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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

1
Department of Ecology and Environmental Science, Umeå University, Umeå 90736, Sweden
2
Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, France
3
Department of Geosciences, UiT the Arctic University of Norway, 9019 Tromsø, Norway
4
Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
5
Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
6
The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Norway
7
Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, Germany
8
GeoBio-Center LMU, Ludwig-Maximilians-Universität München, 80331 Munich, Germany
9
Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland
10
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
11
School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
12
Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO 80309, USA
13
LMGE, UMR CNRS 6023, University Clermont Auvergne, 63000 Clermont-Ferrand, France
14
Department of Environmental Science and Policy, University of Milan, 20122 Milan, Italy
15
Laboratoire d’Écologie Alpine (LECA), University Grenoble Alpes, CNRS, F-38000 Grenoble, France
16
Department of Biology, Concordia University, Montréal, QC H3G 1M8, Canada
17
Groupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, Canada
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Department of Biology, University McGill, Montréal, QC H3A 0G4, Canada
19
Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, Germany
20
Institute for Mathematics, University of Potsdam, 14469 Potsdam, Germany
21
Institute for Environmental Sciences and Geography, University of Potsdam, 14469 Potsdam, Germany
22
Department of Biology, University of Konstanz, 78464 Konstanz, Germany
23
Institute of Technology, University of Tartu, 50090 Tartu, Estonia
24
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
25
Department of Environmental Sciences and Lake Erie Center, University of Toledo, Toledo, OH 43606, USA
26
Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK
27
Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley 6102, Australia
28
Limnological Institute, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
29
INRAE, University Savoie Mont Blanc, CARRTEL, 74200 Thonon les bains, France
30
UMR CARRTEL, Pôle R&D ECLA, 74200 Thonon les bains, France
31
Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
*
Authors to whom correspondence should be addressed.
Joint second authors.
Joint last authors.
Academic Editor: Matthew Peros
Received: 27 November 2020 / Revised: 22 January 2021 / Accepted: 29 January 2021 / Published: 13 February 2021
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. View Full-Text
Keywords: sedimentary ancient DNA; sedimentary DNA; lake sediments; paleolimnology; paleoecology; paleogenetics; paleogenomics; metabarcoding; metagenomics; biodiversity sedimentary ancient DNA; sedimentary DNA; lake sediments; paleolimnology; paleoecology; paleogenetics; paleogenomics; metabarcoding; metagenomics; biodiversity
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Figure 1

MDPI and ACS Style

Capo, E.; Giguet-Covex, C.; Rouillard, A.; Nota, K.; Heintzman, P.D.; Vuillemin, A.; Ariztegui, D.; Arnaud, F.; Belle, S.; Bertilsson, S.; Bigler, C.; Bindler, R.; Brown, A.G.; Clarke, C.L.; Crump, S.E.; Debroas, D.; Englund, G.; Ficetola, G.F.; Garner, R.E.; Gauthier, J.; Gregory-Eaves, I.; Heinecke, L.; Herzschuh, U.; Ibrahim, A.; Kisand, V.; Kjær, K.H.; Lammers, Y.; Littlefair, J.; Messager, E.; Monchamp, M.-E.; Olajos, F.; Orsi, W.; Pedersen, M.W.; Rijal, D.P.; Rydberg, J.; Spanbauer, T.; Stoof-Leichsenring, K.R.; Taberlet, P.; Talas, L.; Thomas, C.; Walsh, D.A.; Wang, Y.; Willerslev, E.; van Woerkom, A.; Zimmermann, H.H.; Coolen, M.J.L.; Epp, L.S.; Domaizon, I.; G. Alsos, I.; Parducci, L. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary 2021, 4, 6. https://0-doi-org.brum.beds.ac.uk/10.3390/quat4010006

AMA Style

Capo E, Giguet-Covex C, Rouillard A, Nota K, Heintzman PD, Vuillemin A, Ariztegui D, Arnaud F, Belle S, Bertilsson S, Bigler C, Bindler R, Brown AG, Clarke CL, Crump SE, Debroas D, Englund G, Ficetola GF, Garner RE, Gauthier J, Gregory-Eaves I, Heinecke L, Herzschuh U, Ibrahim A, Kisand V, Kjær KH, Lammers Y, Littlefair J, Messager E, Monchamp M-E, Olajos F, Orsi W, Pedersen MW, Rijal DP, Rydberg J, Spanbauer T, Stoof-Leichsenring KR, Taberlet P, Talas L, Thomas C, Walsh DA, Wang Y, Willerslev E, van Woerkom A, Zimmermann HH, Coolen MJL, Epp LS, Domaizon I, G. Alsos I, Parducci L. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary. 2021; 4(1):6. https://0-doi-org.brum.beds.ac.uk/10.3390/quat4010006

Chicago/Turabian Style

Capo, Eric, 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 F. 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, and Laura Parducci. 2021. "Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations" Quaternary 4, no. 1: 6. https://0-doi-org.brum.beds.ac.uk/10.3390/quat4010006

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