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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] [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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C Martins C, Adams JK, Yang H, Shchetnikov AA, Di Domenico M, Rose NL, Mackay AW. Earthquake, floods and changing land use history: A 200-year overview of environmental changes in Selenga River basin as indicated by n-alkanes and related proxies in sediments from shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162245. [PMID: 36805057 DOI: 10.1016/j.scitotenv.2023.162245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The Selenga River basin, located in southern Siberia, is an important component of the Lake Baikal ecosystem, and comprises approximately 80 % of the Baikal watershed. Within the Selenga River basin, two localized study regions were chosen. The first, the Selenga Delta, is one of the largest inland freshwater floodplains in the world and plays an important role in the ecosystem functioning of Baikal. It purifies the river waters before they enter the lake and acts as a refuge for many of Baikal's endemic species. The second location, the Gusinoozersk region, is southwest of Lake Baikal and the Selenga Delta, and was chosen as a more heavily industrialized region within the Selenga River basin. Anthropogenic activities, including industry, urban settlements, aquaculture and agriculture, have historically increased ecological damage within this area. We assessed possible drivers of changes in sedimentary organic matter (OM) composition within two shallow lakes (SLNG04 and Black Lake), located in the Selenga Delta and the Selenga watershed, respectively. We focused on individual n-alkanes, one of the most abundant and common lipids used to provide information on past vegetation and used multivariate statistics to disentangle changes in the sources of sedimentary OM over time. The depositional OM history of SLNG04B core can be divided in four zones: (i) major influence of non-emergent vascular plants, typically found in transitional environments (ca. 1835 to ca. 1875); (ii) increased influence of grasses/herbs (ca. 1880 to ca. 1910); (iii) transition from non-emergent vascular plants and grasses/herbs to submerged and floating macrophytes and phytoplankton (ca. 1915 to ca. 1945); (iv) maintenance of autochthonous OM from submerged and floating macrophytes and phytoplankton (ca. 1945 to ca. 2014). The depositional OM history of the Black Lake core can be divided in two main zones: (i) major influence of non-emergent vascular plants and submerged and floating macrophytes (ca. 1915 to ca. 1980); (ii) increased influence of grasses/herbs and phytoplankton (ca. 1980 to ca. 2010). Natural events (e.g., an earthquake in 1862 caused flooding and subsidence of much of the land surrounding SLNG04 lake and a further catastrophic flood event in 1897) and anthropogenic activities (e.g., nutrient pollution from expansion of agricultural and livestock population) changed the composition of sedimentary OM resulting in ecological shifts across trophic levels in the Selenga River basin.
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Affiliation(s)
- César C Martins
- Centro de Estudos do Mar, Campus Pontal do Paraná, Universidade Federal do Paraná, Caixa Postal 61, 83255-976 Pontal do Paraná, PR, Brazil; Environmental Change Research Centre, Department of Geography, University College London, Gower Street, London WC1E 6BT, UK.
| | - Jennifer K Adams
- Environmental Change Research Centre, Department of Geography, University College London, Gower Street, London WC1E 6BT, UK; Biology Department, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada.
| | - Handong Yang
- Environmental Change Research Centre, Department of Geography, University College London, Gower Street, London WC1E 6BT, UK
| | - Alexander A Shchetnikov
- Institute of the Earth's Crust, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; Vinogradov Institute of Geochemistry, Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; Irkutsk State University, Irkutsk, 664025, Russia
| | - Maikon Di Domenico
- Centro de Estudos do Mar, Campus Pontal do Paraná, Universidade Federal do Paraná, Caixa Postal 61, 83255-976 Pontal do Paraná, PR, Brazil
| | - Neil L Rose
- Environmental Change Research Centre, Department of Geography, University College London, Gower Street, London WC1E 6BT, UK
| | - Anson W Mackay
- Environmental Change Research Centre, Department of Geography, University College London, Gower Street, London WC1E 6BT, UK
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Everett R, Cribdon B. MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.888421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.
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Garcés-Pastor S, Coissac E, Lavergne S, Schwörer C, Theurillat JP, Heintzman PD, Wangensteen OS, Tinner W, Rey F, Heer M, Rutzer A, Walsh K, Lammers Y, Brown AG, Goslar T, Rijal DP, Karger DN, Pellissier L, Heiri O, Alsos IG. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change. Nat Commun 2022; 13:6559. [PMID: 36333301 PMCID: PMC9636257 DOI: 10.1038/s41467-022-34010-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.
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Affiliation(s)
- Sandra Garcés-Pastor
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Eric Coissac
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Sébastien Lavergne
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Christoph Schwörer
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Jean-Paul Theurillat
- grid.8591.50000 0001 2322 4988Fondation Aubert, 1938 Champex-Lac, Switzerland, Department of Plant Sciences, University of Geneva, 1292 Chambésy, Switzerland
| | - Peter D. Heintzman
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Owen S. Wangensteen
- grid.10919.300000000122595234Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway ,grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Catalonia Spain
| | - Willy Tinner
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Fabian Rey
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Martina Heer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Astrid Rutzer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Kevin Walsh
- grid.5685.e0000 0004 1936 9668Department of Archaeology, University of York, York, 11 YO1 7EP UK
| | - Youri Lammers
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Antony G. Brown
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Tomasz Goslar
- grid.5633.30000 0001 2097 3545Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, 61-680 Poznań, Poland
| | - Dilli P. Rijal
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Dirk N. Karger
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute for Forest, Snow, and Landscape Research (WSL), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Loïc Pellissier
- grid.5801.c0000 0001 2156 2780Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zurich, Zürich, Switzerland ,grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Oliver Heiri
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Inger Greve Alsos
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
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ter Schure AT, Bruch AA, Kandel AW, Gasparyan B, Bussmann RW, Brysting AK, de Boer HJ, Boessenkool S. Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. J Hum Evol 2022; 172:103258. [DOI: 10.1016/j.jhevol.2022.103258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022]
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Moore MA, Scheible MK, Robertson JB, Meiklejohn KA. Assessing the lysis of diverse pollen from bulk environmental samples for DNA metabarcoding. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.89753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pollen is ubiquitous year-round in bulk environmental samples and can provide useful information on previous and current plant communities. Characterization of pollen has traditionally been completed based on morphology, requiring significant time and expertise. DNA metabarcoding is a promising approach for characterizing pollen from bulk environmental samples, but accuracy hinges on successful lysis of pollen grains to free template DNA. In this study, we assessed the lysis of morphologically and taxonomically diverse pollen from one of the most common bulk environmental sample types for DNA metabarcoding, surface soil. To achieve this, a four species artificial pollen mixture was spiked into surface soils collected from Colorado, North Carolina, and Pennsylvania, and subsequently subjected to DNA extraction using both the PowerSoil and PowerSoil Pro Kits (Qiagen) with a heated incubation (either 65 °C or 90 °C). Amplification and Illumina sequencing of the internal transcribed spacer subunit 2 (ITS2) was completed in duplicate for each sample (total n, 76), and the resulting sequencing reads taxonomically identified using GenBank. The PowerSoil Pro Kit statistically outperformed the PowerSoil Kit for total DNA yield. When using either kit, incubation temperature (65 °C or 90 °C) used had no impact on the recovery of DNA, plant amplicon sequence variants (ASVs), or total plant ITS2 reads. This study highlighted that lysis of pollen in bulk environmental samples is feasible using commercially available kits, and downstream DNA metabarcoding can be used to accurately characterize pollen DNA from such sample types.
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Geng R, Andreev A, Kruse S, Heim B, van Geffen F, Pestryakova L, Zakharov E, Troeva E, Shevtsova I, Li F, Zhao Y, Herzschuh U. Modern Pollen Assemblages From Lake Sediments and Soil in East Siberia and Relative Pollen Productivity Estimates for Major Taxa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.837857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Modern pollen–vegetation–climate relationships underpin palaeovegetation and palaeoclimate reconstructions from fossil pollen records. East Siberia is an ideal area for investigating the relationships between modern pollen assemblages and near natural vegetation under cold continental climate conditions. Reliable pollen-based quantitative vegetation and climate reconstructions are still scarce due to the limited number of modern pollen datasets. Furthermore, differences in pollen representation of samples from lake sediments and soils are not well understood. Here, we present a new pollen dataset of 48 moss/soil and 24 lake surface-sediment samples collected in Chukotka and central Yakutia in East Siberia. The pollen–vegetation–climate relationships were investigated by ordination analyses. Generally, tundra and taiga vegetation types can be well distinguished in the surface pollen assemblages. Moss/soil and lake samples contain generally similar pollen assemblages as revealed by a Procrustes comparison with some exceptions. Overall, modern pollen assemblages reflect the temperature and precipitation gradients in the study areas as revealed by constrained ordination analysis. We estimate the relative pollen productivity (RPP) of major taxa and the relevant source area of pollen (RSAP) for moss/soil samples from Chukotka and central Yakutia using Extended R-Value (ERV) analysis. The RSAP of the tundra-forest transition area in Chukotka and taiga area in central Yakutia are ca. 1300 and 360 m, respectively. For Chukotka, RPPs relative to both Poaceae and Ericaceae were estimated while RPPs for central Yakutia were relative only to Ericaceae. Relative to Ericaceae (reference taxon, RPP = 1), Larix, Betula, Picea, and Pinus are overrepresented while Alnus, Cyperaceae, Poaceae, and Salix are underrepresented in the pollen spectra. Our estimates are in general agreement with previously published values and provide the basis for reliable quantitative reconstructions of East Siberian vegetation.
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Messager E, Giguet-Covex C, Doyen E, Etienne D, Gielly L, Sabatier P, Banjan M, Develle AL, Didier J, Poulenard J, Julien A, Arnaud F. Two Millennia of Complexity and Variability in a Perialpine Socioecological System (Savoie, France): The Contribution of Palynology and sedaDNA Analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the last two millennia, European Alpine ecosystems have experienced major changes in response to the important, yet fluctuating, impact of human activities. This study aims to reconstruct the environmental history of the last 1800 years on the western edge of the Alps by analyzing sediments from Lake Aiguebelette, a large lake located in the perialpine area. We have combined analyses of pollen and other palynomorphs, such as coprophilous fungal spores, together with sedimentary DNA (from plants and mammals) in order to reconstruct both vegetation and land-use histories. A sedimentological and geochemical analysis was also conducted in order to gain an understanding of changes in erosion dynamics in response to landscape modifications that were influenced by climate and human activities. This work highlights alternating phases of anthropization and agricultural abandonment allowing forest recovery. While pollen reflects the major phases of regional deforestation and afforestation related to the dynamic of farming activities, plant DNA provides precise information on the plants cultivated in fields, orchards and vegetable gardens over the past centuries. The combination of mammal DNA and coprophilous fungal spores completes this work by documenting the history of pastoral practices.
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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Huang S, Stoof-Leichsenring KR, Liu S, Courtin J, Andreev AA, Pestryakova LA, Herzschuh U. Plant Sedimentary Ancient DNA From Far East Russia Covering the Last 28,000 Years Reveals Different Assembly Rules in Cold and Warm Climates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.763747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plant communities is not well understood due to the limited knowledge about plant assembly rules. Records of past plant diversity over long time series are rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation biomass could be highest. We reveal highest richness during 28–23 ka and a second richness peak during 13–9 ka, with both periods being accompanied by low relative abundance of shrubs. During the cold period before 14 ka, rich plant assemblages were phylogenetically clustered, suggesting low genetic divergence in the assemblages despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich plant assemblages were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness might overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.
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Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. DIVERSITY 2021. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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12
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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] [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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13
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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] [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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14
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Crump SE, Fréchette B, Power M, Cutler S, de Wet G, Raynolds MK, Raberg JH, Briner JP, Thomas EK, Sepúlveda J, Shapiro B, Bunce M, Miller GH. Ancient plant DNA reveals High Arctic greening during the Last Interglacial. Proc Natl Acad Sci U S A 2021; 118:e2019069118. [PMID: 33723011 PMCID: PMC8020792 DOI: 10.1073/pnas.2019069118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.
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Affiliation(s)
- Sarah E Crump
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303;
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Bianca Fréchette
- Geotop, Université du Québec à Montréal, Montréal, H2L 2C4, Canada
| | - Matthew Power
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, 6845 Bentley, Australia
| | - Sam Cutler
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Gregory de Wet
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
- Department of Geosciences, Smith College, Northampton, MA 01063
| | - Martha K Raynolds
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Jonathan H Raberg
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
| | - Jason P Briner
- Department of Geology, University at Buffalo, Buffalo, NY 14260
| | | | - Julio Sepúlveda
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
- HHMI, University of California, Santa Cruz, CA 95064
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, 6845 Bentley, Australia
- New Zealand Environment Protection Authority, 6011 Wellington, New Zealand
| | - Gifford H Miller
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
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15
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Meucci S, Schulte L, Zimmermann HH, Stoof‐Leichsenring KR, Epp L, Bronken Eidesen P, Herzschuh U. Holocene chloroplast genetic variation of shrubs ( Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses. Ecol Evol 2021; 11:2173-2193. [PMID: 33717447 PMCID: PMC7920767 DOI: 10.1002/ece3.7183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.
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Affiliation(s)
- Stefano Meucci
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Luise Schulte
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Heike H. Zimmermann
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
| | - Kathleen R. Stoof‐Leichsenring
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
| | - Laura Epp
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | | | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Institute of Environmental Sciences and GeographyUniversity of PotsdamPotsdamGermany
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16
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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17
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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18
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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] [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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19
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Liu S, Stoof-Leichsenring KR, Kruse S, Pestryakova LA, Herzschuh U. Holocene Vegetation and Plant Diversity Changes in the North-Eastern Siberian Treeline Region From Pollen and Sedimentary Ancient DNA. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.560243] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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20
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Crump SE, Miller GH, Power M, Sepúlveda J, Dildar N, Coghlan M, Bunce M. Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada. GLOBAL CHANGE BIOLOGY 2019; 25:4244-4256. [PMID: 31603617 DOI: 10.1111/gcb.14836] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 08/08/2019] [Indexed: 12/29/2022]
Abstract
Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic 10 Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen-based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags.
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Affiliation(s)
- Sarah E Crump
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Organic Geochemistry Laboratory, University of Colorado Boulder, Boulder, CO, USA
| | - Gifford H Miller
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Julio Sepúlveda
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Organic Geochemistry Laboratory, University of Colorado Boulder, Boulder, CO, USA
| | - Nadia Dildar
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA.,Organic Geochemistry Laboratory, University of Colorado Boulder, Boulder, CO, USA
| | - Megan Coghlan
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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21
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Giguet-Covex C, Ficetola GF, Walsh K, Poulenard J, Bajard M, Fouinat L, Sabatier P, Gielly L, Messager E, Develle AL, David F, Taberlet P, Brisset E, Guiter F, Sinet R, Arnaud F. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Sci Rep 2019; 9:14676. [PMID: 31604959 PMCID: PMC6789010 DOI: 10.1038/s41598-019-50339-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/12/2019] [Indexed: 11/09/2022] Open
Abstract
Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).
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Affiliation(s)
- C Giguet-Covex
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK. .,EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France.
| | - G F Ficetola
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - K Walsh
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK
| | - J Poulenard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - M Bajard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Fouinat
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - P Sabatier
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Messager
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - A L Develle
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - F David
- CEREGE, UMR CNRS 7330, IRD 161-Marseille Université, Technopôle de l'Arbois Méditerranée, BP 80, 13545, Aix en Provence cedex 4, France
| | - P Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Brisset
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - F Guiter
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - R Sinet
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - F Arnaud
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
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22
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Zimmermann HH, Harms L, Epp LS, Mewes N, Bernhardt N, Kruse S, Stoof-Leichsenring KR, Pestryakova LA, Wieczorek M, Trense D, Herzschuh U. Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly. PLoS One 2019; 14:e0216966. [PMID: 31291259 PMCID: PMC6619608 DOI: 10.1371/journal.pone.0216966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.
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MESH Headings
- Chromosome Mapping
- DNA, Ancient
- DNA, Chloroplast/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Genetic Variation
- Genetics, Population
- Genome, Chloroplast
- Genome, Mitochondrial
- Genome, Plant
- Haplotypes
- History, Ancient
- Larix/classification
- Larix/genetics
- Polymorphism, Single Nucleotide
- Siberia
- Taiga
- Tundra
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Affiliation(s)
- Heike H. Zimmermann
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
| | - Lars Harms
- Scientific Computing, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Laura S. Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nick Mewes
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Nadine Bernhardt
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Stefan Kruse
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Kathleen R. Stoof-Leichsenring
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | | | - Mareike Wieczorek
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Daronja Trense
- Institute for Integrated Natural Sciences, Biology, Koblenz-Landau University, Koblenz, Germany
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute of Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
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23
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Parducci L, Alsos IG, Unneberg P, Pedersen MW, Han L, Lammers Y, Salonen JS, Väliranta MM, Slotte T, Wohlfarth B. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00189] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Epp LS, Kruse S, Kath NJ, Stoof-Leichsenring KR, Tiedemann R, Pestryakova LA, Herzschuh U. Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling. Sci Rep 2018; 8:17436. [PMID: 30498238 PMCID: PMC6265258 DOI: 10.1038/s41598-018-35550-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 11/01/2018] [Indexed: 12/01/2022] Open
Abstract
Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
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Affiliation(s)
- Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany.
| | - Stefan Kruse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Nadja J Kath
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Ralph Tiedemann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Luidmila A Pestryakova
- Department for Geography and Biology, North-Eastern Federal University of Yakutsk, Belinskogo 58, 67700, Yakutsk, Russia
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
- Institute of Earth and Environmental Science, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
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25
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Dormontt EE, van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM, Waycott M, Lowe AJ. Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00134] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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26
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Bell KL, Burgess KS, Botsch JC, Dobbs EK, Read TD, Brosi BJ. Quantitative and qualitative assessment of pollen
DNA
metabarcoding using constructed species mixtures. Mol Ecol 2018; 28:431-455. [DOI: 10.1111/mec.14840] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/20/2018] [Accepted: 07/28/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Karen L. Bell
- Department of Environmental Sciences Emory University Atlanta Georgia
| | - Kevin S. Burgess
- Columbus State University Department of Biology Columbus Georgia
| | | | - Emily K. Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia
| | - Timothy D. Read
- Division of Infectious Diseases Department of Human Genetics School of Medicine Emory University Atlanta Georgia
| | - Berry J. Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia
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27
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Bálint M, Nowak C, Márton O, Pauls SU, Wittwer C, Aramayo JL, Schulze A, Chambert T, Cocchiararo B, Jansen M. Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs. Mol Ecol Resour 2018; 18:1415-1426. [DOI: 10.1111/1755-0998.12934] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 06/20/2018] [Accepted: 07/05/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Miklós Bálint
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Orsolya Márton
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research; Hungarian Academy of Sciences; Budapest Hungary
| | - Steffen U. Pauls
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Claudia Wittwer
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
| | - José Luis Aramayo
- Museo de Historia Natural Noel Kempff Mercado - Facultad Cs; Farmacéutica y Bioquímicas - UAGRM; Santa Cruz Bolivia
| | - Arne Schulze
- Hessisches Landesmuseum Darmstadt (HLMD); Darmstadt Germany
| | - Thierry Chambert
- Department of Ecosystem Science and Management; Pennsylvania State University; University Park Pennsylvania
| | - Berardino Cocchiararo
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG); Frankfurt Germany
| | - Martin Jansen
- Senckenberg Research Institute and Natural History Museum Frankfurt; Frankfurt Germany
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28
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Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B. Minimizing polymerase biases in metabarcoding. Mol Ecol Resour 2018; 18:927-939. [PMID: 29797549 DOI: 10.1111/1755-0998.12895] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 01/24/2023]
Abstract
DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.
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Affiliation(s)
- Ruth V Nichols
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Lee A Newsom
- Department of Social Sciences, Flagler College, St. Augustine, Florida
| | - Yue Wang
- Department of Geography, University of Wisconsin-Madison, Madison, Wisconsin
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
- Tromsø University Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - McKenna Leighton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
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29
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Alsos IG, Lammers Y, Yoccoz NG, Jørgensen T, Sjögren P, Gielly L, Edwards ME. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS One 2018; 13:e0195403. [PMID: 29664954 PMCID: PMC5903670 DOI: 10.1371/journal.pone.0195403] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Youri Lammers
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nigel Giles Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Tina Jørgensen
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Per Sjögren
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Ludovic Gielly
- University Grenoble Alpes, LECA, Grenoble, France
- CNRS, LECA, Grenoble, France
| | - Mary E. Edwards
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- Geography and Environment, University of Southampton, Highfield, Southampton, United Kingdom
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30
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Zimmermann HH, Raschke E, Epp LS, Stoof-Leichsenring KR, Schirrmeister L, Schwamborn G, Herzschuh U. The History of Tree and Shrub Taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data. Genes (Basel) 2017; 8:E273. [PMID: 29027988 PMCID: PMC5664123 DOI: 10.3390/genes8100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/27/2017] [Accepted: 10/04/2017] [Indexed: 11/21/2022] Open
Abstract
Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.
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Affiliation(s)
- Heike H Zimmermann
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Elena Raschke
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Laura S Epp
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Kathleen R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Lutz Schirrmeister
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Georg Schwamborn
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Ulrike Herzschuh
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
- Institute of Earth and Environmental Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
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