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

129 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

Access to Document

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.

@article{7b08132085fb4e1d8df32a2838300928,

title = "Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations",

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

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

year = "2021",

doi = "10.3390/quat4010006",

language = "English",

volume = "4",

journal = "Quaternary",

issn = "2571-550X",

publisher = "MDPI",

number = "1",

}

TY - JOUR

T1 - Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity

T2 - Overview and Recommendations

AU - Capo, Eric

AU - Giguet-Covex, Charline

AU - Rouillard, Alexandra

AU - Nota, Kevin

AU - Heintzman, Peter D.

AU - Vuillemin, Aurele

AU - Ariztegui, Daniel

AU - Arnaud, Fabien

AU - Belle, Simon

AU - Bertilsson, Stefan

AU - Bigler, Christian

AU - Bindler, Richard

AU - Brown, Antony G.

AU - Clarke, Charlotte L.

AU - Crump, Sarah E.

AU - Debroas, Didier

AU - Englund, Göran

AU - Ficetola, Gentile Francesco

AU - Garner, Rebecca E.

AU - Gauthier, Joanna

AU - Gregory-Eaves, Irene

AU - Heinecke, Liv

AU - Herzschuh, Ulrike

AU - Ibrahim, Anan

AU - Kisand, Veljo

AU - Kjær, Kurt H.

AU - Lammers, Youri

AU - Littlefair, Joanne

AU - Messager, Erwan

AU - Monchamp, Marie-Eve

AU - Olajos, Fredrik

AU - Orsi, William

AU - Pedersen, Mikkel W.

AU - Rijal, Dilli P.

AU - Rydberg, Johan

AU - Spanbauer, Trisha

AU - Stoof-Leichsenring, Kathleen R.

AU - Taberlet, Pierre

AU - Talas, Liisi

AU - Thomas, Camille

AU - Walsh, David A.

AU - Wang, Yucheng

AU - Willerslev, Eske

AU - van Woerkom, Anne

AU - Zimmermann, Heike H.

AU - Coolen, Marco J. L.

AU - Epp, Laura S.

AU - Domaizon, Isabelle

AU - Alsos, Inger G.

AU - Parducci, Laura

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - sedimentary ancient DNA

KW - sedimentary DNA

KW - lake sediments

KW - paleolimnology

KW - paleoecology

KW - paleogenetics

KW - paleogenomics

KW - metabarcoding

KW - metagenomics

KW - biodiversity

U2 - 10.3390/quat4010006

DO - 10.3390/quat4010006

M3 - Review

VL - 4

JO - Quaternary

JF - Quaternary

SN - 2571-550X

IS - 1

M1 - 6

ER -