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Anderson TM, Hepler SA, Holdo RM, Donaldson JE, Erhardt RJ, Hopcraft JGC, Hutchinson MC, Huebner SE, Morrison TA, Muday J, Munuo IN, Palmer MS, Pansu J, Pringle RM, Sketch R, Packer C. Interplay of competition and facilitation in grazing succession by migrant Serengeti herbivores. Science 2024; 383:782-788. [PMID: 38359113 DOI: 10.1126/science.adg0744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Competition, facilitation, and predation offer alternative explanations for successional patterns of migratory herbivores. However, these interactions are difficult to measure, leaving uncertainty about the mechanisms underlying body-size-dependent grazing-and even whether succession occurs at all. We used data from an 8-year camera-trap survey, GPS-collared herbivores, and fecal DNA metabarcoding to analyze the timing, arrival order, and interactions among migratory grazers in Serengeti National Park. Temporal grazing succession is characterized by a "push-pull" dynamic: Competitive grazing nudges zebra ahead of co-migrating wildebeest, whereas grass consumption by these large-bodied migrants attracts trailing, small-bodied gazelle that benefit from facilitation. "Natural experiments" involving intense wildfires and rainfall respectively disrupted and strengthened these effects. Our results highlight a balance between facilitative and competitive forces in co-regulating large-scale ungulate migrations.
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Affiliation(s)
- T Michael Anderson
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Staci A Hepler
- Department of Statistical Sciences, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Ricardo M Holdo
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Jason E Donaldson
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Robert J Erhardt
- Department of Statistical Sciences, Wake Forest University, Winston-Salem, NC 27109, USA
| | - J Grant C Hopcraft
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Matthew C Hutchinson
- Department of Life & Environmental Sciences, University of California Merced, Merced, CA 95343, USA
| | - Sarah E Huebner
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Thomas A Morrison
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Jeffry Muday
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Issack N Munuo
- Serengeti Wildlife Research Centre, 2113 Lemara, Arusha, TZ
| | - Meredith S Palmer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Johan Pansu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert Sketch
- Department of Statistical Sciences, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Craig Packer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
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Reji Chacko M, Altermatt F, Fopp F, Guisan A, Keggin T, Lyet A, Rey PL, Richards E, Valentini A, Waldock C, Pellissier L. Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes. Oecologia 2023; 202:699-713. [PMID: 37558733 PMCID: PMC10475001 DOI: 10.1007/s00442-023-05428-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/22/2023] [Indexed: 08/11/2023]
Abstract
Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.
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Affiliation(s)
- Merin Reji Chacko
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland.
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Fabian Fopp
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Geopolis, Lausanne, Switzerland
| | - Thomas Keggin
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Arnaud Lyet
- World Wildlife Fund, Wildlife Conservation Team, Washington, DC, USA
| | - Pierre-Louis Rey
- Institute of Earth Surface Dynamics, University of Lausanne, Geopolis, Lausanne, Switzerland
| | - Eilísh Richards
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | | | - Conor Waldock
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Loïc Pellissier
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
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Hervé V, Sabatier P, Lambourdière J, Poulenard J, Lopez PJ. Temporal pesticide dynamics alter specific eukaryotic taxa in a coastal transition zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161205. [PMID: 36603640 DOI: 10.1016/j.scitotenv.2022.161205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/02/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Land use change and anthropogenic forcing can drastically alter the rates and patterns of sediment transport and modify biodiversity and ecosystem functions in coastal transition zones, such as the coastal ecosystems. Molecular studies of sediment extracted DNAs provide information on currently living organisms within the upper layers or buried from various periods of time, but might also provide knowledge on species dynamics, replacement and turnover. In this study, we evaluated the eukaryotic communities of a marine core that present a shift in soil erosion that was linked to glyphosate usage and correlated to chlordecone resurgence since 2000. We show differences in community composition between samples from the second half of the last century and those from the last two decades. Temporal analyses of the relative abundance, alpha diversity, and beta diversity for the two periods demonstrated different temporal dynamics depending on the considered taxonomic group. In particular, Ascomycetes showed a decrease in abundance over the most recent period associated with changes in community membership but not community structure. Two photosynthetic groups, Bacillariophyceae and Prasinophytes clade VII, showed a different pattern with an increase in abundance since the beginning of the 21st century with a decrease in diversity and evenness to form more heterogeneous communities dominated by a few abundant OTUs. Altogether, our data reveal that agricultural usages such as pesticide use can have long-term and species-dependent implications for microeukaryotic coastal communities on a tropical island.
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Affiliation(s)
- Vincent Hervé
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Pierre Sabatier
- EDYTEM, Université Savoie Mont Blanc, CNRS, UMR-5204, 73370 Le Bourget-Du-Lac, France
| | - Josie Lambourdière
- Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique UMR-8067, Sorbonne Université, Institut de Recherche pour le Développement, Université de Caen Normandie, Université des Antilles, 75005 Paris, France
| | - Jérôme Poulenard
- EDYTEM, Université Savoie Mont Blanc, CNRS, UMR-5204, 73370 Le Bourget-Du-Lac, France
| | - Pascal Jean Lopez
- Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique UMR-8067, Sorbonne Université, Institut de Recherche pour le Développement, Université de Caen Normandie, Université des Antilles, 75005 Paris, France.
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4
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Kalneniece K, Gudra D, Lielauss L, Selga T, Fridmanis D, Terauds J, Muter O. Batch-mode stimulation of hydrocarbons biodegradation in freshwater sediments from historically contaminated Alūksne lake. JOURNAL OF CONTAMINANT HYDROLOGY 2023; 253:104103. [PMID: 36435695 DOI: 10.1016/j.jconhyd.2022.104103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Historical contamination of freshwater lakes with hydrocarbons (HC) due to anthropogenic activities represents a serious problem worldwide. This study was focused on hydrocarbons-contaminated sediments sampled in Lake Alūksne of glacial origin in Northeast Latvia. The batch experiments were aimed at evaluating the effect of bio-stimulation and bioaugmentation on the biodegradation of hydrocarbons in lake sediments (LS), as well as changes in microbial community structure and metabolic activity. The sediments were sampled from two points of the lake, 4-5 m and 8 m depth, respectively. These samples slightly differed by colour, count of diatoms, microbial respiration intensity and colour intensity of 2,6- dichlorophenolindophenol. Nevertheless, the trend in biodegradation activity was similar for both LS samples. The concentration of HC in LS during the 32-day incubation decreased in average from 465 mg/kg to 165 mg/kg and 117.5 mg/kg in the LS amended with nutrients and nutrients+microbial community, respectively. Different treatment types of LS resulted in differences in microbial respiration and HC-degrading activity. The Shotgun sequencing has revealed the main phyla present in the intact LS being Proteobacteria (48.8%), Actinobacteria (24.4%), Firmicutes (10.4%) and Bacteroidetes (5.0%). Incubation of LS for 32 days resulted in increasing abundance of Proteobacteria from 48.8% in the raw LS to 58-62%, mainly due to the increase of Betaproteobacteria. The functional annotation of gene families revealed that the most abundant gene families were associated with ATP binding, metal ion, magnesium ion, sulfur cluster, zinc ion binding, DNA binding and other essential components for cell functioning. The Shannon biodiversity index of culturable microorganisms in EcoPlates™ ranged from 2.28 to 2.85. The data obtained in this study indicated that the suggested approach is a potent remediation technology for further ex situ scaling up.
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Affiliation(s)
- Kristine Kalneniece
- Department of Microbiology & Biotechnology, Faculty of Biology, University of Latvia, 1 Jelgavas Str., Riga LV-1004, Latvia
| | - Dita Gudra
- Latvian Biomedical Research and Study Center, 1 Ratsupites Str., Riga LV-1067, Latvia
| | - Ludvigs Lielauss
- Baltijas Juras Geologijas Centrs Ltd., 67A Ieriku Str., LV-1084 Riga, Latvia
| | - Turs Selga
- Faculty of Medicine, University of Latvia, 1 Jelgavas Str., Riga LV-1004, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Center, 1 Ratsupites Str., Riga LV-1067, Latvia
| | - Janis Terauds
- Baltijas Juras Geologijas Centrs Ltd., 67A Ieriku Str., LV-1084 Riga, Latvia
| | - Olga Muter
- Department of Microbiology & Biotechnology, Faculty of Biology, University of Latvia, 1 Jelgavas Str., Riga LV-1004, Latvia.
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Everett R, Cribdon B. MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.888421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.
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Garcés-Pastor S, Coissac E, Lavergne S, Schwörer C, Theurillat JP, Heintzman PD, Wangensteen OS, Tinner W, Rey F, Heer M, Rutzer A, Walsh K, Lammers Y, Brown AG, Goslar T, Rijal DP, Karger DN, Pellissier L, Heiri O, Alsos IG. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change. Nat Commun 2022; 13:6559. [PMID: 36333301 PMCID: PMC9636257 DOI: 10.1038/s41467-022-34010-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.
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Affiliation(s)
- Sandra Garcés-Pastor
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Eric Coissac
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Sébastien Lavergne
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Christoph Schwörer
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Jean-Paul Theurillat
- grid.8591.50000 0001 2322 4988Fondation Aubert, 1938 Champex-Lac, Switzerland, Department of Plant Sciences, University of Geneva, 1292 Chambésy, Switzerland
| | - Peter D. Heintzman
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Owen S. Wangensteen
- grid.10919.300000000122595234Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway ,grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Catalonia Spain
| | - Willy Tinner
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Fabian Rey
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Martina Heer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Astrid Rutzer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Kevin Walsh
- grid.5685.e0000 0004 1936 9668Department of Archaeology, University of York, York, 11 YO1 7EP UK
| | - Youri Lammers
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Antony G. Brown
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Tomasz Goslar
- grid.5633.30000 0001 2097 3545Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, 61-680 Poznań, Poland
| | - Dilli P. Rijal
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Dirk N. Karger
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute for Forest, Snow, and Landscape Research (WSL), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Loïc Pellissier
- grid.5801.c0000 0001 2156 2780Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zurich, Zürich, Switzerland ,grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Oliver Heiri
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Inger Greve Alsos
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
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Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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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] [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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Abstract
Lake sediments are a valuable archive to document past flood occurrence and magnitude, and their evolution over centuries to millennia. This information has the potential to greatly improve current flood design and risk assessment approaches, which are hampered by the shortness and scarcity of gauge records. For this reason, paleoflood hydrology from lake sediments received fast-growing attention over the last decade. This allowed an extensive development of experience and methodologies and, thereby, the reconstruction of paleoflood series with increasingly higher accuracy. In this review, we provide up-to-date knowledge on flood sedimentary processes and systems, as well as on state-of-the-art methods for reconstructing and interpreting paleoflood records. We also discuss possible perspectives in the field of paleoflood hydrology from lake sediments by highlighting the remaining challenges. This review intends to guide the research interest in documenting past floods from lake sediments. In particular, we offer here guidance supported by the literature in how: to choose the most appropriate lake in a given region, to find the best suited sedimentary environments to take the cores, to identify flood deposits in the sedimentary sequence, to distinguish them from other instantaneous deposits, and finally, to rigorously interpret the flood chronicle thus produced.
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Foster NR, van Dijk KJ, Biffin E, Young JM, Thomson VA, Gillanders BM, Jones AR, Waycott M. A Multi-Gene Region Targeted Capture Approach to Detect Plant DNA in Environmental Samples: A Case Study From Coastal Environments. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.735744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes, and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilised gene region for metabarcoding plants due to the short fragment length and subsequent ease of recovery from degraded DNA, which is characteristic of environmental samples. However, the taxonomic resolution for this gene region is limited, often precluding species level identification. Additionally, targeting gene regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase the ability of DNA metabarcoding to better resolve flowering plant species (angiosperms) within environmental samples, and reduce bias in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species. Using this approach, we effectively recovered multiple chloroplast gene regions for three species within artificial DNA mixtures down to 0.001 ng/μL of DNA. We tested the detection level of this approach, successfully recovering target genes for 10 flowering plant species. Finally, we applied this approach to sediment samples containing unknown compositions of eDNA and confidently detected plant species that were later verified with observation data. Targeting multiple chloroplast gene regions in environmental samples, enabled species-level information to be recovered from complex DNA mixtures. Thus, the method developed here, confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.
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12
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Pearman JK, Biessy L, Howarth JD, Vandergoes MJ, Rees A, Wood SA. Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives. Mol Ecol Resour 2021; 22:877-890. [PMID: 34562066 DOI: 10.1111/1755-0998.13515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 01/04/2023]
Abstract
Lake sediments accumulate information on biological communities thus acting as natural archives. Traditionally paleolimnology has focussed on fossilized remains of organisms, however, many organisms do not leave fossil evidence, meaning major ecosystem components are missing from environmental reconstructions. Many paleolimnology studies now incorporate molecular methods, including investigating microbial communities using environmental DNA (eDNA), but there is uncertainty about the contribution of living organisms to molecular inventories. In the present study, we obtained DNA and RNA inventories from sediment spanning 700 years to investigate the contribution of past and active communities to the molecular signal from sedimentary archives. Additionally, a droplet digital PCR (ddPCR) targeting the 16S ribosomal RNA (16S rRNA) gene of the photosynthetic cyanobacterial genera Microcystis was used to explore if RNA signals were from legacy RNA. We posit that the RNA signal is a mixture of legacy RNA, dormant cells, living bacteria and modern-day trace level contaminants that were introduced during sampling and preferentially amplified. The presence of legacy RNA was confirmed by the detection of Microcystis in sediments aged to ~200 years ago. Recent comparisons between 16S rRNA gene metabarcoding and traditional paleo proxies showed that past changes in bacterial communities can be reconstructed from sedimentary archives. The recovery of RNA in the present study has provided new insights into the origin of these signals. However, caution is required during analysis and interpretation of 16S rRNA gene metabarcoding data especially in recent sediments were there are potentially active bacteria.
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Affiliation(s)
- John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Andrew Rees
- University of Victoria, Wellington, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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13
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Osathanunkul M, Sawongta N, Pheera W, Pechlivanis N, Psomopoulos F, Madesis P. Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning. PeerJ 2021; 9:e11753. [PMID: 34414025 PMCID: PMC8340909 DOI: 10.7717/peerj.11753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited. Methods Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron. Results The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5-10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.
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Affiliation(s)
- Maslin Osathanunkul
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand.,Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Nipitpong Sawongta
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Wittaya Pheera
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece.,Development and Molecular Biology, School of Biology, Department of Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece.,Crop Production and Rural Environment, Laboratory of Molecular Biology of Plants, Department of Agriculture, University of Thessaly, Volos, Magnesia, Greece
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14
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Rijal DP, Heintzman PD, Lammers Y, Yoccoz NG, Lorberau KE, Pitelkova I, Goslar T, Murguzur FJA, Salonen JS, Helmens KF, Bakke J, Edwards ME, Alm T, Bråthen KA, Brown AG, Alsos IG. Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia. SCIENCE ADVANCES 2021; 7:eabf9557. [PMID: 34330702 PMCID: PMC8324056 DOI: 10.1126/sciadv.abf9557] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/15/2021] [Indexed: 05/22/2023]
Abstract
The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.
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Affiliation(s)
- Dilli P Rijal
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway.
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nigel G Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kelsey E Lorberau
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Iva Pitelkova
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tomasz Goslar
- Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
- Poznań Park of Science and Technology, Poznań, Poland
| | - Francisco J A Murguzur
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - J Sakari Salonen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Karin F Helmens
- Swedish Museum of Natural History, P.O. Box 50007, 10405 Stockholm, Sweden
- Värriö Research Station, Institute for Atmospheric and Earth System Research INAR/Physics, University of Helsinki, P.O. Box 64, 00014 Helsinki, Finland
| | - Jostein Bakke
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Mary E Edwards
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Alaska Quaternary Center, University of Alaska, Fairbanks, AK 99775, USA
| | - Torbjørn Alm
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kari Anne Bråthen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Antony G Brown
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway.
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15
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Pearman JK, Thomson-Laing G, Howarth JD, Vandergoes MJ, Thompson L, Rees A, Wood SA. Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores. PLoS One 2021; 16:e0250783. [PMID: 33939728 PMCID: PMC8092796 DOI: 10.1371/journal.pone.0250783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- * E-mail:
| | | | | | | | - Lucy Thompson
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Andrew Rees
- Victoria University of Wellington, Wellington, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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16
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Arribas P, Andújar C, Bidartondo MI, Bohmann K, Coissac É, Creer S, deWaard JR, Elbrecht V, Ficetola GF, Goberna M, Kennedy S, Krehenwinkel H, Leese F, Novotny V, Ronquist F, Yu DW, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Vogler AP, Papadopoulou A, Emerson BC. Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Mol Ecol 2021; 30:1120-1135. [PMID: 33432777 PMCID: PMC7986105 DOI: 10.1111/mec.15797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023]
Abstract
High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Carmelo Andújar
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Martin I. Bidartondo
- Department of Life SciencesImperial College LondonLondonUK
- Comparative Plant and Fungal BiologyRoyal Botanic GardensLondonUK
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Éric Coissac
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Jeremy R. deWaard
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphCanada
- School of Environmental SciencesUniversity of GuelphGuelphCanada
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM)Zoological Research Museum Alexander KoenigBonnGermany
| | - Gentile F. Ficetola
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
- Department of Environmental Sciences and PolicyUniversity of MilanoMilanoItaly
| | - Marta Goberna
- Department of Environment and AgronomyINIAMadridSpain
| | - Susan Kennedy
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Department of BiogeographyTrier UniversityTrierGermany
| | | | - Florian Leese
- Aquatic Ecosystem Research, Faculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU) EssenUniversity of Duisburg‐EssenEssenGermany
| | - Vojtech Novotny
- Biology Centre, Institute of EntomologyCzech Academy of SciencesCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Fredrik Ronquist
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Lucie Zinger
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | | | | | | | - Isaac Overcast
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
- Division of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkUSA
| | - Hélène Morlon
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Alfried P. Vogler
- Department of Life SciencesImperial College LondonLondonUK
- Department of Life SciencesNatural History MuseumLondonUK
| | | | - Brent C. Emerson
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
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17
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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18
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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19
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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] [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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20
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Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes. Sci Rep 2020; 10:10502. [PMID: 32601368 PMCID: PMC7324595 DOI: 10.1038/s41598-020-67452-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/19/2020] [Indexed: 11/08/2022] Open
Abstract
eDNA refers to DNA extracted from an environmental sample with the goal of identifying the occurrence of past or current biological communities in aquatic and terrestrial environments. However, there is currently a lack of knowledge regarding the soil memory effect and its potential impact on lake sediment eDNA records. To investigate this issue, two contrasted sites located in cultivated environments in France were studied. In the first site, soil samples were collected (n = 30) in plots for which the crop rotation history was documented since 1975. In the second site, samples were collected (n = 40) to compare the abundance of currently observed taxa versus detected taxa in cropland and other land uses. The results showed that the last cultivated crop was detected in 100% of the samples as the most abundant. In addition, weeds were the most abundant taxa identified in both sites. Overall, these results illustrate the potential of eDNA analyses for identifying the recent (< 10 years) land cover history of soils and outline the detection of different taxa in cultivated plots. The capacity of detection of plant species grown on soils delivering sediments to lacustrine systems is promising to improve our understanding of sediment transfer processes over short timescales.
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21
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Kuefner W, Hofmann AM, Geist J, Raeder U. Evaluating climate change impacts on mountain lakes by applying the new silicification value to paleolimnological samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136913. [PMID: 32007888 DOI: 10.1016/j.scitotenv.2020.136913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The evaluation of climate change impact on lakes typically relies on statistical methods like the reorganisation of organism communities (beta diversity) or transfer functions. A new method uses the silicification of diatoms that correlates with temperature and nutrients. The so-called silicification value (SiVa) overcomes problems of descriptive statistics or absent indicator species. Averaged over diatom communities, it related inversely to lake surface temperatures in mountain lakes. Hence, its change over time (δ SiVa) in a lake was hypothesised to reflect global change-driven lake warming quantitatively, which supposedly climaxes in shallow lakes. Sixteen different δ SiVa calculation approaches were tested. They (1) included or excluded planktic diatoms, (2) integrated fixed or variable time series referring to climate data or changes in diatom assemblages, (3) employed a top-bottom or regression approach and (4) expressed the δ SiVa as relative or absolute values. Subfossil diatom assemblages from 24 sediment cores from Bavarian and north Tyrolian mountain lakes served as sample set. All possible approaches were evaluated for their explanatory power for lake characteristics using GLMs. The top-bottom benthic approach with fixed climate data-based time series appeared to be the best model based on AIC and the extent of variable integration. In line with the hypothesis, the strongest decrease of δ SiVa was evident in most shallow lakes. Segmented regression further highlighted a positive correlation with depth if shallower than 10 m. By referring to the negative SiVa-summer temperature relation, δ SiVa also enabled the quantification of lake warming within the last decades, which ranged mainly between 0.1 °C and 1.1 °C per decade, consistent with existing literature. Additionally, a 100 year temperature reconstruction from a varved sediment core successfully validated the approach. Further studies may focus and extend its application to deeper lakes, but it can already serve as a powerful tool in palaeolimnological studies of shallow lakes like hard-water mountain lakes.
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Affiliation(s)
- Wolfgang Kuefner
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Department of Ecology and Ecosystem Management, Technical University of Munich, Hofmark 1-3, D-82393 Iffeldorf, Germany.
| | - Andrea M Hofmann
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Department of Ecology and Ecosystem Management, Technical University of Munich, Hofmark 1-3, D-82393 Iffeldorf, Germany.
| | - Juergen Geist
- Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management, Technical University of Munich, Mühlenweg 22, D-85354 Freising, Germany.
| | - Uta Raeder
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Department of Ecology and Ecosystem Management, Technical University of Munich, Hofmark 1-3, D-82393 Iffeldorf, Germany.
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22
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Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan. PLoS One 2020; 15:e0226654. [PMID: 32130218 PMCID: PMC7055813 DOI: 10.1371/journal.pone.0226654] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/01/2019] [Indexed: 11/21/2022] Open
Abstract
Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th–19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.
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23
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Guyton JA, Pansu J, Hutchinson MC, Kartzinel TR, Potter AB, Coverdale TC, Daskin JH, da Conceição AG, Peel MJS, Stalmans ME, Pringle RM. Trophic rewilding revives biotic resistance to shrub invasion. Nat Ecol Evol 2020; 4:712-724. [PMID: 31932702 DOI: 10.1038/s41559-019-1068-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/20/2019] [Indexed: 11/09/2022]
Abstract
Trophic rewilding seeks to rehabilitate degraded ecosystems by repopulating them with large animals, thereby re-establishing strong top-down interactions. Yet there are very few tests of whether such initiatives can restore ecosystem structure and functions, and on what timescales. Here we show that war-induced collapse of large-mammal populations in Mozambique's Gorongosa National Park exacerbated woody encroachment by the invasive shrub Mimosa pigra-considered one of the world's 100 worst invasive species-and that one decade of concerted trophic rewilding restored this invasion to pre-war baseline levels. Mimosa occurrence increased between 1972 and 2015, a period encompassing the near extirpation of large herbivores during the Mozambican Civil War. From 2015 to 2019, mimosa abundance declined as ungulate biomass recovered. DNA metabarcoding revealed that ruminant herbivores fed heavily on mimosa, and experimental exclosures confirmed the causal role of mammalian herbivory in containing shrub encroachment. Our results provide mechanistic evidence that trophic rewilding has rapidly revived a key ecosystem function (biotic resistance to a notorious woody invader), underscoring the potential for restoring ecological health in degraded protected areas.
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Affiliation(s)
- Jennifer A Guyton
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Johan Pansu
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Station Biologique de Roscoff, UMR 7144 CNRS-Sorbonne Université, Roscoff, France.,CSIRO Ocean & Atmosphere, Lucas Heights, New South Wales, Australia
| | - Matthew C Hutchinson
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Tyler R Kartzinel
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Ecology & Evolutionary Biology, Brown University, Providence, RI, USA
| | - Arjun B Potter
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Tyler C Coverdale
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Joshua H Daskin
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Mike J S Peel
- ARC-Animal Production Institute, Rangeland Ecology Group, Nelspruit, South Africa
| | - Marc E Stalmans
- Department of Scientific Services, Parque Nacional da Gorongosa, Sofala, Mozambique
| | - Robert M Pringle
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA. .,Department of Scientific Services, Parque Nacional da Gorongosa, Sofala, Mozambique.
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24
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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] [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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25
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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] [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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26
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Parducci L, Alsos IG, Unneberg P, Pedersen MW, Han L, Lammers Y, Salonen JS, Väliranta MM, Slotte T, Wohlfarth B. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00189] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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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28
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Atkins JL, Long RA, Pansu J, Daskin JH, Potter AB, Stalmans ME, Tarnita CE, Pringle RM. Cascading impacts of large-carnivore extirpation in an African ecosystem. Science 2019; 364:173-177. [PMID: 30846612 DOI: 10.1126/science.aau3561] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 02/22/2019] [Indexed: 01/06/2023]
Abstract
Populations of the world's largest carnivores are declining and now occupy mere fractions of their historical ranges. Theory predicts that when apex predators disappear, large herbivores become less fearful, occupy new habitats, and modify those habitats by eating new food plants. Yet experimental support for this prediction has been difficult to obtain in large-mammal systems. After the extirpation of leopards and African wild dogs from Mozambique's Gorongosa National Park, forest-dwelling antelopes [bushbuck (Tragelaphus sylvaticus)] expanded into treeless floodplains, where they consumed novel diets and suppressed a common food plant [waterwort (Bergia mossambicensis)]. By experimentally simulating predation risk, we demonstrate that this behavior was reversible. Thus, whereas anthropogenic predator extinction disrupted a trophic cascade by enabling rapid differentiation of prey behavior, carnivore restoration may just as rapidly reestablish that cascade.
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Affiliation(s)
- Justine L Atkins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Ryan A Long
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Johan Pansu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Station Biologique de Roscoff, UMR 7144 CNRS-Sorbonne Université, 29688 Roscoff, France.,CSIRO Ocean and Atmosphere, Lucas Heights, NSW 2234, Australia
| | - Joshua H Daskin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Arjun B Potter
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Marc E Stalmans
- Department of Scientific Services, Parque Nacional da Gorongosa, Sofala, Mozambique
| | - Corina E Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
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29
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Epp LS, Zimmermann HH, Stoof-Leichsenring KR. Sampling and Extraction of Ancient DNA from Sediments. Methods Mol Biol 2019; 1963:31-44. [PMID: 30875042 DOI: 10.1007/978-1-4939-9176-1_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.
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Affiliation(s)
- Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany. .,Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Heike H Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
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30
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Bálint M, Pfenninger M, Grossart HP, Taberlet P, Vellend M, Leibold MA, Englund G, Bowler D. Environmental DNA Time Series in Ecology. Trends Ecol Evol 2018; 33:945-957. [DOI: 10.1016/j.tree.2018.09.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/28/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022]
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32
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Cristescu ME, Hebert PD. Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062306] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.
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Affiliation(s)
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Ontario N1G 2W1, Canada
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33
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Chen W, Ficetola GF. Conditionally autoregressive models improve occupancy analyses of autocorrelated data: An example with environmental DNA. Mol Ecol Resour 2018; 19:163-175. [DOI: 10.1111/1755-0998.12949] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Wentao Chen
- Laboratoire d’Écologie Alpine (LECA) CNRS Univ. Grenoble Alpes Grenoble France
| | - Gentile Francesco Ficetola
- Laboratoire d’Écologie Alpine (LECA) CNRS Univ. Grenoble Alpes Grenoble France
- Department of Environmental Science and Policy Università degli Studi di Milano Milano Italy
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34
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Mata VA, Rebelo H, Amorim F, McCracken GF, Jarman S, Beja P. How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis. Mol Ecol 2018; 28:165-175. [PMID: 29940083 PMCID: PMC7379978 DOI: 10.1111/mec.14779] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 11/29/2022]
Abstract
DNA metabarcoding is increasingly used in dietary studies to estimate diversity, composition and frequency of occurrence of prey items. However, few studies have assessed how technical and biological replication affect the accuracy of diet estimates. This study addresses these issues using the European free‐tailed bat Tadarida teniotis, involving high‐throughput sequencing of a small fragment of the COI gene in 15 separate faecal pellets and a 15‐pellet pool per each of 20 bats. We investigated how diet descriptors were affected by variability among (a) individuals, (b) pellets of each individual and (c) PCRs of each pellet. In addition, we investigated the impact of (d) analysing separate pellets vs. pellet pools. We found that diet diversity estimates increased steadily with the number of pellets analysed per individual, with seven pellets required to detect ~80% of prey species. Most variation in diet composition was associated with differences among individual bats, followed by pellets per individual and PCRs per pellet. The accuracy of frequency of occurrence estimates increased with the number of pellets analysed per bat, with the highest error rates recorded for prey consumed infrequently by many individuals. Pools provided poor estimates of diet diversity and frequency of occurrence, which were comparable to analysing a single pellet per individual, and consistently missed the less common prey items. Overall, our results stress that maximizing biological replication is critical in dietary metabarcoding studies and emphasize that analysing several samples per individual rather than pooled samples produce more accurate results.
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Affiliation(s)
- Vanessa A Mata
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Hugo Rebelo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,CEABN-InBIO, Centro de Ecologia Aplicada "Professor Baeta Neves", Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Francisco Amorim
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Gary F McCracken
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee
| | - Simon Jarman
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Trace and Environmental DNA (TrEnD) Laboratory, Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, Australia
| | - Pedro Beja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,CEABN-InBIO, Centro de Ecologia Aplicada "Professor Baeta Neves", Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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35
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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. SCIENCE ADVANCES 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] [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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36
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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] [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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37
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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38
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Bálint M, Márton O, Schatz M, Düring R, Grossart H. Proper experimental design requires randomization/balancing of molecular ecology experiments. Ecol Evol 2018; 8:1786-1793. [PMID: 29435253 PMCID: PMC5792580 DOI: 10.1002/ece3.3687] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/21/2017] [Accepted: 10/26/2017] [Indexed: 12/12/2022] Open
Abstract
Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.
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Affiliation(s)
- Miklós Bálint
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Orsolya Márton
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Soil Sciences and Agricultural ChemistryCentre for Agricultural ResearchHungarian Academy of SciencesBudapestHungary
| | | | | | - Hans‐Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland FisheriesStechlinGermany
- Institute of Biochemistry and BiologyPotsdam UniversityPotsdamGermany
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39
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Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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40
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Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol 2017; 26:5872-5895. [PMID: 28921802 DOI: 10.1111/mec.14350] [Citation(s) in RCA: 590] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
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Affiliation(s)
- Kristy Deiner
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Holly M Bik
- Department of Nematology, University of California, Riverside, CA, USA
| | - Elvira Mächler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | | | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | - Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David M Lodge
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Natasha de Vere
- Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
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41
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Salmona J, Heller R, Quéméré E, Chikhi L. Climate change and human colonization triggered habitat loss and fragmentation in Madagascar. Mol Ecol 2017; 26:5203-5222. [DOI: 10.1111/mec.14173] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Jordi Salmona
- Instituto Gulbenkian de Ciênca; Oeiras Portugal
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS; Université Paul Sabatier; Toulouse France
- UMR 5174 EDB; Université de Toulouse; Toulouse France
| | - Rasmus Heller
- Department of Biology; University of Copenhagen; Copenhagen N Denmark
| | - Erwan Quéméré
- CEFS; Université de Toulouse; INRA; Castanet-Tolosan France
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciênca; Oeiras Portugal
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS; Université Paul Sabatier; Toulouse France
- UMR 5174 EDB; Université de Toulouse; Toulouse France
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42
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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43
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Somervuo P, Yu DW, Xu CC, Ji Y, Hultman J, Wirta H, Ovaskainen O. Quantifying uncertainty of taxonomic placement in
DNA
barcoding and metabarcoding. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12721] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Panu Somervuo
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Charles C.Y. Xu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- Groningen Institute for Evolutionary Life Sciences University of Groningen P.O. Box 11103 9700 CC Groningen The Netherlands
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
| | - Jenni Hultman
- Department of Food and Environmental Sciences University of Helsinki P.O. Box 56 Helsinki FI‐00014 Finland
| | - Helena Wirta
- Department of Agricultural Sciences University of Helsinki P.O. Box 27 Helsinki FI‐00014 Finland
| | - Otso Ovaskainen
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology N‐7491 Trondheim Norway
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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. THE NEW PHYTOLOGIST 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] [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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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM. The ecologist's field guide to sequence‐based identification of biodiversity. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12574] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Environment Centre Wales Building Bangor University Deiniol Road Bangor Gwynedd LL57 2UW UK
| | - Kristy Deiner
- Eawag: Aquatic Ecology Überlandstrasse 133 8600 Dübendorf Switzerland
| | - Serita Frey
- Natural Resources and the Environment University of New Hampshire Durham NH 03824 USA
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder Boulder CO 80309 USA
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 F‐38041 Grenoble Cedex 9 France
| | - W. Kelley Thomas
- Department of Molecular, Cellular, & Biomedical Sciences University of New Hampshire Durham NH 03824 USA
| | - Caitlin Potter
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Environment Centre Wales Building Bangor University Deiniol Road Bangor Gwynedd LL57 2UW UK
| | - Holly M. Bik
- Center for Genomics and Systems Biology Department of Biology New York University, New York NY 10003 USA
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Birks HJB, Birks HH. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? THE NEW PHYTOLOGIST 2016; 209:499-506. [PMID: 26402315 DOI: 10.1111/nph.13657] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/03/2015] [Indexed: 06/05/2023]
Abstract
499 I. 499 II. 500 III. 500 IV. 500 V. 500 VI. 501 VII. 502 VIII. 504 504 References 505 SUMMARY: Ancient DNA (aDNA) from lake sediments, peats, permafrost soils, preserved megafaunal gut contents and coprolites has been used to reconstruct late-Quaternary floras. aDNA is either used alone for floristic reconstruction or compared with pollen and/or macrofossil results. In comparative studies, aDNA may complement pollen and macrofossil analyses by increasing the number of taxa found. We discuss the relative contributions of each fossil group to taxon richness and the number of unique taxa found, and situations in which aDNA has refined pollen identifications. Pressing problems in aDNA studies are contamination and ignorance about taphonomy (transportation, incorporation, and preservation in sediments). Progress requires that these problems are reduced to allow aDNA to reach its full potential contribution to reconstructions of Quaternary floras.
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Affiliation(s)
- H John B Birks
- Department of Biology, University of Bergen, and Bjerknes Centre for Climate Research, Postbox 7803, N-5020, Bergen, Norway
- Environmental Change Research Centre, University College London, Gower Street, London, WC1E 6BT, UK
| | - Hilary H Birks
- Department of Biology, University of Bergen, and Bjerknes Centre for Climate Research, Postbox 7803, N-5020, Bergen, Norway
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