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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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2
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Teixeira DF, Hilário HO, Santos GB, Carvalho DC. DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent. Ecol Evol 2023; 13:e10649. [PMID: 37869433 PMCID: PMC10587807 DOI: 10.1002/ece3.10649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%-87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.
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Affiliation(s)
- Daniel Fonseca Teixeira
- Post-Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte Brazil
- Post-Graduate Program in Genetics Federal University of Minas Gerais Belo Horizonte Brazil
| | - Heron Oliveira Hilário
- Post-Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte Brazil
| | - Gilmar Bastos Santos
- Post-Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte Brazil
| | - Daniel Cardoso Carvalho
- Post-Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte Brazil
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3
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Li H, Zhang H, Chang F, Liu Q, Zhang Y, Liu F, Zhang X. Sedimentary DNA for tracking the long-term changes in biodiversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17039-17050. [PMID: 36622608 DOI: 10.1007/s11356-023-25130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
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4
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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5
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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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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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8
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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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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Schulte L, Meucci S, Stoof-Leichsenring KR, Heitkam T, Schmidt N, von Hippel B, Andreev AA, Diekmann B, Biskaborn BK, Wagner B, Melles M, Pestryakova LA, Alsos IG, Clarke C, Krutovsky KV, Herzschuh U. Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA. Commun Biol 2022; 5:570. [PMID: 35681049 PMCID: PMC9184489 DOI: 10.1038/s42003-022-03455-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.
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11
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Han X, Tolu J, Deng L, Fiskal A, Schubert CJ, Winkel LHE, Lever MA. Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls. PNAS NEXUS 2022; 1:pgac076. [PMID: 36741427 PMCID: PMC9896894 DOI: 10.1093/pnasnexus/pgac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023]
Abstract
Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.
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Affiliation(s)
| | - Julie Tolu
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Longhui Deng
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Carsten Johnny Schubert
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Lenny H E Winkel
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
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12
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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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Ahlquist KD, Bañuelos MM, Funk A, Lai J, Rong S, Villanea FA, Witt KE. Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture. Genome Biol Evol 2021; 13:evab115. [PMID: 34028527 PMCID: PMC8480178 DOI: 10.1093/gbe/evab115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022] Open
Abstract
The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.
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Affiliation(s)
- K D Ahlquist
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mayra M Bañuelos
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Jiaying Lai
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Brown Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
| | - Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Fernando A Villanea
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Anthropology, University of Colorado Boulder, Colorado, USA
| | - Kelsey E Witt
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
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14
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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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15
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Courtin J, Andreev AA, Raschke E, Bala S, Biskaborn BK, Liu S, Zimmermann H, Diekmann B, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. Vegetation Changes in Southeastern Siberia During the Late Pleistocene and the Holocene. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.625096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last ∼35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake’s vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the “keystone herbivore” hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.
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16
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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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17
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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18
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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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19
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Leewis MC, Berlemont R, Podgorski DC, Srinivas A, Zito P, Spencer RGM, McFarland J, Douglas TA, Conaway CH, Waldrop M, Mackelprang R. Life at the Frozen Limit: Microbial Carbon Metabolism Across a Late Pleistocene Permafrost Chronosequence. Front Microbiol 2020; 11:1753. [PMID: 32849382 PMCID: PMC7403407 DOI: 10.3389/fmicb.2020.01753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022] Open
Abstract
Permafrost is an extreme habitat yet it hosts microbial populations that remain active over millennia. Using permafrost collected from a Pleistocene chronosequence (19 to 33 ka), we hypothesized that the functional genetic potential of microbial communities in permafrost would reflect microbial strategies to metabolize permafrost soluble organic matter (OM) in situ over geologic time. We also hypothesized that changes in the metagenome across the chronosequence would correlate with shifts in carbon chemistry, permafrost age, and paleoclimate at the time of permafrost formation. We combined high-resolution characterization of water-soluble OM by Fourier-transform ion-cyclotron-resonance mass spectrometry (FT-ICR MS), quantification of organic anions in permafrost water extracts, and metagenomic sequencing to better understand the relationships between the molecular-level composition of potentially bioavailable OM, the microbial community, and permafrost age. Both age and paleoclimate had marked effects on both the molecular composition of dissolved OM and the microbial community. The relative abundance of genes associated with hydrogenotrophic methanogenesis, carbohydrate active enzyme families, nominal oxidation state of carbon (NOSC), and number of identifiable molecular formulae significantly decreased with increasing age. In contrast, genes associated with fermentation of short chain fatty acids (SCFAs), the concentration of SCFAs and ammonium all significantly increased with age. We present a conceptual model of microbial metabolism in permafrost based on fermentation of OM and the buildup of organic acids that helps to explain the unique chemistry of ancient permafrost soils. These findings imply long-term in situ microbial turnover of ancient permafrost OM and that this pooled biolabile OM could prime ancient permafrost soils for a larger and more rapid microbial response to thaw compared to younger permafrost soils.
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Affiliation(s)
- Mary-Cathrine Leewis
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, United States
| | - Renaud Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA, United States
| | - David C Podgorski
- Pontchartrain Institute for Environmental Sciences, Department of Chemistry, University of New Orleans, New Orleans, LA, United States
| | - Archana Srinivas
- Department of Biology, California State University Northridge, Northridge, CA, United States
| | - Phoebe Zito
- Pontchartrain Institute for Environmental Sciences, Department of Chemistry, University of New Orleans, New Orleans, LA, United States
| | - Robert G M Spencer
- National High Magnetic Field Laboratory Geochemistry Group, Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Jack McFarland
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, United States
| | - Thomas A Douglas
- U.S. Army Cold Regions Research and Engineering Laboratory, Fort Wainwright, AK, United States
| | | | - Mark Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, United States
| | - Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, CA, United States
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20
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Seersholm FV, Werndly DJ, Grealy A, Johnson T, Keenan Early EM, Lundelius EL, Winsborough B, Farr GE, Toomey R, Hansen AJ, Shapiro B, Waters MR, McDonald G, Linderholm A, Stafford TW, Bunce M. Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change. Nat Commun 2020; 11:2770. [PMID: 32488006 PMCID: PMC7265304 DOI: 10.1038/s41467-020-16502-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall’s Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene. The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.
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Affiliation(s)
- Frederik V Seersholm
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| | - Daniel J Werndly
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Alicia Grealy
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.,Division of Ecology and Evolution, Research School of Biology, ANU College of Science The Australian National University, Canberra, ACT, 2600, Australia
| | - Taryn Johnson
- Bioarchaeology and Genomics Laboratory, Department of Anthropology, Texas A&M University, College Station, TX, 77843, USA
| | - Erin M Keenan Early
- Department of Geosciences, Jackson School of Geological Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ernest L Lundelius
- Department of Geosciences, Vertebrate Paleontology Laboratory, Jackson School of Geological Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Barbara Winsborough
- Department of Integrative Biology, The University of Texas, Austin, TX, 78712, USA.,Winsborough Consulting, Leander, TX, 78641, USA
| | - Grayal Earle Farr
- Department of Anthropology, Florida State University, Tallahassee, FL, 32310, USA
| | - Rickard Toomey
- Mammoth Cave National Park, PO Box 7, Mammoth Cave, KY, 42259, USA
| | - Anders J Hansen
- Centre for GeoGenetics, Department of Biology, University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Michael R Waters
- Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX, 77843-4352, USA
| | - Gregory McDonald
- Bureau of Land Management, Utah State Office, 440 West 200 South, Salt Lake City, UT, 84101-1345, USA
| | - Anna Linderholm
- Bioarchaeology and Genomics Laboratory, Department of Anthropology, Texas A&M University, College Station, TX, 77843, USA
| | | | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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21
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Kuefner W, Hofmann AM, Geist J, Raeder U. Evaluating climate change impacts on mountain lakes by applying the new silicification value to paleolimnological samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136913. [PMID: 32007888 DOI: 10.1016/j.scitotenv.2020.136913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The evaluation of climate change impact on lakes typically relies on statistical methods like the reorganisation of organism communities (beta diversity) or transfer functions. A new method uses the silicification of diatoms that correlates with temperature and nutrients. The so-called silicification value (SiVa) overcomes problems of descriptive statistics or absent indicator species. Averaged over diatom communities, it related inversely to lake surface temperatures in mountain lakes. Hence, its change over time (δ SiVa) in a lake was hypothesised to reflect global change-driven lake warming quantitatively, which supposedly climaxes in shallow lakes. Sixteen different δ SiVa calculation approaches were tested. They (1) included or excluded planktic diatoms, (2) integrated fixed or variable time series referring to climate data or changes in diatom assemblages, (3) employed a top-bottom or regression approach and (4) expressed the δ SiVa as relative or absolute values. Subfossil diatom assemblages from 24 sediment cores from Bavarian and north Tyrolian mountain lakes served as sample set. All possible approaches were evaluated for their explanatory power for lake characteristics using GLMs. The top-bottom benthic approach with fixed climate data-based time series appeared to be the best model based on AIC and the extent of variable integration. In line with the hypothesis, the strongest decrease of δ SiVa was evident in most shallow lakes. Segmented regression further highlighted a positive correlation with depth if shallower than 10 m. By referring to the negative SiVa-summer temperature relation, δ SiVa also enabled the quantification of lake warming within the last decades, which ranged mainly between 0.1 °C and 1.1 °C per decade, consistent with existing literature. Additionally, a 100 year temperature reconstruction from a varved sediment core successfully validated the approach. Further studies may focus and extend its application to deeper lakes, but it can already serve as a powerful tool in palaeolimnological studies of shallow lakes like hard-water mountain lakes.
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Affiliation(s)
- Wolfgang Kuefner
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Department of Ecology and Ecosystem Management, Technical University of Munich, Hofmark 1-3, D-82393 Iffeldorf, Germany.
| | - Andrea M Hofmann
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Department of Ecology and Ecosystem Management, Technical University of Munich, Hofmark 1-3, D-82393 Iffeldorf, Germany.
| | - Juergen Geist
- Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management, Technical University of Munich, Mühlenweg 22, D-85354 Freising, Germany.
| | - Uta Raeder
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Department of Ecology and Ecosystem Management, Technical University of Munich, Hofmark 1-3, D-82393 Iffeldorf, Germany.
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22
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Clarke CL, Edwards ME, Gielly L, Ehrich D, Hughes PDM, Morozova LM, Haflidason H, Mangerud J, Svendsen JI, Alsos IG. Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals. Sci Rep 2019; 9:19613. [PMID: 31873100 PMCID: PMC6927971 DOI: 10.1038/s41598-019-55989-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
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Affiliation(s)
- C L Clarke
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - M E Edwards
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L Gielly
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, C2 40700 38058, Grenoble, Cedex 9, France
| | - D Ehrich
- Department of Arctic and Marine Biology, UiT- The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - P D M Hughes
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L M Morozova
- Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Ekaterinburg, Russia
| | - H Haflidason
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J Mangerud
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J I Svendsen
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - I G Alsos
- Tromsø University Museum, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
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23
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Epp LS, Zimmermann HH, Stoof-Leichsenring KR. Sampling and Extraction of Ancient DNA from Sediments. Methods Mol Biol 2019; 1963:31-44. [PMID: 30875042 DOI: 10.1007/978-1-4939-9176-1_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.
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Affiliation(s)
- Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany. .,Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Heike H Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
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24
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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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25
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Tse TJ, Doig LE, Tang S, Zhang X, Sun W, Wiseman SB, Feng CX, Liu H, Giesy JP, Hecker M, Jones PD. Combining High-Throughput Sequencing of sedaDNA and Traditional Paleolimnological Techniques To Infer Historical Trends in Cyanobacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6842-6853. [PMID: 29782156 DOI: 10.1021/acs.est.7b06386] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA ( sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional paleolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production, and paleoenvironmental proxies. DNA was extracted from two sediment cores collected from a northern Canadian Great Plains reservoir. Diversity indices illustrated significant community-level changes since reservoir formation. Furthermore, higher relative abundances in more recent years were observed for potentially toxic cyanobacterial genera including Dolichospermum. Correlation-based network analysis revealed this trend significantly and positively correlated to abundances of the microcystin synthetase gene ( mcyA) and other paleoproxies (nutrients, pigments, stanols, sterols, and certain diatom species), demonstrating synchrony between molecular and more standard proxies. These findings demonstrate a novel approach to infer long-term dynamics of cyanobacterial diversity in inland waters and highlight the power of high-throughput sequencing to reconstruct trends in environmental quality and inform lake and reservoir management and monitoring program design.
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Affiliation(s)
- Timothy J Tse
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
| | - Lorne E Doig
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
| | - Song Tang
- School of Environment and Sustainability , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C3 , Canada
- National Institute of Environmental Health , Chinese Center for Disease Control and Prevention , No. 7 Panjiayuan Nanli , Chaoyang District, Beijing 100021 , China
| | - Xiaohui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-environment Science & Technology , Guangzhou , Guangdong 510650 , China
| | - Steve B Wiseman
- Department of Biological Sciences , University of Lethbridge , Lethbridge , AB T1K 3M4 , Canada
| | - Cindy Xin Feng
- School of Public Health , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Hongling Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - John P Giesy
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
- Zoology Department, Center for Integrative Toxicology , Michigan State University , East Lansing , Michigan 48824 , United States
- School of Biological Sciences , University of Hong Kong , Hong Kong , SAR 999077 , China
| | - Markus Hecker
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
- School of Environment and Sustainability , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C3 , Canada
| | - Paul D Jones
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
- School of Environment and Sustainability , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C3 , Canada
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26
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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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27
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Wagner S, Lagane F, Seguin-Orlando A, Schubert M, Leroy T, Guichoux E, Chancerel E, Bech-Hebelstrup I, Bernard V, Billard C, Billaud Y, Bolliger M, Croutsch C, Čufar K, Eynaud F, Heussner KU, Köninger J, Langenegger F, Leroy F, Lima C, Martinelli N, Momber G, Billamboz A, Nelle O, Palomo A, Piqué R, Ramstein M, Schweichel R, Stäuble H, Tegel W, Terradas X, Verdin F, Plomion C, Kremer A, Orlando L. High-Throughput DNA sequencing of ancient wood. Mol Ecol 2018; 27:1138-1154. [PMID: 29412519 DOI: 10.1111/mec.14514] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023]
Abstract
Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.
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Affiliation(s)
- Stefanie Wagner
- BIOGECO, INRA, University of Bordeaux, Cestas, France.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Vincent Bernard
- Dendro-Archaeology, CNRS, UMR 6566 CReAAH, University of Rennes, Rennes cedex, France
| | | | - Yves Billaud
- MCC/DRASSM, Marseille, France.,Edytem, University of Savoie, Le Bourget-du-Lac, France
| | | | - Christophe Croutsch
- Archéologie Alsace 11, Sélestat, France.,UMR 7044, ARCHIMEDE, Strasbourg Cedex, France
| | - Katarina Čufar
- Biotechnical Faculty, Department of Wood Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Karl Uwe Heussner
- Deutsches Archäologisches Institut, Zentrale, Referat Naturwissenschaften/Dendrochronologie, Berlin, Germany
| | - Joachim Köninger
- Janus Verlag Freiburg im Breisgau, Freiburg im Breisgau, Germany
| | | | - Frédéric Leroy
- Département des Recherches Archéologiques Subaquatiques et Sous-Marines, Marseille, France
| | - Christine Lima
- Département des Recherches Archéologiques Subaquatiques et Sous-Marines, Marseille, France
| | | | - Garry Momber
- National Oceanography Centre, Maritime Archaeology Trust, Southampton, UK
| | - André Billamboz
- Baden-Wuerttemberg State Office for Cultural Heritage, Tree-ring Lab, Hemmenhofen, Germany
| | - Oliver Nelle
- Baden-Wuerttemberg State Office for Cultural Heritage, Tree-ring Lab, Hemmenhofen, Germany
| | - Antoni Palomo
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Piqué
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | | - Willy Tegel
- Institute for Forest Growth, University of Freiburg, Freiburg, Germany
| | - Xavier Terradas
- Spanish National Research Council, IMF - Archaeology of Social Dynamics, Barcelona, Spain
| | - Florence Verdin
- CNRS, UMR 5607 Ausonius, Maison de l'Archéologie, Pessac cedex, France
| | | | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France
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28
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Molecular-Assisted Pollen Grain Analysis Reveals Spatiotemporal Origin of Long-Distance Migrants of a Noctuid Moth. Int J Mol Sci 2018; 19:ijms19020567. [PMID: 29438348 PMCID: PMC5855789 DOI: 10.3390/ijms19020567] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/04/2018] [Accepted: 02/08/2018] [Indexed: 11/30/2022] Open
Abstract
Pollen grains are regularly used as markers to determine an insect’s movement patterns or host (plant) feeding behavior, yet conventional morphology-based pollen grain analysis (or palynology) encounters a number of important limitations. In the present study, we combine conventional analytical approaches with DNA meta-barcoding to identify pollen grains attached to migrating adults of the turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) in Northeast China. More specifically, pollen grains were dislodged from 2566 A. segetum long-distance migrants captured on Beihuang Island (Bohai Sea) and identified to many (plant) species level. Pollen belonged to 26 families of plants, including Fagaceae, Oleaceae, Leguminosae, Asteraceae, Pinaceae and Rosaceae, including common species such as Citrus sinensis, Olea europaea, Ligustrum lucidum, Robinia pseudoacacia, Castanopsis echinocarpa, Melia azedarach and Castanea henryi. As the above plants are indigenous to southern climes, we deduce that A. segetum forage on plants in those locales prior to engaging in northward spring migration. Our work validates the use of DNA-assisted approaches in lepidopteran pollination ecology research and provides unique and valuable information on the adult feeding range and geographical origin of A. segetum. Our findings also enable targeted (area-wide) pest management interventions or guide the future isolation of volatile attractants.
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29
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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30
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Buxton AS, Groombridge JJ, Griffiths RA. Seasonal variation in environmental DNA detection in sediment and water samples. PLoS One 2018; 13:e0191737. [PMID: 29352294 PMCID: PMC5774844 DOI: 10.1371/journal.pone.0191737] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/10/2018] [Indexed: 11/18/2022] Open
Abstract
The use of aquatic environmental DNA (eDNA) to detect the presence of species depends on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments for longer than it does in water, and analysing sediment could potentially extend the seasonal window for species assessment. Using the great crested newt as a model, we compare how detection probability changes across the seasons in eDNA samples collected from both pond water and pond sediments. Detection of both aquatic and sedimentary eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter (January): in all seasons, detection probability of eDNA from water exceeded that from sediment. Detection probability of eDNA also varied between study areas, and according to great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA show the same seasonal fluctuations, the patterns observed in both sample types likely reflect current or recent presence of the target species. However, given the low detection probabilities found in the autumn and winter we would not recommend using either aquatic or sedimentary eDNA for year-round sampling without further refinement and testing of the methods.
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Affiliation(s)
- Andrew S. Buxton
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
- * E-mail:
| | - Jim J. Groombridge
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
| | - Richard A. Griffiths
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
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31
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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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32
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Olajos F, Bokma F, Bartels P, Myrstener E, Rydberg J, Öhlund G, Bindler R, Wang X, Zale R, Englund G. Estimating species colonization dates using
DNA
in lake sediment. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fredrik Olajos
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Folmer Bokma
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Pia Bartels
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Erik Myrstener
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Johan Rydberg
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Gunnar Öhlund
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Richard Bindler
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Xiao‐Ru Wang
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Rolf Zale
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Göran Englund
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
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33
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Kouduka M, Tanabe AS, Yamamoto S, Yanagawa K, Nakamura Y, Akiba F, Tomaru H, Toju H, Suzuki Y. Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea. GEOBIOLOGY 2017; 15:715-727. [PMID: 28434198 DOI: 10.1111/gbi.12233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/25/2017] [Indexed: 06/07/2023]
Abstract
Marine sediments contain eukaryotic DNA deposited from overlying water columns. However, a large proportion of deposited eukaryotic DNA is aerobically biodegraded in shallow marine sediments. Cold seep sediments are often anaerobic near the sediment-water interface, so eukaryotic DNA in such sediments is expected to be preserved. We investigated deeply buried marine sediments in the Japan Sea, where a methane hydrate deposit is associated with cold seeps. Quantitative PCR analysis revealed the reproducible recovery of eukaryotic DNA in marine sediments at depths up to 31.0 m in the vicinity of the methane hydrate deposit. In contrast, the reproducible recovery of eukaryotic DNA was limited to a shallow depth (8.3 m) in marine sediments not adjacent to the methane hydrate deposit in the same area. Pyrosequencing of an 18S rRNA gene variable region generated 1,276-3,307 reads per sample, which was sufficient to cover the biodiversity based on rarefaction curves. Phylogenetic analysis revealed that most of the eukaryotic DNA originated from radiolarian genera of the class Chaunacanthida, which have SrSO4 skeletons, the sea grass genus Zostera, and the seaweed genus Sargassum. Eukaryotic DNA originating from other planktonic fauna and land plants was also detected. Diatom sequences closely related to Thalassiosira spp., indicative of cold climates, were obtained from sediments deposited during the last glacial period (MIS-2). Plant sequences of the genera Alnus, Micromonas, and Ulmus were found in sediments deposited during the warm interstadial period (MIS-3). These results suggest the long-term persistence of eukaryotic DNA from terrestrial and aquatic sources in marine sediments associated with cold seeps, and that the genetic information from eukaryotic DNA from deeply buried marine sediments associated with cold seeps can be used to reconstruct environments and ecosystems from the past.
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Affiliation(s)
- M Kouduka
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo, Japan
| | - A S Tanabe
- Graduate School of Science, Kobe University, Kobe, Japan
| | - S Yamamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - K Yanagawa
- Graduate School of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Y Nakamura
- Institute of Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - F Akiba
- Diatom Minilab Akiba Ltd., Saitama, Japan
| | - H Tomaru
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - H Toju
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Y Suzuki
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo, Japan
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34
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Niemeyer B, Epp LS, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline. Mol Ecol Resour 2017; 17:e46-e62. [DOI: 10.1111/1755-0998.12689] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Bastian Niemeyer
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
| | - Laura S. Epp
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | | | - Luidmila A. Pestryakova
- Department for Geography and Biology; North-Eastern Federal University of Yakutsk; Yakutsk Russia
| | - Ulrike Herzschuh
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam-Golm Germany
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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Andruszkiewicz EA, Starks HA, Chavez FP, Sassoubre LM, Block BA, Boehm AB. Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS One 2017; 12:e0176343. [PMID: 28441466 PMCID: PMC5404852 DOI: 10.1371/journal.pone.0176343] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/10/2017] [Indexed: 02/03/2023] Open
Abstract
Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.
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Affiliation(s)
- Elizabeth A. Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Hilary A. Starks
- Center for Ocean Solutions, Stanford University, Stanford, CA, United States of America
| | - Francisco P. Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - Lauren M. Sassoubre
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Barbara A. Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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Sjögren P, Edwards ME, Gielly L, Langdon CT, Croudace IW, Merkel MKF, Fonville T, Alsos IG. Lake sedimentary DNA accurately records 20 th Century introductions of exotic conifers in Scotland. THE NEW PHYTOLOGIST 2017; 213:929-941. [PMID: 27678125 PMCID: PMC5215665 DOI: 10.1111/nph.14199] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/08/2016] [Indexed: 05/08/2023]
Abstract
Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20th Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen.
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Affiliation(s)
- Per Sjögren
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
| | - Mary E. Edwards
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Ludovic Gielly
- Laboratoire d'Ecologie AlpineUniversité Grenoble AlpesF‐38000GrenobleFrance
- Laboratoire d'Ecologie AlpineCNRSF‐38000GrenobleFrance
| | - Catherine T. Langdon
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Ian W. Croudace
- Ocean and Earth ScienceUniversity of SouthamptonNational Oceanography CentreSouthamptonSO14 3ZHUK
| | | | - Thierry Fonville
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Inger Greve Alsos
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
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Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, Gauthier E, Massa C, Develle AL, Pignol C, Lejzerowicz F, Domaizon I. Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA. Mol Ecol 2016; 25:5925-5943. [DOI: 10.1111/mec.13893] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/08/2016] [Accepted: 10/07/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Eric Capo
- CARRTEL; INRA; Université de Savoie Mont Blanc; 74200 Thonon-les-bains France
| | - Didier Debroas
- Université Clermont Auvergne; Laboratoire “Microorganismes: Génome et Environnement”; Université Blaise Pascal; BP 10448 F-63000 Clermont-Ferrand France
- CNRS; UMR 6023; LMGE; Campus Universitaire des Cézeaux 63171 Aubière France
| | - Fabien Arnaud
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Typhaine Guillemot
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Vincent Bichet
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Laurent Millet
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Emilie Gauthier
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Charly Massa
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Anne-Lise Develle
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Cécile Pignol
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Franck Lejzerowicz
- Department of Genetics and Evolution; University of Geneva; 4 Boulevard d'Yvoy, 1205 Geneva Switzerland
| | - Isabelle Domaizon
- CARRTEL; INRA; Université de Savoie Mont Blanc; 74200 Thonon-les-bains France
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DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago. Nat Commun 2016; 7:13389. [PMID: 27824339 PMCID: PMC5105157 DOI: 10.1038/ncomms13389] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/29/2016] [Indexed: 01/21/2023] Open
Abstract
The demographic history of Greenland is characterized by recurrent migrations and extinctions since the first humans arrived 4,500 years ago. Our current understanding of these extinct cultures relies primarily on preserved fossils found in their archaeological deposits, which hold valuable information on past subsistence practices. However, some exploited taxa, though economically important, comprise only a small fraction of these sub-fossil assemblages. Here we reconstruct a comprehensive record of past subsistence economies in Greenland by sequencing ancient DNA from four well-described midden deposits. Our results confirm that the species found in the fossil record, like harp seal and ringed seal, were a vital part of Inuit subsistence, but also add a new dimension with evidence that caribou, walrus and whale species played a more prominent role for the survival of Paleo-Inuit cultures than previously reported. Most notably, we report evidence of bowhead whale exploitation by the Saqqaq culture 4,000 years ago.
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Wood JR, Perry GLW, Wilmshurst JM. Using palaeoecology to determine baseline ecological requirements and interaction networks for de‐extinction candidate species. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jamie R. Wood
- Long‐term Ecology Lab Landcare Research PO Box 69040 Lincoln7640 New Zealand
| | - George L. W. Perry
- School of Environment The University of Auckland Private Bag 92019 Auckland1142 New Zealand
| | - Janet M. Wilmshurst
- Long‐term Ecology Lab Landcare Research PO Box 69040 Lincoln7640 New Zealand
- School of Environment The University of Auckland Private Bag 92019 Auckland1142 New Zealand
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Bell KL, de Vere N, Keller A, Richardson RT, Gous A, Burgess KS, Brosi BJ. Pollen DNA barcoding: current applications and future prospects. Genome 2016; 59:629-40. [DOI: 10.1139/gen-2015-0200] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
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Affiliation(s)
- Karen L. Bell
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | | | - Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Berry J. Brosi
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
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Tesson SV, Okamura B, Dudaniec RY, Vyverman W, Löndahl J, Rushing C, Valentini A, Green AJ. Integrating microorganism and macroorganism dispersal: modes, techniques and challenges with particular focus on co-dispersal. ECOSCIENCE 2016. [DOI: 10.1080/11956860.2016.1148458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Birks HJB, Birks HH. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? THE NEW PHYTOLOGIST 2016; 209:499-506. [PMID: 26402315 DOI: 10.1111/nph.13657] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/03/2015] [Indexed: 06/05/2023]
Abstract
499 I. 499 II. 500 III. 500 IV. 500 V. 500 VI. 501 VII. 502 VIII. 504 504 References 505 SUMMARY: Ancient DNA (aDNA) from lake sediments, peats, permafrost soils, preserved megafaunal gut contents and coprolites has been used to reconstruct late-Quaternary floras. aDNA is either used alone for floristic reconstruction or compared with pollen and/or macrofossil results. In comparative studies, aDNA may complement pollen and macrofossil analyses by increasing the number of taxa found. We discuss the relative contributions of each fossil group to taxon richness and the number of unique taxa found, and situations in which aDNA has refined pollen identifications. Pressing problems in aDNA studies are contamination and ignorance about taphonomy (transportation, incorporation, and preservation in sediments). Progress requires that these problems are reduced to allow aDNA to reach its full potential contribution to reconstructions of Quaternary floras.
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Affiliation(s)
- H John B Birks
- Department of Biology, University of Bergen, and Bjerknes Centre for Climate Research, Postbox 7803, N-5020, Bergen, Norway
- Environmental Change Research Centre, University College London, Gower Street, London, WC1E 6BT, UK
| | - Hilary H Birks
- Department of Biology, University of Bergen, and Bjerknes Centre for Climate Research, Postbox 7803, N-5020, Bergen, Norway
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Torti A, Lever MA, Jørgensen BB. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 2015; 24 Pt 3:185-96. [DOI: 10.1016/j.margen.2015.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 12/17/2022]
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Parducci L, Väliranta M, Salonen JS, Ronkainen T, Matetovici I, Fontana SL, Eskola T, Sarala P, Suyama Y. Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130382. [PMID: 25487333 DOI: 10.1098/rstb.2013.0382] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ØsterVoldgade 5-7, 1350 Copenhagen, Denmark
| | - Minna Väliranta
- Department of Environmental Sciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - J Sakari Salonen
- Department of Geosciences and Geography, University of Helsinki, PO Box 64, 00014 Helsinki, Finland
| | - Tiina Ronkainen
- Department of Environmental Sciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Irina Matetovici
- Molecular Biology Centre, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babes-Bolyai-University ClujNapoca, 42 TreboniuLaurian Street, 400271 Cluj-Napoca, Romania
| | - Sonia L Fontana
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, UK
| | - Tiina Eskola
- Department of Geosciences, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Pertti Sarala
- Geological Survey of Finland, PO Box 77, 96101 Rovaniemi, Finland
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P. Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Mol Ecol 2015; 24:1485-98. [PMID: 25735209 DOI: 10.1111/mec.13136] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 02/24/2015] [Accepted: 02/27/2015] [Indexed: 11/30/2022]
Abstract
Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.
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Affiliation(s)
- Johan Pansu
- Univ. Grenoble Alpes, LECA, F-38000, Grenoble, France; CNRS, LECA, F-38000, Grenoble, France
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Pedersen MW, Overballe-Petersen S, Ermini L, Sarkissian CD, Haile J, Hellstrom M, Spens J, Thomsen PF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AMZ, Gilbert MTP, Hansen AJ, Orlando L, Willerslev E. Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130383. [PMID: 25487334 PMCID: PMC4275890 DOI: 10.1098/rstb.2013.0383] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Affiliation(s)
- Mikkel Winther Pedersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Søren Overballe-Petersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - James Haile
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Trace and Environmental DNA Laboratory, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
| | - Micaela Hellstrom
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Johan Spens
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Department of Wildlife, Fish and Environmental Studies, SLU, Umeå S-901 83, Sweden
| | - Philip Francis Thomsen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Kristine Bohmann
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Enrico Cappellini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ida Bærholm Schnell
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nathan A Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Astrid M Z Schmidt
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
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Orlando L, Cooper A. Using Ancient DNA to Understand Evolutionary and Ecological Processes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091712] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark;,
| | - Alan Cooper
- Australian Center for Ancient DNA, University of Adelaide, Adelaide, South Australia
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Galimberti A, De Mattia F, Bruni I, Scaccabarozzi D, Sandionigi A, Barbuto M, Casiraghi M, Labra M. A DNA barcoding approach to characterize pollen collected by honeybees. PLoS One 2014; 9:e109363. [PMID: 25296114 PMCID: PMC4190116 DOI: 10.1371/journal.pone.0109363] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/02/2014] [Indexed: 11/18/2022] Open
Abstract
In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno), characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella) at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands.
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Affiliation(s)
- Andrea Galimberti
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Fabrizio De Mattia
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Ilaria Bruni
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | | | - Anna Sandionigi
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Michela Barbuto
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Maurizio Casiraghi
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Massimo Labra
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
- * E-mail:
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