• 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Inference of natural selection from ancient DNA 

      Dehasque, Marianne; Ávila-Arcos, María C; Díez-del-Molino, David; Fumagalli, Matteo; Guschanski, Katerina; Lorenzen, Eline D.; Malaspinas, Anna-Sapfo; Marques-Bonet, Tomas; Martin, Michael David; Murray, Gemma G.R.; Papadopulos, Alexander; Therkildsen, Nina Overgaard; Wegmann, Daniel; Dalén, Love; Foote, Andrew (Peer reviewed; Journal article, 2020)
      Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral ...
    • Population genomics of grey wolves and wolf-like canids in North America 

      Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Vieira, Filipe G.; Samaniego, Jose A; Raundrup, Katrine; Heide Jørgensen, Mads Peter; Meldgaard, Morten; Petersen, Bent; Sicheritz-Ponten, Thomas; Mikkelsen, Johan Brus; Marquard-Petersen, Ulf; Dietz, Rune; Sonne, Christian; Dalén, Love; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2018)
      North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. ...
    • 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 ...
    • Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic 

      Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Hulme-Beaman, Ardern; Lebrasseur, Ophelie; Sinding, Mikkel Holger Strander; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; Bachmann, Lutz; Betts, Matthew; Britton, Kate; Darwent, John; Dietz, Rune; Fredholm, Merethe; Gopalakrishnan, Shyam; Goruinova, Olga I.; Grønnow, Bjarne; Haile, James; Hallsson, Jón Hallsteinn; Harrison, Ramona; Heide-Jørgensen, Mads-Peter; Knecht, Rick; Losey, Robert J.; Masson-MacLean, Edouard; McGovern, Thomas H.; McMagnus-Fry, Ellen; Meldgaard, Morten; Midtdal, Åslaug; Moss, Madonna L.; Nikitin, Iurii G.; Nomokonova, Tatiana; Palsdottir, Albina Hulda; Perri, Angela; Popov, Aleksandr N.; Rankin, Lisa; Reuther, Joshua D.; Sablin, Mikhail V.; Schmidt, Anne Lisbeth; Shirar, Scott; Smiarowski, Konrad; Sonne, Christian; Stiner, Mary C.; Vasyukov, Mitya; West, Catherine F.; Ween, Gro Birgit; Wennerberg, Sanne Eline; Wiig, Øystein; Woollett, James; Dalén, Love; Hansen, Anders J.; Gilbert, Marcus Thomas Pius; Sacks, Benjamin N; Frantz, Laurent A.F.; Larson, Greger; Dobney, Keith; Darwent, Christyann M.; Evin, Allowen (Journal article; Peer reviewed, 2019)
      Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but ...
    • The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics 

      Gopalakrishnan, Shyam; Samaniego Castruita, José Alfredo; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Räikkönen, Jannikke; Petersen, Bent; Sicheritz-Ponten, Thomas; Larson, Greger; Orlando, Ludovic; Marques-Bonet, Tomas; Hansen, Anders J.; Dalén, Love; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled ...