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; Aurele 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

doi:10.3390/quat4010006

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, Aurele 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 GauthierIrene 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

Section for Geogenetics

Research output: Contribution to journal › Review › Research › peer-review

127 Citations (Scopus)

122 Downloads (Pure)

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.

Original language	English
Article number	6
Journal	Quaternary
Volume	4
Issue number	1
Number of pages	58
ISSN	2571-550X
DOIs	https://doi.org/10.3390/quat4010006
Publication status	Published - 2021

Keywords

sedimentary ancient DNA
sedimentary DNA
lake sediments
paleolimnology
paleoecology
paleogenetics
paleogenomics
metabarcoding
metagenomics
biodiversity

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10.3390/quat4010006Licence: CC BY

Lake Sedimentary DNA Research on Past Terrestrial andAquatic BiodiversityFinal published version, 5.91 MBLicence: CC BY

Cite this

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., ... Parducci, L. (2021). Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary, 4(1), [6]. https://doi.org/10.3390/quat4010006

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity : Overview and Recommendations. / Capo, Eric; Giguet-Covex, Charline; Rouillard, Alexandra; Nota, Kevin; Heintzman, Peter D.; Vuillemin, Aurele; Ariztegui, Daniel; Arnaud, Fabien; Belle, Simon; Bertilsson, Stefan; Bigler, Christian; Bindler, Richard; Brown, Antony G.; Clarke, Charlotte L.; Crump, Sarah E.; Debroas, Didier; Englund, Göran; Ficetola, Gentile Francesco; Garner, Rebecca E.; Gauthier, Joanna; Gregory-Eaves, Irene; Heinecke, Liv; Herzschuh, Ulrike; Ibrahim, Anan; Kisand, Veljo; Kjær, Kurt H.; Lammers, Youri; Littlefair, Joanne; Messager, Erwan; Monchamp, Marie-Eve; Olajos, Fredrik; Orsi, William; Pedersen, Mikkel W.; Rijal, Dilli P.; Rydberg, Johan; Spanbauer, Trisha; Stoof-Leichsenring, Kathleen R.; Taberlet, Pierre; Talas, Liisi; Thomas, Camille; Walsh, David A.; Wang, Yucheng ; Willerslev, Eske; van Woerkom, Anne; Zimmermann, Heike H.; Coolen, Marco J. L.; Epp, Laura S.; Domaizon, Isabelle; Alsos, Inger G.; Parducci, Laura.

In: Quaternary, Vol. 4, No. 1, 6, 2021.

Research output: Contribution to journal › Review › Research › peer-review

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, Alsos, IG & Parducci, L 2021, 'Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations', Quaternary, vol. 4, no. 1, 6. https://doi.org/10.3390/quat4010006

Capo, Eric ; Giguet-Covex, Charline ; Rouillard, Alexandra ; Nota, Kevin ; Heintzman, Peter D. ; Vuillemin, Aurele ; Ariztegui, Daniel ; Arnaud, Fabien ; Belle, Simon ; Bertilsson, Stefan ; Bigler, Christian ; Bindler, Richard ; Brown, Antony G. ; Clarke, Charlotte L. ; Crump, Sarah E. ; Debroas, Didier ; Englund, Göran ; Ficetola, Gentile Francesco ; Garner, Rebecca E. ; Gauthier, Joanna ; Gregory-Eaves, Irene ; Heinecke, Liv ; Herzschuh, Ulrike ; Ibrahim, Anan ; Kisand, Veljo ; Kjær, Kurt H. ; Lammers, Youri ; Littlefair, Joanne ; Messager, Erwan ; Monchamp, Marie-Eve ; Olajos, Fredrik ; Orsi, William ; Pedersen, Mikkel W. ; Rijal, Dilli P. ; Rydberg, Johan ; Spanbauer, Trisha ; Stoof-Leichsenring, Kathleen R. ; Taberlet, Pierre ; Talas, Liisi ; Thomas, Camille ; Walsh, David A. ; Wang, Yucheng ; Willerslev, Eske ; van Woerkom, Anne ; Zimmermann, Heike H. ; Coolen, Marco J. L. ; Epp, Laura S. ; Domaizon, Isabelle ; Alsos, Inger G. ; Parducci, Laura. / Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity : Overview and Recommendations. In: Quaternary. 2021 ; Vol. 4, No. 1.

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AU - Nota, Kevin

AU - Heintzman, Peter D.

AU - Vuillemin, Aurele

AU - Ariztegui, Daniel

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AU - Gauthier, Joanna

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AU - Heinecke, Liv

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AU - Ibrahim, Anan

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AU - Kjær, Kurt H.

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