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

Eric Capo (1) , Charline Giguet-Covex (2) , Alexandra Rouillard (3, 4) , Kevin Nota (5) , Peter Heintzman (3) , Aurèle Vuillemin (6, 7) , Daniel Ariztegui (8) , Fabien Arnaud (2) , Simon Belle (9) , Stefan Bertilsson (9) , Christian Bigler (1) , Richard Bindler (1) , Antony Brown (10, 3) , Charlotte Clarke (3) , Sarah Crump (11) , Didier Debroas (12) , Göran Englund (1) , Gentile Francesco Ficetola (13, 14) , Rebecca Garner (15, 16) , Joanna Gauthier (16, 17) , Irene Gregory-Eaves (16, 17) , Liv Heinecke (18, 19) , Ulrike Herzschuh (18, 20) , Anan Ibrahim (21) , Veljo Kisand (22) , Kurt Kjær (5) , Youri Lammers (3) , Joanne Littlefair (23) , Erwan Messager (2) , Marie-Eve Monchamp (16, 17) , Fredrik Olajos (1) , William Orsi (6, 7) , Mikkel Pedersen (4) , Dilli Rijal (3) , Johan Rydberg (1) , Trisha Spanbauer (24) , Kathleen Stoof-Leichsenring (18) , Pierre Taberlet (3, 14) , Liisi Talas (22) , Camille Thomas (8) , David Walsh (15) , Yucheng Wang (4, 25) , Eske Willerslev (4) , Anne van Woerkom (1) , Heike Zimmermann (18) , Marco Coolen (26) , Laura Epp (27) , Isabelle Domaizon (28) , Inger G. Alsos (3) , Laura Parducci (5, 29)

1 Umeå University
2 EDYTEM - Environnements, Dynamiques et Territoires de Montagne
3 UiT - The Arctic University of Norway [Tromsø, Norway]
4 UCPH - University of Copenhagen = Københavns Universitet
5 Uppsala University
6 Department of Earth and Environmental Sciences [München]
7 GeoBio-CenterLMU
8 UNIGE - Université de Genève = University of Geneva
9 SLU - Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet
10 University of Southampton
11 INSTAAR - Institute of Arctic Alpine Research [University of Colorado Boulder]
12 LMGE - Laboratoire Microorganismes : Génome et Environnement
13 Department of Environmental Science and Policy [Milano]
14 LECA - Laboratoire d'Ecologie Alpine
15 Department of Biology [Concordia]
16 Groupe de recherche interuniversitaire en limnologie et en environnement aquatique - GRIL (Montréal, Canada)
17 Department of Biology [McGill University]
18 ALFRED WEGENER INSTITUTE HELMHOLTZ CENTRE FOR POLAR AND MARINE RESEARCH POTSDAM DEU
19 Institute of Mathematics
20 Institute for Environmental Sciences and Geography, University of Potsdam
21 Department of Biology, University of Konstanz, Konstanz, Germany
22 University of Tartu
23 School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
24 Department of Environmental Sciences and Lake Erie Center, University of Toledo, Toledo, OH 43606
25 CAM - University of Cambridge [UK]
26 Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley 6102
27 Limnological Institute, Department of Biology, University of Konstanz, 78464 Konstanz
28 CARRTEL - Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques
29 UNIROMA - Università degli Studi di Roma "La Sapienza" = Sapienza University [Rome]

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.

Mots clés: sedimentary ancient DNA; sedimentary DNA; lake sediments; paleolimnology; paleoecology; paleogenetics; paleogenomics; metabarcoding; metagenomics; biodiversity

Domaines: Sciences du Vivant [q-bio]; Sciences de l'environnement

Eric Capo, Charline Giguet-Covex, Alexandra Rouillard, Kevin Nota, Peter Heintzman, et al.. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary, 2021, 4 (1), pp.6. ⟨10.3390/quat4010006⟩. ⟨hal-03218984⟩