Quaternary (Feb 2021)
Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
- Eric Capo,
- Charline Giguet-Covex,
- Alexandra Rouillard,
- Kevin Nota,
- Peter D. Heintzman,
- Aurèle Vuillemin,
- Daniel Ariztegui,
- Fabien Arnaud,
- Simon Belle,
- Stefan Bertilsson,
- Christian Bigler,
- Richard Bindler,
- Antony G. Brown,
- Charlotte L. Clarke,
- Sarah E. Crump,
- Didier Debroas,
- Göran Englund,
- Gentile Francesco Ficetola,
- Rebecca E. Garner,
- Joanna Gauthier,
- Irene Gregory-Eaves,
- Liv Heinecke,
- Ulrike Herzschuh,
- Anan Ibrahim,
- Veljo Kisand,
- Kurt H. Kjær,
- Youri Lammers,
- Joanne Littlefair,
- Erwan Messager,
- Marie-Eve Monchamp,
- Fredrik Olajos,
- William Orsi,
- Mikkel W. Pedersen,
- Dilli P. Rijal,
- Johan Rydberg,
- Trisha Spanbauer,
- Kathleen R. Stoof-Leichsenring,
- Pierre Taberlet,
- Liisi Talas,
- Camille Thomas,
- David A. Walsh,
- Yucheng Wang,
- Eske Willerslev,
- Anne van Woerkom,
- Heike H. Zimmermann,
- Marco J. L. Coolen,
- Laura S. Epp,
- Isabelle Domaizon,
- Inger G. Alsos,
- Laura Parducci
Affiliations
- Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- Charline Giguet-Covex
- Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, France
- Alexandra Rouillard
- Department of Geosciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway
- Kevin Nota
- Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
- Peter D. Heintzman
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Aurèle Vuillemin
- Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, Germany
- Daniel Ariztegui
- Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland
- Fabien Arnaud
- Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, France
- Simon Belle
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Christian Bigler
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- Richard Bindler
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- Antony G. Brown
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Charlotte L. Clarke
- School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
- Sarah E. Crump
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO 80309, USA
- Didier Debroas
- LMGE, UMR CNRS 6023, University Clermont Auvergne, 63000 Clermont-Ferrand, France
- Göran Englund
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, 20122 Milan, Italy
- Rebecca E. Garner
- Department of Biology, Concordia University, Montréal, QC H3G 1M8, Canada
- Joanna Gauthier
- Groupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, Canada
- Irene Gregory-Eaves
- Groupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, Canada
- Liv Heinecke
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, Germany
- Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, Germany
- Anan Ibrahim
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
- Veljo Kisand
- Institute of Technology, University of Tartu, 50090 Tartu, Estonia
- Kurt H. Kjær
- Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
- Youri Lammers
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Joanne Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
- Erwan Messager
- Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, France
- Marie-Eve Monchamp
- Groupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, Canada
- Fredrik Olajos
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- William Orsi
- Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, Germany
- Mikkel W. Pedersen
- Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
- Dilli P. Rijal
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Johan Rydberg
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- Trisha Spanbauer
- Department of Environmental Sciences and Lake Erie Center, University of Toledo, Toledo, OH 43606, USA
- Kathleen R. Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, Germany
- Pierre Taberlet
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Liisi Talas
- Institute of Technology, University of Tartu, 50090 Tartu, Estonia
- Camille Thomas
- Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland
- David A. Walsh
- Department of Biology, Concordia University, Montréal, QC H3G 1M8, Canada
- Yucheng Wang
- Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
- Eske Willerslev
- Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
- Anne van Woerkom
- Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
- Heike H. Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, Germany
- Marco J. L. Coolen
- Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley 6102, Australia
- Laura S. Epp
- Limnological Institute, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
- Isabelle Domaizon
- INRAE, University Savoie Mont Blanc, CARRTEL, 74200 Thonon les bains, France
- Inger G. Alsos
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Laura Parducci
- Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
- DOI
- https://doi.org/10.3390/quat4010006
- Journal volume & issue
-
Vol. 4,
no. 1
p. 6
Abstract
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 case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
Keywords
