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  • Biagioni, Cristian
    et al.
    Università di Pisa, Italy..
    Hålenius, Ulf
    Swedish Museum of Natural History, Department of Geology.
    Miyawaki, Ritsuro
    National Museum of Nature and Science, Tsukuba, Japan.
    Pasero, Marco
    Università di Pisa, Italy..
    Nuove specie mineralogiche Italiane2019In: Rivista Mineralogica Italiana, Vol. 43, no 4, p. 256-262Article in journal (Other (popular science, discussion, etc.))
  • Stanton, David William Graham
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    More grist for the mill? Species delimitation in the genomic era and its implications for conservation2019In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 20, no 1, p. 101-113Article in journal (Refereed)
  • 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.

  • Sinding, Mikkel-Holger S.
    et al.
    Gopalakrishan, Shyam
    Vieira, Filipe G.
    Castruita, Jose A. Samaniego
    Raundrup, Katrine
    Jorgensen, Mads Peter Heide
    Meldgaard, Morten
    Petersen, Bent
    Sicheritz-Ponten, Thomas
    Mikkelsen, Johan Brus
    Marquard-Petersen, Ulf
    Dietz, Rune
    Sonne, Christian
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Bachmann, Lutz
    Wiig, Oystein
    Hansen, Anders J.
    Gilbert, M. Thomas P.
    Population genomics of grey wolves and wolf-like canids in North America2018In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 14, no 11, article id e1007745Article in journal (Refereed)
    Abstract [en]

    North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified "Polar wolf" population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.

  • Ameen, Carly
    et al.
    Feuerborn, Tatiana R.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    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
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    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 Arctic2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1916, article id 20191929Article in journal (Refereed)
    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.

  • Saremi, Nedda F.
    et al.
    Supple, Megan A.
    Byrne, Ashley
    Cahill, James A.
    Coutinho, Luiz Lehmann
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Figueiro, Henrique V.
    Johnson, Warren E.
    Milne, Heather J.
    O'Brien, Stephen J.
    O'Connell, Brendan
    Onorato, David P.
    Riley, Seth P. D.
    Sikich, Jeff A.
    Stahler, Daniel R.
    Villela, Priscilla Marqui Schmidt
    Vollmers, Christopher
    Wayne, Robert K.
    Eizirik, Eduardo
    Corbett-Detig, Russell B.
    Green, Richard E.
    Wilmers, Christopher C.
    Shapiro, Beth
    Puma genomes from North and South America provide insights into the genomic consequences of inbreeding (vol 10, 4769, 2019)2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 5276Article in journal (Refereed)
  • 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
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Olsen, Jesper V.
    Lordkipanidze, David
    Willerslev, Eske
    Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 574, no 7776, p. 103-+Article in journal (Refereed)
    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.

  • van der Valk, Tom
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Diez-del-Molino, David
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Marques-Bonet, Tomas
    Guschanski, Katerina
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. 165-+Article in journal (Refereed)
    Abstract [en]

    Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.

  • Naud, Lucy
    et al.
    Masviken, Johannes
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Freire, Susana
    Angerbjorn, Anders
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dalerum, Fredrik
    Altitude effects on spatial components of vascular plant diversity in a subarctic mountain tundra2019In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, no 8, p. 4783-4795Article in journal (Refereed)
    Abstract [en]

    Environmental gradients are caused by gradual changes in abiotic factors, which affect species abundances and distributions, and are important for the spatial distribution of biodiversity. One prominent environmental gradient is the altitude gradient. Understanding ecological processes associated with altitude gradients may help us to understand the possible effects climate change could have on species communities. We quantified vegetation cover, species richness, species evenness, beta diversity, and spatial patterns of community structure of vascular plants along altitude gradients in a subarctic mountain tundra in northern Sweden. Vascular plant cover and plant species richness showed unimodal relationships with altitude. However, species evenness did not change with altitude, suggesting that no individual species became dominant when species richness declined. Beta diversity also showed a unimodal relationship with altitude, but only for an intermediate spatial scale of 1km. A lack of relationships with altitude for either patch or landscape scales suggests that any altitude effects on plant spatial heterogeneity occurred on scales larger than individual patches but were not effective across the whole landscape. We observed both nested and modular patterns of community structures, but only the modular patterns corresponded with altitude. Our observations point to biotic regulations of plant communities at high altitudes, but we found both scale dependencies and inconsistent magnitude of the effects of altitude on different diversity components. We urge for further studies evaluating how different factors influence plant communities in high altitude and high latitude environments, as well as studies identifying scale and context dependencies in any such influences.

  • Ersmark, Erik
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    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
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Genetic turnovers and northern survival during the last glacial maximum in European brown bears2019In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, no 10, p. 5891-5905Article in journal (Refereed)
    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.