Now showing items 21-40 of 73

    • A draft genome sequence of the elusive giant squid, Architeuthis dux 

      Da Fonseca, Rute R.; Couto, Alvarina; Machado, Andre M; Brejova, Brona; Albertin, Carolin B; Silva, Filipe; Gardner, Paul; Baril, Tobias; Hayward, Alex; Campos, Alexandre; Ribeiro, Ângela M; Barrio-Hernandez, Inigo; Hoving, Henk-Jan; Tafur-Jimenez, Ricardo; Chu, Chong; Frazão, Barbara; Petersen, Bent; Peñaloza, Fernando; Musacchia, Francesco; Alexander, Graham C; Osório, Hugo; Winkelmann, Inger; Simakov, Oleg; Rasmussen, Simon; Rahman, M. Ziaur; Pisani, Davide; Vinther, Jakob; Jarvis, Erich D.; Zhang, Guojie; Strugnell, Jan M.; Castro, L. Filipe C; Fedrigo, Olivier; Patricio, Mateus; Li, Qiye; Rocha, Sara; Antunes, Agostinho; Wu, Yufeng; Ma, Bin; Sanges, Remo; Vinar, Tomas; Blagoev, Blagoy; Sicheritz-Pontén, Thomas; Nielsen, Rasmus; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)
      Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the ...
    • Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny 

      Cappellini, Enrico; Welker, Frido; Pandolfi, Luca; Ramos-Madrigal, Jazmín; Samodova, Diana; Rüther, Patrick L.; Fotakis, Anna K.; Lyon, David; Moreno-Mayar, J. Víctor; Bukhsianidze, Maia; Jersie-Christensen, Rosa Rakownikow; Mackie, Meaghan; Ginolhac, Aurélien; Ferring, Reid; Tappen, Martha; Palkopoulou, Eleftheria; Dickinson, Marc R.; Stafford, Jr., Thomas W.; Chan, Yvonne L.; Götherström, Anders; Nathan, Senthilvel K.S.S.; Heintzman, Peter D.; Kapp, Joshua D.; Kirillova, Irina V.; Moodley, Yoshan; Agusti, Jordi; Kahlke, Ralf-Dietrich; Kiladze, Gocha; Martínez-Navarro, Bienvenido; Liu, Shanlin; Sandoval Velasco, Marcela; Sinding, Mikkel-Holger S.; Kelstrup, Christian D.; Allentoft, Morten E.; Orlando, Ludovic; Penkman, Kirsty; Shapiro, Beth; Rook, Lorenzo; Dalén, Love; Gilbert, Marcus Thomas Pius; Olsen, Jesper V.; Lordkipanidze, David; Willerslev, Eske (Journal article; Peer reviewed, 2019)
      The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its ...
    • eDNA-based biomonitoring at an experimental German vineyard to characterize how management regimes shape ecosystem diversity 

      Agerbo Rasmussen, Jacob; Nielsen, Martin; Mak, Sarah Siu Tze; Döring, Johanna; Klincke, Franziska; Gopalakrishnan, Shyam; Dunn, Robert R.; Kauer, Randolf; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2021)
      There is growing interest in the application of sustainable agricultural methods to minimize the environmental impact of farming and thus aiding quantification of the actual benefit that such approaches may confer. We ...
    • Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet 

      Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; de Manuel, Marc; Renom, Pere; Margaryan, Ashot; Stiller, Josefin; De-Dios, Toni; Fang, Qi; Feng, Shaohong; Mañosa, Santi; Pacheco, George; Ferrando-Bernal, Manuel; Shi, Guolin; Hao, Fei; Chen, Xianqing; Petersen, Bent; Olsen, Remi-André; Navarro, Arcadi; Deng, Yuan; Dalén, Love; Marques-Bonet, Tomas; Zhang, Guojie; Antunes, Agostinho; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles (Peer reviewed; Journal article, 2020)
      As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati ...
    • Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū 

      Niemann, Jonas; Gopalakrishnan, Shyam; Yamaguchi, Nobuyuki; Ramos-Madrigal, Jazmín; Wales, Nathan; Gilbert, Marcus Thomas Pius; Sinding, Mikkel-Holger S. (Peer reviewed; Journal article, 2021)
      The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was ...
    • Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches 

      Pereira, Cátia Lúcio; Gilbert, Marcus Thomas Pius; Araújo, Miguel B.; Matias, Miguel Graça (Peer reviewed; Journal article, 2021)
      Accurate quantification of biodiversity can be demanding and expensive. Although environmental DNA (eDNA) metabarcoding can facilitate biodiversity assessments through non-invasive, cost-efficient and rapid surveys, the ...
    • Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features 

      Seki, Ryohei; Li, Caí; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang; Xu, Luohao; Pan, Hailin; Kondo, Mao; Sato, Tomohiko; Matsubara, Haruka; Kamiyama, Namiko; Kitajima, Keiichi; Saito, Daisuke; Liu, Yang; Gilbert, Marcus Thomas Pius; Zhou, Qi; Xu, Xing; Shiroishi, Toshihiko; Irie, Naoki; Tamura, Koji; Zhang, Guojie (Journal article; Peer reviewed, 2017)
      Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous ...
    • Genetic affinities of an eradicated european plasmodium falciparum strain 

      De-Dios, Toni; van Dorp, Lucy; Gelabert, Pere; Carøe, Christian; Sandoval-Velasco, Marcela; Fregel, Rosa; Escosa, Raül; Aranda, Carles; Huijben, Silvie; Balloux, Francois; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles (Journal article; Peer reviewed, 2019)
      Malaria was present in most of Europe until the second half of the 20th century, when it was eradicated through a combination of increased surveillance and mosquito control strategies, together with cross-border and political ...
    • The genetic impact of an Ebola outbreak on a wild gorilla population 

      Fontsere, Claudia; Frandsen, Peter; Hernandez-Rodriguez, Jessica; Niemann, Jonas; Scharff-Olsen, Camilla Hjorth; Vallet, Dominique; Le Gouar, Pascaline; Ménard, Nelly; Navarro, Arcadi; Siegismund, Hans Redlef; Hvilsom, Christina; Gilbert, Marcus Thomas Pius; Kuhlwilm, Martin; Hughes, David; Marques-Bonet, Tomas (Peer reviewed; Journal article, 2021)
      Background Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the ...
    • Genetisk opphav til den norsksvenske ulvestammen (Canis lupus lupus) 

      Stenøien, Hans K.; Sun, Xin; Martin, Michael David; Scharff-Olsen, Camilla Hjorth; Alonso, Germán Hernàndez; Martins, Nuno Filipe Gomes; Lanigan, Liam T; Ciucani, Marta M.; Sinding, Mikkel-Holger S.; Gopalakrishnan, Shyam; Gilbert, Marcus Thomas Pius (NTNU Vitenskapsmuseet naturhistorisk rapport;, Research report, 2021)
      Den genetiske opprinnelsen til den norsk-svenske ulvebestanden har vært debattert helt siden den tilsynelatende ble reetablert på 1980-tallet. Det er stilt spørsmål om bestanden kan være nedstammet fra andre ulver enn de ...
    • The genome sequence of the grey wolf, Canis lupus Linnaeus 1758 

      Sinding, Mikkel-Holger S.; Gopalakrishnan, Shyam; Raundrup, Katrine; Dalén, Love; Threlfall, Jonathan; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2021)
      We present a genome assembly from an individual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf; Chordata; Mammalia; Carnivora; Canidae). The genome sequence is 2,447 megabases in span. The majority of ...
    • Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts 

      Rasmussen, Jacob A.; Villumsen, Kasper Rømer; Duchêne, David; Puetz, Lara; Delmont, Tom; Sveier, Harald; von Gersdorff Jørgensen, Louise; Præbel, Kim; Martin, Michael David; Bojesen, Anders Miki; Gilbert, Marcus Thomas Pius; Kristiansen, Karsten; Limborg, Morten T. (Peer reviewed; Journal article, 2021)
      Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite ...
    • Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages 

      Ramos-Madrigal, Jazmín; Sinding, Mikkel Holger Strander; Carøe, Christian; Mak, Sarah Siu Tze; Niemann, Jonas; Samaniego Castruita, José A.; Fedorov, Sergey; Kandyba, Alexander; Germonpré, Mietje; Bocherens, Hervé; Feuerborn, Tatiana R.; Pitulko, Vladimir V.; Pavlova, Elena Y.; Nikolskiy, Pavel A.; Kasparov, Aleksei K.; Ivanova, Varvara V.; Larson, Greger; Frantz, Laurent A.F.; Willerslev, Eske; Meldgaard, Morten; Petersen, Bent; Sicheritz-Pontén, Thomas; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam (Peer reviewed; Journal article, 2020)
      Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf ...
    • Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat, Homotherium latidens 

      Barnett, Ross; Westbury, Michael V; Sandoval-Velasco, Marcela; Vieira, Filipe G.; Jeon, Sungwon; Zazula, Grant; Martin, Michael David; Ho, Simon Y.W.; Mather, Niklas; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; de Manuel, Marc; Zepeda-Mendoza, Marie Lisandra; Antunes, Agostinho; Carmona Baez, Aldo; De Cahsan, Binia; Larson, Greger; O'Brien, Stephen J.; Eizirik, Eduardo; Johnson, Warren E.; Koepfli, Klaus-Peter; Wilting, Andreas; Fickel, Jörns; Dalén, Love; Lorenzen, Eline D.; Marques-Bonet, Tomas; Hansen, Anders J.; Zhang, Guojie; Bhak, Jong; Yamaguchi, Nobuyuki; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2020)
      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 ...
    • A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives 

      Westbury, Michael V; Barnett, Ross; Sandoval-Velasco, Marcela; Gower, Graham; Vieira, Filipe G.; de Manuel, Marc; Hansen, Anders J.; Yamaguchi, Nobuyuki; Werdelin, Lars; Marquès-Bonet, Tomás; Gilbert, Marcus Thomas Pius; Lorenzen, Eline D. (Peer reviewed; Journal article, 2021)
      Background: The evolutionary relationships of Felidae during their Early–Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is ...
    • Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations 

      von Seth, Johanna; Dussex, Nicolas; Díez-del-Molino, David; van der Valk, Tom; Kutschera, Verena E.; Kierczak, Marcin; Steiner, Cynthia C.; Liu, Shanlin; Gilbert, Marcus Thomas Pius; Sinding, Mikkel-Holger S.; Prost, Stefan; Guschanski, Katerina; Nathan, Senthilvel K. S. S.; Brace, Selina; Chan, Yvonne L.; Wheat, Christopher W.; Skoglund, Pontus; Ryder, Oliver A.; Goossens, Benoit; Götherström, Anders; Dalén, Love (Peer reviewed; Journal article, 2021)
      Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated ...
    • The germline mutational process in rhesus macaque and its implications for phylogenetic dating 

      Bergeron, Lucie A.; Besenbacher, Søren; Bakker, Jaco; Zheng, Jiao; Li, Panyi; Pacheco, George; Sinding, Mikkel-Holger S.; Kamilari, Maria; Gilbert, Marcus Thomas Pius; Schiedrup, Mikkel H.; Zhang, Guojie (Peer reviewed; Journal article, 2021)
      Background Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Results Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca ...
    • High-coverage genomes to elucidate the evolution of penguins 

      Pan, Hailin; Cole, Theresa L.; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao; Ksepka, Daniel T.; Hart, Tom; Bouzat, Juan L.; Argilla, Lisa S.; Bertelsen, Mads F.; Boersma, P. Dee; Bost, Charles-André; Cherel, Yves; Dann, Peter; Fiddaman, Steven R.; Howard, Pauline; Labuschagne, Kim; Mattern, Thomas; Miller, Gary; Parker, Patricia; Phillips, Richard A.; Quillfeldt, Petra; Ryan, Peter G.; Taylor, Helen; Thompson, David R.; Young, Melanie J.; Ellegaard, Martin; Gilbert, Marcus Thomas Pius; Sinding, Mikkel Holger Strander; Pacheco, George; Shepherd, Lara D.; Tennyson, Alan J.D.; Grosser, Stefanie; Kay, Emily; Nupen, Lisa J.; Ellenberg, Ursula; Houston, David M.; Reeve, Andrew Hart; Johnson, Kathryn; Masello, Juan F.; Stracke, Thomas; McKinlay, Bruce; Borboroglu, Pablo García; Zhang, De-Xing; Zhang, Guojie (Peer reviewed; Journal article, 2019)
      Background Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes ...
    • Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum) 

      Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès-Bonet, Tomás; Moodley, Yoshan; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)
      Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a ...
    • Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum) 

      Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès-Bonet, Tomás; Moodley, Yoshan; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)
      Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a ...