Blar i NTNU Open på forfatter "Sinding, Mikkel-Holger S."
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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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos
Sinding, Mikkel-Holger S.; Ciucani, Marta M.; Ramos-Madrigal, Jazmín; Carmagnini, Alberto; Rasmussen, Jacob A.; Feng, Shaohong; Chen, Guangji; Vieira, Filipe G.; Mattiangeli, Valeria; Ganjoo, Rajinder K.; Larson, Greger; Sicheritz-Pontén, Thomas; Petersen, Bent; Frantz, Laurent A.F.; Gilbert, Marcus Thomas Pius; Bradley, Daniel G. (Peer reviewed; Journal article, 2021)The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely ... -
Pre-extinction demographic stability and genomic signatures of adaptation in the woolly rhinoceros
Lord, Edana; Dussex, Nicolas; Kierczak, Marcin; Díez-del-Molino, David; Ryder, Oliver A.; Stanton, David W. G.; Gilbert, Marcus Thomas Pius; Sánchez-Barreiro, Fatima; Zhang, Guojie; Sinding, Mikkel-Holger S.; Lorenzen, Eline D.; Willerslev, Eske; Protopov, Albert; Shidlovskiy, Fedor K.; Fedorov, Sergey; Bocherens, Hervé; Nathan, Senthilvel K.S.S.; Goossens, Benoit; Johannes, van der Plicht; Chan, Yvonne L.; Prost, Stefan; Potapova, Olga R; Kirillova, Irina V.; Lister, Adrian M.; Heintzman, Peter D.; Kapp, Joshua D.; Shapiro, Beth; Vartanyan, Sergey; Götherström, Anders; Dalén, Love (Peer reviewed; Journal article, 2020)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 ... -
Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences
Hernández-Alonso, Germán; Ramos-Madrigal, Jazmín; van Grouw, Hein; Ciucani, MartaMaria; Cavill, Emily Louisa; Sinding, Mikkel-Holger S.; Gopalakrishnan, Shyam; Pacheco, George; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2023)The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, ...