1
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Charrier E, Chen R, Thundathil N, Gilleard JS. A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding. Mol Ecol Resour 2024:e13965. [PMID: 38733216 DOI: 10.1111/1755-0998.13965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/25/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free-living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS-1 intergenic spacer and the region spanning ITS-1_5.8S_ITS-2. These databases comprise 2645, 254, 13,461 and 10,107 unique full-length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS-1 database includes the largest number of unique full-length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short-read or long-read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum.
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Affiliation(s)
- Eléonore Charrier
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - Rebecca Chen
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - Noelle Thundathil
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - John S Gilleard
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
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3
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Ekram MAE, Campbell M, Kose SH, Plet C, Hamilton R, Bijaksana S, Grice K, Russell J, Stevenson J, Vogel H, Coolen MJL. A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia). Geobiology 2024; 22:e12599. [PMID: 38745401 DOI: 10.1111/gbi.12599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/24/2023] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.
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Affiliation(s)
- Md Akhtar-E Ekram
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Matthew Campbell
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Sureyya H Kose
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Chloe Plet
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Rebecca Hamilton
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Indonesia
| | - Kliti Grice
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - James Russell
- Department of Earth, Environmental, and Planetary Sciences (DEEPS), Brown University, Providence, Rhode Island, USA
| | - Janelle Stevenson
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Marco J L Coolen
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
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4
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Espinosa Prieto A, Hardion L, Debortoli N, Beisel JN. Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13937. [PMID: 38363053 DOI: 10.1111/1755-0998.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
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Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Laurent Hardion
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Nicolas Debortoli
- Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium
- E-BIOM SA, Namur, Belgium
| | - Jean-Nicolas Beisel
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
- École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Setsuko S, Yoshimura K, Ueno S, Worth JRP, Ujino-Ihara T, Katsuki T, Noshiro S, Fujii T, Arai T, Yoshimaru H. A DNA barcode reference library for the native woody seed plants of Japan. Mol Ecol Resour 2023; 23:855-871. [PMID: 36694075 DOI: 10.1111/1755-0998.13748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/25/2022] [Accepted: 12/08/2022] [Indexed: 01/26/2023]
Abstract
DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.
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Affiliation(s)
- Suzuki Setsuko
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Kensuke Yoshimura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - James Raymond Peter Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Toshio Katsuki
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tokyo, Japan
| | - Shuichi Noshiro
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tomoyuki Fujii
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Takahisa Arai
- Tohoku University Botanical Gardens, Tohoku University, Miyagi, Japan
| | - Hiroshi Yoshimaru
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
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8
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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] [What about the content of this article? (0)] [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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9
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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022; 612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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Affiliation(s)
- Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Binia De Cahsan
- Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Michelsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina K Sand
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Astrid M A Schmidt
- Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
- DIS Study Abroad in Scandinavia, University of Copenhagen, Copenhagen, Denmark
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Alexey S Tesakov
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Ian Snowball
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - John C Gosse
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Yucheng Wang
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeppe Å Kristensen
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
- Geological Survey of Denmark and Greenland, (GEUS), Copenhagen, Denmark
| | - Morten Bjerager
- Department of Geophysics and Sedimentary Basins, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL, Paris, France
| | - Marc Macias-Fauria
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alan J Hidy
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Collins
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolaj K Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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10
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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] [What about the content of this article? (0)] [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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11
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AoB Plants 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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13
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Picard M, Pochon X, Atalah J, Pearman JK, Rees A, Howarth JD, Moy CM, Vandergoes MJ, Hawes I, Khan S, Wood SA. Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes. Sci Rep 2022; 12:12810. [PMID: 35896561 PMCID: PMC9329365 DOI: 10.1038/s41598-022-14216-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.
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Affiliation(s)
- Maïlys Picard
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand. .,Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand.
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand.,Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Andrew Rees
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Christopher M Moy
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | | | - Ian Hawes
- Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand
| | - Samiullah Khan
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
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14
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Lunghi E, Valle B, Guerrieri A, Bonin A, Cianferoni F, Manenti R, Ficetola GF. Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils. Sci Total Environ 2022; 826:154022. [PMID: 35202680 DOI: 10.1016/j.scitotenv.2022.154022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/01/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Subterranean environments host a substantial amount of biodiversity, however assessing the distribution of species living underground is still extremely challenging. Environmental DNA (eDNA) metabarcoding is a powerful tool to estimate biodiversity in poorly known environments and has excellent performance for soil organisms. Here, we tested 1) whether eDNA metabarcoding from cave soils/sediments allows to successfully detect springtails (Hexapoda: Collembola) and insects (Hexapoda: Insecta); 2) whether eDNA mostly represents autochthonous (cave-dwelling) organisms or it also incorporates information from species living in surface environments; 3) whether eDNA detection probability changes across taxa with different ecology. Environmental DNA metabarcoding analyses detected a large number of Molecular Operational Taxonomic Units (MOTUs) for both insects and springtails. For springtails, detection probability was high, with a substantial proportion of hypogean species, suggesting that eDNA provides good information on the distribution of these organisms in caves. Conversely, for insects most of MOTUs represented taxa living outside caves, and the majority of them represented taxa/organisms living in freshwater environments (Ephemeroptera, Plecoptera and Trichoptera). The eDNA of freshwater insects was particularly abundant in deep sectors of caves, far from the entrance. Furthermore, average detection probability of insects was significantly lower than the one of springtails. This suggests that cave soils/sediments act as "conveyer belts of biodiversity information", possibly because percolating water lead to the accumulation of eDNA of organisms living in nearby areas. Cave soils hold a complex mix of autochthonous and allochthonous eDNA. eDNA provided unprecedented information on the understudied subterranean cave organisms; analyses of detection probability and occupancy can help teasing apart local eDNA from the eDNA representing spatially-integrated biodiversity for whole landscape.
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Affiliation(s)
- Enrico Lunghi
- Division of Molecular Biology Ruđer Bošković Institute, Zagreb, Croatia; Natural Oasis, Prato, Italy.
| | - Barbara Valle
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy; Unità di Climatologia ed Ecologia, MUSE-Museo delle Scienze di Trento, Italy
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Fabio Cianferoni
- Istituto di Ricerca sugli Ecosistemi Terrestri (IRET), Consiglio Nazionale delle Ricerche (CNR), Sesto Fiorentino (Firenze), Italy; Zoologia, La Specola, Museo di Storia Naturale, Università degli Studi di Firenze, Firenze, Italy
| | - Raoul Manenti
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratorio di Biologia Sotterranea "Enrico Pezzoli", Parco Regionale del Monte Barro, Galbiate, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratoire d'Écologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
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15
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Messager E, Giguet-Covex C, Doyen E, Etienne D, Gielly L, Sabatier P, Banjan M, Develle AL, Didier J, Poulenard J, Julien A, Arnaud F. Two Millennia of Complexity and Variability in a Perialpine Socioecological System (Savoie, France): The Contribution of Palynology and sedaDNA Analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the last two millennia, European Alpine ecosystems have experienced major changes in response to the important, yet fluctuating, impact of human activities. This study aims to reconstruct the environmental history of the last 1800 years on the western edge of the Alps by analyzing sediments from Lake Aiguebelette, a large lake located in the perialpine area. We have combined analyses of pollen and other palynomorphs, such as coprophilous fungal spores, together with sedimentary DNA (from plants and mammals) in order to reconstruct both vegetation and land-use histories. A sedimentological and geochemical analysis was also conducted in order to gain an understanding of changes in erosion dynamics in response to landscape modifications that were influenced by climate and human activities. This work highlights alternating phases of anthropization and agricultural abandonment allowing forest recovery. While pollen reflects the major phases of regional deforestation and afforestation related to the dynamic of farming activities, plant DNA provides precise information on the plants cultivated in fields, orchards and vegetable gardens over the past centuries. The combination of mammal DNA and coprophilous fungal spores completes this work by documenting the history of pastoral practices.
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16
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Schulte L, Meucci S, Stoof-Leichsenring KR, Heitkam T, Schmidt N, von Hippel B, Andreev AA, Diekmann B, Biskaborn BK, Wagner B, Melles M, Pestryakova LA, Alsos IG, Clarke C, Krutovsky KV, Herzschuh U. Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA. Commun Biol 2022; 5:570. [PMID: 35681049 PMCID: PMC9184489 DOI: 10.1038/s42003-022-03455-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.
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Jeliazkov A, Gavish Y, Marsh CJ, Geschke J, Brummitt N, Rocchini D, Haase P, Kunin WE, Henle K. Sampling and modelling rare species: Conceptual guidelines for the neglected majority. Glob Chang Biol 2022; 28:3754-3777. [PMID: 35098624 DOI: 10.1111/gcb.16114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 11/18/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Biodiversity conservation faces a methodological conundrum: Biodiversity measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the most challenging to sample and model. Predicting the distribution change of rare species using conventional species distribution models is challenging because rare species are hardly captured by most survey systems. When enough data are available, predictions are usually spatially biased towards locations where the species is most likely to occur, violating the assumptions of many modelling frameworks. Workflows to predict and eventually map rare species distributions imply important trade-offs between data quantity, quality, representativeness and model complexity that need to be considered prior to survey and analysis. Our opinion is that study designs need to carefully integrate the different steps, from species sampling to modelling, in accordance with the different types of rarity and available data in order to improve our capacity for sound assessment and prediction of rare species distribution. In this article, we summarize and comment on how different categories of species rarity lead to different types of occurrence and distribution data depending on choices made during the survey process, namely the spatial distribution of samples (where to sample) and the sampling protocol in each selected location (how to sample). We then clarify which species distribution models are suitable depending on the different types of distribution data (how to model). Among others, for most rarity forms, we highlight the insights from systematic species-targeted sampling coupled with hierarchical models that allow correcting for overdispersion and spatial and sampling sources of bias. Our article provides scientists and practitioners with a much-needed guide through the ever-increasing diversity of methodological developments to improve the prediction of rare species distribution depending on rarity type and available data.
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Affiliation(s)
| | - Yoni Gavish
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Charles J Marsh
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Ecology and Evolution & Yale Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
| | - Jonas Geschke
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Neil Brummitt
- Department of Life Sciences, Natural History Museum, London, UK
| | - Duccio Rocchini
- BIOME Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Department of Spatial Sciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha - Suchdol, Czech Republic
| | - Peter Haase
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
- Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Klaus Henle
- Department of Conservation Biology & Social-Ecological Systems, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
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18
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Hudson SM, Pears B, Jacques D, Fonville T, Hughes P, Alsos I, Snape L, Lang A, Brown A. Life before Stonehenge: The hunter-gatherer occupation and environment of Blick Mead revealed by sedaDNA, pollen and spores. PLoS One 2022; 17:e0266789. [PMID: 35476794 PMCID: PMC9045597 DOI: 10.1371/journal.pone.0266789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
The Neolithic and Bronze Age construction and habitation of the Stonehenge Landscape has been extensively explored in previous research. However, little is known about the scale of pre-Neolithic activity and the extent to which the later monumental complex occupied an ‘empty’ landscape. There has been a long-running debate as to whether the monumental archaeology of Stonehenge was created in an uninhabited forested landscape or whether it was constructed in an already partly open area of pre-existing significance to late Mesolithic hunter-gatherers. This is of significance to a global discussion about the relationship between incoming farmers and indigenous hunter-gatherer societies that is highly relevant to both Old and New World archaeology. Here we present the results of plant sedaDNA, palynological and geoarchaeological analysis at the Late hunter-gatherer site complex of Blick Mead at the junction of the drylands of Salisbury Plain and the floodplain of the River Avon, on the edge of the Stonehenge World Heritage Site. The findings are placed within a chronological framework built on OSL, radiocarbon and relative archaeological dating. We show that Blick Mead existed in a clearing in deciduous woodland, exploited by aurochsen, deer and hunter-gatherers for approximately 4000 years. Given its rich archaeology and longevity this strongly supports the arguments of continuity between the Late Mesolithic hunter-gatherers activity and Neolithic monument builders, and more specifically that this was a partially open environment important to both groups. This study also demonstrates that sediments from low-energy floodplains can provide suitable samples for successful environmental assaying using sedaDNA, provided they are supported by secure dating and complementary environmental proxies.
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Affiliation(s)
- Samuel M. Hudson
- Department of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
- * E-mail:
| | - Ben Pears
- Department of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - David Jacques
- School of Humanities, The University of Buckingham, Buckingham, United Kingdom
| | - Thierry Fonville
- Department of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Paul Hughes
- Department of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Inger Alsos
- Department of Natural Sciences, Tromsø University Museum, Arctic University of Tromsø, Tromsø, Norway
| | - Lisa Snape
- Department of Geography and Geology, University of Salzburg, Salzburg, Austria
| | - Andreas Lang
- Department of Geography and Geology, University of Salzburg, Salzburg, Austria
| | - Antony Brown
- Department of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
- Department of Natural Sciences, Tromsø University Museum, Arctic University of Tromsø, Tromsø, Norway
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19
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Ariza M, Fouks B, Mauvisseau Q, Halvorsen R, Alsos IG, de Boer H. Plant biodiversity assessment through soil
eDNA
reflects temporal and local diversity. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- María Ariza
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
| | - Bertrand Fouks
- Westfälische Wilhelms‐Universität Institute for Evolution and Biodiversity Molecular Evolution and Bioinformatics. Hüfferstraße 1 Münster Germany
| | | | | | - Inger Greve Alsos
- The Arctic University Museum of Norway UiT ‐ The Arctic University of Norway Norway
| | - Hugo de Boer
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
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20
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Nota K, Klaminder J, Milesi P, Bindler R, Nobile A, van Steijn T, Bertilsson S, Svensson B, Hirota SK, Matsuo A, Gunnarsson U, Seppä H, Väliranta MM, Wohlfarth B, Suyama Y, Parducci L. Norway spruce postglacial recolonization of Fennoscandia. Nat Commun 2022; 13:1333. [PMID: 35288569 PMCID: PMC8921311 DOI: 10.1038/s41467-022-28976-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/18/2022] [Indexed: 01/25/2023] Open
Abstract
Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial. Contrasting theories exist regarding how Norway spruce recolonized Fennoscandia after the last glaciation. Here, the authors provide evidences from sedimentary ancient DNA and modern population genomics to support that Norway spruce was present in southern Fennoscandia shortly after deglaciation and the early Holocene migration from the east.
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21
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Keck F, Blackman RC, Bossart R, Brantschen J, Couton M, Hürlemann S, Kirschner D, Locher N, Zhang H, Altermatt F. Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Mol Ecol 2022; 31:1820-1835. [PMID: 35075700 PMCID: PMC9303474 DOI: 10.1111/mec.16364] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
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Affiliation(s)
- François Keck
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Rosetta C Blackman
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Raphael Bossart
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Marjorie Couton
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Samuel Hürlemann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Dominik Kirschner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental System Science, ETH Zürich, Universitätstr. 16, 8092, Zürich, Switzerland.,Landscape Ecology, Land Change Science, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nadine Locher
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Heng Zhang
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
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22
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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] [What about the content of this article? (0)] [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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23
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Vasconcelos S, Nunes GL, Dias MC, Lorena J, Oliveira RRM, Lima TGL, Pires ES, Valadares RBS, Alves R, Watanabe MTC, Zappi DC, Hiura AL, Pastore M, Vasconcelos LV, Mota NFO, Viana PL, Gil ASB, Simões AO, Imperatriz‐Fonseca VL, Harley RM, Giulietti AM, Oliveira G. Unraveling the plant diversity of the Amazonian canga through DNA barcoding. Ecol Evol 2021; 11:13348-13362. [PMID: 34646474 PMCID: PMC8495817 DOI: 10.1002/ece3.8057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 01/04/2023] Open
Abstract
The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.
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Affiliation(s)
| | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Renato R. M. Oliveira
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Daniela C. Zappi
- Instituto Tecnológico ValeBelémBrazil
- Instituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | | | - Mayara Pastore
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Liziane V. Vasconcelos
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em EcologiaUniversidade Federal do ParáBelémBrazil
| | - Nara F. O. Mota
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Pedro L. Viana
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André S. B. Gil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André O. Simões
- Departamento de Biologia VegetalUniversidade Estadual de CampinasCampinasBrazil
| | | | | | - Ana M. Giulietti
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em BotânicaUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
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24
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Tommasi N, Ferrari A, Labra M, Galimberti A, Biella P. Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. Diversity 2021; 13:437. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.
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25
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Osathanunkul M, Sawongta N, Pheera W, Pechlivanis N, Psomopoulos F, Madesis P. Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning. PeerJ 2021; 9:e11753. [PMID: 34414025 PMCID: PMC8340909 DOI: 10.7717/peerj.11753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited. Methods Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron. Results The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5-10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.
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Affiliation(s)
- Maslin Osathanunkul
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand.,Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Nipitpong Sawongta
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Wittaya Pheera
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece.,Development and Molecular Biology, School of Biology, Department of Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece.,Crop Production and Rural Environment, Laboratory of Molecular Biology of Plants, Department of Agriculture, University of Thessaly, Volos, Magnesia, Greece
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26
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Ji F, Yan L, Yan S, Qin T, Shen J, Zha J. Estimating aquatic plant diversity and distribution in rivers from Jingjinji region, China, using environmental DNA metabarcoding and a traditional survey method. Environ Res 2021; 199:111348. [PMID: 34029550 DOI: 10.1016/j.envres.2021.111348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Traditional survey methods (TSMs) are difficult to use to perform a census of aquatic plant diversity completely in river ecosystems, and improved aquatic plant community monitoring programs are becoming increasingly crucial with a continuous decline in diversity. Although environmental DNA (eDNA) metabarcoding has been applied successfully to assess aquatic biodiversity, limited work has been reported regarding aquatic plant diversity in rivers. In this study, the efficiency of eDNA to estimate the aquatic plant diversity and spatial distribution of rivers from the Jingjinji (JJJ) region was evaluated by comparing results obtained by the TSM. Based on a combination of the two methods, 157 aquatic plant species, including 24 hydrophytes, 61 amphibious plants, and 72 mesophytes, were identified. The spatial patterns in species richness and abundance by eDNA exhibited agreement with the TSM results with a gradual decline from the mountain area (MA) to the agricultural area (AA) and then to the urban area (UA). Compared to the TSM, eDNA identified a significantly greater number of species per site (p < 0.01) and obtained a significantly higher abundance in hydrophytes (p < 0.01), supplementing the unavailable abundance data from the TSM. Furthermore, the aquatic plant assemblages from the different areas were discriminated well using eDNA (p < 0.05), but they were better discriminated by the TSM (p < 0.01). Thus, our study provides more detailed data on aquatic plant diversity in rivers from the JJJ region, which is essential for biodiversity conservation. Our findings also highlight that eDNA can be reliable for evaluating aquatic plant diversity and has the potential to respond to landscape heterogeneity in river ecosystems.
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Affiliation(s)
- Fenfen Ji
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Liang Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Saihong Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianlong Qin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jianzhong Shen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China.
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Grant DM, Brodnicke OB, Evankow AM, Ferreira AO, Fontes JT, Hansen AK, Jensen MR, Kalaycı TE, Leeper A, Patil SK, Prati S, Reunamo A, Roberts AJ, Shigdel R, Tyukosova V, Bendiksby M, Blaalid R, Costa FO, Hollingsworth PM, Stur E, Ekrem T. The Future of DNA Barcoding: Reflections from Early Career Researchers. Diversity 2021; 13:313. [DOI: 10.3390/d13070313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.
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28
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Brown AG, Van Hardenbroek M, Fonville T, Davies K, Mackay H, Murray E, Head K, Barratt P, McCormick F, Ficetola GF, Gielly L, Henderson ACG, Crone A, Cavers G, Langdon PG, Whitehouse NJ, Pirrie D, Alsos IG. Ancient DNA, lipid biomarkers and palaeoecological evidence reveals construction and life on early medieval lake settlements. Sci Rep 2021; 11:11807. [PMID: 34083588 PMCID: PMC8175756 DOI: 10.1038/s41598-021-91057-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/04/2021] [Indexed: 11/17/2022] Open
Abstract
Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery.
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Affiliation(s)
- A G Brown
- Tromsø Museum, Artic University of Norway, Tromsø, Norway. .,School of Geography and Environmental Science, University of Southampton, Southampton, UK.
| | - M Van Hardenbroek
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - T Fonville
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - K Davies
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK.,IMSET, Bournemouth University, Poole, UK
| | - H Mackay
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK.,Department of Geography, Durham University, Durham, UK
| | - E Murray
- Archaeology, Queens University, Belfast, Northern Ireland, UK
| | - K Head
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - P Barratt
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - F McCormick
- Archaeology, Queens University, Belfast, Northern Ireland, UK
| | - G F Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,LECA, Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France
| | - L Gielly
- LECA, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France
| | - A C G Henderson
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - A Crone
- AOC Group Ltd., Edinburgh, Scotland, UK
| | - G Cavers
- AOC Group Ltd., Edinburgh, Scotland, UK
| | - P G Langdon
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - N J Whitehouse
- Department of Archaeology, School of Humanities, University of Glasgow, Glasgow, UK
| | - D Pirrie
- School of Applied Sciences, University of South Wales, Pontypridd, UK
| | - I G Alsos
- Tromsø Museum, Artic University of Norway, Tromsø, Norway
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30
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Liu S, Kruse S, Scherler D, Ree RH, Zimmermann HH, Stoof-Leichsenring KR, Epp LS, Mischke S, Herzschuh U. Sedimentary ancient DNA reveals a threat of warming-induced alpine habitat loss to Tibetan Plateau plant diversity. Nat Commun 2021; 12:2995. [PMID: 34016962 PMCID: PMC8137883 DOI: 10.1038/s41467-021-22986-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/16/2021] [Indexed: 11/19/2022] Open
Abstract
Studies along elevational gradients worldwide usually find the highest plant taxa richness in mid-elevation forest belts. Hence, an increase in upper elevation diversity is expected in the course of warming-related treeline rise. Here, we use a time-series approach to infer past taxa richness from sedimentary ancient DNA from the south-eastern Tibetan Plateau over the last ~18,000 years. We find the highest total plant taxa richness during the cool phase after glacier retreat when the area contained extensive and diverse alpine habitats (14-10 ka); followed by a decline when forests expanded during the warm early- to mid-Holocene (10-3.6 ka). Livestock grazing since 3.6 ka promoted plant taxa richness only weakly. Based on these inferred dependencies, our simulation yields a substantive decrease in plant taxa richness in response to warming-related alpine habitat loss over the next centuries. Accordingly, efforts of Tibetan biodiversity conservation should include conclusions from palaeoecological evidence.
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Affiliation(s)
- Sisi Liu
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany
| | - Stefan Kruse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Dirk Scherler
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Richard H Ree
- Negaunee Integrative Research Center, Department of Science and Education, Field Museum, Chicago, USA
| | - 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
| | - Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Steffen Mischke
- Institute of Earth Sciences, University of Iceland, Reykjavík, Iceland
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany.
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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31
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Liu S, Li K, Jia W, Stoof-Leichsenring KR, Liu X, Cao X, Herzschuh U. Vegetation Reconstruction From Siberia and the Tibetan Plateau Using Modern Analogue Technique–Comparing Sedimentary (Ancient) DNA and Pollen Data. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.668611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To reconstruct past vegetation from pollen or, more recently, lake sedimentary DNA (sedDNA) data is a common goal in palaeoecology. To overcome the bias of a researcher’s subjective assessment and to assign past assemblages to modern vegetation types quantitatively, the modern analogue technique (MAT) is often used for vegetation reconstruction. However, a rigorous comparison of MAT-derived pollen-based and sedDNA-based vegetation reconstruction is lacking. Here, we assess the dissimilarity between modern taxa assemblages from lake surface-sediments and fossil taxa assemblages from four lake sediment cores from the south-eastern Tibetan Plateau and northern Siberia using receiver operating characteristic (ROC) curves, ordination methods, and Procrustes analyses. Modern sedDNA samples from 190 lakes and pollen samples from 136 lakes were collected from a variety of vegetation types. Our results show that more modern analogues are found with sedDNA than pollen when applying similarly derived thresholds. In particular, there are few modern pollen analogues for open vegetation such as alpine or arctic tundra, limiting the ability of treeline shifts to be clearly reconstructed. In contrast, the shifts in the main vegetation communities are well captured by sedimentary ancient DNA (sedaDNA). For example, pronounced shifts from late-glacial alpine meadow/steppe to early–mid-Holocene coniferous forests to late Holocene Tibetan shrubland vegetation types are reconstructed for Lake Naleng on the south-eastern Tibetan Plateau. Procrustes and PROTEST analyses reveal that intertaxa relationships inferred from modern sedaDNA datasets align with past relationships generally, while intertaxa relationships derived from modern pollen spectra are mostly significantly different from fossil pollen relationships. Overall, we conclude that a quantitative sedaDNA-based vegetation reconstruction using MAT is more reliable than a pollen-based reconstruction, probably because of the more straightforward taphonomy that can relate sedDNA assemblages to the vegetation surrounding the lake.
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Chua PYS, Crampton-Platt A, Lammers Y, Alsos IG, Boessenkool S, Bohmann K. Metagenomics: A viable tool for reconstructing herbivore diet. Mol Ecol Resour 2021; 21:2249-2263. [PMID: 33971086 PMCID: PMC8518049 DOI: 10.1111/1755-0998.13425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
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Affiliation(s)
- Physilia Y S Chua
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Youri Lammers
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Inger G Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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34
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Courtin J, Andreev AA, Raschke E, Bala S, Biskaborn BK, Liu S, Zimmermann H, Diekmann B, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. Vegetation Changes in Southeastern Siberia During the Late Pleistocene and the Holocene. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.625096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last ∼35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake’s vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the “keystone herbivore” hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.
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35
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Rucińska A, Olszak M, Świerszcz S, Nobis M, Zubek S, Kusza G, Boczkowska M, Nowak A. Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities. Biomolecules 2021; 11:318. [PMID: 33669773 PMCID: PMC7921978 DOI: 10.3390/biom11020318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/02/2022] Open
Abstract
Despite the raising preoccupation, the critical question of how the plant community is composed belowground still remains unresolved, particularly for the conservation priority types of vegetation. The usefulness of metabarcoding analysis of the belowground parts of the plant community is subjected to a considerable bias, that often impedes detection of all species in a sample due to insufficient DNA quality or quantity. In the presented study we have attempted to find environmental factors that determine the amount and quality of DNA extracted from total plant tissue from above- and belowground samples (1000 and 10,000 cm2). We analyzed the influence of land use intensity, soil properties, species composition, and season on DNA extraction. The most important factors for DNA quality were vegetation type, soil conductometry (EC), and soil pH for the belowground samples. The species that significantly decreased the DNA quality were Calamagrostis epigejos, Coronilla varia, and Holcus lanatus. For the aboveground part of the vegetation, the season, management intensity, and certain species-with the most prominent being Centaurea rhenana and Cirsium canum-have the highest influence. Additionally, we found that sample size, soil granulation, MgO, organic C, K2O, and total soil N content are important for DNA extraction effectiveness. Both low EC and pH reduce significantly the yield and quality of DNA. Identifying the potential inhibitors of DNA isolation and predicting difficulties of sampling the vegetation plots for metabarcoding analysis will help to optimize the universal, low-cost multi-stage DNA extraction procedure in molecular ecology studies.
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Affiliation(s)
- Anna Rucińska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
| | - Marcin Olszak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Sebastian Świerszcz
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
- Research Laboratory ‘Herbarium’, National Research Tomsk State University, 634050 Tomsk, Russia
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
| | - Grzegorz Kusza
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
| | - Maja Boczkowska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR)–National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
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Lammers Y, Heintzman PD, Alsos IG. Environmental palaeogenomic reconstruction of an Ice Age algal population. Commun Biol 2021; 4:220. [PMID: 33594237 DOI: 10.1038/s42003-021-01710-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA. Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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Capo E, Giguet-covex C, Rouillard A, Nota K, Heintzman PD, Vuillemin A, Ariztegui D, Arnaud F, Belle S, Bertilsson S, Bigler C, Bindler R, Brown AG, Clarke CL, Crump SE, Debroas D, Englund G, Ficetola GF, Garner RE, Gauthier J, Gregory-eaves I, Heinecke L, Herzschuh U, Ibrahim A, Kisand V, Kjær KH, Lammers Y, Littlefair J, Messager E, Monchamp M, Olajos F, Orsi W, Pedersen MW, Rijal DP, Rydberg J, Spanbauer T, Stoof-leichsenring KR, Taberlet P, Talas L, Thomas C, Walsh DA, Wang Y, Willerslev E, van Woerkom A, Zimmermann HH, Coolen MJL, Epp LS, Domaizon I, G. Alsos I, Parducci L. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary 2021; 4:6. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Varotto C, Pindo M, Bertoni E, Casarotto C, Camin F, Girardi M, Maggi V, Cristofori A. A pilot study of eDNA metabarcoding to estimate plant biodiversity by an alpine glacier core (Adamello glacier, North Italy). Sci Rep 2021; 11:1208. [PMID: 33441696 PMCID: PMC7807053 DOI: 10.1038/s41598-020-79738-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
Current biodiversity loss is a major concern and thus biodiversity assessment of modern ecosystems is compelling and needs to be contextualized on a longer timescale. High Throughput Sequencing (HTS) is progressively becoming a major source of data on biodiversity time series. In this multi proxy study, we tested, for the first time, the potential of HTS to estimate plant biodiversity archived in the surface layers of a temperate alpine glacier, amplifying the trnL barcode for vascular plants from eDNA of firn samples. A 573 cm long core was drilled by the Adamello glacier and cut into sections; produced samples were analyzed for physical properties, stable isotope ratio, and plant biodiversity by eDNA metabarcoding and conventional light microscopy analysis. Results highlighted the presence of pollen and plant remains within the distinct layers of snow, firn and ice. While stable isotope ratio showed a scarcely informative pattern, DNA metabarcoding described distinct plant species composition among the different samples, with a broad taxonomic representation of the biodiversity of the catchment area and a high-ranking resolution. New knowledge on climate and plant biodiversity changes of large catchment areas can be obtained by this novel approach, relevant for future estimates of climate change effects.
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Affiliation(s)
- Claudio Varotto
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | | | | | - Federica Camin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | - Matteo Girardi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | - Valter Maggi
- Earth and Environmental Sciences, University of Milano Bicocca, Milan, Italy
| | - Antonella Cristofori
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy.
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40
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Hobbs WO, Dreher TW, Davis EW, Vinebrooke RD, Wong S, Weissman T, Dawson M. Using a lake sediment record to infer the long-term history of cyanobacteria and the recent rise of an anatoxin producing Dolichospermum sp. Harmful Algae 2021; 101:101971. [PMID: 33526187 DOI: 10.1016/j.hal.2020.101971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Lakes that experience recurrent toxic cyanobacterial harmful algae blooms (cyanoHABS) are often subject to cultural eutrophication, where landscape development and upland activities increase the nutrient inputs to the water column and fuel cyanoHABS. Few studies have focused on the response of a lake to nutrient inputs for which the natural geomorphic setting predisposes a nutrient-rich water column to already support abundant cyanobacteria. Here, we present a sediment core record from a lake surrounded by parkland that experiences recurrent cyanoHABs which produce dangerous levels of the neurotoxin, anatoxin-a, impacting the recreational use of the lake and park. Using photoautotrophic pigments in the sediment record, we establish cyanobacteria have long been part of the diverse and abundant phytoplankton community within the lake. Despite this long record, shotgun metagenome and other DNA analyses of the sediment record suggest that the current anatoxin-a producer Dolichospermum sp. WA102 only emerged to dominate the cyanobacterial community in the mid-1990s. A period of lakeshore farming that finished in the 1950s-1960s and possibly the stocking of rainbow trout fry (1970-2016) coincide with a progressive shift in primary production, together with a change in bacterial communities. Based on the history of the lake and contemporary ecology of Dolichospermum, we propose that the legacy of nutrient inputs and changes in nutrient cycling within the lake has encouraged the development of an ecosystem where the toxin producing Dolichospermum sp WA102 is highly competitive. Understanding the historical presence of cyanobacteria in the lake provides a context for current-day management strategies of cyanoHABs.
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Affiliation(s)
- William O Hobbs
- Washington State Department of Ecology, PO Box 47600, Olympia, WA 98502 United States.
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 United States; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 United States
| | - Edward W Davis
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 United States
| | - Rolf D Vinebrooke
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9 Canada
| | - Siana Wong
- Washington State Department of Ecology, PO Box 47600, Olympia, WA 98502 United States
| | - Tim Weissman
- Jefferson County Public Health, 615 Sheridan St, Port Townsend, Washington 98368 United States
| | - Michael Dawson
- Jefferson County Public Health, 615 Sheridan St, Port Townsend, Washington 98368 United States
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41
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Stoof-Leichsenring KR, Liu S, Jia W, Li K, Pestryakova LA, Mischke S, Cao X, Liu X, Ni J, Neuhaus S, Herzschuh U. Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China). Biodivers Data J 2020; 8:e57089. [PMID: 33364896 PMCID: PMC7752886 DOI: 10.3897/bdj.8.e57089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/26/2020] [Indexed: 11/15/2022] Open
Abstract
Background Plant diversity in the Arctic and at high altitudes strongly depends on and rebounds to climatic and environmental variability and is nowadays tremendously impacted by recent climate warming. Therefore, past changes in plant diversity in the high Arctic and high-altitude regions are used to infer climatic and environmental changes through time and allow future predictions. Sedimentary DNA (sedDNA) is an established proxy for the detection of local plant diversity in lake sediments, but still relationships between environmental conditions and preservation of the plant sedDNA proxy are far from being fully understood. Studying modern relationships between environmental conditions and plant sedDNA will improve our understanding under which conditions sedDNA is well-preserved helping to a.) evaluate suitable localities for sedDNA approaches, b.) provide analogues for preservation conditions and c.) conduct reconstruction of plant diversity and climate change. This study investigates modern plant diversity applying a plant-specific metabarcoding approach on sedimentary DNA of surface sediment samples from 262 lake localities covering a large geographical, climatic and ecological gradient. Latitude ranges between 25°N and 73°N and longitude between 81°E and 161°E, including lowland lakes and elevated lakes up to 5168 m a.s.l. Further, our sampling localities cover a climatic gradient ranging in mean annual temperature between -15°C and +18°C and in mean annual precipitation between 36 and 935 mm. The localities in Siberia span over a large vegetational gradient including tundra, open woodland and boreal forest. Lake localities in China include alpine meadow, shrub, forest and steppe and also cultivated areas. The assessment of plant diversity in the underlying dataset was conducted by a specific plant metabarcoding approach. New information We provide a large dataset of genetic plant diversity retrieved from surface sedimentary DNA from lakes in Siberia and China spanning over a large environmental gradient. Our dataset encompasses sedDNA sequence data of 259 surface lake sediments and three soil samples originating from Siberian and Chinese lakes. We used the established chloroplastidal P6 loop trnL marker for plant diversity assessment. The merged, filtered and assigned dataset includes 15,692,944 read counts resulting in 623 unique plant DNA sequence types which have a 100% match to either the EMBL or to the specific Arctic plant reference database. The underlying dataset includes a taxonomic list of identified plants and results from PCR replicates, as well as extraction blanks (BLANKs) and PCR negative controls (NTCs), which were run along with the investigated lake samples. This collection of plant metabarcoding data from modern lake sediments is still ongoing and additional data will be released in the future.
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Affiliation(s)
- Kathleen Rosmarie Stoof-Leichsenring
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany
| | - Sisi Liu
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany Institute of Environmental Science and Geography, University of Potsdam Potsdam Germany.,Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany
| | - Weihan Jia
- College of Resource Environment and Tourism, Capital Normal University, Beijing, China College of Resource Environment and Tourism, Capital Normal University Beijing China.,Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany
| | - Kai Li
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany.,College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China College of Chemistry and Life Sciences, Zhejiang Normal University Jinhua China
| | - Luidmila A Pestryakova
- Department for Geography and Biology, North-Eastern Federal University of Yakutsk, Yakutsk, Russia Department for Geography and Biology, North-Eastern Federal University of Yakutsk Yakutsk Russia
| | - Steffen Mischke
- Institute of Earth Sciences, University of Iceland, Reykjavík, Iceland Institute of Earth Sciences, University of Iceland Reykjavík Iceland
| | - Xianyong Cao
- Alpine Paleoecology and Human Adaptation Group (ALPHA), Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Beijing, China Alpine Paleoecology and Human Adaptation Group (ALPHA), Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research Beijing China
| | - Xingqi Liu
- College of Resource Environment and Tourism, Capital Normal University, Beijing, China College of Resource Environment and Tourism, Capital Normal University Beijing China
| | - Jian Ni
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China College of Chemistry and Life Sciences, Zhejiang Normal University Jinhua China
| | - Stefan Neuhaus
- Computing and Data Centre, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany Computing and Data Centre, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Ulrike Herzschuh
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany Institute of Environmental Science and Geography, University of Potsdam Potsdam Germany.,Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany Institute of Biochemistry and Biology, University of Potsdam Potsdam Germany
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42
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Banchi E, Ametrano CG, Greco S, Stanković D, Muggia L, Pallavicini A. PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding. Database (Oxford) 2020; 2020:5722079. [PMID: 32016319 PMCID: PMC6997939 DOI: 10.1093/database/baz155] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/11/2019] [Accepted: 12/23/2019] [Indexed: 01/02/2023]
Abstract
DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called 'better clustering for QIIME' (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151, Trieste, Italy
| | - Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy
| | - David Stanković
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy.,Marine Biology Station, National Institute of Biology, Fornače 41, Piran, Slovenia
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151, Trieste, Italy.,Department of Biology and Evoliution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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43
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Ghosh-harihar M, Gurung N, Shukla H, Sinha I, Pandit A, Prakash V, Green RE, Ramakrishnan U. Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures. CONSERV GENET RESOUR 2021; 13:61-77. [DOI: 10.1007/s12686-020-01171-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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45
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Foucher A, Evrard O, Ficetola GF, Gielly L, Poulain J, Giguet-Covex C, Laceby JP, Salvador-Blanes S, Cerdan O, Poulenard J. 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 DOI: 10.1038/s41598-020-67452-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [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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46
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Gostel MR, Zúñiga JD, Kress WJ, Funk VA, Puente-Lelievre C. Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding. Sci Rep 2020; 10:8701. [PMID: 32457375 PMCID: PMC7250904 DOI: 10.1038/s41598-020-64919-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/20/2020] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.
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Affiliation(s)
- Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107-3400, USA.
| | - Jose D Zúñiga
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA
| | - W John Kress
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
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47
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Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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48
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Epp LS. A global perspective for biodiversity history with ancient environmental DNA. Mol Ecol 2020; 28:2456-2458. [PMID: 31216119 DOI: 10.1111/mec.15118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
The past centuries have seen tremendous turnovers in species distributions and biodiversity due to anthropogenic impacts on a global scale. The processes are ongoing and mostly not well documented. Long-term records of biotic change can be recovered from sedimentary deposits, but traditional analyses were restricted to organisms that leave behind visible traces and molecular genetic tools were mostly employed on samples that promised good DNA preservation. In this issue of Molecular Ecology, Shaw, Weyrich, Hallegraeff and Cooper (2019) and Gomez Cabrera et al. (2019) present two studies on marine sedimentary records from warm environments, in which they successfully analyze ancient environmental DNA (aeDNA) on a decadal and centennial scale. Notably, the studies were conducted on novel samples with nonoptimal preservation conditions for ancient DNA - historical collections of ship ballast tank sediments from Australia and two coral reef cores spanning up to 750 years (Figure 1) - but yielded a high diversity of taxa. This highlights that aeDNA is a promising tool to globally study biodiversity history on scales of decades to centuries - the timeframe most relevant to human society in the context of both current climate change and direct anthropogenic modifications of the environment.
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Affiliation(s)
- Laura S Epp
- Limnological Institute, Environmental Genomics, University of Konstanz, Konstanz, Germany
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49
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Clarke CL, Edwards ME, Gielly L, Ehrich D, Hughes PDM, Morozova LM, Haflidason H, Mangerud J, Svendsen JI, Alsos IG. Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals. Sci Rep 2019; 9:19613. [PMID: 31873100 PMCID: PMC6927971 DOI: 10.1038/s41598-019-55989-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
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Affiliation(s)
- C L Clarke
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - M E Edwards
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L Gielly
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, C2 40700 38058, Grenoble, Cedex 9, France
| | - D Ehrich
- Department of Arctic and Marine Biology, UiT- The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - P D M Hughes
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L M Morozova
- Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Ekaterinburg, Russia
| | - H Haflidason
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J Mangerud
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J I Svendsen
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - I G Alsos
- Tromsø University Museum, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
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50
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deWaard JR, Ratnasingham S, Zakharov EV, Borisenko AV, Steinke D, Telfer AC, Perez KHJ, Sones JE, Young MR, Levesque-Beaudin V, Sobel CN, Abrahamyan A, Bessonov K, Blagoev G, deWaard SL, Ho C, Ivanova NV, Layton KKS, Lu L, Manjunath R, McKeown JTA, Milton MA, Miskie R, Monkhouse N, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Radulovici AE, Steinke C, Warne CP, Hebert PDN. A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples. Sci Data 2019; 6:308. [PMID: 31811161 PMCID: PMC6897906 DOI: 10.1038/s41597-019-0320-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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Affiliation(s)
- Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Alex V Borisenko
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kara K S Layton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Norm Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Connor P Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
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