• 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 (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-08-24)
      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 and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and ...
    • Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge 

      Vershinina, Alisa; Heintzman, Peter D.; Froese, Duane G.; Zazula, Grant D.; Cassatt-Johnstone, Molly; Dalén, Love; Der Sarkissian, Clio; Dunn, Shelby G.; Ermini, Luca; Gamba, Cristina; Groves, Pamela; Kapp, Joshua D.; Mann, Daniel H.; Seguin-Orlando, Andaine; Southon, John R.; Stiller, Mathias; Wooller, Matthew J.; Baryshnikov, Gennady; Gimranov, Dmitry; Scott, Eric; Hall, Elizabeth; Hewitson, Susan; Kirillova, Irina V.; Kosintsev, Pavel; Shidlovsky, Fedor; Tong, Hao-Wen; Tiunov, Mikhail P.; Vartanyan, Sergey; Orlando, Ludovic; Corbett-Detig, Russell B.; MacPhee, Ross D. E.; Shapiro, Beth (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-05-10)
      The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations ...
    • A detailed life history of a Pleistocene steppe bison (Bison priscus) skeleton unearthed in Arctic Alaska 

      Funck, Juliette; Heintzman, Peter D.; Murray, Gemma G.R.; Shapiro, Beth; McKinney, Holly; Huchet, Jean-Bernard; Bigelow, Nancy H; Druckenmiller, Patrick; Wooller, Matthew J. (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-10-12)
      Detailed paleoecological evidence from Arctic Alaska’s past megafauna can help reconstruct paleoenvironmental conditions and can illustrate ecological adaptation to varying environments. We examined a rare, largely articulated and almost complete skeleton of a steppe bison (<i>Bison priscus</i>) recently unearthed in Northern Alaska. We used a multi-proxy paleoecological approach to reconstruct the ...
    • 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 ...
    • Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age 

      Cahill, James A.; Heintzman, Peter D.; Harris, Kelley; Teasdale, Matthew D.; Kapp, Joshua D.; Soares, Andre, E. R.; Stirling, Ian; Bradley, Daniel; Edwards, Ceiridwen J.; Graim, Kiley; Kisleika, Aliaksandr A.; Malev, Alexander V.; Monaghan, Nigel; Green, Richard E.; Shapiro, Beth (Journal article; Tidsskriftartikkel, 2018-02-20)
      Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (<i>Ursus maritimus</i>) into Alaskan brown bears (<i>Ursus arctos</i>), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, frequency, and evolutionary significance ...
    • Million-year-old DNA sheds light on the genomic history of mammoths 

      van der Valk, Tom; Pečnerová, Patrícia; Díez-del-Molino, David; Bergström, Anders; Oppenheimer, Jonas; Hartmann, Stefanie; Xenikoudakis, Georgios; Thomas, Jessica A.; Dehasque, Marianne; Sağlıcan, Ekin; Rabia Fidan, Fatma; Barnes, Ian; Liu, Shanlin; Somel, Mehmet; Heintzman, Peter D.; Nikolskiy, Pavel; Shapiro, Beth; Skoglund, Pontus; Hofreiter, Michael; Lister, Adrian M.; Götherström, Anders; Dalén, Love (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-02-17)
      Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen ...
    • Minimizing polymerase biases in metabarcoding 

      Nichols, Ruth V.; Vollmers, Christopher; Newsom, Lee A.; Wang, Yue; Heintzman, Peter D.; Leighton, McKenna; Green, Richard E.; Shapiro, Beth (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-24)
      DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or “barcode,” from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as ...
    • Natural selection shaped the rise and fall of passenger pigeon genomic diversity 

      Murray, Gemma G.R.; Soares, André E.R.; Novak, Ben J.; Schaefer, Nathan K.; Cahill, James A.; Baker, Allan J.; Demboski, John R.; Doll, Andrew; Da Fonseca, Rute R.; Fulton, Tara L.; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Letts, Brandon; McIntosh, George; O'Connell, Brendan L.; Peck, Mark; Pipes, Marie-Lorraine; Rice, Edward S.; Santos, Kathryn M.; Sohrweide, A. Gregory; Vohr, Samuel H.; Corbett-Detig, Russell B.; Green, Richard E.; Shapiro, Beth (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-11-17)
      The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are ...
    • A new genus of horse from Pleistocene North America 

      Heintzman, Peter D.; Zazula, Grant D.; MacPhee, Ross D. E.; Scott, Eric; Cahill, James A.; McHorse, Brianna K.; Kapp, Joshua D.; Stiller, Mathias; Wooller, Matthew J.; Orlando, Ludovic; Southon, John R.; Froese, Duane G.; Shapiro, Beth (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-11-28)
      The extinct ‘New World stilt-legged’, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear ...
    • 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 ...