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  • 1.
    Dussex, Nicolas
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Alberti, Federica
    Heino, Matti T.
    Olsen, Remi-Andre
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    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
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Díez-del-Molino, David
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Moose genomes reveal past glacial demography and the origin of modern lineages2020In: BMC Genomics, E-ISSN 1471-2164, Vol. 21, no 1Article in journal (Refereed)
    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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  • 2. Dussex, Nicolas
    et al.
    Tørresen, Ole K.
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Le Moullec, Mathilde
    Veiberg, Vebjørn
    Tooming-Klunderud, Ave
    Skage, Morten
    Garmann-Aarhus, Benedicte
    Wood, Jonathan
    Rasmussen, Jacob A.
    Pedersen, Åshild Ø.
    Martin, Sarah L.F.
    Røed, Knut H.
    Jakobsen, Kjetill S.
    Dalén, Love
    Hansen, Brage B.
    Martin, Michael D.
    Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer2023In: iScience, ISSN 2589-0042, Vol. 26, no 10, p. 107811-107811, article id 107811Article in journal (Refereed)
  • 3.
    Dussex, Nicolas
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Morales, Hernán E.
    Wheat, Christopher W.
    Díez-del-Molino, David
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    von Seth, Johanna
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    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
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Population genomics of the critically endangered kākāpō2021In: Cell Genomics, ISSN 2666-979X, Vol. 1, no 1Article in journal (Refereed)
    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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  • 4. Díez-del-Molino, David
    et al.
    Dehasque, Marianne
    Chacón-Duque, J. Camilo
    Pečnerová, Patrícia
    Tikhonov, Alexei
    Protopopov, Albert
    Plotnikov, Valeri
    Kanellidou, Foteini
    Nikolskiy, Pavel
    Mortensen, Peter
    Swedish Museum of Natural History, Department of Zoology.
    Danilov, Gleb K.
    Vartanyan, Sergey
    Gilbert, M. Thomas P.
    Lister, Adrian M.
    Heintzman, Peter D.
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dalén, Love
    Genomics of adaptive evolution in the woolly mammoth2023In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 33, no 9, p. 1753-1764.e4Article in journal (Refereed)
  • 5. Feuerborn, Tatiana R.
    et al.
    Palkopoulou, Eleftheria
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    von Seth, Johanna
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Munters, Arielle R.
    Pečnerová, Patrícia
    Dehasque, Marianne
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ureña, Irene
    Ersmark, Erik
    Lagerholm, Vendela Kempe
    Krzewińska, Maja
    Rodríguez-Varela, Ricardo
    Götherström, Anders
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Díez-del-Molino, David
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets2020In: BMC Genomics, E-ISSN 1471-2164, Vol. 21, no 1Article in journal (Refereed)
    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.

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  • 6. Pawar, Harvinder
    et al.
    Rymbekova, Aigerim
    Cuadros-Espinoza, Sebastian
    Huang, Xin
    de Manuel, Marc
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lobon, Irene
    Alvarez-Estape, Marina
    Haber, Marc
    Dolgova, Olga
    Han, Sojung
    Esteller-Cucala, Paula
    Juan, David
    Ayub, Qasim
    Bautista, Ruben
    Kelley, Joanna L.
    Cornejo, Omar E.
    Lao, Oscar
    Andrés, Aida M.
    Guschanski, Katerina
    Ssebide, Benard
    Cranfield, Mike
    Tyler-Smith, Chris
    Xue, Yali
    Prado-Martinez, Javier
    Marques-Bonet, Tomas
    Kuhlwilm, Martin
    Ghost admixture in eastern gorillas2023In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 7, no 9, p. 1503-1514Article in journal (Refereed)
  • 7.
    Pecnerova, P
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Diez-del-Molino, D
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    van der Valk, T
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dehasque, M
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gotherstrom, A
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Mammuthus sp. (Early and Middle Pleistocene Mammoths)2021In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 37, no 7, p. 682-683Article in journal (Refereed)
  • 8. Pochon, Zoé
    et al.
    Bergfeldt, Nora
    Kırdök, Emrah
    Vicente, Mário
    Naidoo, Thijessen
    van der Valk, Tom
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Altınışık, N. Ezgi
    Krzewińska, Maja
    Dalén, Love
    Götherström, Anders
    Mirabello, Claudio
    Unneberg, Per
    Oskolkov, Nikolay
    aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow2023In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, no 1, article id 242Article in journal (Refereed)
  • 9.
    van der Valk, T
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pecnerova, P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Diez-del-Molino, D
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Bergstrom, A
    Oppenheimer, J
    Hartmann, S
    Xenikoudakis, G
    Thomas, J A
    Dehasque, M
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Saglican, E
    Fidan, F R
    Barnes, I
    Liu, S L
    Somel, M
    Heintzman, P D
    Nikolskiy, P
    Shapiro, B
    Skoglund, P
    Hofreiter, M
    Lister, A M
    Gotherstrom, A
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Million-year-old DNA sheds light on the genomic history of mammoths2021In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 591, no 7849, p. 265-+Article in journal (Refereed)
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  • 10.
    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.

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  • 11.
    von Seth, J
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dussex, N
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Diez-del-Molino, D
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    van der Valk, T
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Kutschera, V E
    Kierczak, M
    Steiner, C C
    Liu, S L
    Gilbert, M T P
    Sinding, M H S
    Prost, S
    Guschanski, K
    Nathan, S K S S
    Brace, S
    Chan, Y L
    Wheat, C W
    Skoglund, P
    Ryder, O A
    Goossens, B
    Gotherstrom, A
    Dalen, L
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1Article in journal (Refereed)
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1 - 11 of 11
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