jr.
    Chan, Yvonne L.
    Gotherstrom, Anders
    Nathan, Senthilvel K. S. S.
    Heintzman, Peter D.
    Kapp, Joshua D.
    Kirillova, Irina
    Moodley, Yoshan
    Agusti, Jordi
    Kahlke, Ralf-Dietrich
    Kiladze, Gocha
    Martinez-Navarro, Bienvenido
    Liu, Shanlin
    Velasco, Marcela Sandoval
    Sinding, Mikkel-Holger S.
    Kelstrup, Christian D.
    Allentoft, Morten E.
    Orlando, Ludovic
    Penkman, Kirsty
    Shapiro, Beth
    Rook, Lorenzo
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gilbert, M. Thomas P.
    Olsen, Jesper V.
    Lordkipanidze, David
    Willerslev, Eske
    Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny2019Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 574, nr 7776, s. 103-+Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

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  • 15. 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
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 analysis2017Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 7, artikel-id 44585Artikel i tidskrift (Refereegranskat)
  • 16. Cockerill, Christopher A
    et al.
    Hasselgren, Malin
    Dussex, Nicolas
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Angerbjörn, Anders
    Wallén, Johan F
    Landa, Arild
    Eide, Nina E
    Flagstad, Øystein
    Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus)2022Ingår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 13, nr 11Artikel i tidskrift (Refereegranskat)
  • 17. Cotton, James A.
    et al.
    Berriman, Matthew
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Barnes, Ian
    Eradication genomics-lessons for parasite control2018Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 361, nr 6398, s. 130-131Artikel i tidskrift (Refereegranskat)
  • 18.
    Dalen, L
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Elmhagen, B
    Angerbjorn, A
    DNA analysis on fox faeces and competition induced niche shifts2004Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, nr 8, s. 2389-2392Artikel i tidskrift (Refereegranskat)
  • 19.
    Dalen, L
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 fox2005Ingår i: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 84, nr 1, s. 79-89Artikel i tidskrift (Refereegranskat)
  • 20.
    Dalen, L
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gotherstrom, A
    Angerbjorn, A
    Identifying species from pieces of faeces2004Ingår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 5, nr 1, s. 109-111Artikel i tidskrift (Refereegranskat)
  • 21.
    Dalen, L
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gotherstrom, A
    Tannerfeldt, M
    Angerbjorn, A
    Is the endangered Fennoscandian arctic fox (Alopex lagopus) population genetically isolated?2002Ingår i: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 105, nr 2, s. 171-178, artikel-id PII S0006-3207(01)00180-XArtikel i tidskrift (Refereegranskat)
  • 22.
    Dalen, L.
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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?2006Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, nr 10, s. 2809-2819Artikel i tidskrift (Refereegranskat)
  • 23.
    Dalen, Love
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gotherstrom, Anders
    Meijer, Tomas
    Shapiro, Beth
    Recovery of DNA from Footprints in the Snow2007Ingår i: Canadian field-naturalist, ISSN 0008-3550, Vol. 121, nr 3, s. 321-324Artikel i tidskrift (Refereegranskat)
  • 24.
    Dalen, Love
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lagerholm, Vendela K.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Nylander, Johan A. A.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017Ingår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, nr 6, artikel-id 169Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 25.
    Dalen, Love
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 fox2007Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, nr 16, s. 6726-6729Artikel i tidskrift (Refereegranskat)
  • 26.
    Dalen, Love
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 West2012Ingår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, nr 8, s. 1893-1897Artikel i tidskrift (Refereegranskat)
  • 27. Dalerum, F.
    et al.
    Freire, S.
    Angerbjorn, A.
    Lecomte, N.
    Lindgren, A.
    Meijer, T.
    Pecnerova, P.
    Dalen, L.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Exploring the diet of arctic wolves (Canis lupus arctos) at their northern range limit2018Ingår i: Canadian Journal of Zoology, ISSN 0008-4301, E-ISSN 1480-3283, Vol. 96, nr 3, s. 277-281Artikel i tidskrift (Refereegranskat)
  • 28. Dalerum, Fredrik
    et al.
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Frojd, Christina
    Lecomte, Nicolas
    Lindgren, Asa
    Meijer, Tomas
    Pecnerova, Patricia
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Angerbjorn, Anders
    Spatial variation in Arctic hare (Lepus arcticus) populations around the Hall Basin2017Ingår i: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, nr 10, s. 2113-2118Artikel i tidskrift (Refereegranskat)
  • 29.
    Dehasque, M
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Pecnerova, P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Muller, H
    Tikhonov, A
    Nikolskiy, P
    Tsigankova, V I
    Danilov, G K
    Diez-del-Molino, D
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Vartanyan, S
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lister, A M
    Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia2021Ingår i: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 259Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 30.
    Dehasque, Marianne
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    avila-Arcos, Maria C.
    Diez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Fumagalli, Matteo
    Guschanski, Katerina
    Lorenzen, Eline D.
    Malaspinas, Anna-Sapfo
    Marques-Bonet, Tomas
    Martin, Michael D.
    Murray, Gemma G. R.
    Papadopulos, Alexander S. T.
    Therkildsen, Nina Overgaard
    Wegmann, Daniel
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Foote, Andrew D.
    Inference of natural selection from ancient DNA2020Ingår i: EVOLUTION LETTERS, Vol. 4, nr 2, s. 94-108Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.

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  • 31. Dehasque, Marianne
    et al.
    Pečnerová, Patrícia
    Kempe Lagerholm, Vendela
    Ersmark, Erik
    Danilov, Gleb K
    Mortensen, Peter
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Vartanyan, Sergey
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA2022Ingår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 13, nr 4Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 32.
    Diez-del-Molino, David
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials2020Ingår i: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 181, nr 6, s. 1200-1201Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world’s most famous and influential sets of ancient parchments.

    Ladda ner fulltext (pdf)
    fulltext
  • 33. Diez-del-Molino, David
    et al.
    Sanchez-Barreiro, Fatima
    Barnes, Ian
    Gilbert, M. Thomas P.
    Dalen, Love
    Quantifying Temporal Genomic Erosion in Endangered Species2018Ingår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 33, nr 3, s. 176-185Artikel i tidskrift (Refereegranskat)
  • 34. Doan, Karolina
    et al.
    Mackiewicz, Pawel
    Sandoval-Castellanos, Edson
    Stefaniak, Krzysztof
    Ridush, Bogdan
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Weglenski, Piotr
    Stankovic, Ana
    The history of Crimean red deer population and Cervus phylogeography in Eurasia2018Ingår i: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 183, nr 1, s. 208-225Artikel i tidskrift (Refereegranskat)
  • 35.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Alberti, Federica
    Heino, Matti T.
    Olsen, Remi-Andre
    van der Valk, Tom
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ryman, Nils
    Laikre, Linda
    Ahlgren, Hans
    Askeyev, Igor V.
    Askeyev, Oleg V.
    Shaymuratova, Dilyara N.
    Askeyev, Arthur O.
    Döppes, Doris
    Friedrich, Ronny
    Lindauer, Susanne
    Rosendahl, Wilfried
    Aspi, Jouni
    Hofreiter, Michael
    Lidén, Kerstin
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Díez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Moose genomes reveal past glacial demography and the origin of modern lineages2020Ingår i: BMC Genomics, E-ISSN 1471-2164, Vol. 21, nr 1Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.

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    fulltext
  • 36. Dussex, Nicolas
    et al.
    Robertson, Bruce C
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Jarvis, Erich D
    The kākāpō (Strigops habroptilus)2022Ingår i: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 38, nr 8Artikel i tidskrift (Refereegranskat)
  • 37.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Stanton, David W. G.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Sigeman, Hanna
    Ericson, Per G. P.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gill, Jacquelyn
    Fisher, Daniel C.
    Protopopov, Albert V.
    Herridge, Victoria L.
    Plotnikov, Valery
    Hansson, Bengt
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass2020Ingår i: COMMUNICATIONS BIOLOGY, Vol. 3, nr 1Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44-49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids. Nicolas Dussex et al. identify a 44,000-49,000 year old bird found in Siberian permafrost as a female horned lark using ancient DNA. This exceptionally well-preserved specimen illustrates the potential contribution to science of permafrost deposits, such as the study of ecology and evolution of ancient ecosystems, calibration of molecular clocks, and furthering our understanding of processes such as biological regulation and gene expression in relation to climate change.

    Ladda ner fulltext (pdf)
    fulltext
  • 38.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    van der Valk, Tom
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Morales, Hernán E.
    Wheat, Christopher W.
    Díez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Foster, Yasmin
    Kutschera, Verena E.
    Guschanski, Katerina
    Rhie, Arang
    Phillippy, Adam M.
    Korlach, Jonas
    Howe, Kerstin
    Chow, William
    Pelan, Sarah
    Mendes Damas, Joanna D.
    Lewin, Harris A.
    Hastie, Alex R.
    Formenti, Giulio
    Fedrigo, Olivier
    Guhlin, Joseph
    Harrop, Thomas W.R.
    Le Lec, Marissa F.
    Dearden, Peter K.
    Haggerty, Leanne
    Martin, Fergal J.
    Kodali, Vamsi
    Thibaud-Nissen, Françoise
    Iorns, David
    Knapp, Michael
    Gemmell, Neil J.
    Robertson, Fiona
    Moorhouse, Ron
    Digby, Andrew
    Eason, Daryl
    Vercoe, Deidre
    Howard, Jason
    Jarvis, Erich D.
    Robertson, Bruce C.
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Population genomics of the critically endangered kākāpō2021Ingår i: Cell Genomics, ISSN 2666-979X, Vol. 1, nr 1Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.

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    fulltext
  • 39.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Knapp, Michael
    Kardailsky, Olga
    Robertson, Bruce C.
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction2019Ingår i: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 15, nr 9, artikel-id 20190491Artikel i tidskrift (Refereegranskat)
    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.

    Ladda ner fulltext (pdf)
    fulltext
  • 40.
    Díez-del-Molino, David
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gyllenstrand, Niclas
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning.
    Widemo, Fredrik
    Liljebäck, Niklas
    Svensson, Mikael
    Sjögren-Gulve, Per
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose2020Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Interspecific introgression is considered a potential threat to endangered taxa. One example where this has had a major impact on conservation policy is the lesser white-fronted goose (LWfG). After a dramatic decline in Sweden, captive breeding birds were released between 1981–1999 with the aim to reinforce the population. However, the detection of greater white-fronted goose (GWfG) mitochondrial DNA in the LWfG breeding stock led to the release program being dismantled, even though the presence of GWfG introgression in the actual wild Swedish LWfG population was never documented. To examine this, we sequenced the complete genomes of 21 LWfG birds from the Swedish, Russian and Norwegian populations, and compared these with genomes from other goose species, including the GWfG. We found no evidence of interspecific introgression into the wild Swedish LWfG population in either nuclear genomic or mitochondrial data. Moreover, Swedish LWfG birds are genetically distinct from the Russian and Norwegian populations and display comparatively low genomic diversity and high levels of inbreeding. Our findings highlight the utility of genomic approaches in providing scientific evidence that can help improve conservation management as well as policies for breeding and reinforcement programmes.

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    fulltext
  • 41. Elmhagen, Bodil
    et al.
    Destouni, Georgia
    Angerbjorn, Anders
    Borgstrom, Sara
    Boyd, Emily
    Cousins, Sara A. O.
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 services2015Ingår i: Ecology & Society, E-ISSN 1708-3087, Vol. 20, nr 1, artikel-id UNSP 23Artikel i tidskrift (Refereegranskat)
  • 42.
    Ersmark, Erik
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Baryshnikov, Gennady
    Higham, Thomas
    Argant, Alain
    Castanos, Pedro
    Doeppes, Doris
    Gasparik, Mihaly
    Germonpre, Mietje
    Liden, Kerstin
    Lipecki, Grzegorz
    Marciszak, Adrian
    Miller, Rebecca
    Moreno-Garcia, Marta
    Pacher, Martina
    Robu, Marius
    Rodriguez-Varela, Ricardo
    Rojo Guerra, Manuel
    Sabol, Martin
    Spassov, Nikolai
    Stora, Jan
    Valdiosera, Christina
    Villaluenga, Aritza
    Stewart, John R.
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Genetic turnovers and northern survival during the last glacial maximum in European brown bears2019Ingår i: Ecology and Evolution, E-ISSN 2045-7758, Vol. 9, nr 10, s. 5891-5905Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

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    fulltext
  • 43.
    Ersmark, Erik
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Orlando, Ludovic
    Sandoval-Castellanos, Edson
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Barnes, Ian
    Barnett, Ross
    Stuart, Anthony
    Lister, Adrian
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Population Demography and Genetic Diversity in the Pleistocene Cave Lion2015Ingår i: Open Quaternary, Vol. 1, nr 4, s. 1-14Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 44. Feng, S H
    et al.
    Stiller, J
    Deng, Y
    Armstrong, J
    Fang, Q
    Reeve, A H
    Xie, D
    Chen, G J
    Guo, C X
    Faircloth, B C
    Petersen, B
    Wang, Z J
    Zhou, Q
    Diekhans, M
    Chen, W J
    Andreu-Sanchez, S
    Margaryan, A
    Howard, J T
    Parent, C
    Pacheco, G
    Sinding, M H S
    Puetz, L
    Cavill, E
    Ribeiro, A M
    Eckhart, L
    Fjeldsa, J
    Hosner, P A
    Brumfield, R T
    Christidis, L
    Bertelsen, M F
    Sicheritz-Ponten, T
    Tietze, D T
    Robertson, B C
    Song, G
    Borgia, G
    Claramunt, S
    Lovette, I J
    Cowen, S J
    Njoroge, P
    Dumbacher, J P
    Ryder, O A
    Fuchs, J
    Bunce, M
    Burt, D W
    Cracraft, J
    Meng, G L
    Hackett, S J
    Ryan, P G
    Jonsson, K A
    Jamieson, I G
    da Fonseca, R R
    Braun, E L
    Houde, P
    Mirarab, S
    Suh, A
    Hansson, B
    Ponnikas, S
    Sigeman, H
    Stervander, M
    Frandsen, P B
    van der Zwan, H
    van der Sluis, R
    Visser, C
    Balakrishnan, C N
    Clark, A G
    Fitzpatrick, J W
    Bowman, R
    Chen, N
    Cloutier, A
    Sackton, T B
    Edwards, S V
    Foote, D J
    Shakya, S B
    Sheldon, F H
    Vignal, A
    Soares, A E R
    Shapiro, B
    Gonzalez-Solis, J
    Ferrer-Obiol, J
    Rozas, J
    Riutort, M
    Tigano, A
    Friesen, V
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Urrutia, A O
    Szekely, T
    Liu, Y
    Campana, M G
    Corvelo, A
    Fleischer, R C
    Rutherford, K M
    Gemmell, N J
    Dussex, N
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Mouritsen, H
    Thiele, N
    Delmore, K
    Liedvogel, M
    Franke, A
    Hoeppner, M P
    Krone, O
    Fudickar, A M
    Mila, B
    Ketterson, E D
    Fidler, A E
    Friis, G
    Parody-Merino, A M
    Battley, P F
    Cox, M P
    Lima, N C B
    Prosdocimi, F
    Parchman, T L
    Schlinger, B A
    Loiselle, B A
    Blake, J G
    Lim, H C
    Day, L B
    Fuxjager, M J
    Baldwin, M W
    Braun, M J
    Wirthlin, M
    Dikow, R B
    Ryder, T B
    Camenisch, G
    Keller, L F
    DaCosta, J M
    Hauber, M E
    Louder, M I M
    Witt, C C
    McGuire, J A
    Mudge, J
    Megna, L C
    Carling, M D
    Wang, B
    Taylor, S A
    Del-Rio, G
    Aleixo, A
    Vasconcelos, A T R
    Mello, C V
    Weir, J T
    Haussler, D
    Li, Q Y
    Yang, H M
    Wang, J
    Lei, F M
    Rahbek, C
    Gilbert, M T P
    Graves, G R
    Jarvis, E D
    Paten, B
    Zhang, G J
    Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)2021Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 592, nr 7856, s. E24-E24Artikel i tidskrift (Refereegranskat)
  • 45. Feng, Shaohong
    et al.
    Stiller, Josefin
    Deng, Yuan
    Armstrong, Joel
    Fang, Qi
    Reeve, Andrew Hart
    Xie, Duo
    Chen, Guangji
    Guo, Chunxue
    Faircloth, Brant C.
    Petersen, Bent
    Wang, Zongji
    Zhou, Qi
    Diekhans, Mark
    Chen, Wanjun
    Andreu-Sanchez, Sergio
    Margaryan, Ashot
    Howard, Jason Travis
    Parent, Carole
    Pacheco, George
    Sinding, Mikkel-Holger S.
    Puetz, Lara
    Cavill, Emily
    Ribeiro, Angela M.
    Eckhart, Leopold
    Fjeldsa, Jon
    Hosner, Peter A.
    Brumfield, Robb T.
    Christidis, Les
    Bertelsen, Mads F.
    Sicheritz-Ponten, Thomas
    Tietze, Dieter Thomas
    Robertson, Bruce C.
    Song, Gang
    Borgia, Gerald
    Claramunt, Santiago
    Lovette, Irby J.
    Cowen, Saul J.
    Njoroge, Peter
    Dumbacher, John Philip
    Ryder, Oliver A.
    Fuchs, Jerome
    Bunce, Michael
    Burt, David W.
    Cracraft, Joel
    Meng, Guanliang
    Hackett, Shannon J.
    Ryan, Peter G.
    Jonsson, Knud Andreas
    Jamieson, Ian G.
    da Fonseca, Rute R.
    Braun, Edward L.
    Houde, Peter
    Mirarab, Siavash
    Suh, Alexander
    Hansson, Bengt
    Ponnikas, Suvi
    Sigeman, Hanna
    Stervander, Martin
    Frandsen, Paul B.
    van der Zwan, Henriette
    van der Sluis, Rencia
    Visser, Carina
    Balakrishnan, Christopher N.
    Clark, Andrew G.
    Fitzpatrick, John W.
    Bowman, Reed
    Chen, Nancy
    Cloutier, Alison
    Sackton, Timothy B.
    Edwards, Scott V.
    Foote, Dustin J.
    Shakya, Subir B.
    Sheldon, Frederick H.
    Vignal, Alain
    Soares, Andre E. R.
    Shapiro, Beth
    Gonzalez-Solis, Jacob
    Ferrer-Obiol, Joan
    Rozas, Julio
    Riutort, Marta
    Tigano, Anna
    Friesen, Vicki
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Urrutia, Araxi O.
    Szekely, Tamas
    Liu, Yang
    Campana, Michael G.
    Corvelo, Andre
    Fleischer, Robert C.
    Rutherford, Kim M.
    Gemmell, Neil J.
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Mouritsen, Henrik
    Thiele, Nadine
    Delmore, Kira
    Liedvogel, Miriam
    Franke, Andre
    Hoeppner, Marc P.
    Krone, Oliver
    Fudickar, Adam M.
    Mila, Borja
    Ketterson, Ellen D.
    Fidler, Andrew Eric
    Friis, Guillermo
    Parody-Merino, Angela M.
    Battley, Phil F.
    Cox, Murray P.
    Lima, Nicholas Costa Barroso
    Prosdocimi, Francisco
    Parchman, Thomas Lee
    Schlinger, Barney A.
    Loiselle, Bette A.
    Blake, John G.
    Lim, Haw Chuan
    Day, Lainy B.
    Fuxjager, Matthew J.
    Baldwin, Maude W.
    Braun, Michael J.
    Wirthlin, Morgan
    Dikow, Rebecca B.
    Ryder, T. Brandt
    Camenisch, Glauco
    Keller, Lukas F.
    DaCosta, Jeffrey M.
    Hauber, Mark E.
    Louder, Matthew I. M.
    Witt, Christopher C.
    McGuire, Jimmy A.
    Mudge, Joann
    Megna, Libby C.
    Carling, Matthew D.
    Wang, Biao
    Taylor, Scott A.
    Del-Rio, Glaucia
    Aleixo, Alexandre
    Vasconcelos, Ana Tereza Ribeiro
    Mello, Claudio V.
    Weir, Jason T.
    Haussler, David
    Li, Qiye
    Yang, Huanming
    Wang, Jian
    Lei, Fumin
    Rahbek, Carsten
    Gilbert, M. Thomas P.
    Graves, Gary R.
    Jarvis, Erich D.
    Paten, Benedict
    Zhang, Guojie
    Dense sampling of bird diversity increases power of comparative genomics2020Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 587, nr 7833Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

  • 46.
    Feuerborn, T R
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Carmagnini, A
    Losey, R J
    Nomokonova, T
    Askeyev, A
    Askeyev, I
    Askeyev, O
    Antipina, E E
    Appelt, M
    Bachura, O P
    Beglane, F
    Bradley, D G
    Daly, K G
    Gopalakrishnan, S
    Gregersen, K M
    Guo, C X
    Gusev, A V
    Jones, C
    Kosintsev, P A
    Kuzmin, Y V
    Mattiangeli, V
    Perri, A R
    Plekhanov, A V
    Ramos-Madrigal, J
    Schmidt, A L
    Shaymuratova, D
    Smith, O
    Yavorskaya, L V
    Zhang, G J
    Willerslev, E
    Meldgaard, M
    Gilbert, M T P
    Larson, G
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Hansen, A J
    Sinding, M H S
    Frantz, L
    Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal2021Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, nr 39Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 47. Feuerborn, Tatiana R.
    et al.
    Palkopoulou, Eleftheria
    van der Valk, Tom
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Munters, Arielle R.
    Pečnerová, Patrícia
    Dehasque, Marianne
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ureña, Irene
    Ersmark, Erik
    Lagerholm, Vendela Kempe
    Krzewińska, Maja
    Rodríguez-Varela, Ricardo
    Götherström, Anders
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Díez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets2020Ingår i: BMC Genomics, E-ISSN 1471-2164, Vol. 21, nr 1Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.

    Ladda ner fulltext (pdf)
    fulltext
  • 48. Fromm, B
    et al.
    Tarbier, M
    Smith, O
    Marmol-Sanchez, E
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gilbert, M T P
    Friedlander, M R
    Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene2021Ingår i: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 27, nr 3, s. 324-334Artikel i tidskrift (Refereegranskat)
  • 49. Fromm, B
    et al.
    Tarbier, M
    Smith, O
    Marmol-Sanchez, E
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gilbert, M T P
    Friedlander, M R
    Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene (vol 15, pg 324, 2020)2021Ingår i: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 27, nr 10, s. 1291-1291Artikel i tidskrift (Refereegranskat)
  • 50. Geffen, Eli
    et al.
    Kam, Michael
    Hefner, Reuven
    Hersteinsson, Pall
    Angerbjorn, Anders
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 canids2011Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, nr 24, s. 5348-5358Artikel i tidskrift (Refereegranskat)
1234 1 - 50 av 156
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