• A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA 

      Kjær, Kurt H.; Winther Pedersen, Mikkel; De Sanctis, Bianca; De Cahsan, Binia; Korneliussen, Thorfinn S.; Michelsen, Christian S.; Sand, Karina K.; Jelavić, Stanislav; Ruter, Anthony H.; Schmidt, Astrid M. A.; Kjeldsen, Kristian K.; Tesakov, Alexey S.; Snowball, Ian; Gosse, John C.; Alsos, Inger Greve; Wang, Yucheng; Dockter, Christoph; Rasmussen, Magnus; Jørgensen, Morten E.; Skadhauge, Birgitte; Prohaska, Ana; Kristensen, Jeppe Å.; Bjerager, Morten; Allentoft, Morten E.; Coissac, Eric; Rouillard, Alexandra; Simakova, Alexandra; Fernandez-Guerra, Antonio; Bowler, Chris; Macias-Fauria, Marc; Vinner, Lasse; Welch, John J.; Hidy, Alan J.; Sikora, Martin; Collins, Matthew J.; Durbin, Richard; Larsen, Nicolaj K.; Willerslev, Eske (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-12-07)
      Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago had climates resembling those forecasted under future warming. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare. Here we report an ancient ...
    • 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; Tidsskriftartikkel; Peer reviewed, 2019-09-11)
      The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa. However, the irreversible post-mortem degradation of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr). By contrast, tandem mass spectrometry has enabled the sequencing of approximately ...
    • Environmental genomics of Late Pleistocene black bears and giant short-faced bears 

      Pedersen, Mikkel W.; De Sanctis, Bianca; Saremi, Nedda F.; Sikora, Martin; Puckett, Emily E.; Gu, Zhenquan; Moon, Katherine L.; Kapp, Joshua D.; Vinner, Lasse; Vardanyan, Zaruhi; Ardelean, Ciprian F.; Arroyo-Cabrales, Joaquin; Cahill, James A.; Heintzman, Peter D.; Zazula, Grant D.; MacPhee, Ross D. E.; Shapiro, Beth; Durbin, Richard; Willerslev, Eske (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-04-19)
      Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1, 2, 3 by allowing for parallel sequencing of DNA from all trophic levels.4, 5, 6, 7, 8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far ...
    • Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations 

      Capo, Eric; Giguet-Covex, Charline; Rouillard, Alexandra; Nota, Kevin; Heintzman, Peter D.; Vuillemin, Aurèle; Ariztegui, Daniel; Arnaud, Fabien; Belle, Simon; Bertilsson, Stefan; Bigler, Christian; Bindler, Richard; Brown, Antony G.; Clarke, Charlotte L.; Crump, Sarah E.; Debroas, Didier; Englund, Göran; Ficetola, Gentile Francesco; Garner, Rebecca E.; Gauthier, Joanna; Gregory-Eaves, Irene; Heinecke, Liv; Herzschuh, Ulrike; Ibrahim, Anan; Kisand, Veljo; Kjær, Kurt H.; Lammers, Youri; Littlefair, Joanne; Messager, Erwan; Monchamp, Marie-Eve; Olajos, Fredrik; Orsi, William; Pedersen, Mikkel W.; Rijal, Dilli P.; Rydberg, Johan; Spanbauer, Trisha; Stoof-Leichsenring, Kathleen R.; Taberlet, Pierre; Talas, Liisi; Thomas, Camille; Walsh, David A.; Wang, Yucheng; Willerslev, Eske; van Woerkom, Anne; Zimmermann, Heike H.; Coolen, Marco J. L.; Epp, Laura S.; Domaizon, Isabelle; Alsos, Inger G.; Parducci, Laura (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-02-13)
      The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original ...
    • Late Quaternary dynamics of Arctic biota from ancient environmental genomics 

      Wang, Yucheng; Pedersen, Mikkel W.; Alsos, Inger Greve; De Sanctis, Bianca; Racimo, Fernando; Prohaska, Ana; Coissac, Eric; Owens, Hannah L.; Merkel, Marie Føreid; Fernandez-Guerra, Antonio; Rouillard, Alexandra; Lammers, Youri; Alberti, Adriana; Denoeud, France; Money, Daniel; Ruter, Anthony H.; McColl, Hugh; Larsen, Nicolaj K.; Cherezova, Anna A.; Edwards, Mary E.; Fedorov, Grigory B.; Haile, James; Orlando, Ludovic; Vinner, Lasse; Korneliussen, Thorfinn S.; Beilman, David W.; Bjørk, Anders A.; Cao, Jialu; Dockter, Christoph; Esdale, Julie; Gusarova, Galina; Kjeldsen, Kristian K.; Mangerud, Jan; Rasic, Jeffrey T.; Skadhauge, Birgitte; Svendsen, John Inge; Tikhonov, Alexei N.; Wincker, Patrick; Xing, Yingchun; Zhang, Yubin; Froese, Duane G.; Rahbek, Carsten; Nogues, David B; Holden, Philip B.; Edwards, Neil R.; Durbin, Richard; Meltzer, David J.; Kjær, Kurt H.; Moller, Per; Willerslev, Eske (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-10-20)
      During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1,2,3,4,5,6,7,8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. ...
    • 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; van der Plicht, Johannes; 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 (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-08-13)
      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 prior to extinction. The woolly rhinoceros (<i>Coelodonta antiquitatis</i>) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene ...
    • Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms 

      Harms, Klaus; Lunnan, Asbjørn; Hulter, Nils; Mourier, Tobias; Vinner, Lasse; Andam, Cheryl P; Marttinen, Pekka; Fridholm, Helena; Hansen, Anders Johannes; Hanage, William P; Nielsen, Kaare Magne; Willerslev, Eske; Johnsen, Pål Jarle (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-12-27)
      In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by ...