• 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 ...
    • Environmental DNA of aquatic macrophytes: The potential for reconstructing past and present vegetation and environments 

      Revéret, Aloïs Nicolas; Rijal, Dilli Prasad; Heintzman, Peter D.; Brown, Antony Gavin; Stoof-Leichsenring, Kathleen R.; Alsos, Inger Greve (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-07-29)
      1. Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments.<p> <p>2. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding ...
    • The era of reference genomes in conservation genomics 

      Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph; Ciofi, Claudio; Crottini, Angelica; Godoy, José A.; Höglund, Jacob; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah Alice; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Svardal, Hannes; Theofanopoulou, Constantina; de Vries, Jantina; Waldvogel, Ann-Marie; Zhang, Guojie; Mazzoni, Camila J.; Jarvis, Erich D.; Bálint, Miklós; Čiampor, Fedor; Aghayan, Sargis A.; Alioto, Tyler S.; Almudí, Isabel; Alvarez, Nadir; Alves, Paulo C.; Amorim, Isabel R.; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Berg, Paul Ragnar; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli-Alquati, Andrea; Boštjančić, Ljudevit L.; Boussau, Bastien; Breton, Catherine M.; Buzan, Elena; Campos, Paula F.; Carreras, Carlos; Castro, L. Filipe; Chueca, Luis J.; Conti, Elena; Cook-Deegan, Robert; Croll, Daniel; Cunha, Mónica V.; Delsuc, Frédéric; Dennis, Alice B.; Dimitrov, Dimitar; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Jakobsen, Kjetill Sigurd; Jentoft, Sissel; Matschiner, Michael (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-01-24)
      Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize ...
    • Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome 

      van der Valk, Tom; Dehasque, Marianne; Chacón-Duque, J. Camilo; Oskolkov, Nikolay; Vartanyan, Sergey; Heintzman, Peter D.; Pečnerová, Patrícia; Díez-del-Molino, David; Dalén, Love (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-08-01)
      Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and ...
    • 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 ...
    • High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change 

      Garces Pastor, Sandra; Alsos, Inger Greve; Coissac, Eric; Lavergne, Sébastien; Schwörer, Christoph; Theurillat, Jean-Paul; Heintzman, Peter D.; Wangensteen, Owen S.; Tinner, Willy; Rey, Fabian; Heer, Martina; Rutzer, Astrid; Walsh, Kevin; Lammers, Youri; Brown, Antony G.; Goslar, Tomasz; Rijal, Dilli P.; Karger, Dirk N.; Pellissier, Loïc; Heiri, Oliver (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-11-04)
      The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA ...
    • Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient DNA (sedaDNA) and pollen 

      Clarke, Charlotte; Edwards, Mary Elizabeth; Brown, Antony Gavin; Gielly, Ludovic; Lammers, Youri; Heintzman, Peter D.; Murguzur, Francisco Javier Ancin; Bråthen, Kari Anne; Goslar, Tomasz; Alsos, Inger Greve (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-10-30)
      We present a Holocene record of floristic diversity and environmental change for the central Varanger Peninsula, Finnmark, based on ancient DNA extracted from the sediments of a small lake (<i>sed</i>aDNA). The record covers the period c. 10 700 to 3300 cal. a BP and is complemented by pollen data. Measures of species richness, sample evenness and beta diversity were calculated based on <i>sed</i>aDNA ...
    • 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 ...
    • Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway 

      Brown, Antony; Rijal, Dilli Prasad; Heintzman, Peter D.; Clarke, Charlotte, L.; Blankholm, Hans Peter; Høeg, Helge I.; Lammers, Youri; Bråthen, Kari Anne; Edwards, M E; Alsos, Inger Greve (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-10-07)
      Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccagea ¯dgi, 70◦N) ...
    • Postglacial species arrival and diversity buildup of northern ecosystems took millennia 

      Alsos, Inger Greve; Rijal, Dilli Prasad; Ehrich, Dorothee; Karger, Dirk Nikolaus; Yoccoz, Nigel; Heintzman, Peter D.; Brown, Antony; Lammers, Youri; Pellissier, Loïc; Alm, Torbjørn; Bråthen, Kari Anne; Coissac, Eric; Merkel, Marie Føreid; Alberti, Adriana; Denoeud, France; Bakke, Jostein (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-09-28)
      What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, ...
    • Sedimentary ancient DNA reveals local vegetation changes driven by glacial activity and climate. 

      Elliott, Lucas Dane; Rijal, Dilli Prasad; Brown, Antony; Bakke, Jostein; Topstad, Lasse; Heintzman, Peter D.; Alsos, Inger Greve (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-01-07)
      Disentangling the effects of glaciers and climate on vegetation is complicated by the confounding role that climate plays in both systems. We reconstructed changes in vegetation occurring over the Holocene at Jøkelvatnet, a lake located directly downstream from the Langfjordjøkel glacier in northern Norway. We used a sedimentary ancient DNA (sedaDNA) metabarcoding dataset of 38 samples from a ...
    • The sedimentary ancient DNA workflow 

      Heintzman, Peter D.; Nota, Kevin; Rouillard, Alexandra; Lammers, Youri; Murchie, Tyler; Armbrecht, Linda; Garcés-Pastor, Sandra; Vernot, Benjamin (Chapter; Bokkapittel, 2023)
      Sedimentary ancient DNA (sedaDNA) is continuing to revolutionise our understanding of past biological and geological processes by retrieving and analysing the ancient DNA preserved in lake, cave, open terrestrial, midden, permafrozen, and marine environments (Crump, 2021). The study of sedaDNA began in the late 1990s (Coolen and Overmann, 1998) with the first reports of extinct animal sedaDNA in ...