Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
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 re...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Quaternary |
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| Online Access: | https://www.mdpi.com/2571-550X/4/1/6 |
| _version_ | 1797396638082269184 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Eric Capo |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T00:54:17Z |
| format | Article |
| id | doaj.art-304e806f23974cc6854bb6f02cd62121 |
| institution | Directory Open Access Journal |
| issn | 2571-550X |
| language | English |
| last_indexed | 2024-03-09T00:54:17Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Quaternary |
| spelling | doaj.art-304e806f23974cc6854bb6f02cd621212023-12-11T16:57:13ZengMDPI AGQuaternary2571-550X2021-02-0141610.3390/quat4010006Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and RecommendationsEric Capo0Charline Giguet-Covex1Alexandra Rouillard2Kevin Nota3Peter D. Heintzman4Aurèle Vuillemin5Daniel Ariztegui6Fabien Arnaud7Simon Belle8Stefan Bertilsson9Christian Bigler10Richard Bindler11Antony G. Brown12Charlotte L. Clarke13Sarah E. Crump14Didier Debroas15Göran Englund16Gentile Francesco Ficetola17Rebecca E. Garner18Joanna Gauthier19Irene Gregory-Eaves20Liv Heinecke21Ulrike Herzschuh22Anan Ibrahim23Veljo Kisand24Kurt H. Kjær25Youri Lammers26Joanne Littlefair27Erwan Messager28Marie-Eve Monchamp29Fredrik Olajos30William Orsi31Mikkel W. Pedersen32Dilli P. Rijal33Johan Rydberg34Trisha Spanbauer35Kathleen R. Stoof-Leichsenring36Pierre Taberlet37Liisi Talas38Camille Thomas39David A. Walsh40Yucheng Wang41Eske Willerslev42Anne van Woerkom43Heike H. Zimmermann44Marco J. L. Coolen45Laura S. Epp46Isabelle Domaizon47Inger G. Alsos48Laura Parducci49Department of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenDepartment Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, FranceDepartment of Geosciences, UiT the Arctic University of Norway, 9019 Tromsø, NorwayDepartment of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, SwedenThe Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, NorwayDepartment of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, GermanyDepartment of Earth Sciences, University of Geneva, 1205 Geneva, SwitzerlandDepartment Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, FranceDepartment of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, SwedenDepartment of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, SwedenDepartment of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenDepartment of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenThe Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, NorwaySchool of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UKInstitute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO 80309, USALMGE, UMR CNRS 6023, University Clermont Auvergne, 63000 Clermont-Ferrand, FranceDepartment of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenDepartment of Environmental Science and Policy, University of Milan, 20122 Milan, ItalyDepartment of Biology, Concordia University, Montréal, QC H3G 1M8, CanadaGroupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, CanadaGroupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, CanadaAlfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, GermanyAlfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, GermanyDepartment of Biology, University of Konstanz, 78464 Konstanz, GermanyInstitute of Technology, University of Tartu, 50090 Tartu, EstoniaSection for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, DenmarkThe Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, NorwaySchool of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UKDepartment Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204 CNRS, University Savoie Mont Blanc, 73370 Le Bourget du Lac, FranceGroupe de recherche interuniversitaire en limnologie, Montréa, QC H3C 3J7, CanadaDepartment of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenDepartment of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, GermanySection for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, DenmarkThe Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, NorwayDepartment of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenDepartment of Environmental Sciences and Lake Erie Center, University of Toledo, Toledo, OH 43606, USAAlfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, GermanyThe Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, NorwayInstitute of Technology, University of Tartu, 50090 Tartu, EstoniaDepartment of Earth Sciences, University of Geneva, 1205 Geneva, SwitzerlandDepartment of Biology, Concordia University, Montréal, QC H3G 1M8, CanadaSection for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, DenmarkSection for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, DenmarkDepartment of Ecology and Environmental Science, Umeå University, Umeå 90736, SwedenAlfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Potsdam, GermanyWestern Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley 6102, AustraliaLimnological Institute, Department of Biology, University of Konstanz, 78464 Konstanz, GermanyINRAE, University Savoie Mont Blanc, CARRTEL, 74200 Thonon les bains, FranceThe Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, NorwayDepartment of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, SwedenThe 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.https://www.mdpi.com/2571-550X/4/1/6sedimentary ancient DNAsedimentary DNAlake sedimentspaleolimnologypaleoecologypaleogenetics |
| spellingShingle | 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 Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations Quaternary sedimentary ancient DNA sedimentary DNA lake sediments paleolimnology paleoecology paleogenetics |
| title | Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations |
| title_full | Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations |
| title_fullStr | Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations |
| title_full_unstemmed | Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations |
| title_short | Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations |
| title_sort | lake sedimentary dna research on past terrestrial and aquatic biodiversity overview and recommendations |
| topic | sedimentary ancient DNA sedimentary DNA lake sediments paleolimnology paleoecology paleogenetics |
| url | https://www.mdpi.com/2571-550X/4/1/6 |
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