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Alsos IG, Boussange V, Rijal DP, Beaulieu M, Brown AG, Herzschuh U, Svenning JC, Pellissier L. Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230017. [PMID: 38583481 PMCID: PMC10999269 DOI: 10.1098/rstb.2023.0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/22/2023] [Indexed: 04/09/2024] Open
Abstract
Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.
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Affiliation(s)
- Inger Greve Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Victor Boussange
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Dilli Prasad Rijal
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Marieke Beaulieu
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Antony Gavin Brown
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ulrike Herzschuh
- Alfred Wegener Institute for Polar and Marine Research, Telegraphenberg A43, 14473 Potsdam, Germany
- Institute of Environmental Sciences and Geography, Potsdam University, 14479 Potsdam, Germany
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Loïc Pellissier
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
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2
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Thomson-Laing G, Howarth JD, Atalah J, Vandergoes MJ, Li X, Pearman JK, Fitzsimons S, Moy C, Moody A, Shepherd C, McKay N, Wood SA. Sedimentary ancient DNA reveals the impact of anthropogenic land use disturbance and ecological shifts on fish community structure in small lowland lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171266. [PMID: 38417515 DOI: 10.1016/j.scitotenv.2024.171266] [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: 12/20/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Freshwater fish biodiversity and abundance are decreasing globally. The drivers of decline are primarily anthropogenic; however, the causative links between disturbances and fish community change are complex and challenging to investigate. We used a suite of sedimentary DNA methods (droplet digital PCR and metabarcoding) and traditional paleolimnological approaches, including pollen and trace metal analysis, ITRAX X-ray fluorescence and hyperspectral core scanning to explore changes in fish abundance and drivers over 1390 years in a small lake. This period captured a disturbance trajectory from pre-human settlement through subsistence living to intensive agriculture. Generalized additive mixed models explored the relationships between catchment inputs, internal drivers, and fish community structure. Fish community composition distinctly shifted around 1350 CE, with the decline of a sensitive Galaxias species concomitant with early land use changes. Total fish abundance significantly declined around 1950 CE related to increases in ruminant bacterial DNA (a proxy for ruminant abundance) and cadmium flux (a proxy for phosphate fertilizers), implicating land use intensification as a key driver. Concurrent shifts in phytoplankton and zooplankton suggested that fish communities were likely impacted by food web dynamics. This study highlights the potential of sedDNA to elucidate the long-term disturbance impacts on biological communities in lakes.
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Affiliation(s)
- Georgia Thomson-Laing
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand; School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand.
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Javier Atalah
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand
| | | | - Xun Li
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand
| | - John K Pearman
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Sean Fitzsimons
- School of Geography, University of Otago, 360 Leith Street, North Dunedin, Dunedin 9054, New Zealand
| | - Chris Moy
- Department of Geology, University of Otago, 360 Leith Street, North Dunedin, Dunedin 9054, New Zealand
| | - Adelaine Moody
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Claire Shepherd
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand
| | - Nicholas McKay
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Susanna A Wood
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand
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3
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Harning DJ, Sacco S, Anamthawat-Jónsson K, Ardenghi N, Thordarson T, Raberg JH, Sepúlveda J, Geirsdóttir Á, Shapiro B, Miller GH. Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic. eLife 2023; 12:RP87749. [PMID: 37955570 PMCID: PMC10642962 DOI: 10.7554/elife.87749] [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] [Indexed: 11/14/2023] Open
Abstract
As the Arctic continues to warm, woody shrubs are expected to expand northward. This process, known as 'shrubification,' has important implications for regional biodiversity, food web structure, and high-latitude temperature amplification. While the future rate of shrubification remains poorly constrained, past records of plant immigration to newly deglaciated landscapes in the Arctic may serve as useful analogs. We provide one new postglacial Holocene sedimentary ancient DNA (sedaDNA) record of vascular plants from Iceland and place a second Iceland postglacial sedaDNA record on an improved geochronology; both show Salicaceae present shortly after deglaciation, whereas Betulaceae first appears more than 1000 y later. We find a similar pattern of delayed Betulaceae colonization in eight previously published postglacial sedaDNA records from across the glaciated circum North Atlantic. In nearly all cases, we find that Salicaceae colonizes earlier than Betulaceae and that Betulaceae colonization is increasingly delayed for locations farther from glacial-age woody plant refugia. These trends in Salicaceae and Betulaceae colonization are consistent with the plant families' environmental tolerances, species diversity, reproductive strategies, seed sizes, and soil preferences. As these reconstructions capture the efficiency of postglacial vascular plant migration during a past period of high-latitude warming, a similarly slow response of some woody shrubs to current warming in glaciated regions, and possibly non-glaciated tundra, may delay Arctic shrubification and future changes in the structure of tundra ecosystems and temperature amplification.
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Affiliation(s)
- David J Harning
- Institute of Arctic and Alpine Research, University of Colorado BoulderBoulderUnited States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta CruzUnited States
| | | | - Nicolò Ardenghi
- Institute of Arctic and Alpine Research, University of Colorado BoulderBoulderUnited States
| | - Thor Thordarson
- Faculty of Earth Sciences, University of IcelandReykjavikIceland
| | - Jonathan H Raberg
- Institute of Arctic and Alpine Research, University of Colorado BoulderBoulderUnited States
| | - Julio Sepúlveda
- Institute of Arctic and Alpine Research, University of Colorado BoulderBoulderUnited States
- Department of Geological Sciences, University of Colorado BoulderBoulderUnited States
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta CruzUnited States
| | - Gifford H Miller
- Institute of Arctic and Alpine Research, University of Colorado BoulderBoulderUnited States
- Department of Geological Sciences, University of Colorado BoulderBoulderUnited States
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4
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Williams JW, Spanbauer TL, Heintzman PD, Blois J, Capo E, Goring SJ, Monchamp ME, Parducci L, Von Eggers JM. Strengthening global-change science by integrating aeDNA with paleoecoinformatics. Trends Ecol Evol 2023; 38:946-960. [PMID: 37230884 DOI: 10.1016/j.tree.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.
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Affiliation(s)
- John W Williams
- Department of Geography, University of Wisconsin-Madison, Madison, WI 53704, USA.
| | - Trisha L Spanbauer
- Department of Environmental Science and Lake Erie Center, University of Toledo, Toledo, OH 43606, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Jessica Blois
- Department of Life and Environmental Sciences, University of California -Merced, Merced, CA 95343, USA
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, 907 36 Umeå, Sweden
| | - Simon J Goring
- Department of Geography, University of Wisconsin-Madison, Madison, WI 53704, USA
| | | | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Jordan M Von Eggers
- Department of Geology and Geophysics, University of Wyoming, Laramie, WY 82071, USA
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5
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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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6
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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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7
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ter Schure AT, Bruch AA, Kandel AW, Gasparyan B, Bussmann RW, Brysting AK, de Boer HJ, Boessenkool S. Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. J Hum Evol 2022; 172:103258. [DOI: 10.1016/j.jhevol.2022.103258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022]
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8
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Alsos IG, Rijal DP, Ehrich D, Karger DN, Yoccoz NG, Heintzman PD, Brown AG, Lammers Y, Pellissier L, Alm T, Bråthen KA, Coissac E, Merkel MKF, Alberti A, Denoeud F, Bakke J. Postglacial species arrival and diversity buildup of northern ecosystems took millennia. SCIENCE ADVANCES 2022; 8:eabo7434. [PMID: 36170372 PMCID: PMC9519041 DOI: 10.1126/sciadv.abo7434] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/12/2022] [Indexed: 05/31/2023]
Abstract
What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.
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Affiliation(s)
- Inger Greve Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dilli Prasad Rijal
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
- Institute of Marine Research, Tromsø, Norway
| | - Dorothee Ehrich
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dirk Nikolaus Karger
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Nigel Gilles Yoccoz
- 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
| | - Antony G. Brown
- 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
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Department of Environmental System Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - 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
| | - Eric Coissac
- Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, France
| | | | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - France Denoeud
- Department of Environmental System Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Jostein Bakke
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
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9
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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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10
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Murchie TJ, Karpinski E, Eaton K, Duggan AT, Baleka S, Zazula G, MacPhee RDE, Froese D, Poinar HN. Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Curr Biol 2022; 32:851-860.e7. [PMID: 35016010 DOI: 10.1016/j.cub.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Box 2703, Whitehorse, YT Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON K1P 6P4, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; CIFAR, Humans and the Microbiome Program, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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11
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Huang S, Stoof-Leichsenring KR, Liu S, Courtin J, Andreev AA, Pestryakova LA, Herzschuh U. Plant Sedimentary Ancient DNA From Far East Russia Covering the Last 28,000 Years Reveals Different Assembly Rules in Cold and Warm Climates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.763747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plant communities is not well understood due to the limited knowledge about plant assembly rules. Records of past plant diversity over long time series are rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation biomass could be highest. We reveal highest richness during 28–23 ka and a second richness peak during 13–9 ka, with both periods being accompanied by low relative abundance of shrubs. During the cold period before 14 ka, rich plant assemblages were phylogenetically clustered, suggesting low genetic divergence in the assemblages despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich plant assemblages were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness might overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.
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12
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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13
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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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14
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Fediajevaite J, Priestley V, Arnold R, Savolainen V. Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards. Ecol Evol 2021; 11:4803-4815. [PMID: 33976849 PMCID: PMC8093654 DOI: 10.1002/ece3.7382] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost-effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta-analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently "better."Environmental DNA publications for multiple species or single macro-organism detection were identified using the Web of Science, by searching "eDNA" and "environmental DNA" across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa-dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance. Synthesis and applications: The results of this meta-analysis demonstrate that where there is a direct comparison, eDNA surveys of macro-organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods-based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.
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Affiliation(s)
| | | | - Richard Arnold
- Thomson Environmental Consultants Compass House Surrey Research Park Guildford UK
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15
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Jones L, Twyford AD, Ford CR, Rich TCG, Davies H, Forrest LL, Hart ML, McHaffie H, Brown MR, Hollingsworth PM, de Vere N. Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom. Mol Ecol Resour 2021; 21:2050-2062. [PMID: 33749162 DOI: 10.1111/1755-0998.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/09/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding and metabarcoding provide new avenues for investigating biological systems. These techniques require well-curated reference libraries with extensive coverage. Generating an exhaustive national DNA barcode reference library can open up new avenues of research in ecology, evolution and conservation, yet few studies to date have created such a resource. In plant DNA barcoding, herbarium collections provide taxonomically robust material but also pose challenges in lab processing. Here, we present a national DNA barcoding resource covering all of the native flowering plants and conifers of the United Kingdom. This represents 1,482 plant species, with the majority of specimens (81%) sourced from herbaria. Using Sanger sequencing of the plant DNA barcode markers, rbcL, matK, and ITS2, at least one DNA barcode was retrieved from 98% of the UK flora. We sampled from multiple individuals, resulting in a species coverage for rbcL of 96% (4,477 sequences), 90% for matK (3,259 sequences) and 75% for ITS2 (2,585 sequences). Sequence recovery was lower for herbarium material compared to fresh collections, with the age of the specimen having a significant effect on the success of sequence recovery. Species level discrimination was highest with ITS2, however, the ability to successfully retrieve a sequence was lowest for this region. Analyses of the genetic distinctiveness of species across a complete flora showed DNA barcoding to be informative for all but the most taxonomically complex groups. The UK flora DNA barcode reference library provides an important resource for many applications that require plant identification from DNA.
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Affiliation(s)
- Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Alex D Twyford
- Royal Botanic Garden Edinburgh, Edinburgh, UK.,School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | - Col R Ford
- National Botanic Garden of Wales, Llanarthne, UK
| | | | | | | | | | | | - Max R Brown
- School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | | | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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16
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Crump SE, Fréchette B, Power M, Cutler S, de Wet G, Raynolds MK, Raberg JH, Briner JP, Thomas EK, Sepúlveda J, Shapiro B, Bunce M, Miller GH. Ancient plant DNA reveals High Arctic greening during the Last Interglacial. Proc Natl Acad Sci U S A 2021; 118:e2019069118. [PMID: 33723011 PMCID: PMC8020792 DOI: 10.1073/pnas.2019069118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.
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Affiliation(s)
- Sarah E Crump
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303;
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Bianca Fréchette
- Geotop, Université du Québec à Montréal, Montréal, H2L 2C4, Canada
| | - Matthew Power
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, 6845 Bentley, Australia
| | - Sam Cutler
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Gregory de Wet
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
- Department of Geosciences, Smith College, Northampton, MA 01063
| | - Martha K Raynolds
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Jonathan H Raberg
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
| | - Jason P Briner
- Department of Geology, University at Buffalo, Buffalo, NY 14260
| | | | - Julio Sepúlveda
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
- HHMI, University of California, Santa Cruz, CA 95064
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, 6845 Bentley, Australia
- New Zealand Environment Protection Authority, 6011 Wellington, New Zealand
| | - Gifford H Miller
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
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17
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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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18
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Ibrahim A, Capo E, Wessels M, Martin I, Meyer A, Schleheck D, Epp LS. Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA. Mol Ecol 2020; 30:3040-3056. [PMID: 33070403 DOI: 10.1111/mec.15696] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/12/2020] [Accepted: 10/05/2020] [Indexed: 01/04/2023]
Abstract
During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change in the past and comparison of pre- and postimpact communities. Peri-Alpine Lake Constance (Germany) underwent a mid-century period of eutrophication followed by re-oligotrophication since the 1980s and is now experiencing warm temperatures. We extended the period for which monitoring data of indicator organisms exist by analysing historical environmental DNA (eDNA) from a sediment core dating back some 110 years. Using three metabarcoding markers-for microbial eukaryotes, diatoms and cyanobacteria-we revealed two major breakpoints of community change, in the 1930s and the mid-1990s. In our core, the latest response was exhibited by diatoms, which are classically used as palaeo-bioindicators for the trophic state of lakes. Following re-oligotrophication, overall diversity values reverted to similar ones of the early 20th century, but multivariate analysis indicated that the present community is substantially dissimilar. Community changes of all three groups were strongly correlated to phosphorus concentration changes, whereas significant relationships to temperature were only observed when we did not account for temporal autocorrelation. Our results indicate that each microbial group analysed exhibited a unique response, highlighting the particular strength of multimarker analysis of eDNA, which is not limited to organisms with visible remains and can therefore discover yet unknown responses and abiotic-biotic relationships.
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Affiliation(s)
- Anan Ibrahim
- Department of Biology, University of Konstanz, Konstanz, Germany.,Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - Eric Capo
- Chemistry Department, Umeå University, Umeå, Sweden
| | | | - Isabel Martin
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany.,Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - Laura S Epp
- Department of Biology, University of Konstanz, Konstanz, Germany.,Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
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19
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Liu S, Stoof-Leichsenring KR, Kruse S, Pestryakova LA, Herzschuh U. Holocene Vegetation and Plant Diversity Changes in the North-Eastern Siberian Treeline Region From Pollen and Sedimentary Ancient DNA. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.560243] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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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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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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22
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Li F, Zhang X, Xie Y, Wang J. Sedimentary DNA reveals over 150 years of ecosystem change by human activities in Lake Chao, China. ENVIRONMENT INTERNATIONAL 2019; 133:105214. [PMID: 31665682 DOI: 10.1016/j.envint.2019.105214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/22/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
Understanding the extent and directionality of the impact of human activities on ecosystems is directly related to their management and protection. However, the lack of historical data limits our understanding of ecosystem changes with long-term exposure to human activities. Recently, lake sedimentary DNA (sedDNA) has become a powerful tool for revealing changes in ecosystems at the century and millennium scales. Here, we used sedDNA to reveal the dynamic of the microbial community (including bacteria and micro-eukaryotes) in Lake Chao over the past 150 years, and further explored the effects of long-term nutrient and heavy metal loads on these communities. Our data show that nutrient and heavy metal loads in Lake Chao have increased by ca. 2 to 4-fold since the 1960s. In response, the community structure, diversity, and ecological network of bacteria and micro-eukaryotes changed significantly during the 1960s, the 1980s and the 2010s. Importantly, community structure was more sensitive to human activities than diversity. We also found that the relative abundance of some taxa associated with nitrification and algal blooms (e.g., taxa in Nitrospira sp., Peridinales) has increased ca. 100-fold since the 1960s. Nutrient could better explain the variation in the bacterial community (ca. twice as much as heavy metal), while heavy metal explained micro-eukaryotes better (ca. 3 or 5-fold as much as nutrient). In particular, based on parsimonious models from distance-based linear model (distLM), we further identified that Pb is the key factor affecting the bacterial and micro-eukaryotes community in Lake Chao in addition to nutrient. Our study reveals the impacts of long-term human activities on lake ecosystems from multiple perspectives of nutrient and heavy metal loads, community structure, diversity and ecological network, these findings will contribute to the management and conservation of lakes in the future.
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Affiliation(s)
- Feilong Li
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Jizhong Wang
- Guangzhou GRG Metrology & Test (Hefei) CO., LID, Hefei 230088, PR China; School of Environment and Energy Engineering, Anhui Jianzhu University, Hefei 230601, PR China
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23
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Crump SE, Miller GH, Power M, Sepúlveda J, Dildar N, Coghlan M, Bunce M. Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada. GLOBAL CHANGE BIOLOGY 2019; 25:4244-4256. [PMID: 31603617 DOI: 10.1111/gcb.14836] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 08/08/2019] [Indexed: 12/29/2022]
Abstract
Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic 10 Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen-based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags.
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Affiliation(s)
- Sarah E Crump
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Organic Geochemistry Laboratory, University of Colorado Boulder, Boulder, CO, USA
| | - Gifford H Miller
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Julio Sepúlveda
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Organic Geochemistry Laboratory, University of Colorado Boulder, Boulder, CO, USA
| | - Nadia Dildar
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Organic Geochemistry Laboratory, University of Colorado Boulder, Boulder, CO, USA
| | - Megan Coghlan
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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24
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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: 27] [Impact Index Per Article: 5.4] [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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25
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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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26
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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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27
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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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28
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Epp LS, Kruse S, Kath NJ, Stoof-Leichsenring KR, Tiedemann R, Pestryakova LA, Herzschuh U. Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling. Sci Rep 2018; 8:17436. [PMID: 30498238 PMCID: PMC6265258 DOI: 10.1038/s41598-018-35550-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 11/01/2018] [Indexed: 12/01/2022] Open
Abstract
Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
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Affiliation(s)
- Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany.
| | - Stefan Kruse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Nadja J Kath
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Ralph Tiedemann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Luidmila A Pestryakova
- Department for Geography and Biology, North-Eastern Federal University of Yakutsk, Belinskogo 58, 67700, Yakutsk, Russia
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
- Institute of Earth and Environmental Science, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
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29
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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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30
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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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31
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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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Harbert RS. Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1034. [PMID: 29732264 PMCID: PMC5895191 DOI: 10.1002/aps3.1034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/22/2017] [Indexed: 05/09/2023]
Abstract
PREMISE OF THE STUDY DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants. METHODS To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants. RESULTS Performance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession. DISCUSSION Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.
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Affiliation(s)
- Robert S. Harbert
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York10024USA
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Niemeyer B, Epp LS, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline. Mol Ecol Resour 2017; 17:e46-e62. [DOI: 10.1111/1755-0998.12689] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Bastian Niemeyer
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
| | - Laura S. Epp
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | | | - Luidmila A. Pestryakova
- Department for Geography and Biology; North-Eastern Federal University of Yakutsk; Yakutsk Russia
| | - Ulrike Herzschuh
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam-Golm Germany
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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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