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

Now showing items 1-20 of 106

    • A 5700 year-old human genome and oral microbiome from chewed birch pitch 

      Jensen, Theis Zetner Trolle; Niemann, Jonas; Iversen, Katrine Højholt; Fotakis, Anna K.; Gopalakrishnan, Shyam; Vågene, Åshild J; Pedersen, Mikkel Winther; Sinding, Mikkel-Holger S.; Ellegaard, Martin R; Allentoft, Morten E.; Lanigan, Liam T; Taurozzi, Alberto J; Nielsen, Sofie Holtsmark; Dee, Michael W; Mortensen, Martin; Christensen, Mads C; Sørensen, Søren; Collins, Matthew J; Gilbert, Marcus Thomas Pius; Sikora, Martin; Rasmussen, Simon; Schroeder, Hannes (Peer reviewed; Journal article, 2019)
      The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancienthuman genome and oral microbiome sequenced ...

    • An expanded mammal mitogenome dataset from Southeast Asia 

      Salleh, Faezah Mohd; Ramos-Madrigal, Jazmín; Peñaloza, Fernando; Liu, Shanlin; Sinding, Mikkel Holger Strander; Patel, Riddhi P.; Martins, Renata; Lenz, Dorina; Fickel, Jörns; Roos, Christian; Shamsir, Mohd Shahir; Azman, Mohammad Shahfiz; Lim, Burton K.; Rossiter, Stephen J.; Wilting, Andreas; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing ...

    • An ‛Aukward’ tale: a genetic approach to discover the whereabouts of the last Great Auks 

      Thomas, Jessica E; Carvalho, Gary R.; Haile, James; Martin, Michael David; Castruita, Jose A. Samaniego; Niemann, Jonas; Sinding, Mikkel Holger Strander; Sandoval-Velasco, Marcela; Rawlence, Nicolas J.; Fuller, Errol; Fjeldså, Jon; Hofreiter, Michael; Stewart, John R; Gilbert, Marcus Thomas Pius; Knapp, Michael (Journal article; Peer reviewed, 2017)
      One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the ...

    • The ancestry and geographical origins of St Helena's liberated Africans 

      Sandoval-Velasco, Marcela; Jagadeesan, Anuradha; Ramos-Madrigal, Jazmín; Ávila-Arcos, María C.; Fortes-Lima, Cesar A.; Watson, Judy; Johannesdóttir, Erna; Cruz-Dávalos, Diana I.; Gopalakrishnan, Shyam; Moreno-Mayar, J. Víctor; Niemann, Jonas; Renaud, Gabriel; Robson Brown, Katharine A.; Bennett, Helena; Pearson, Andrew; Helgason, Agnar; Gilbert, Marcus Thomas Pius; Schroeder, Hannes (Peer reviewed; Journal article, 2023)
      The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception ...

    • Ancient and historical DNA in conservation policy 

      Jensen, Evelyn L.; Díez-del-Molino, David; Gilbert, Marcus Thomas Pius; Bertola, Laura D.; Borges, Filipa; Cubric-Curik, Vlatka; de Navascués, Miguel; Frandsen, Peter; Heuertz, Myriam; Hvilsom, Christina; Jiménez-Mena, Belén; Miettinen, Antti; Moest, Markus; Pečnerová, Patrícia; Barnes, Ian; Vernesi, Cristiano (Peer reviewed; Journal article, 2022)
      Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even ...

    • Ancient and modern genomes unravel the evolutionary history of the rhinoceros family 

      Liu, Shanlin; Westbury, Michael V; Dussex, Nicolas; Mitchell, Kieren J.; Sinding, Mikkel-Holger S.; Heintzman, Peter D.; Duchêne, David A.; Kapp, Joshua D.; von Seth, Johanna; Heiniger, Holly; Sánchez-Barreiro, Fatima; Margaryan, Ashot; André-Olsen, Remi; De Cahsan, Binia; Meng, Guanliang; Yang, Chentao; Chen, Lei; van der Valk, Tom; Moodley, Yoshan; Rookmaaker, Kees; Bruford, Michael W.; Ryder, Oliver; Steiner, Cynthia; Bruins-van Sonsbeek, Linda G. R.; Vartanyan, Sergey; Guo, Chunxue; Cooper, Alan; Kosintsev, Pavel; Kirillova, Irina V.; Lister, Adrian M.; Marques-Bonet, Tomas; Gopalakrishnan, Shyam; Dunn, Robert R.; Lorenzen, Eline D.; Shapiro, Beth; Zhang, Guojie; Antoine, Pierre-Olivier; Dalén, Love; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2021)
      Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct ...

    • Ancient and modern stickleback genomes reveal the demographic constraints on adaptation 

      Kirch, Melanie; Romundset, Anders; Gilbert, Marcus Thomas Pius; Jones, Felicity C.; Foote, Andrew (Peer reviewed; Journal article, 2021)
      Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it ...

    • Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage 

      Cohen, Pnina; Bacilieri, Roberto; Ramos-Madrigal, Jazmín; Privman, Eyal; Boaretto, Elisabetta; Weber, Audrey; Fuks, Daniel; Weiss, Ehud; Erickson-Gini, Tali; Bucking, Scott; Tepper, Yotam; Cvikel, Deborah; Schmidt, Joshua; Gilbert, Marcus Thomas Pius; Wales, Nathan; Bar-Oz, Guy; Meiri, Meirav (Peer reviewed; Journal article, 2023)
      Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. ...

    • Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement 

      Wales, Nathan; Akman, Melis; Watson, Ray H B; Sánchez Barreiro, Fatima; Smith, Bruce D; Gremillion, Kristen J; Gilbert, Marcus Thomas Pius; Blackman, Benjamin K (Journal article; Peer reviewed, 2019)
      Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient ...

    • Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia 

      Loog, Liisa; Thalmann, Olaf; Sinding, Mikkel Holger Strander; Schuenemann, Verena J.; Perri, Angela; Germonpré, Mietje; Bocherens, Herve; Witt, Kelsey E.; Samaniego Castruita, José Alfredo; Velasco, Marcela Sandoval; Lundstrøm, Inge K.C.; Wales, Nathan; Sonet, Gontran; Frantz, Laurent; Schroeder, Hannes; Budd, Jane; Jimenez, Elodie-Laure; Fedorov, Sergey; Gasparyan, Boris; Kandel, Andrew W.; Lázničková-Galetová, Martina; Napierala, Hannes; Uerpmann, Hans-Peter; Nikolskiy, Pavel A.; Pavlova, Elena Y.; Pitulko, Vladimir V.; Herzig, Karl-Heinz; Malhi, Ripan S.; Willerslev, Eske; Hansen, Anders J.; Dobney, Keith; Gilbert, Marcus Thomas Pius; Krause, Johannes; Larson, Greger; Eriksson, Anders; Manica, Andrea (Journal article; Peer reviewed, 2019)
      Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies ...

    • Ancient genomes from Iceland reveal the making of a human population 

      Ebenesersdóttir, Sigríður Sunna; Sandoval-Velasco, Marcela; Gunnarsdóttir, Ellen D.; Jagadeesan, Anuradha; Guðmundsdóttir, Valdís B.; Thordardóttir, Elísabet L.; Einarsdóttir, Margrét S.; Moore, Kristjan H. S.; Sigurðsson, Ásgeir; Magnúsdóttir, Droplaug N.; Jónsson, Hákon; Snorradóttir, Steinunn; Hovig, Eivind; Møller, Pål; Kockum, Ingrid; Olsson, Tomas; Alfredsson, Lars; Hansen, Thomas F.; Werge, Thomas; Cavalleri, Gianpiero L.; Gilbert, Edmund; Lalueza-Fox, Carles; Walser III, Joe W.; Kristjánsdóttir, Steinunn; Gopalakrishnan, Shyam; Arnadottir, Lilja; Magnússon, Ólafur Þ.; Gilbert, Marcus Thomas Pius; Stefánsson, Kári; Helgason, Agnar (Journal article; Peer reviewed, 2018)
      Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of ...

    • Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene 

      Fromm, Bastian; Tarbier, Marcel; Smith, Oliver; Mármol-Sánchez, Emilio; Dalén, Love; Gilbert, Marcus Thomas Pius; Friedländer, Marc R. (Peer reviewed; Journal article, 2021)
      DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular ...

    • Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival 

      Smith, Oliver; Dunshea, Glenn; Sinding, Mikkel-Holger; Fedorov, Sergey; Germonpre, Mietje; Bocherens, Hervé; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2019)
      While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. ...

    • Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic 

      Patrono, Livia V.; Vrancken, Bram; Budt, Matthias; Düx, Ariane; Lequime, Sebastian; Boral, Sengül; Gilbert, Marcus Thomas Pius; Gogarten, Jan F.; Hoffmann, Luisa; Horst, David; Merkel, Kevin; Morens, David; Prepoint, Baptiste; Schlotterbeck, Jasmin; Schuenemann, Verena J.; Suchard, Marc A.; Taubenberger, Jeffery K.; Tenkhoff, Luisa; Urban, Christian; Widulin, Navena; Winter, Eduard; Worobey, Michael; Schnalke, Thomas; Wolff, Thorsten; Lemey, Philippe; Calvignac-Spencer, Sébastien (Peer reviewed; Journal article, 2022)
      The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from ...

    • Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact 

      Rasmussen, Linett; Fontsere, Claudia; Soto-Calderón, Iván D.; Guillen, Rosamira; Savage, Anne; Hansen, Anders Johannes; Hvilsom, Christina; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2023)
      During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic ...

    • The Australian dingo is an early offshoot of modern breed dogs 

      Field, Matt A.; Yadav, Sonu; Dudchenko, Olga; Esvaran, Meera; Rosen, Benjamin D.; Skvortsova, Ksenia; Edwards, Richard J.; Keilwagen, Jens; Cochran, Blake J.; Manandhar, Bikash; Bustamante, Sonia; Rasmussen, Jacob Agerbo; Melvin, Richard G.; Chernoff, Barry; Omer, Arina; Colaric, Zane; Chan, Eva K.F.; Minoche, Andre E.; Smith, Timothy P.L.; Gilbert, Marcus Thomas Pius; Bogdanovic, Ozren; Zammit, Robert A.; Thomas, Torsten; Aiden, Erez L.; Ballard, J. William O. (Journal article; Peer reviewed, 2022)

    • Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification 

      Bohmann, Kristine; Mirarab, Siavash; Bafna, Vineet; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)
      Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I ...

    • Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community 

      Eriksen, Anne Marie Høier; Nielsen, Tue Kjærgaard; Matthiesen, Henning; Carøe, Christian; Hansen, Lars Hestbjerg; Gregory, David John; Turner-Walker, Gordon; Collins, Matthew James; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)
      Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their ...

    • Co-diversification of an intestinal Mycoplasma and its salmonid host 

      Rasmussen, Jacob A.; Kiilerich, Pia; Madhun, Abdullah Sami; Waagbø, Rune; Lock, Erik Jan Robert; Madsen, Lise; Gilbert, Marcus Thomas Pius; Kristiansen, Karsten; Limborg, Morten T. (Peer reviewed; Journal article, 2023)
      Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably ...

    • Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing 

      Mak, Sarah S.T.; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G.; Germonpre, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant ...