Browsing NTNU Open by Author "Gilbert, Marcus Thomas Pius"

Now showing items 21-40 of 106

    • Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum): a unique insight into the history of a precious endemic bird 

      Cavill, Emily L.; Gopalakrishnan, Shyam; Puetz, Lara C.; Ribeiro, Ângela M.; Mak, Sarah S. T.; da Fonseca, Rute R.; Pacheco, George; Dunlop, Bronwyn; Accouche, Wilna; Shah, Nirmal; Zora, Anna; Calabrese, Licia; Genner, Martin; Jones, Gareth; Guo, Chunxue; Zhang, Guojie; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)
      The Seychelles Magpie-Robin Copsychus sechellarum is an IUCN Red-List Endangered species endemic to the Seychelles, whose population was reduced to eight individuals on a single island in the 1960s. Translocations from the ...

    • Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing 

      Hernández-Alonso, Germán; Ramos-Madrigal, Jazmín; Sun, Xin; Scharff-Olsen, Camilla Hjorth; Sinding, Mikkel Holger Strander; Martins, Nuno F.; Ciucani, Marta Maria; Mak, Sarah S. T.; Lanigan, Liam Thomas; Clausen, Cecilie G.; Bhak, Jong; Jeon, Sungwon; Kim, Changjae; Eo, Kyung Yeon; Cho, Seong-Ho; Boldgiv, Bazartseren; Gantulga, Gankhuyag; Unudbayasgalan, Zunduibaatar; Kosintsev, Pavel A.; Stenøien, Hans Kristen; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam (Peer reviewed; Journal article, 2023)
      The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic ...

    • Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds 

      Pacheco, George; Van Grouw, Hein; Shapiro, Michael D.; Gilbert, Marcus Thomas Pius; Vieira, Filipe G. (Peer reviewed; Journal article, 2020)
      Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has ...

    • Demographic reconstruction from ancient DNA supports rapid extinction of the Great Auk 

      Thomas, Jessica E; Carvalho, Gary R.; James, Haile; Rawlence, Nicolas J.; Martin, Michael David; Ho, Simon Y.W.; Sigfússon, Arnór; Jósefsson, Vigfús A.; Frederiksen, Morten; Linnebjerg, Jannie F.; Castruita, Jose A. Samaniego; Niemann, Jonas; Sinding, Mikkel-Holger S.; Sandoval-Velasco, Marcela; Soares, André E.R.; Lacy, Robert; Barilaro, Christina; Best, Julia; Brandis, Dirk; Cavallo, Chiara; Elorza, Mikelo; Garrett, Kimball L; Groot, Maaike; Johansson, Friederike; Lifjeld, Jan Terje; Nilson, Göran; Serjeanston, Dale; Sweet, Paul; Fuller, Errol; Hufthammer, Anne Karin; Meldgaard, Morten; Fjeldså, Jon; Shapiro, Beth; Hofreiter, Michael; Gilbert, Marcus Thomas Pius; Knapp, Michael (Journal article; Peer reviewed, 2019)
      The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by ...

    • Dense sampling of bird diversity increases power of comparative genomics 

      Feng, Shaohong; 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-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel-Holger S.; Puetz, Lara; Cavill, Emily; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)
      Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures ...

    • Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria 

      Kieler, Ida Nordang; Osto, Melania; Hugentobler, Leoni; Puetz, Lara; Gilbert, Marcus Thomas Pius; Hansen, Torben; Pedersen, Oluf; Reusch, Claudia E.; Zini, Eric; Lutz, Thomas A.; Bjørnvad, Charlotte Reinhard (Peer reviewed; Journal article, 2019)
      Obesity and inactivity are major risk factors of feline diabetes mellitus (FDM) and human type II diabetes mellitus (T2DM). In recent years, changes in the gut microbiota have been suggested as a contributing factor to ...

    • Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome 

      Neves, Ricardo A. Cardoso; Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Gilbert, Marcus Thomas Pius; Møbjerg, Nadja (Peer reviewed; Journal article, 2022)
      Tardigrades are renowned for their extreme stress tolerance, which includes the ability to endure complete desiccation, high levels of radiation and very low sub-zero temperatures. Nevertheless, tardigrades appear to be ...

    • DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats 

      Alberdi, Antton; Razgour, Orly; Aizpurua, Ostaizka; Novella-Fernandez, Roberto; Aihartza, Joxerra; Budinski, Ivana; Garin, Inazio; Ibáñez, Carlos; Izagirre, Eñaut; Rebelo, Hugo; Russo, Danilo; Vlaschenko, Anton; Zhelyazkova, Violeta; Zrncic, Vida; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)
      Inferences of the interactions between species’ ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the ...

    • DNA-Based Arthropod Diversity Assessment in Amazonian Iron Mine Lands Show Ecological Succession Towards Undisturbed Reference Sites 

      Lynggaard, Christina; Yu, Douglas W.; Oliveira, Guilherme; Caldeira, Cecilio F.; Ramos, Silvio J.; Ellegaard, Martin; Gilbert, Marcus Thomas Pius; Gastauer, Markus; Bohmann, Kristine (Peer reviewed; Journal article, 2020)
      Human activities change natural landscapes, and in doing so endanger biodiversity and associated ecosystem services. To reduce the net impacts of these activities, such as mining, disturbed areas are rehabilitated and ...

    • 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 ...

    • The Earth BioGenome Project 2020: Starting the clock 

      Lewin, Harris A.; Richards, Stephen; Aiden, Erez Lieberman; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós; Barker, Katharine B.; Baumgartner, Bridget; Belov, Katherine; Bertorelle, Giorgio; Blaxter, Mark L.; Cai, Jing; Caperello, Nicolette D.; Carlson, Keith; Castilla-Rubio, Juan Carlos; Chaw, Shu-Miaw; Chen, Lei; Childers, Anna K.; Coddington, Jonathan A.; Conde, Dalia A.; Corominas, Montserrat; Crandall, Keith A.; Crawford, Andrew J.; DiPalma, Federica; Durbin, Richard; Ebenezer, ThankGod E.; Edwards, Scott V.; Fedrigo, Olivier; Flicek, Paul; Formenti, Giulio; Gibbs, Richard A.; Gilbert, Marcus Thomas Pius; Goldstein, Melissa M.; Graves, Jennifer Marshall; Greely, Henry T.; Grigoriev, Igor V.; Hackett, Kevin J.; Hall, Neil; Haussler, David; Helgen, Kristofer M.; Hogg, Carolyn J.; Isobe, Sachiko; Jakobsen, Kjetill Sigurd; Janke, Axel; Jarvis, Erich D.; Johnson, Warren E.; Jones, Steven J.M.; Karlsson, Elinor K.; Kersey, Paul J.; Kim, Jin-Hyoung; Kress, W. John; Kuraku, Shigehiro; Lawniczak, Mara K.N.; Leebens-Mack, James H.; Li, Xueyan; Lindblad-Toh, Kerstin; Liu, Xin; Lopez, Jose V.; Marques-Bonet, Tomas; Mazard, Sophie; Mazet, Jonna A.K.; Mazzoni, Camila J.; Myers, Eugene W.; O’Neill, Rachel J.; Paez, Sadye; Park, Hyun; Robinson, Gene E.; Roquet, Cristina; Ryder, Oliver A.; Sabir, Jamal S.M.; Shaffer, H. Bradley; Shank, Timothy M.; Sherkow, Jacob S.; Soltis, Pamela S.; Tang, Boping; Tedersoo, Leho; Uliano-Silva, Marcela; Wang, Kun; Wei, Xiaofeng; Wetzer, Regina; Wilson, Julia L.; Xu, Xun; Yang, Huanming; Yoder, Anne D.; Zhang, Guojie (Peer reviewed; Journal article, 2022)

    • 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 ...

    • Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals 

      Koziol, Adam; Odriozola, Iñaki; Nyholm, Lasse; Leonard, Aoife; San José, Carlos; Pauperio, Joana; Ferreira, Clara; Hansen, Anders J.; Aizpurua, Ostaizka; Gilbert, Marcus Thomas Pius; Alberdi, Antton (Journal article; Peer reviewed, 2022)

    • The era of reference genomes in conservation genomics 

      Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph; Ciofi, Claudio; Crottini, Angelica; Godoy, José A.; Höglund, Jacob; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah Alice; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Svardal, Hannes; Theofanopoulou, Constantina; de Vries, Jantina; Waldvogel, Ann-Marie; Zhang, Guojie; Mazzoni, Camila J.; Jarvis, Erich D.; Bálint, Miklós; Čiampor, Fedor; Aghayan, Sargis A.; Alioto, Tyler S.; Almudí, Isabel; Alvarez, Nadir; Alves, Paulo C.; Amorim, Isabel R.; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Berg, Paul Ragnar; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli-Alquati, Andrea; Boštjančić, Ljudevit L.; Boussau, Bastien; Breton, Catherine M.; Buzan, Elena; Campos, Paula F.; Carreras, Carlos; Castro, L. Filipe; Chueca, Luis J.; Conti, Elena; Cook-Deegan, Robert; Croll, Daniel; Cunha, Mónica V.; Delsuc, Frédéric; Dennis, Alice B.; Dimitrov, Dimitar; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Jakobsen, Kjetill Sigurd; Jentoft, Sissel; Matschiner, Michael (Peer reviewed; Journal article, 2022)
      Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique ...

    • Evolution of the germline mutation rate across vertebrates 

      Bergeron, Lucie A.; Besenbacher, Søren; Zheng, Jiao; Li, Panyi; Bertelsen, Mads Frost; Quintard, Benoit; Hoffman, Joseph I.; Li, Zhipeng; St. Leger, Judy; Shao, Changwei; Stiller, Josefin; Gilbert, Marcus Thomas Pius; Schierup, Mikkel H.; Zhang, Guojie (Peer reviewed; Journal article, 2023)
      The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single ...

    • 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 ...

    • The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs 

      Ciucani, Marta Maria; Ramos-Madrigal, Jazmín; Hernández-Alonso, Germán; Carmagnini, Alberto; Aninta, Sabhrina Gita; Sun, Xin; Scharff-Olsen, Camilla Hjorth; Lanigan, Liam Thomas; Fracasso, Ilaria; Clausen, Cecilie G.; Aspi, Jouni; Kojola, Ilpo; Baltrūnaitė, Laima; Balčiauskas, Linas; Moore, Jane; Åkesson, Mikael; Saarma, Urmas; Hindrikson, Maris; Hulva, Pavel; Bolfíková, Barbora Černá; Nowak, Carsten; Godinho, Raquel; Smith, Steve; Paule, Ladislav; Nowak, Sabina; Mysłajek, Robert W.; Lo Brutto, Sabrina; Ciucci, Paolo; Boitani, Luigi; Vernesi, Cristiano; Stenøien, Hans Kristen; Smith, Oliver; Frantz, Laurent; Rossi, Lorenzo; Angelici, Francesco Maria; Cilli, Elisabetta; Sinding, Mikkel Holger Strander; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam (Peer reviewed; Journal article, 2023)
      The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s–1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the ...

    • Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data 

      Aizpurua, Ostaizka; Dunn, Robert R.; Hansen, Lars H.; Gilbert, Marcus Thomas Pius; Alberdi, Antton (Peer reviewed; Journal article, 2023)
      Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required ...