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  • 1. Cole, Theresa
    et al.
    Rawlence, Nic
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Elleberg, Ursulla
    Houston, Dave
    Mattern, Thomas
    Miskelly, Colin
    Morrisson, Kyle
    Scofield, Paul
    Tennyson, Alan
    Tompson, David
    Wood, Jamie
    Waters, Jonathan
    Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade2018Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 131, s. 72-79Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as ‘Eudyptes spp.’, we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.

  • 2.
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’s most diverse penguin clade2018Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513Artikel i tidskrift (Refereegranskat)
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  • 3.
    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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  • 4.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Bergfeldt, Nora
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    de Anca Prado, Violeta
    Dehasque, Marianne
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Díez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ersmark, Erik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Kanellidou, Foteini
    Larsson, Petter
    Lemež, Špela
    Lord, Edana
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics2021Ingår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 288, nr 1957Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 5.
    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.

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  • 6.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Taylor, Helen
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Robertson, Bruce
    When genetic and phenotypic data do not agree: the conservation implications of ignoring inconvenient taxonomic evidence2018Ingår i: New Zealand Journal of Ecology, ISSN 11777788, Vol. 42, nr 2, s. 1-7Artikel i tidskrift (Refereegranskat)
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  • 7.
    Dussex, Nicolas
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Taylor, Helen
    Stovall, William
    Rutherford, Kim
    Dodds, Ken
    Clarke, Shannon
    Gemmel, Neil
    Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species2018Ingår i: Ecology and Evolution, ISSN 20457758, Vol. 8, nr 17, s. 8736-8749Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation‐by‐distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10‐fold and 250‐fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next‐generation markers and methods are powerful tools for resolving fine‐scale structure and informing conservation and management efforts.

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  • 8. Dussex, Nicolas
    et al.
    Tørresen, Ole K.
    van der Valk, Tom
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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 reindeer2023Ingår i: iScience, ISSN 2589-0042, Vol. 26, nr 10, s. 107811-107811, artikel-id 107811Artikel i tidskrift (Refereegranskat)
  • 9.
    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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  • 10.
    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.

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  • 11. 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)
  • 12. 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.

  • 13. Liu, S L
    et al.
    Westbury, M V
    Dussex, N
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Mitchell, K J
    Sinding, M H S
    Heintzman, P D
    Duchene, D A
    Kapp, J D
    von Seth, J
    Naturhistoriska riksmuseet.
    Heiniger, H
    Sanchez-Barreiro, F
    Margaryan, A
    Andre-Olsen, R
    De Cahsan, B
    Meng, G L
    Yang, C T
    Chen, L
    van der Valk, T
    Moodley, Y
    Rookmaaker, K
    Bruford, M W
    Ryder, O
    Steiner, C
    Bruins-van Sonsbeek, L G R
    Vartanyan, S
    Guo, C X
    Cooper, A
    Kosintsev, P
    Kirillova, I
    Lister, A M
    Marques-Bonet, T
    Gopalakrishnan, S
    Dunn, R R
    Lorenzen, E D
    Shapiro, B
    Zhang, G J
    Antoine, P O
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gilbert, M T P
    Ancient and modem genomes unravel the evolutionary history of the rhinoceros family2021Ingår i: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 184, nr 19, s. 4874-+Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 14.
    Lord, Edana
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Kierczak, Marcin
    Diez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ryder, Oliver A.
    Stanton, David W. G.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Gilbert, M. Thomas P.
    Sanchez-Barreiro, Fatima
    Zhang, Guojie
    Sinding, Mikkel-Holger S.
    Lorenzen, Eline D.
    Willerslev, Eske
    Protopopov, Albert
    Shidlovskiy, Fedor
    Fedorov, Sergey
    Bocherens, Herve
    Nathan, Senthilvel K. S. S.
    Goossens, Benoit
    van der Plicht, Johannes
    Chan, Yvonne L.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Prost, Stefan
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Potapova, Olga
    Kirillova, Irina
    Lister, Adrian M.
    Heintzman, Peter D.
    Kapp, Joshua D.
    Shapiro, Beth
    Vartanyan, Sergey
    Gotherstrom, Anders
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros2020Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 30, nr 19Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species’ extinction. Analysis of the nuclear genome from a similar to 18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bolling-Allerod interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.

    Ladda ner fulltext (pdf)
    fulltext
  • 15.
    Pecnerova, Patricia
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Diez-del-Molino, David
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Feuerborn, Tatiana
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    van der Plicht, Johannes
    Nikolskiy, Pavel
    Tikhonov, Alexei
    Vartanyan, Sergey
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth2017Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, nr 22, s. 3505-+Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 16.
    von Seth, J
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Dussex, N
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Diez-del-Molino, D
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    van der Valk, T
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    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
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations2021Ingår i: Nature Communications, E-ISSN 2041-1723, Vol. 12, nr 1Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
1 - 16 av 16
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