1
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Carteron A, Cantera I, Guerrieri A, Marta S, Bonin A, Ambrosini R, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague JJ, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses RI, Peyre G, Pittino F, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Taberlet P, Diolaiuti GA, Poulenard J, Thuiller W, Caccianiga M, Ficetola GF. Dynamics and drivers of mycorrhizal fungi after glacier retreat. New Phytol 2024; 242:1739-1752. [PMID: 38581206 DOI: 10.1111/nph.19682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/17/2023] [Indexed: 04/08/2024]
Abstract
The development of terrestrial ecosystems depends greatly on plant mutualists such as mycorrhizal fungi. The global retreat of glaciers exposes nutrient-poor substrates in extreme environments and provides a unique opportunity to study early successions of mycorrhizal fungi by assessing their dynamics and drivers. We combined environmental DNA metabarcoding and measurements of local conditions to assess the succession of mycorrhizal communities during soil development in 46 glacier forelands around the globe, testing whether dynamics and drivers differ between mycorrhizal types. Mycorrhizal fungi colonized deglaciated areas very quickly (< 10 yr), with arbuscular mycorrhizal fungi tending to become more diverse through time compared to ectomycorrhizal fungi. Both alpha- and beta-diversity of arbuscular mycorrhizal fungi were significantly related to time since glacier retreat and plant communities, while microclimate and primary productivity were more important for ectomycorrhizal fungi. The richness and composition of mycorrhizal communities were also significantly explained by soil chemistry, highlighting the importance of microhabitat for community dynamics. The acceleration of ice melt and the modifications of microclimate forecasted by climate change scenarios are expected to impact the diversity of mycorrhizal partners. These changes could alter the interactions underlying biotic colonization and belowground-aboveground linkages, with multifaceted impacts on soil development and associated ecological processes.
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Affiliation(s)
- Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
- Université de Toulouse, Ecole d'Ingénieurs de PURPAN, UMR INRAE-INPT DYNAFOR, Toulouse, 31076, France
| | - Isabel Cantera
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
- Argaly, Bâtiment CleanSpace, 354 Voie Magellan, 73800, Sainte-Hélène-du-Lac, France
| | - Silvio Marta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
- Institute of Geosciences and Earth Resources, CNR, Via Moruzzi 1, 56124, Pisa, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
- Argaly, Bâtiment CleanSpace, 354 Voie Magellan, 73800, Sainte-Hélène-du-Lac, France
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
| | - Fabien Anthelme
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, 34398, France
| | - Roberto Sergio Azzoni
- Dipartimento di Scienze della Terra 'Ardito Desio', Università degli Studi di Milano, Via L. Mangiagalli 34, 20133, Milano, Italy
| | - Peter Almond
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Pablo Alviz Gazitúa
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, CW76+76, Osorno, Chile
| | | | | | - Pritam Chand
- Department of Geography, School of Environment and Earth Sciences, Central University of Punjab, VPO-Ghudda, Bathinda, 151401, Punjab, India
| | - Milap Chand Sharma
- Centre for the Study of Regional Development - School of Social Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067, New Delhi, India
| | - John J Clague
- Department of Earth Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | | | - Chiara Compostella
- Dipartimento di Scienze della Terra 'Ardito Desio', Università degli Studi di Milano, Via L. Mangiagalli 34, 20133, Milano, Italy
| | | | - Olivier Dangles
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 34090, Montpellier, France
| | - Andre Eger
- Mannaki Whenua - Landcare Research, Soils and Landscapes, 54 Gerald St., Lincoln, 7608, New Zealand
| | - Sergey Erokhin
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Frunze, 533, 720033, Bishkek, Kyrgyzstan
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, 20126, Milano, Italy
| | - Ludovic Gielly
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
| | - Fabrizio Gili
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Mauro Gobbi
- Research and Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Corso del Lavoro e della Scienza, 3, 38122, Trento, Italy
| | - Sigmund Hågvar
- Faculty of Environmental Sciences and Natural Resource Management (INA), Norwegian University of Life Sciences, Universitetstunet 3, 1433, Ås, Norway
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, 9006, Norway
| | - Norine Khedim
- Université Savoie Mont Blanc, Université Grenoble Alpes, EDYTEM, F-73000, Chambéry, France
| | - Rosa Isela Meneses
- Herbario Nacional de Bolivia: La Paz, FW6J+RP2, La Paz, Bolivia
- Universidad Católica del Norte, 8HCR+94, Antofagasta, Chile
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, 111711, Bogotá, Colombia
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, 20126, Milano, Italy
- Swiss Federal Institute for Forest, Snow and Landscape Research, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Antoine Rabatel
- Université Grenoble Alpes, CNRS, IRD, INRAE, Grenoble-INP, Institut des Géosciences de l'Environnement (IGE, UMR 5001), F-38000, Grenoble, France
| | - Nurai Urseitova
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Frunze, 533, 720033, Bishkek, Kyrgyzstan
| | - Yan Yang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Vitalii Zaginaev
- Mountain Societies Research Institute, University of Central Asia, Toktogula 125/1, 720001, Bishkek, Kyrgyzstan
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra 'Ardito Desio', Università degli Studi di Milano, Via L. Mangiagalli 34, 20133, Milano, Italy
| | - Anaïs Zimmer
- Department of Geography and the Environment, University of Texas at Austin, Austin, TX, 78712, USA
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, 9006, Norway
| | - Guglielmina Adele Diolaiuti
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
| | - Jerome Poulenard
- Université Savoie Mont Blanc, Université Grenoble Alpes, EDYTEM, F-73000, Chambéry, France
| | - Wilfried Thuiller
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
| | - Marco Caccianiga
- Dipartimento di Bioscienze, Universitá degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
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2
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Lin Q, Zhang K, Giguet-Covex C, Arnaud F, McGowan S, Gielly L, Capo E, Huang S, Ficetola GF, Shen J, Dearing JA, Meadows ME. Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape. Proc Natl Acad Sci U S A 2024; 121:e2321303121. [PMID: 38640342 PMCID: PMC11046650 DOI: 10.1073/pnas.2321303121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024] Open
Abstract
Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.
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Affiliation(s)
- Qi Lin
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing210008, People’s Republic of China
| | - Ke Zhang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing210008, People’s Republic of China
| | - Charline Giguet-Covex
- Laboratoire Environnements, Dyamiques et Teritoires de la Montagne, Université Savoie Mont Blanc, CNRS, Chambéry73000, France
| | - Fabien Arnaud
- Laboratoire Environnements, Dyamiques et Teritoires de la Montagne, Université Savoie Mont Blanc, CNRS, Chambéry73000, France
| | - Suzanne McGowan
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen6708PB, Netherlands
| | - Ludovic Gielly
- Laboratoire d’Écologie Alpine, CNRS, Université Grenoble Alpes, GrenobleF-38000, France
| | - Eric Capo
- Department of Ecology and Environmental Sciences, Umeå University, UmeåSE-90187, Sweden
| | - Shixin Huang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing210008, People’s Republic of China
| | - Gentile Francesco Ficetola
- Laboratoire d’Écologie Alpine, CNRS, Université Grenoble Alpes, GrenobleF-38000, France
- Department of Environmental Science and Policy, University of Milan, Milan20133, Italy
| | - Ji Shen
- School of Geography and Ocean Science, Nanjing University, Nanjing210023, People’s Republic of China
| | - John A. Dearing
- School of Geography and Environmental Science, University of Southampton, SouthamptonSO17 1BJ, United Kingdom
| | - Michael E. Meadows
- School of Geography and Ocean Science, Nanjing University, Nanjing210023, People’s Republic of China
- Department of Environmental & Geographical Science, University of Cape Town, Rondebosch7701, South Africa
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3
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Cantera I, Carteron A, Guerrieri A, Marta S, Bonin A, Ambrosini R, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses RI, Peyre G, Pittino F, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Taberlet P, Diolaiuti GA, Poulenard J, Thuiller W, Caccianiga M, Ficetola GF. The importance of species addition 'versus' replacement varies over succession in plant communities after glacier retreat. Nat Plants 2024; 10:256-267. [PMID: 38233559 DOI: 10.1038/s41477-023-01609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024]
Abstract
The mechanisms underlying plant succession remain highly debated. Due to the local scope of most studies, we lack a global quantification of the relative importance of species addition 'versus' replacement. We assessed the role of these processes in the variation (β-diversity) of plant communities colonizing the forelands of 46 retreating glaciers worldwide, using both environmental DNA and traditional surveys. Our findings indicate that addition and replacement concur in determining community changes in deglaciated sites, but their relative importance varied over time. Taxa addition dominated immediately after glacier retreat, as expected in harsh environments, while replacement became more important for late-successional communities. These changes were aligned with total β-diversity changes, which were more pronounced between early-successional communities than between late-successional communities (>50 yr since glacier retreat). Despite the complexity of community assembly during plant succession, the observed global pattern suggests a generalized shift from the dominance of facilitation and/or stochastic processes in early-successional communities to a predominance of competition later on.
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Affiliation(s)
- Isabel Cantera
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy.
| | - Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Université de Toulouse, Ecole d'Ingénieurs de Purpan, UMR INRAE-INPT DYNAFOR, Toulouse, France
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Silvio Marta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Institute of Geosciences and Earth Resources, CNR, Pisa, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Fabien Anthelme
- Laboratory AMAP, IRD, University of Montpellier, CIRAD, CNRS, INRA, Montpellier, France
| | - Roberto Sergio Azzoni
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Dipartimento di Scienze della Terra 'Ardito Desio', Milano, Italy
| | - Peter Almond
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Pablo Alviz Gazitúa
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | | | | | - Pritam Chand
- Department of Geography, School of Environment and Earth Sciences, Central University of Punjab, VPO- Ghudda, Bathinda, Punjab, India
| | - Milap Chand Sharma
- Centre for the Study of Regional Development - School of Social Sciences, Jawaharlal Nehru University, New Delhi, India
| | - John Clague
- Department of Earth Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | | | | | - Olivier Dangles
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Andre Eger
- Mannaki Whenua - Landcare Research, Soils and Landscapes, Lincoln, New Zealand
| | - Sergey Erokhin
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), - University of Milano-Bicocca, Milano, Italy
| | - Ludovic Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Fabrizio Gili
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Mauro Gobbi
- Research and Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Trento, Italy
| | - Sigmund Hågvar
- Faculty of Environmental Sciences and Natural Resource Management (INA), Norwegian University of Life Sciences, Ås, Norway
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Norine Khedim
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Rosa Isela Meneses
- Herbario Nacional de Bolivia: La Paz, La Paz, Bolivia
- Universidad Católica del Norte, Antofagasta, Chile
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogotá, Colombia
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), - University of Milano-Bicocca, Milano, Italy
| | - Antoine Rabatel
- Univ. Grenoble Alpes, CNRS, IRD, Grenoble-INP, Institut des Géosciences de l'Environnement (IGE, UMR 5001), Grenoble, France
| | - Nurai Urseitova
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Yan Yang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Vitalii Zaginaev
- Mountain Societies Research Institute, University of Central Asia, Bishkek, Kyrgyzstan
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra 'Ardito Desio', Milano, Italy
| | - Anaïs Zimmer
- Department of Geography and the Environment, University of Texas at Austin, Austin, TX, USA
| | - Pierre Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | | | - Jerome Poulenard
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Marco Caccianiga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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4
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Guerrieri A, Cantera I, Marta S, Bonin A, Carteron A, Ambrosini R, Caccianiga M, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Deline P, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses RI, Peyre G, Pittino F, Proietto A, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Taberlet P, Diolaiuti GA, Poulenard J, Fontaneto D, Thuiller W, Ficetola GF. Local climate modulates the development of soil nematode communities after glacier retreat. Glob Chang Biol 2024; 30:e17057. [PMID: 38273541 DOI: 10.1111/gcb.17057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 01/27/2024]
Abstract
The worldwide retreat of glaciers is causing a faster than ever increase in ice-free areas that are leading to the emergence of new ecosystems. Understanding the dynamics of these environments is critical to predicting the consequences of climate change on mountains and at high latitudes. Climatic differences between regions of the world could modulate the emergence of biodiversity and functionality after glacier retreat, yet global tests of this hypothesis are lacking. Nematodes are the most abundant soil animals, with keystone roles in ecosystem functioning, but the lack of global-scale studies limits our understanding of how the taxonomic and functional diversity of nematodes changes during the colonization of proglacial landscapes. We used environmental DNA metabarcoding to characterize nematode communities of 48 glacier forelands from five continents. We assessed how different facets of biodiversity change with the age of deglaciated terrains and tested the hypothesis that colonization patterns are different across forelands with different climatic conditions. Nematodes colonized ice-free areas almost immediately. Both taxonomic and functional richness quickly increased over time, but the increase in nematode diversity was modulated by climate, so that colonization started earlier in forelands with mild summer temperatures. Colder forelands initially hosted poor communities, but the colonization rate then accelerated, eventually leveling biodiversity differences between climatic regimes in the long term. Immediately after glacier retreat, communities were dominated by colonizer taxa with short generation time and r-ecological strategy but community composition shifted through time, with increased frequency of more persister taxa with K-ecological strategy. These changes mostly occurred through the addition of new traits instead of their replacement during succession. The effects of local climate on nematode colonization led to heterogeneous but predictable patterns around the world that likely affect soil communities and overall ecosystem development.
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Affiliation(s)
- Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Isabel Cantera
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Silvio Marta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Institute of Geosciences and Earth Resources, CNR, Pisa, Italy
| | - Aurélie Bonin
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Marco Caccianiga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Fabien Anthelme
- Laboratory AMAP, IRD, University of Montpellier, CIRAD, CNRS, INRA, Montpellier, France
| | - Roberto Sergio Azzoni
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | - Peter Almond
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Pablo Alviz Gazitúa
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | | | | | - Pritam Chand
- Department of Geography, School of Environment and Earth Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Milap Chand Sharma
- Centre for the Study of Regional Development - School of Social Sciences, Jawaharlal Nehru University, New Delhi, India
| | - John Clague
- Department of Earth Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Chiara Compostella
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | | | - Olivier Dangles
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Philip Deline
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Andre Eger
- Mannaki Whenua - Landcare Research, Soils and Landscapes, Lincoln, New Zealand
| | - Sergey Erokhin
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milano, Italy
| | - Ludovic Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Fabrizio Gili
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Mauro Gobbi
- Research and Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Corso del Lavoro e della Scienza, Trento, Italy
| | - Sigmund Hågvar
- Faculty of Environmental Sciences and Natural Resource Management (INA), Norwegian University of Life Sciences, Ås, Norway
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Norine Khedim
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Rosa Isela Meneses
- Herbario Nacional de Bolivia: La Paz, La Paz, Bolivia
- Universidad Católica del Norte, Antofagasta, Chile
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogotá, Colombia
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milano, Italy
| | - Angela Proietto
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | - Antoine Rabatel
- Univ. Grenoble Alpes, CNRS, IRD, Grenoble-INP, Institut des Géosciences de l'Environnement (IGE, UMR 5001), Grenoble, France
| | - Nurai Urseitova
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Yan Yang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Vitalii Zaginaev
- Mountain Societies Research Institute, University of Central Asia, Bishkek, Kyrgyzstan
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | - Anaïs Zimmer
- Department of Geography and the Environment, University of Texas at Austin, Austin, Texas, USA
| | - Pierre Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | | | - Jerome Poulenard
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Diego Fontaneto
- CNR - Water Research Institute, Verbania, Italy
- NBFC - National Biodiversity Future Center, Palermo, Italy
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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5
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Guerrieri A, Carteron A, Bonin A, Marta S, Ambrosini R, Caccianiga M, Cantera I, Compostella C, Diolaiuti G, Fontaneto D, Gielly L, Gili F, Gobbi M, Poulenard J, Taberlet P, Zerboni A, Thuiller W, Ficetola GF. Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands. Mol Ecol 2023; 32:6304-6319. [PMID: 35997629 DOI: 10.1111/mec.16669] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022]
Abstract
Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0-5 cm) and deeper (7.5-20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.
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Affiliation(s)
- Alessia Guerrieri
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Alexis Carteron
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Aurélie Bonin
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Silvio Marta
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Marco Caccianiga
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Isabel Cantera
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Chiara Compostella
- Department of Earth Sciences, "A. Desio," Università degli Studi di Milano, Milan, Italy
| | - Guglielmina Diolaiuti
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | | | - Ludovic Gielly
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Fabrizio Gili
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Mauro Gobbi
- Research & Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Trento, Italy
| | | | - Pierre Taberlet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Andrea Zerboni
- Department of Earth Sciences, "A. Desio," Università degli Studi di Milano, Milan, Italy
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
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6
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Messager E, Giguet-Covex C, Doyen E, Etienne D, Gielly L, Sabatier P, Banjan M, Develle AL, Didier J, Poulenard J, Julien A, Arnaud F. Two Millennia of Complexity and Variability in a Perialpine Socioecological System (Savoie, France): The Contribution of Palynology and sedaDNA Analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the last two millennia, European Alpine ecosystems have experienced major changes in response to the important, yet fluctuating, impact of human activities. This study aims to reconstruct the environmental history of the last 1800 years on the western edge of the Alps by analyzing sediments from Lake Aiguebelette, a large lake located in the perialpine area. We have combined analyses of pollen and other palynomorphs, such as coprophilous fungal spores, together with sedimentary DNA (from plants and mammals) in order to reconstruct both vegetation and land-use histories. A sedimentological and geochemical analysis was also conducted in order to gain an understanding of changes in erosion dynamics in response to landscape modifications that were influenced by climate and human activities. This work highlights alternating phases of anthropization and agricultural abandonment allowing forest recovery. While pollen reflects the major phases of regional deforestation and afforestation related to the dynamic of farming activities, plant DNA provides precise information on the plants cultivated in fields, orchards and vegetable gardens over the past centuries. The combination of mammal DNA and coprophilous fungal spores completes this work by documenting the history of pastoral practices.
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7
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Calderón‐Sanou I, Zinger L, Hedde M, Martinez‐Almoyna C, Saillard A, Renaud J, Gielly L, Khedim N, Lionnet C, Ohlmann M, Consortium O, Münkemüller T, Thuiller W. Energy and physiological tolerance explain multi‐trophic soil diversity in temperate mountains. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Irene Calderón‐Sanou
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Lucie Zinger
- Département de biologie Institut de Biologie de l’ENS (IBENS) École normale supérieure CNRS INSERM Université PSL Paris France
| | - Mickael Hedde
- Eco&Sols Univ Montpellier CIRAD INRA IRD Montpellier SupAgro Montpellier France
| | - Camille Martinez‐Almoyna
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Amelie Saillard
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Julien Renaud
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Norine Khedim
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
- Univ. Savoie Mont‐Blanc Univ. Grenoble Alpes CNRS EDYTEM Chambéry France
| | - Clement Lionnet
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Marc Ohlmann
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | | | - Tamara Münkemüller
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
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8
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Calderón-Sanou I, Münkemüller T, Zinger L, Schimann H, Yoccoz NG, Gielly L, Foulquier A, Hedde M, Ohlmann M, Roy M, Si-Moussi S, Thuiller W. Cascading effects of moth outbreaks on subarctic soil food webs. Sci Rep 2021; 11:15054. [PMID: 34301993 PMCID: PMC8302651 DOI: 10.1038/s41598-021-94227-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/06/2021] [Indexed: 11/18/2022] Open
Abstract
The increasing severity and frequency of natural disturbances requires a better understanding of their effects on all compartments of biodiversity. In Northern Fennoscandia, recent large-scale moth outbreaks have led to an abrupt change in plant communities from birch forests dominated by dwarf shrubs to grass-dominated systems. However, the indirect effects on the belowground compartment remained unclear. Here, we combined eDNA surveys of multiple trophic groups with network analyses to demonstrate that moth defoliation has far-reaching consequences on soil food webs. Following this disturbance, diversity and relative abundance of certain trophic groups declined (e.g., ectomycorrhizal fungi), while many others expanded (e.g., bacterivores and omnivores) making soil food webs more diverse and structurally different. Overall, the direct and indirect consequences of moth outbreaks increased belowground diversity at different trophic levels. Our results highlight that a holistic view of ecosystems improves our understanding of cascading effects of major disturbances on soil food webs.
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Affiliation(s)
- Irene Calderón-Sanou
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000, Grenoble, France.
| | - Tamara Münkemüller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000, Grenoble, France
| | - Lucie Zinger
- Institut de Biologie de L'ENS (IBENS), Département de biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Heidy Schimann
- INRA EcoFoG (AgroParisTech, CNRS, CIRAD, INRA, Université Des Antilles, Université de Guyane), Kourou, France
| | - Nigel Gilles Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ludovic Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000, Grenoble, France
| | - Arnaud Foulquier
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000, Grenoble, France
| | - Mickael Hedde
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, 34398, Montpellier, France
| | - Marc Ohlmann
- Université Savoie Mont-Blanc, LAMA, 73000, Chambéry, France
| | - Mélanie Roy
- Laboratoire Évolution Et Diversité Biologique, CNRS, UMR 5174 UPS CNRS IRD, Université Toulouse 3 Paul Sabatier, Toulouse, France
- Instituto Franco-Argentino Para El Estudio del Clima Y Sus Impactos (UMI IFAECI/CNRS-CONICET-UBA-IRD), Dpto. de Ciencias de La Atmosfera Y Los Oceanos, FCEN, Universidad de Buenos Aires, Intendente Guiraldes 2160 - Ciudad Universitaria (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sara Si-Moussi
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, 34398, Montpellier, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000, Grenoble, France
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9
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Stewart A, Rioux D, Boyer F, Gielly L, Pompanon F, Saillard A, Thuiller W, Valay JG, Maréchal E, Coissac E. Altitudinal Zonation of Green Algae Biodiversity in the French Alps. Front Plant Sci 2021; 12:679428. [PMID: 34163510 PMCID: PMC8215661 DOI: 10.3389/fpls.2021.679428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.
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Affiliation(s)
- Adeline Stewart
- Laboratoire de Physiologie Cellulaire et Végétale, CEA, CNRS, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
- Jardin du Lautaret, CNRS, Université Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Delphine Rioux
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Fréderic Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Ludovic Gielly
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Amélie Saillard
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Wilfried Thuiller
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, CEA, CNRS, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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10
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Brown AG, Van Hardenbroek M, Fonville T, Davies K, Mackay H, Murray E, Head K, Barratt P, McCormick F, Ficetola GF, Gielly L, Henderson ACG, Crone A, Cavers G, Langdon PG, Whitehouse NJ, Pirrie D, Alsos IG. Ancient DNA, lipid biomarkers and palaeoecological evidence reveals construction and life on early medieval lake settlements. Sci Rep 2021; 11:11807. [PMID: 34083588 PMCID: PMC8175756 DOI: 10.1038/s41598-021-91057-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/04/2021] [Indexed: 11/17/2022] Open
Abstract
Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery.
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Affiliation(s)
- A G Brown
- Tromsø Museum, Artic University of Norway, Tromsø, Norway. .,School of Geography and Environmental Science, University of Southampton, Southampton, UK.
| | - M Van Hardenbroek
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - T Fonville
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - K Davies
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK.,IMSET, Bournemouth University, Poole, UK
| | - H Mackay
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK.,Department of Geography, Durham University, Durham, UK
| | - E Murray
- Archaeology, Queens University, Belfast, Northern Ireland, UK
| | - K Head
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - P Barratt
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - F McCormick
- Archaeology, Queens University, Belfast, Northern Ireland, UK
| | - G F Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,LECA, Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France
| | - L Gielly
- LECA, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France
| | - A C G Henderson
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - A Crone
- AOC Group Ltd., Edinburgh, Scotland, UK
| | - G Cavers
- AOC Group Ltd., Edinburgh, Scotland, UK
| | - P G Langdon
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - N J Whitehouse
- Department of Archaeology, School of Humanities, University of Glasgow, Glasgow, UK
| | - D Pirrie
- School of Applied Sciences, University of South Wales, Pontypridd, UK
| | - I G Alsos
- Tromsø Museum, Artic University of Norway, Tromsø, Norway
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11
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Khedim N, Cécillon L, Poulenard J, Barré P, Baudin F, Marta S, Rabatel A, Dentant C, Cauvy‐Fraunié S, Anthelme F, Gielly L, Ambrosini R, Franzetti A, Azzoni RS, Caccianiga MS, Compostella C, Clague J, Tielidze L, Messager E, Choler P, Ficetola GF. Topsoil organic matter build-up in glacier forelands around the world. Glob Chang Biol 2021; 27:1662-1677. [PMID: 33342032 PMCID: PMC8048894 DOI: 10.1111/gcb.15496] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Since the last glacial maximum, soil formation related to ice-cover shrinkage has been one major sink of carbon accumulating as soil organic matter (SOM), a phenomenon accelerated by the ongoing global warming. In recently deglacierized forelands, processes of SOM accumulation, including those that control carbon and nitrogen sequestration rates and biogeochemical stability of newly sequestered carbon, remain poorly understood. Here, we investigate the build-up of SOM during the initial stages (up to 410 years) of topsoil development in 10 glacier forelands distributed on four continents. We test whether the net accumulation of SOM on glacier forelands (i) depends on the time since deglacierization and local climatic conditions (temperature and precipitation); (ii) is accompanied by a decrease in its stability and (iii) is mostly due to an increasing contribution of organic matter from plant origin. We measured total SOM concentration (carbon, nitrogen), its relative hydrogen/oxygen enrichment, stable isotopic (13 C, 15 N) and carbon functional groups (C-H, C=O, C=C) compositions, and its distribution in carbon pools of different thermal stability. We show that SOM content increases with time and is faster on forelands experiencing warmer climates. The build-up of SOM pools shows consistent trends across the studied soil chronosequences. During the first decades of soil development, the low amount of SOM is dominated by a thermally stable carbon pool with a small and highly thermolabile pool. The stability of SOM decreases with soil age at all sites, indicating that SOM storage is dominated by the accumulation of labile SOM during the first centuries of soil development, and suggesting plant carbon inputs to soil (SOM depleted in nitrogen, enriched in hydrogen and in aromatic carbon). Our findings highlight the potential vulnerability of SOM stocks from proglacial areas to decomposition and suggest that their durability largely depends on the relative contribution of carbon inputs from plants.
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Affiliation(s)
- Norine Khedim
- Univ. Savoie Mont‐BlancUniv. Grenoble AlpesCNRSEDYTEMChambéryFrance
- Univ. Grenoble AlpesUniv. Savoie Mont‐BlancCNRSLECAGrenobleFrance
| | - Lauric Cécillon
- Univ. NormandieUNIROUENINRAEECODIVFR Scale CNRS 3730RouenFrance
- Laboratoire de GéologieCNRSÉcole normale supérieurePSL UniversityIPSLParisFrance
| | - Jérôme Poulenard
- Univ. Savoie Mont‐BlancUniv. Grenoble AlpesCNRSEDYTEMChambéryFrance
| | - Pierre Barré
- Laboratoire de GéologieCNRSÉcole normale supérieurePSL UniversityIPSLParisFrance
| | | | - Silvio Marta
- Department of Environmental Science and PolicyUniv. of MilanMilanItaly
| | - Antoine Rabatel
- Institut des Géosciences de l'EnvironnementUMR 5001Univ. Grenoble AlpesCNRSIRDGrenobleFrance
| | | | | | | | - Ludovic Gielly
- Univ. Grenoble AlpesUniv. Savoie Mont‐BlancCNRSLECAGrenobleFrance
| | - Roberto Ambrosini
- Department of Environmental Science and PolicyUniv. of MilanMilanItaly
| | - Andrea Franzetti
- Department of Earth and Environmental ScienceUniv. of Milano BicoccaMilanItaly
| | | | | | | | - John Clague
- Department of Earth SciencesSimon Fraser UniversityBurnabyBCCanada
| | - Levan Tielidze
- Antarctic Research CentreVictoria University of WellingtonWellingtonNew Zealand
- School of GeographyEnvironment and Earth SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Erwan Messager
- Univ. Savoie Mont‐BlancUniv. Grenoble AlpesCNRSEDYTEMChambéryFrance
| | - Philippe Choler
- Univ. Grenoble AlpesUniv. Savoie Mont‐BlancCNRSLECAGrenobleFrance
| | - Gentile Francesco Ficetola
- Univ. Grenoble AlpesUniv. Savoie Mont‐BlancCNRSLECAGrenobleFrance
- Department of Environmental Science and PolicyUniv. of MilanMilanItaly
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12
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Guerrieri A, Bonin A, Münkemüller T, Gielly L, Thuiller W, Francesco Ficetola G. Effects of soil preservation for biodiversity monitoring using environmental DNA. Mol Ecol 2020; 30:3313-3325. [PMID: 33034070 DOI: 10.1111/mec.15674] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]
Abstract
Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6 hr, preservation at 4°C for 3 days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6 hr at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
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Affiliation(s)
- Alessia Guerrieri
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Aurélie Bonin
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Tamara Münkemüller
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Ludovic Gielly
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy.,Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
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13
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Zawierucha K, Porazinska DL, Ficetola GF, Ambrosini R, Baccolo G, Buda J, Ceballos JL, Devetter M, Dial R, Franzetti A, Fuglewicz U, Gielly L, Łokas E, Janko K, Novotna Jaromerska T, Kościński A, Kozłowska A, Ono M, Parnikoza I, Pittino F, Poniecka E, Sommers P, Schmidt SK, Shain D, Sikorska S, Uetake J, Takeuchi N. A hole in the nematosphere: tardigrades and rotifers dominate the cryoconite hole environment, whereas nematodes are missing. J Zool (1987) 2020. [DOI: 10.1111/jzo.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- K. Zawierucha
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - D. L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville FL USA
| | - G. F. Ficetola
- Department of Environmental Science and Policy University of Milan Milan Italy
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - R. Ambrosini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - G. Baccolo
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - J. Buda
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. L. Ceballos
- Institute of Hydrology, Meteorology and Environmental Studies IDEAM Bogota' Colombia
| | - M. Devetter
- Institute of soil Biology Biology Centre CAS České Budějovice Czech Republic
- Centre for Polar Ecology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - R. Dial
- Institute of Culture and the Environment Alaska Pacific University Anchorage AK USA
| | - A. Franzetti
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | | | - L. Gielly
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - E. Łokas
- Department of Mass Spectroscopy Institute of Nuclear Physics Polish Academy of Sciences Kraków Poland
| | - K. Janko
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Libechov Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | | | - A. Kozłowska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - M. Ono
- Graduate School of Science and Engineering Chiba University Chiba Japan
| | - I. Parnikoza
- State Institution National Antarctic Center of Ministry of Education and Science of Ukraine Kyiv Ukraine
- Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine
| | - F. Pittino
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - E. Poniecka
- School of Earth and Ocean Sciences Cardiff University Cardiff UK
| | - P. Sommers
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - S. K. Schmidt
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - D. Shain
- Biology Department Rutgers, The State University of New Jersey Camden NJ USA
| | - S. Sikorska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. Uetake
- The Arctic Environment Research Center National Institute of Polar Research Tachikawa Japan
| | - N. Takeuchi
- Department of Earth Sciences Graduate School of Science Chiba University Chiba Japan
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14
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Lopes CM, De Barba M, Boyer F, Mercier C, Galiano D, Kubiak BB, Maestri R, da Silva Filho PJS, Gielly L, Coissac E, de Freitas TRO, Taberlet P. Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis. Mol Ecol 2020; 29:3144-3154. [PMID: 32654383 DOI: 10.1111/mec.15549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/20/2020] [Accepted: 07/08/2020] [Indexed: 01/20/2023]
Abstract
Knowledge of how animal species use food resources available in the environment can increase our understanding of many ecological processes. However, obtaining this information using traditional methods is difficult for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an environmental DNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the genus Ctenomys distributed in southern and midwestern Brazil. The metabarcoding approach revealed that these species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The family Poaceae was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and molecular operational taxonomic units consumed, mainly among the southern species. Interspecific differences in diet composition were influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.
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Affiliation(s)
- Carla Martins Lopes
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
| | - Marta De Barba
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
| | - Frédéric Boyer
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
| | - Céline Mercier
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
| | - Daniel Galiano
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Bruno Busnello Kubiak
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Renan Maestri
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Ludovic Gielly
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
| | - Eric Coissac
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
| | | | - Pierre Taberlet
- Laboratoire d'Écologie Alpine, UMR 5553, CNRS, Université Savoie Mont Blanc, Université Grenoble Alpes, Grenoble, France
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15
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Clarke CL, Edwards ME, Gielly L, Ehrich D, Hughes PDM, Morozova LM, Haflidason H, Mangerud J, Svendsen JI, Alsos IG. Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals. Sci Rep 2019; 9:19613. [PMID: 31873100 PMCID: PMC6927971 DOI: 10.1038/s41598-019-55989-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
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Affiliation(s)
- C L Clarke
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - M E Edwards
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L Gielly
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, C2 40700 38058, Grenoble, Cedex 9, France
| | - D Ehrich
- Department of Arctic and Marine Biology, UiT- The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - P D M Hughes
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L M Morozova
- Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Ekaterinburg, Russia
| | - H Haflidason
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J Mangerud
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J I Svendsen
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - I G Alsos
- Tromsø University Museum, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
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16
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Giguet-Covex C, Ficetola GF, Walsh K, Poulenard J, Bajard M, Fouinat L, Sabatier P, Gielly L, Messager E, Develle AL, David F, Taberlet P, Brisset E, Guiter F, Sinet R, Arnaud F. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Sci Rep 2019; 9:14676. [PMID: 31604959 PMCID: PMC6789010 DOI: 10.1038/s41598-019-50339-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/12/2019] [Indexed: 11/09/2022] Open
Abstract
Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).
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Affiliation(s)
- C Giguet-Covex
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK. .,EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France.
| | - G F Ficetola
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - K Walsh
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK
| | - J Poulenard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - M Bajard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Fouinat
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - P Sabatier
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Messager
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - A L Develle
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - F David
- CEREGE, UMR CNRS 7330, IRD 161-Marseille Université, Technopôle de l'Arbois Méditerranée, BP 80, 13545, Aix en Provence cedex 4, France
| | - P Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Brisset
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - F Guiter
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - R Sinet
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - F Arnaud
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
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17
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Evrard O, Laceby JP, Ficetola GF, Gielly L, Huon S, Lefèvre I, Onda Y, Poulenard J. Environmental DNA provides information on sediment sources: A study in catchments affected by Fukushima radioactive fallout. Sci Total Environ 2019; 665:873-881. [PMID: 30790760 DOI: 10.1016/j.scitotenv.2019.02.191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 05/23/2023]
Abstract
An excessive supply of sediment is observed in numerous rivers across the world where it leads to deleterious impacts. Information on the sources delivering this material to waterbodies is required to design effective management measures, and sediment tracing or fingerprinting techniques are increasingly used to quantify the amount of sediment derived from different sources. However, the current methods used to identify the land use contributions to sediment have a limited discrimination power. Here, we investigated the potential of environmental DNA (eDNA) to provide more detailed information on the plant species found in sediment source areas as a next generation fingerprint. To this end, flood sediment deposits (n = 12) were collected in 2017 in two catchments impacted by the Fukushima radioactive fallout along differing river sections draining forests, cropland or a mix of both land uses. Conventional fingerprints (i.e. fallout radionuclides and organic matter properties) were also measured in these samples. The conventional fingerprint model results showed that most sediment samples contained a dominant proportion of subsoil material. Nevertheless, the eDNA information effectively discriminated the three above-mentioned groups of sediment, with the dominance of tree, shrub and fern species in sediment sampled in rivers draining forests versus a majority of grass, algae and cultivated plant species in sediment collected in rivers draining cropland. Based on these encouraging results, future research should examine the potential of eDNA in mixed land use catchments where the contribution of topsoil to sediment dominates and where the cultivation of land has not been abandoned in order to better characterize the memory effect of eDNA in soils and sediment.
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Affiliation(s)
- Olivier Evrard
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL), Unité Mixte de Recherche 8212 (CEA/CNRS/UVSQ), Université Paris-Saclay, Gif-sur-Yvette, France.
| | - J Patrick Laceby
- Environmental Monitoring and Science Division (EMSD), Alberta Environment and Parks (AEP), Calgary, Alberta, Canada
| | - Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine, Grenoble, France; Departement of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Ludovic Gielly
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine, Grenoble, France
| | - Sylvain Huon
- Sorbonne Universités, UPMC Univ Paris 06, Institut d'Ecologie et des Sciences de l'environnement de Paris (iEES), Paris, France
| | - Irène Lefèvre
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL), Unité Mixte de Recherche 8212 (CEA/CNRS/UVSQ), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yuichi Onda
- Center for Research in Isotopes and Environmental Dynamics (CRIED), University of Tsukuba, Tsukuba, Japan
| | - Jérôme Poulenard
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Environnements, DYnamiques et TErritoires de la Montagne), Chambéry, France
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18
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Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, Gaucher P, Gielly L, Giguet‐Covex C, Iribar A, Réjou‐Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, Chave J. Body size determines soil community assembly in a tropical forest. Mol Ecol 2018; 28:528-543. [DOI: 10.1111/mec.14919] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 10/02/2018] [Accepted: 10/14/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Lucie Zinger
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Pierre Taberlet
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Heidy Schimann
- UMR Ecologie des Forets de Guyane (AgroParisTech, CIRAD, CNRS, Université des Antilles, Université de la Guyane)INRA Kourou France
| | - Aurélie Bonin
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Frédéric Boyer
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Marta De Barba
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Philippe Gaucher
- USR 3456CNRSCentre de recherche de Montabo IRDCNRS‐Guyane Cayenne France
| | - Ludovic Gielly
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | | | - Amaia Iribar
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Maxime Réjou‐Méchain
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
- UMR AMAP, IRD Montpellier France
| | - Gilles Rayé
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Delphine Rioux
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Vincent Schilling
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Blaise Tymen
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Jérôme Viers
- CNRS, IRDUMR 5563 GETUniversité Toulouse 3 Paul Sabatier Toulouse France
| | - Cyril Zouiten
- CNRS, IRDUMR 5563 GETUniversité Toulouse 3 Paul Sabatier Toulouse France
| | - Wilfried Thuiller
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Eric Coissac
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Jérôme Chave
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
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19
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Ohlmann M, Mazel F, Chalmandrier L, Bec S, Coissac E, Gielly L, Pansu J, Schilling V, Taberlet P, Zinger L, Chave J, Thuiller W. Mapping the imprint of biotic interactions on β-diversity. Ecol Lett 2018; 21:1660-1669. [DOI: 10.1111/ele.13143] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/01/2018] [Accepted: 07/25/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Marc Ohlmann
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Florent Mazel
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Loïc Chalmandrier
- Landscape Ecology; Institute of Terrestrial Ecosystems; ETH Zürich; Zürich Switzerland
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Stéphane Bec
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Eric Coissac
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Ludovic Gielly
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Johan Pansu
- Princeton University; 110 Morrison Hall Princeton NJ 08544 USA
| | - Vincent Schilling
- Université Toulouse 3 Paul Sabatier; CNRS; IRD; UMR 5174 Evolution et Diversité Biologique (EDB); F-31062 Toulouse France
| | - Pierre Taberlet
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Lucie Zinger
- Ecole Normale Supérieure; PSL Research University; CNRS; Inserm; Institut de Biologie de l'Ecole Normale Supérieure (IBENS); F-75005 Paris France
| | - Jérome Chave
- Université Toulouse 3 Paul Sabatier; CNRS; IRD; UMR 5174 Evolution et Diversité Biologique (EDB); F-31062 Toulouse France
| | - Wilfried Thuiller
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
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Ficetola GF, Poulenard J, Sabatier P, Messager E, Gielly L, Leloup A, Etienne D, Bakke J, Malet E, Fanget B, Støren E, Reyss JL, Taberlet P, Arnaud F. DNA from lake sediments reveals long-term ecosystem changes after a biological invasion. Sci Adv 2018; 4:eaar4292. [PMID: 29750197 PMCID: PMC5942909 DOI: 10.1126/sciadv.aar4292] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 05/30/2023]
Abstract
What are the long-term consequences of invasive species? After invasion, how long do ecosystems require to reach a new equilibrium? Answering these questions requires long-term, high-resolution data that are vanishingly rare. We combined the analysis of environmental DNA extracted from a lake sediment core, coprophilous fungi, and sedimentological analyses to reconstruct 600 years of ecosystem dynamics on a sub-Antarctic island and to identify the impact of invasive rabbits. Plant communities remained stable from AD 1400 until the 1940s, when the DNA of invasive rabbits was detected in sediments. Rabbit detection corresponded to abrupt changes of plant communities, with a continuous decline of a dominant plant species. Furthermore, erosion rate abruptly increased with rabbit abundance. Rabbit impacts were very fast and were stronger than the effects of climate change during the 20th century. Lake sediments can allow an integrated temporal analysis of ecosystems, revealing the impact of invasive species over time and improving our understanding of underlying mechanisms.
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Affiliation(s)
- Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, Laboratoire d’Écologie Alpine, F-38000 Grenoble, France
- Departement of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Jérôme Poulenard
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Pierre Sabatier
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Erwan Messager
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Ludovic Gielly
- Université Grenoble Alpes, CNRS, Laboratoire d’Écologie Alpine, F-38000 Grenoble, France
| | - Anouk Leloup
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - David Etienne
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Jostein Bakke
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Emmanuel Malet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Bernard Fanget
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Eivind Støren
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Jean-Louis Reyss
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, Laboratoire d’Écologie Alpine, F-38000 Grenoble, France
| | - Fabien Arnaud
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
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Alsos IG, Lammers Y, Yoccoz NG, Jørgensen T, Sjögren P, Gielly L, Edwards ME. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS One 2018; 13:e0195403. [PMID: 29664954 PMCID: PMC5903670 DOI: 10.1371/journal.pone.0195403] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Youri Lammers
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nigel Giles Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Tina Jørgensen
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Per Sjögren
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Ludovic Gielly
- University Grenoble Alpes, LECA, Grenoble, France
- CNRS, LECA, Grenoble, France
| | - Mary E. Edwards
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- Geography and Environment, University of Southampton, Highfield, Southampton, United Kingdom
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Soininen EM, Zinger L, Gielly L, Yoccoz NG, Henden JA, Ims RA. Not only mosses: lemming winter diets as described by DNA metabarcoding. Polar Biol 2017. [DOI: 10.1007/s00300-017-2114-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sjögren P, Edwards ME, Gielly L, Langdon CT, Croudace IW, Merkel MKF, Fonville T, Alsos IG. Lake sedimentary DNA accurately records 20 th Century introductions of exotic conifers in Scotland. New Phytol 2017; 213:929-941. [PMID: 27678125 PMCID: PMC5215665 DOI: 10.1111/nph.14199] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/08/2016] [Indexed: 05/08/2023]
Abstract
Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20th Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen.
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Affiliation(s)
- Per Sjögren
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
| | - Mary E. Edwards
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Ludovic Gielly
- Laboratoire d'Ecologie AlpineUniversité Grenoble AlpesF‐38000GrenobleFrance
- Laboratoire d'Ecologie AlpineCNRSF‐38000GrenobleFrance
| | - Catherine T. Langdon
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Ian W. Croudace
- Ocean and Earth ScienceUniversity of SouthamptonNational Oceanography CentreSouthamptonSO14 3ZHUK
| | | | - Thierry Fonville
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Inger Greve Alsos
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
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Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S. Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). Ann Bot 2016; 118:885-896. [PMID: 27443299 PMCID: PMC5055816 DOI: 10.1093/aob/mcw135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/09/2016] [Accepted: 05/12/2016] [Indexed: 05/19/2023]
Abstract
Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
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Affiliation(s)
- Cristina Roquet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
- *For correspondence. E-mail
| | - Éric Coissac
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Corinne Cruaud
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Martí Boleda
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Adriana Alberti
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Jérémie Van Es
- Conservatoire Botanique National Alpin, Domaine de Charance, FR-05000 Gap, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
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25
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Pansu J, Winkworth RC, Hennion F, Gielly L, Taberlet P, Choler P. Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago. Biol Lett 2016; 11:20150408. [PMID: 26333663 DOI: 10.1098/rsbl.2015.0408] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities at sites on the sub-Antarctic Kerguelen Islands with contrasting histories of disturbance by rabbits. Our results suggest that on these islands, the simplification of plant communities and increased erosion resulting from the introduction of rabbits have driven compositional changes, including diversity reductions, in indigenous soil fungal communities. Moreover, there is no indication of recovery at sites from which rabbits were removed 20 years ago. These results imply that introduced herbivores have long-lasting and multifaceted effects on fungal biodiversity as well as highlight the low resiliency of sub-Antarctic ecosystems.
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Affiliation(s)
- Johan Pansu
- LECA, Université de Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - Richard C Winkworth
- Department of Natural Sciences, Unitec Institute of Technology, Auckland, New Zealand Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Ludovic Gielly
- LECA, Université de Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - Pierre Taberlet
- LECA, Université de Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - Philippe Choler
- LECA, Université de Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
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26
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Lopes CM, De Barba M, Boyer F, Mercier C, da Silva Filho PJS, Heidtmann LM, Galiano D, Kubiak BB, Langone P, Garcias FM, Gielly L, Coissac E, de Freitas TRO, Taberlet P. DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents. Heredity (Edinb) 2015; 114:525-36. [PMID: 25649502 PMCID: PMC4815513 DOI: 10.1038/hdy.2014.109] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 10/22/2014] [Accepted: 10/27/2014] [Indexed: 11/09/2022] Open
Abstract
Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents.
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Affiliation(s)
- C M Lopes
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - M De Barba
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - F Boyer
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - C Mercier
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - P J S da Silva Filho
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - L M Heidtmann
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - D Galiano
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - B B Kubiak
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - P Langone
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - F M Garcias
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - L Gielly
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - E Coissac
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - T R O de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - P Taberlet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
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Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P. Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Mol Ecol 2015; 24:1485-98. [PMID: 25735209 DOI: 10.1111/mec.13136] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 02/24/2015] [Accepted: 02/27/2015] [Indexed: 11/30/2022]
Abstract
Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.
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Affiliation(s)
- Johan Pansu
- Univ. Grenoble Alpes, LECA, F-38000, Grenoble, France; CNRS, LECA, F-38000, Grenoble, France
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28
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Soininen EM, Gauthier G, Bilodeau F, Berteaux D, Gielly L, Taberlet P, Gussarova G, Bellemain E, Hassel K, Stenøien HK, Epp L, Schrøder-Nielsen A, Brochmann C, Yoccoz NG. Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding. PLoS One 2015; 10:e0115335. [PMID: 25635852 PMCID: PMC4312081 DOI: 10.1371/journal.pone.0115335] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/21/2014] [Indexed: 01/19/2023] Open
Abstract
Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found that the diets of both collared (Dicrostonyx groenlandicus) and brown lemmings (Lemmus trimucronatus) on Bylot Island were dominated by Salix while mosses, which were significantly consumed only by the brown lemming, were a relatively minor food item. The most abundant plant taxon, Cassiope tetragona, which alone composes more than 50% of the available plant biomass, was not detected in feces and can thus be considered to be non-food. Most plant taxa that were identified as food items were consumed in proportion to their availability and none were clearly selected for. The resulting high diet overlap, together with a lack of habitat segregation, indicates a high potential for resource competition between the two lemming species. However, Salix is abundant in the winter habitats of lemmings on Bylot Island and the non-Salix portion of the diets differed between the two species. Also, lemming grazing impact on vegetation during winter in the study area is negligible. Hence, it seems likely that the high potential for resource competition predicted between these two species did not translate into actual competition. This illustrates that even in environments with low primary productivity food resources do not necessarily generate strong competition among herbivores.
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Affiliation(s)
- Eeva M. Soininen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Gilles Gauthier
- Département de Biologie & Centre d’Études Nordiques, Université Laval, Québec, Canada
| | - Frédéric Bilodeau
- Département de Biologie & Centre d’Études Nordiques, Université Laval, Québec, Canada
| | - Dominique Berteaux
- Chaire de Recherche du Canada en Biodiversité Nordique & Centre d’Études Nordiques, Université du Québec à Rimouski, Québec, Canada
| | - Ludovic Gielly
- Université Grenoble Alpes/CNRS, Laboratoire d’Écologie Alpine (LECA), Grenoble, France
| | - Pierre Taberlet
- Université Grenoble Alpes/CNRS, Laboratoire d’Écologie Alpine (LECA), Grenoble, France
| | - Galina Gussarova
- Natural History Museum, University of Oslo, Oslo, Norway
- Department of Botany, St Petersburg State University, St Petersburg, Russia
| | - Eva Bellemain
- Natural History Museum, University of Oslo, Oslo, Norway
- SPYGEN, Savoie Technolac, Le Bourget du Lac, France
| | - Kristian Hassel
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Laura Epp
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | | | - Nigel G. Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
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Ficetola GF, Pansu J, Bonin A, Coissac E, Giguet-Covex C, De Barba M, Gielly L, Lopes CM, Boyer F, Pompanon F, Rayé G, Taberlet P. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol Ecol Resour 2014; 15:543-56. [PMID: 25327646 DOI: 10.1111/1755-0998.12338] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/27/2014] [Accepted: 10/07/2014] [Indexed: 01/21/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.
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Affiliation(s)
- Gentile F Ficetola
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes Savoie, F-38000, Grenoble, France
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Soininen EM, Ehrich D, Lecomte N, Yoccoz NG, Tarroux A, Berteaux D, Gauthier G, Gielly L, Brochmann C, Gussarova G, Ims RA. Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis. Isotopes Environ Health Stud 2014; 50:361-381. [PMID: 24830842 DOI: 10.1080/10256016.2014.915824] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
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Affiliation(s)
- Eeva M Soininen
- a Department of Arctic and Marine Biology , UiT The Arctic University of Norway , Tromsø , Norway
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31
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Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergård M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Bråthen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sønstebø JH, Murton J, Sher A, Rasmussen M, Rønn R, Mourier T, Cooper A, Austin J, Möller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjær KH, Orlando L, Brochmann C, Taberlet P. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 2014; 506:47-51. [DOI: 10.1038/nature12921] [Citation(s) in RCA: 390] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/28/2013] [Indexed: 11/09/2022]
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Soininen EM, Ravolainen VT, Bråthen KA, Yoccoz NG, Gielly L, Ims RA. Arctic Small Rodents Have Diverse Diets and Flexible Food Selection. PLoS One 2013; 8:e68128. [PMID: 23826371 PMCID: PMC3694920 DOI: 10.1371/journal.pone.0068128] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 05/28/2013] [Indexed: 11/18/2022] Open
Abstract
The ecology of small rodent food selection is poorly understood, as mammalian herbivore food selection theory has mainly been developed by studying ungulates. Especially, the effect of food availability on food selection in natural habitats where a range of food items are available is unknown. We studied diets and selectivity of grey-sided voles (Myodes rufocanus) and tundra voles (Microtus oeconomus), key herbivores in European tundra ecosystems, using DNA metabarcoding, a novel method enabling taxonomically detailed diet studies. In order to cover the range of food availabilities present in the wild, we employed a large-scale study design for sampling data on food availability and vole diets. Both vole species had ingested a range of plant species and selected particularly forbs and grasses. Grey-sided voles also selected ericoid shrubs and tundra voles willows. Availability of a food item rarely affected its utilization directly, although seasonal changes of diets and selection suggest that these are positively correlated with availability. Moreover, diets and selectivity were affected by availability of alternative food items. These results show that the focal sub-arctic voles have diverse diets and flexible food preferences and rarely compensate low availability of a food item with increased searching effort. Diet diversity itself is likely to be an important trait and has previously been underrated owing to methodological constraints. We suggest that the roles of alternative food item availability and search time limitations for small rodent feeding ecology should be investigated. Nomenclature Annotated Checklist of the Panarctic Flora (PAF), Vascular plants. Available at: http://nhm2.uio.no/paf/, accessed 15.6.2012.
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Affiliation(s)
- Eeva M. Soininen
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
- * E-mail:
| | - Virve T. Ravolainen
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Kari Anne Bråthen
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Nigel G. Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Ludovic Gielly
- Laboratoire d’ECologie Alpine, Université Joseph Fourier, Grenoble, France
| | - Rolf A. Ims
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
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Soininen EM, Zinger L, Gielly L, Bellemain E, Bråthen KA, Brochmann C, Epp LS, Gussarova G, Hassel K, Henden JA, Killengreen ST, Rämä T, Stenøien HK, Yoccoz NG, Ims RA. Shedding new light on the diet of Norwegian lemmings: DNA metabarcoding of stomach content. Polar Biol 2013. [DOI: 10.1007/s00300-013-1328-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Taberlet P, Zimmermann NE, Englisch T, Tribsch A, Holderegger R, Alvarez N, Niklfeld H, Coldea G, Mirek Z, Moilanen A, Ahlmer W, Marsan PA, Bona E, Bovio M, Choler P, Cieślak E, Colli L, Cristea V, Dalmas J, Frajman B, Garraud L, Gaudeul M, Gielly L, Gutermann W, Jogan N, Kagalo AA, Korbecka G, Küpfer P, Lequette B, Letz DR, Manel S, Mansion G, Marhold K, Martini F, Negrini R, Niño F, Paun O, Pellecchia M, Perico G, Piękoś‐Mirkowa H, Prosser F, Puşcaş M, Ronikier M, Scheuerer M, Schneeweiss GM, Schönswetter P, Schratt‐Ehrendorfer L, Schüpfer F, Selvaggi A, Steinmann K, Thiel‐Egenter C, Loo M, Winkler M, Wohlgemuth T, Wraber T, Gugerli F. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecol Lett 2012; 15:1439-48. [DOI: 10.1111/ele.12004] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Taberlet
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Niklaus E. Zimmermann
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Thorsten Englisch
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Andreas Tribsch
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Nadir Alvarez
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Harald Niklfeld
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Gheorghe Coldea
- Institute of Biological Research Str. Republicii nr. 48 400015 Cluj‐Napoca Romania
| | - Zbigniew Mirek
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Atte Moilanen
- Department of Biosciences P.O. Box 65 (Biocenter III) FI‐00014 University of Helsinki Finland
| | - Wolfgang Ahlmer
- University of Regensburg Institute of Botany 93040 Regensburg Germany
| | - Paolo Ajmone Marsan
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Enzo Bona
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Maurizio Bovio
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Philippe Choler
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Elżbieta Cieślak
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Licia Colli
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | | | - Jean‐Pierre Dalmas
- Conservatoire Botanique National Alpin ‐ CBNA Domaine de Charance 05000 Gap France
| | - Božo Frajman
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Luc Garraud
- Conservatoire Botanique National Alpin ‐ CBNA Domaine de Charance 05000 Gap France
| | - Myriam Gaudeul
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Ludovic Gielly
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Walter Gutermann
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Nejc Jogan
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Alexander A. Kagalo
- Institute of Ecology of the Carpathians N.A.S. of Ukraine 4 Kozelnitska str. 79026 Lviv Ukraine
| | - Grażyna Korbecka
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Philippe Küpfer
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Benoît Lequette
- Parc national du Mercantour 23 rue d'Italie, BP 1316 06006 Nice Cedex 1 France
| | - Dominik Roman Letz
- Institute of Botany of Slovak Academy of Sciences Department of Vascular Plant Taxonomy Dúbravská cesta 9 845 23 Bratislava Slovakia
| | - Stéphanie Manel
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Guilhem Mansion
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Karol Marhold
- Institute of Botany of Slovak Academy of Sciences Department of Vascular Plant Taxonomy Dúbravská cesta 9 845 23 Bratislava Slovakia
| | - Fabrizio Martini
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Riccardo Negrini
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Fernando Niño
- Medias‐France/IRD CNES ‐ BPi 2102, 18, Av. Edouard Belin F‐31401 Toulouse Cedex 9 France
| | - Ovidiu Paun
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Marco Pellecchia
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Giovanni Perico
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | | | | | - Mihai Puşcaş
- Babes‐Bolyai University 400015 Cluj‐Napoca Romania
| | - Michał Ronikier
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Martin Scheuerer
- University of Regensburg Institute of Botany 93040 Regensburg Germany
| | | | - Peter Schönswetter
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | | | - Fanny Schüpfer
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Alberto Selvaggi
- Istituto per le Piante da Legno e l'Ambiente c.so Casale, 476 10132 Torino Italy
| | - Katharina Steinmann
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Conny Thiel‐Egenter
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Marcela Loo
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Manuela Winkler
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Thomas Wohlgemuth
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Tone Wraber
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
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Manel S, Gugerli F, Thuiller W, Alvarez N, Legendre P, Holderegger R, Gielly L, Taberlet P. Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation. Mol Ecol 2012; 21:3729-38. [PMID: 22680783 PMCID: PMC4003392 DOI: 10.1111/j.1365-294x.2012.05656.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran's eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps.
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Affiliation(s)
- Stéphanie Manel
- Laboratoire Population Environnement Développement, UMR 151 UP/IRD, Aix-Marseille Université, Marseille, France.
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36
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Yoccoz NG, Bråthen KA, Gielly L, Haile J, Edwards ME, Goslar T, Von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, De Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP, Orlando L, Brochmann C, Willerslev E, Taberlet P. DNA from soil mirrors plant taxonomic and growth form diversity. Mol Ecol 2012; 21:3647-55. [PMID: 22507540 DOI: 10.1111/j.1365-294x.2012.05545.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.
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Affiliation(s)
- N G Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
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de Witte LC, Armbruster GFJ, Gielly L, Taberlet P, Stöcklin J. AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species. Mol Ecol 2011; 21:1081-97. [PMID: 22070158 DOI: 10.1111/j.1365-294x.2011.05326.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic-alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left-skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were <200 years old. The oldest genets of D. octopetala, S. herbacea and V. uliginosum were found to be at least 500, 450 and 1400 years old, respectively. These results indicate that individuals in the studied populations have survived pronounced climatic oscillations, including the Little Ice Age and the postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long-lived clonal plants in arctic-alpine ecosystems can persist, despite considerable climatic change.
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Affiliation(s)
- Lucienne C de Witte
- Institute of Botany, University of Basel, Schönbeinstrasse 6, Basel, Switzerland.
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Poncet BN, Herrmann D, Gugerli F, Taberlet P, Holderegger R, Gielly L, Rioux D, Thuiller W, Aubert S, Manel S. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 2010; 19:2896-907. [PMID: 20609082 DOI: 10.1111/j.1365-294x.2010.04696.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.
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Affiliation(s)
- Bénédicte N Poncet
- Laboratoire d'Ecologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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Herrmann D, Poncet BN, Manel S, Rioux D, Gielly L, Taberlet P, Gugerli F. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome 2010; 53:302-10. [DOI: 10.1139/g10-006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.
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Affiliation(s)
- Doris Herrmann
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Bénédicte N. Poncet
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Stéphanie Manel
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Delphine Rioux
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Ludovic Gielly
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Pierre Taberlet
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Felix Gugerli
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
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Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, Sønstebø JH, Ims RA, Yoccoz NG, Taberlet P. Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zool 2009; 6:16. [PMID: 19695081 PMCID: PMC2736939 DOI: 10.1186/1742-9994-6-16] [Citation(s) in RCA: 201] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 08/20/2009] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron. RESULTS Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis. CONCLUSION We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores.
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Affiliation(s)
- Eeva M Soininen
- Department of Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Alice Valentini
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Christian Miquel
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Ludovic Gielly
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Christian Brochmann
- National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway
| | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Jørn H Sønstebø
- National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway
| | - Rolf A Ims
- Department of Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Nigel G Yoccoz
- Department of Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
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Alvarez N, Thiel-Egenter C, Tribsch A, Holderegger R, Manel S, Schönswetter P, Taberlet P, Brodbeck S, Gaudeul M, Gielly L, Küpfer P, Mansion G, Negrini R, Paun O, Pellecchia M, Rioux D, Schüpfer F, Van Loo M, Winkler M, Gugerli F. History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants. Ecol Lett 2009; 12:632-40. [PMID: 19392716 DOI: 10.1111/j.1461-0248.2009.01312.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadir Alvarez
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Valentini A, Miquel C, Nawaz MA, Bellemain E, Coissac E, Pompanon F, Gielly L, Cruaud C, Nascetti G, Wincker P, Swenson JE, Taberlet P. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach. Mol Ecol Resour 2009; 9:51-60. [PMID: 21564566 DOI: 10.1111/j.1755-0998.2008.02352.x] [Citation(s) in RCA: 311] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alice Valentini
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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Gury J, Zinger L, Gielly L, Taberlet P, Geremia RA. Exonuclease activity of proofreading DNA polymerases is at the origin of artifacts in molecular profiling studies. Electrophoresis 2008; 29:2437-44. [PMID: 18429330 DOI: 10.1002/elps.200700667] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
CE fingerprint methods are commonly used in microbial ecology. We have previously noticed that the position and number of peaks in CE-SSCP (single-strand conformation polymorphism) profiles depend on the DNA polymerase used in PCR [1]. Here, we studied the fragments produced by Taq polymerase as well as four commercially available proofreading polymerases, using the V3 region of the Escherichia coli rss gene as a marker. PCR products rendered multiple peaks in denaturing CE; Taq polymerase was observed to produce the longest fragments. Incubation of the fragments with T4 DNA polymerase indicated that the 3'-ends of the proofreading polymerase amplicons were recessed, while the Taq amplicon was partially +A tailed. Treatment of the PCR product with proofreading DNA polymerase rendered trimmed fragments. This was due to the 3'-5' exonuclease activity of these enzymes, which is essential for proofreading. The nuclease activity was reduced by increasing the concentration of dNTP. The Platinum Pfx DNA polymerase generated very few artifacts and could produce 85% of blunted PCR products. Nevertheless, despite the higher error rate, we recommend the use of Taq polymerase rather than proofreading in the framework for molecular fingerprint studies. They are more cost-effective and therefore ideally suited for high-throughput analysis; the +A tail artifact rate can be controlled by modifying the PCR primers and the reaction conditions.
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Affiliation(s)
- Jerome Gury
- Laboratoire d'écologie alpine, UMR UJF-CNRS 5553, Université Joseph Fourier, Grenoble, France
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Zinger L, Gury J, Alibeu O, Rioux D, Gielly L, Sage L, Pompanon F, Geremia RA. Corrigendum to “CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies” [Journal of Microbiological Methods 72 (2008) 42–53]. Journal of Microbiological Methods 2008. [DOI: 10.1016/j.mimet.2008.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Zinger L, Gury J, Alibeu O, Rioux D, Gielly L, Sage L, Pompanon F, Geremia RA. CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies. J Microbiol Methods 2007; 72:42-53. [PMID: 18054096 DOI: 10.1016/j.mimet.2007.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 10/12/2007] [Accepted: 10/12/2007] [Indexed: 11/18/2022]
Abstract
Fungal communities are key components of soil, but the study of their ecological significance is limited by a lack of appropriated methods. For instance, the assessment of fungi occurrence and spatio-temporal variation in soil requires the analysis of a large number of samples. The molecular signature methods provide a useful tool to monitor these microbial communities and can be easily adapted to capillary electrophoresis (CE) allowing high-throughput studies. Here we assess the suitability of CE-FLA (Fragment Length Polymorphism, denaturing conditions) and CE-SSCP (Single-Stranded Conformation Polymorphism, native conditions) applied to environmental studies since they require a short molecular marker and no post-PCR treatments. We amplified the ITS1 region from 22 fungal strains isolated from an alpine ecosystem and from total genomic DNA of alpine and infiltration basin soils. The CE-FLA and CE-SSCP separated 17 and 15 peaks respectively from a mixture of 19 strains. For the alpine soil-metagenomic DNA, the FLA displayed more peaks than the SSCP and the converse result was found for infiltration basin sediments. We concluded that CE-FLA and CE-SSCP of ITS1 region provided complementary information. In order to improve CE-SSCP sensitivity, we tested its resolution according to migration temperature and found 32 degrees C to be optimal. Because of their simplicity, quickness and reproducibility, we found that these two methods were promising for high-throughput studies of soil fungal communities.
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Affiliation(s)
- Lucie Zinger
- Laboratoire d'Ecologie Alpine UMR 5553 UJF/CNRS, Grenoble Cedex 9, France
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Zinger L, Gury J, Giraud F, Krivobok S, Gielly L, Taberlet P, Geremia RA. Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil. Microb Ecol 2007; 54:203-16. [PMID: 17587075 DOI: 10.1007/s00248-006-9151-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 06/27/2006] [Accepted: 07/24/2006] [Indexed: 05/15/2023]
Abstract
The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE-SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE-SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE-SSCP. Studies on PCR and CE-SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE-SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.
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Affiliation(s)
- Lucie Zinger
- Laboratoire d'Ecologie Alpine, Perturbations Environnementales et Xénobiotiques, CNRS UMR 5553, Université Joseph Fourier, Grenoble Cedex 9, France
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Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 2006; 35:e14. [PMID: 17169982 PMCID: PMC1807943 DOI: 10.1093/nar/gkl938] [Citation(s) in RCA: 531] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.
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Affiliation(s)
- Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France.
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Liepelt S, Sperisen C, Deguilloux MF, Petit RJ, Kissling R, Spencer M, de Beaulieu JL, Taberlet P, Gielly L, Ziegenhagen B. Authenticated DNA from ancient wood remains. Ann Bot 2006; 98:1107-11. [PMID: 16987920 PMCID: PMC3292245 DOI: 10.1093/aob/mcl188] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND The reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final 'proof' is still missing for wood, despite some promising studies. SCOPE The goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers. CONCLUSIONS Authentic DNA was retrieved from wood samples up to 1,000 years of age. A new tool for real-time vegetation history and archaeology is ready to use.
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Affiliation(s)
- Sascha Liepelt
- Philipps-University Marburg, Faculty of Biology Nature Conservation Division, Karl-von-Frisch-Str 2, Marburg, Germany.
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Abstract
We address the impact of the ice age cycles on intraspecific cpDNA diversity, for the first time on the full circumboreal-circumarctic scale. The bird-dispersed bog bilberry (or arctic blueberry, Vaccinium uliginosum) is a key component of northern ecosystems and is here used to assess diversity in previously glaciated vs. unglaciated areas and the importance of Beringia as a refugium and source for interglacial expansion. Eighteen chloroplast DNA haplotypes were observed in and among 122 populations, grouping into three main lineages which probably diverged before, and thus were affected more or less independently by, all major glaciations. The boreal 'Amphi-Atlantic lineage' included one haplotype occurring throughout northern Europe and one occurring in eastern North America, suggesting expansion from at least two bottlenecked, glacial refugium populations. The boreal 'Beringian lineage' included seven haplotypes restricted to Beringia and the Pacific coast of USA. The 'Arctic-Alpine lineage' included nine haplotypes, one of them fully circumpolar. This lineage was unexpectedly diverse, also in previously glaciated areas, suggesting that it thrived on the vast tundras during the ice ages and recolonized deglaciated terrain over long distances. Its largest area of persistence during glaciations was probably situated in the north, stretching from Beringia and far into Eurasia, and it probably also survived the last glaciation in southern mountain ranges. Although Beringia apparently was important for the initial divergence and expansion of V. uliginosum as well as for continuous survival of both the Beringian and Arctic-Alpine lineages during all ice ages, this region played a minor role as a source for later interglacial expansions.
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Affiliation(s)
- I G Alsos
- Tromsø Museum, University of Tromsø, NO-9037 Tromsø, Norway
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Abstract
Rhododendron ferrugineum L. (Ericaceae) is a subalpine shrub found throughout the Pyrenees and Alps at elevations of 1600-2200 m. We examined relationships between genetic and geographic distance, using 115 dominant amplified fragment length polymorphism (AFLP) markers to assess genetic structure over a wide range of spatial scales. We sampled 17 sites with distances of 4 km to more than 1000 km between them. At these scales we detected no association between geographic distance and genetic distance between populations. This suggests that genetic drift and gene flow are not in equilibrium for these populations. This pattern could have resulted from recent and rapid postglacial colonization, from more recent human disturbance, or as a function of frequent and random "natural" long-distance colonization. At two of our sites we used transects (two horizontal and two vertical with respect to slope at each site) to sample at distances ranging from 10 m to more than 5000 m. At this scale we observed a positive relationship between genetic and spatial distance along two vertical transects, one at each site. We hypothesize that isolation-by-distance at this smaller scale is a function of restricted gene flow via seed dispersal.
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Affiliation(s)
- P G Wolf
- Department of Biology and Ecology Center, Utah State University, Logan, UT 84322, USA.
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