• 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 ...
    • 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 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 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • The genetic history of Scandinavia from the Roman Iron Age to the present 

      Rodriguez-Varela, Ricardo; Moore, Kristjan H.S.; Ebenesersdottir, Sunna; Kilinc, Gulsah; Kjellström, Anna; Papmehl-Dufay, Ludvig; Alfsdotter, Clara; Berglund, Birgitta; Alrawi, Loey; Kashuba, Natlija; Sobrado, Veronica; Lagerholm, Vendela Kempe; Gilbert, Edmund; Cavalleri, Gianpiero L.; Hovig, Eivind; Kockum, Ingrid; Olsson, Tomas; Alfredsson, Lars; Hansen, Thomas F.; Werge, Thomas; Munters, Arielle R.; Bernhardsson, Carolina; Skar, Birgitte; Christophersen, Axel; Turner-Walker, Gordon; Gopalakrishnan, Shyam; Daskalaki, Evangelia; Omrak, Ayca; Perez-Ramallo, Patxi; Skoglund, Pontus; Girdland-Flink, Linus; Gunnarsson, Fredrik; Hedenstierna-Jonson, Charlotte; Gilbert, Marcus Thomas Pius; Lidén, Kerstin; Jakobsson, Mattias; Einarsson, Lars Petter; Victor, Helena; Krzewinska, Maja; Zachrisson, Torun; Storå, Jan; Stefánsson, Kári; Helgason, Agnar; Götherström, Anders (Peer reviewed; Journal article, 2023)
      We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation ...
    • 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 ...
    • 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 ...
    • Grey wolf genomic history reveals a dual ancestry of dogs 

      Bergström, Anders; Stanton, David W. G.; Taron, Ulrike H.; Frantz, Laurent; Sinding, Mikkel Holger Strander; Ersmark, Erik; Pfrengle, Saskia; Cassatt-Johnstone, Molly; Lebrasseur, Ophélie; Girdland-Flink, Linus; Fernandes, Daniel M.; Ollivier, Morgane; Speidel, Leo; Gopalakrishnan, Shyam; Westbury, Michael V.; Ramos-Madrigal, Jazmin; Feuerborn, Tatiana R.; Reiter, Ella; Gretzinger, Joscha; Münzel, Susanne C.; Swali, Pooja; Conard, Nicholas J.; Carøe, Christian; Haile, James; Linderholm, Anna; Androsov, Semyon; Barnes, Ian; Baumann, Chris; Benecke, Norbert; Bocherens, Hervé; Brace, Selina; Carden, Ruth F.; Drucker, Dorothée G.; Fedorov, Sergey; Gasparik, Mihály; Germonpré, Mietje; Grigoriev, Semyon; Groves, Pam; Hertwig, Stefan T.; Ivanova, Varvara V.; Janssens, Luc; Jennings, Richard P.; Kasparov, Aleksei K.; Kirillova, Irina V.; Kurmaniyazov, Islam; Kuzmin, Yaroslav V.; Kosintsev, Pavel A.; Lázničková-Galetová, Martina; Leduc, Charlotte; Nikolskiy, Pavel; Nussbaumer, Marc; O’Drisceoil, Cóilín; Orlando, Ludovic; Outram, Alan; Pavlova, Elena Y.; Perri, Angela R.; Pilot, Małgorzata; Pitulko, Vladimir V.; Plotnikov, Valerii V.; Protopopov, Albert V.; Rehazek, André; Sablin, Mikhail; Seguin-Orlando, Andaine; Storå, Jan; Verjux, Christian; Zaibert, Victor F.; Zazula, Grant; Crombé, Philippe; Hansen, Anders J.; Willerslev, Eske; Leonard, Jennifer A.; Götherström, Anders; Pinhasi, Ron; Schuenemann, Verena J.; Hofreiter, Michael; Gilbert, Marcus Thomas Pius; Shapiro, Beth; Larson, Greger; Krause, Johannes; Dalén, Love; Skoglund, Pontus (Peer reviewed; Journal article, 2022)
      The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, ...
    • 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 ...
    • Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research 

      Nyholm, Lasse; Koziol, Adam; Marcos, Sofia; Botnen, Amanda Bolt; Aizpurua, Ostaizka; Gopalakrishnan, Shyam; Limborg, Morten T.; Gilbert, Marcus Thomas Pius; Alberdi, Antton (Peer reviewed; Journal article, 2020)
      From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions ...
    • Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark 

      Margaryan, Ashot; Noer, Christina Lehmkuhl; Richter, Stine R.; Restrup, Marlene Elise; Bülow-Hansen, Julie Lee; Leerhøi, Frederik; Langkjær, Emilia Marie Rolander; Gopalakrishnan, Shyam; Carøe, Christian; Gilbert, Marcus Thomas Pius; Bohmann, Kristine (Peer reviewed; Journal article, 2021)
      Biodiversity monitoring projects using environmental DNA techniques are becoming increasingly widespread. However, these techniques depend heavily on the quality and richness of the available DNA reference database against ...