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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. Am J Bot 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 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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2
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Mardini M, Ermolaev A, Khrustaleva L. Hidden Pitfalls of Using Onion Pollen in Molecular Research. Curr Issues Mol Biol 2023; 45:1065-1072. [PMID: 36826015 PMCID: PMC9955844 DOI: 10.3390/cimb45020070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
There is little information on the use of pollen in molecular research, despite the increased interest in genome editing by pollen-mediated transformation. This paper presents an essential toolbox of technical procedures and observations for molecular studies on onion (Allium cepa L.) pollen. PCR is a useful tool as an express method to evaluate editing results before pollination. A direct PCR protocol for pollen suspension has been adapted without needing DNA pre-extraction. We showed that the outer layer of lipids known as pollenkitt is a limiting factor for successful PCR on pollen. A simple pre-washing step of pollen suspension was able to eliminate the pollenkitt and enormously affect the PCR results. Additionally, our pollenkitt study helped us develop a simple and effective pollination method using wetted onion pollen grains. Classical manual pollination usually is conducted by intact pollen without wetting. Most existing methods of the editing system delivery into pollen are carried out in a wet medium with consequent drying before pollination, which adversely affects the viability of pollen. The optimal medium for wet pollination was 12% sucrose water solution. Our method of using wetted pollen grains for pollination might be very beneficial for pollen genetic manipulation.
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Affiliation(s)
- Majd Mardini
- Center of Molecular Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy (RSAU-MTAA), 49, Timiryazevskaya Str., 127550 Moscow, Russia
| | - Aleksey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy (RSAU-MTAA), 49, Timiryazevskaya Str., 127550 Moscow, Russia
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy (RSAU-MTAA), 49, Timiryazevskaya Str., 127550 Moscow, Russia
- Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy (RSAU-MTAA), 49, Timiryazevskaya Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Correspondence: or
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3
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Hassan S, Khurshid Z, Sabreena, Bali BS, Ganai BA, Sayyed RZ, Poczai P, Zaman M. A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. IJERPH 2022; 19:9445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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4
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Messager E, Giguet-Covex C, Doyen E, Etienne D, Gielly L, Sabatier P, Banjan M, Develle AL, Didier J, Poulenard J, Julien A, Arnaud F. Two Millennia of Complexity and Variability in a Perialpine Socioecological System (Savoie, France): The Contribution of Palynology and sedaDNA Analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the last two millennia, European Alpine ecosystems have experienced major changes in response to the important, yet fluctuating, impact of human activities. This study aims to reconstruct the environmental history of the last 1800 years on the western edge of the Alps by analyzing sediments from Lake Aiguebelette, a large lake located in the perialpine area. We have combined analyses of pollen and other palynomorphs, such as coprophilous fungal spores, together with sedimentary DNA (from plants and mammals) in order to reconstruct both vegetation and land-use histories. A sedimentological and geochemical analysis was also conducted in order to gain an understanding of changes in erosion dynamics in response to landscape modifications that were influenced by climate and human activities. This work highlights alternating phases of anthropization and agricultural abandonment allowing forest recovery. While pollen reflects the major phases of regional deforestation and afforestation related to the dynamic of farming activities, plant DNA provides precise information on the plants cultivated in fields, orchards and vegetable gardens over the past centuries. The combination of mammal DNA and coprophilous fungal spores completes this work by documenting the history of pastoral practices.
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6
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Kelley L, Rose E, McCullough B, Martinez M, Baudelet M. Non-destructive DNA analysis of single pollen grains. Forensic Chem 2020. [DOI: 10.1016/j.forc.2020.100275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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8
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Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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9
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Giguet-Covex C, Ficetola GF, Walsh K, Poulenard J, Bajard M, Fouinat L, Sabatier P, Gielly L, Messager E, Develle AL, David F, Taberlet P, Brisset E, Guiter F, Sinet R, Arnaud F. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Sci Rep 2019; 9:14676. [PMID: 31604959 PMCID: PMC6789010 DOI: 10.1038/s41598-019-50339-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/12/2019] [Indexed: 11/09/2022] Open
Abstract
Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).
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Affiliation(s)
- C Giguet-Covex
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK. .,EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France.
| | - G F Ficetola
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - K Walsh
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK
| | - J Poulenard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - M Bajard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Fouinat
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - P Sabatier
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Messager
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - A L Develle
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - F David
- CEREGE, UMR CNRS 7330, IRD 161-Marseille Université, Technopôle de l'Arbois Méditerranée, BP 80, 13545, Aix en Provence cedex 4, France
| | - P Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Brisset
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - F Guiter
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - R Sinet
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - F Arnaud
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
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10
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Zimmermann HH, Harms L, Epp LS, Mewes N, Bernhardt N, Kruse S, Stoof-Leichsenring KR, Pestryakova LA, Wieczorek M, Trense D, Herzschuh U. Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly. PLoS One 2019; 14:e0216966. [PMID: 31291259 PMCID: PMC6619608 DOI: 10.1371/journal.pone.0216966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.
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MESH Headings
- Chromosome Mapping
- DNA, Ancient
- DNA, Chloroplast/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Genetic Variation
- Genetics, Population
- Genome, Chloroplast
- Genome, Mitochondrial
- Genome, Plant
- Haplotypes
- History, Ancient
- Larix/classification
- Larix/genetics
- Polymorphism, Single Nucleotide
- Siberia
- Taiga
- Tundra
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Affiliation(s)
- Heike H. Zimmermann
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
| | - Lars Harms
- Scientific Computing, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Laura S. Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nick Mewes
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Nadine Bernhardt
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Stefan Kruse
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Kathleen R. Stoof-Leichsenring
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | | | - Mareike Wieczorek
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Daronja Trense
- Institute for Integrated Natural Sciences, Biology, Koblenz-Landau University, Koblenz, Germany
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute of Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
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11
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Gous A, Swanevelder DZH, Eardley CD, Willows‐Munro S. Plant-pollinator interactions over time: Pollen metabarcoding from bees in a historic collection. Evol Appl 2019; 12:187-197. [PMID: 30697333 PMCID: PMC6346658 DOI: 10.1111/eva.12707] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/30/2018] [Accepted: 09/02/2018] [Indexed: 12/28/2022] Open
Abstract
Pollination is a key component in agricultural food production and ecosystem maintenance, with plant-pollinator interactions an important research theme in ecological and evolutionary studies. Natural history collections provide unique access to samples collected at different spatial and temporal scales. Identification of the plant origins of pollen trapped on the bodies of pollinators in these collections provides insight into historic plant communities and pollinators' preferred floral taxa. In this study, pollen was sampled from Megachile venusta Smith bees from the National Collection of Insects, South Africa, spanning 93 years. Three barcode regions, the internal transcribed spacer 1 and 2 (ITS1 and ITS2) and ribulose-1,5-biphosphate carboxylase (rbcL), were sequenced from mixed pollen samples using a next-generation sequencing approach (MiSeq, Illumina). Sequenced reads were compared to sequence reference databases that were generated by extracting sequence and taxonomic data from GenBank. ITS1 and ITS2 were amplified successfully across all (or most) samples, while rbcL performed inconsistently. Age of sample had no impact on sequencing success. Plant classification was more informative using ITS2 than ITS1 barcode data. This study also highlights the need for comprehensive reference databases as limited local plant sequence representation in reference databases resulted in higher-level taxon classifications being more confidently interpreted. The results showed that small, insect-carried pollen samples from historic bee specimens collected from as early as 1914 can be used to obtain pollen metabarcodes. DNA metabarcoding of mixed origin pollen samples provided a faster, more accurate method of determining pollen provenance, without the need for expert palynologists. The use of historic collections to sample pollen directly from pollinators provided additional value to these collections. Sampling pollen from historic collections can potentially provide the spatial and temporal scales for investigations into changes in plant community structure or pollinator floral choice in the face of global climate change.
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Affiliation(s)
- Annemarie Gous
- Biotechnology PlatformAgricultural Research CouncilPretoriaSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalScottsville, PietermaritzburgSouth Africa
| | - Dirk Z. H. Swanevelder
- Biotechnology PlatformAgricultural Research CouncilPretoriaSouth Africa
- College of Agriculture and Environmental SciencesUniversity of South AfricaFloridaSouth Africa
| | - Connal D. Eardley
- School of Life SciencesUniversity of KwaZulu‐NatalScottsville, PietermaritzburgSouth Africa
- Plant Protection Research InstituteAgricultural Research InstitutePretoriaSouth Africa
| | - Sandi Willows‐Munro
- School of Life SciencesUniversity of KwaZulu‐NatalScottsville, PietermaritzburgSouth Africa
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12
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Boser CL, Sillett TS, Collins PW, Faulkner KR, Funk WC, Ghalambor CK, Laughrin L, Pauly GB, Robertson JM, Shea R, Vickers W. Equipping Tomorrow's Historical Ecologist: Priorities for Documenting Conditions of the Terrestrial Fauna of Santa Cruz Island, California. WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - T. Scott Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20013
| | - Paul W. Collins
- Santa Barbara Museum of Natural History, Santa Barbara, CA 93105
| | | | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Cameron K. Ghalambor
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Lyndal Laughrin
- University of California Natural Reserve System, UCSB, Santa Barbara, CA 93106
| | - Gregory B. Pauly
- Natural History Museum of Los Angeles County, Los Angeles, CA 90007
| | | | - Robyn Shea
- California State University Channel Islands, Camarillo, CA 93012
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Zimmermann B. Chemical characterization and identification of Pinaceae pollen by infrared microspectroscopy. Planta 2018; 247:171-180. [PMID: 28913637 DOI: 10.1007/s00425-017-2774-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/08/2017] [Indexed: 05/24/2023]
Abstract
FTIR microspectroscopy, in combination with spectral averaging procedure, enables precise analysis of pollen grains for chemical characterization and identification studies of fresh and fossilised pollen in botany, ecology and palaeosciences. Infrared microspectroscopy (µFTIR) of Pinaceae pollen can provide valuable information on plant phenology, ecophysiology and paleoecology, but measurements are challenging, resulting in unreproducible spectra. The comparative analysis of µFTIR spectra belonging to morphologically different Pinaceae pollen, namely bisaccate Pinus and monosaccate Tsuga pollen, was conducted. The study shows that the main cause of spectral variability is non-radial symmetry of bisaccate pollen grains, while additional variation is caused by Mie scattering. Averaging over relatively small number of single pollen grain spectra (approx. 5-10) results with reproducible data on pollen chemical composition. The practical applicability of the µFTIR spectral averaging method has been demonstrated by the partial least-squares regression-based differentiation of the two closely related Pinus species with morphologically indistinguishable pollen: Pinus mugo (mountain pine) and Pinus sylvestris (Scots pine). The study has demonstrated that the µFTIR approach can be used for identification, differentiation and chemical characterization of pollen with complex morphology. The methodology enables analysis of fresh pollen, as well as fossil pollen from sediment core samples, and can be used in botany, ecology and paleoecology for study of biotic and abiotic effects on plants.
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Affiliation(s)
- Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1432, Ås, Norway.
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15
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Di Donato A, Filippone E, Ercolano MR, Frusciante L. Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops. Front Plant Sci 2018; 9:441. [PMID: 29719544 PMCID: PMC5914272 DOI: 10.3389/fpls.2018.00441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/21/2018] [Indexed: 05/08/2023]
Abstract
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.
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16
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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 DOI: 10.3390/genes8100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [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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17
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Vuillemin A, Horn F, Alawi M, Henny C, Wagner D, Crowe SA, Kallmeyer J. Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia. Front Microbiol 2017; 8:1440. [PMID: 28798742 PMCID: PMC5529349 DOI: 10.3389/fmicb.2017.01440] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/17/2017] [Indexed: 01/20/2023] Open
Abstract
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.
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Affiliation(s)
- Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Section 5.3: GeomicrobiologyPotsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section 5.3: GeomicrobiologyPotsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Section 5.3: GeomicrobiologyPotsdam, Germany
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of SciencesCibinong-Bogor, Indonesia
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section 5.3: GeomicrobiologyPotsdam, Germany
| | - Sean A. Crowe
- Department of Microbiology and Immunology, University of British Columbia, VancouverBC, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, VancouverBC, Canada
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section 5.3: GeomicrobiologyPotsdam, Germany
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18
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Cabrera AA, Palsbøll PJ. Inferring past demographic changes from contemporary genetic data: A simulation-based evaluation of the ABC methods implemented indiyabc. Mol Ecol Resour 2017; 17:e94-e110. [DOI: 10.1111/1755-0998.12696] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea A. Cabrera
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
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19
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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20
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Vamosi JC, Gong YB, Adamowicz SJ, Packer L. Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry. New Phytol 2017; 214:11-18. [PMID: 27901268 DOI: 10.1111/nph.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
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22
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Mohanty RP, Buchheim MA, Anderson J, Levetin E. Molecular analysis confirms the long-distance transport of Juniperus ashei pollen. PLoS One 2017; 12:e0173465. [PMID: 28273170 PMCID: PMC5342239 DOI: 10.1371/journal.pone.0173465] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 02/22/2017] [Indexed: 11/18/2022] Open
Abstract
Although considered rare, airborne pollen can be deposited far from its place of origin under a confluence of favorable conditions. Temporally anomalous records of Cupressacean pollen collected from January air samples in London, Ontario, Canada have been cited as a new case of long-distance transport. Data on pollination season implicated Juniperus ashei (mountain cedar), with populations in central Texas and south central Oklahoma, as the nearest source of the Cupressacean pollen in the Canadian air samples. This finding is of special significance given the allergenicity of mountain cedar pollen. While microscopy is used extensively to identify particles in the air spora, pollen from all members of the Cupressaceae, including Juniperus, are morphologically indistinguishable. Consequently, we implemented a molecular approach to characterize Juniperus pollen using PCR in order to test the long-distance transport hypothesis. Our PCR results using species-specific primers confirmed that the anomalous Cupressacean pollen collected in Canada was from J. ashei. Forward trajectory analysis from source areas in Texas and the Arbuckle Mountains in Oklahoma and backward trajectory analysis from the destination area near London, Ontario were completed using models implemented in HYSPLIT4 (Hybrid Single-Particle Lagrangian Integrated Trajectory). Results from these trajectory analyses strongly supported the conclusion that the J. ashei pollen detected in Canada had its origins in Texas or Oklahoma. The results from the molecular findings are significant as they provide a new method to confirm the long-distance transport of pollen that bears allergenic importance.
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Affiliation(s)
- Rashmi Prava Mohanty
- Department of Biological Sciences, The University of Tulsa, Tulsa, Oklahoma, United States of America
| | - Mark Alan Buchheim
- Department of Biological Sciences, The University of Tulsa, Tulsa, Oklahoma, United States of America
| | | | - Estelle Levetin
- Department of Biological Sciences, The University of Tulsa, Tulsa, Oklahoma, United States of America
- * E-mail:
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23
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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. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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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Honsho C, Sakata A, Tanaka H, Ishimura S, Tetsumura T. Single-pollen genotyping to estimate mode of unreduced pollen formation in Citrus tamurana cv. Nishiuchi Konatsu. Plant Reprod 2016; 29:189-97. [PMID: 26968168 DOI: 10.1007/s00497-016-0277-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/22/2016] [Indexed: 05/23/2023]
Abstract
2n pollen formed by FDR in citrus. The Japanese local citrus cultivar, Nishiuchi Konatsu (Citrus tamurana hort. ex Tanaka; NK hereafter), has the ability to produce unreduced 2n pollen grains, allowing generation of polyploid progenies via sexual polyploidization. In this study, we developed a method of single-pollen genotyping for citrus and applied it to the analysis of transmission of heterozygosity in NK 2n pollen grains. Heterozygosity transmission was expressed as the percentage inheritance of a set of heterozygous alleles from the parent to the 2n gamete. The pathway of 2n pollen development was investigated by applying the observed heterozygosity transmission and genetic distance to two different map functions, for first division restitution (FDR) and second division restitution (SDR). The fit of the values observed for both functions was calculated, while virtually moving the centromere position. We screened for six heterozygous SSR (codominant microsatellite marker loci) in NK, all of which were expected to lie within the same linkage group. Pollen germination prior to DNA extraction was essential for this work, and 6-h incubation proved to be optimal for subsequent PCR amplification. Single-pollen genotyping unreduced NK 2n pollen grains revealed that heterozygosity transmission exceeded 50 % in all six alleles, and fitness tests indicated that the FDR map function better fitted the heterozygosity transmission observed rather than the SDR function. Our data thus strongly indicate that 2n pollen in NK is a result of first division restitution.
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Affiliation(s)
- Chitose Honsho
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan.
| | - Aisa Sakata
- Graduate School of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Hikaru Tanaka
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Shuji Ishimura
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Takuya Tetsumura
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
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Georgolopoulos G, Parducci L, Drouzas AD. A short phylogenetically informative cpDNA fragment for the identification of Pinus species. BIOCHEM SYST ECOL 2016; 66:166-72. [DOI: 10.1016/j.bse.2016.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Birks HJB, Birks HH. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sickel W, Ankenbrand MJ, Grimmer G, Holzschuh A, Härtel S, Lanzen J, Steffan-Dewenter I, Keller A. Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. BMC Ecol 2015; 15:20. [PMID: 26194794 PMCID: PMC4509727 DOI: 10.1186/s12898-015-0051-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meta-barcoding of mixed pollen samples constitutes a suitable alternative to conventional pollen identification via light microscopy. Current approaches however have limitations in practicability due to low sample throughput and/or inefficient processing methods, e.g. separate steps for amplification and sample indexing. RESULTS We thus developed a new primer-adapter design for high throughput sequencing with the Illumina technology that remedies these issues. It uses a dual-indexing strategy, where sample-specific combinations of forward and reverse identifiers attached to the barcode marker allow high sample throughput with a single sequencing run. It does not require further adapter ligation steps after amplification. We applied this protocol to 384 pollen samples collected by solitary bees and sequenced all samples together on a single Illumina MiSeq v2 flow cell. According to rarefaction curves, 2,000-3,000 high quality reads per sample were sufficient to assess the complete diversity of 95% of the samples. We were able to detect 650 different plant taxa in total, of which 95% were classified at the species level. Together with the laboratory protocol, we also present an update of the reference database used by the classifier software, which increases the total number of covered global plant species included in the database from 37,403 to 72,325 (93% increase). CONCLUSIONS This study thus offers improvements for the laboratory and bioinformatical workflow to existing approaches regarding data quantity and quality as well as processing effort and cost-effectiveness. Although only tested for pollen samples, it is furthermore applicable to other research questions requiring plant identification in mixed and challenging samples.
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Affiliation(s)
- Wiebke Sickel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Markus J Ankenbrand
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Gudrun Grimmer
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Andrea Holzschuh
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Stephan Härtel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Jonathan Lanzen
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
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Boessenkool S, McGlynn G, Epp LS, Taylor D, Pimentel M, Gizaw A, Nemomissa S, Brochmann C, Popp M. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity. Conserv Biol 2014; 28:446-455. [PMID: 24372820 DOI: 10.1111/cobi.12195] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/17/2013] [Indexed: 06/03/2023]
Abstract
Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.
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Affiliation(s)
- Sanne Boessenkool
- National Centre for Biosystematics, Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, NO-0318, Oslo, Norway.
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Parducci L, Matetovici I, Fontana SL, Bennett KD, Suyama Y, Haile J, Kjaer KH, Larsen NK, Drouzas AD, Willerslev E. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Mol Ecol 2013; 22:3511-24. [PMID: 23587049 DOI: 10.1111/mec.12298] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/18/2013] [Accepted: 01/29/2013] [Indexed: 11/26/2022]
Abstract
Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
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Gismondi A, Rolfo MF, Leonardi D, Rickards O, Canini A. Identification of ancient Olea europaea L. and Cornus mas L. seeds by DNA barcoding. C R Biol 2012; 335:472-9. [PMID: 22847014 DOI: 10.1016/j.crvi.2012.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/17/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
Abstract
The analysis of ancient DNA (aDNA) provides archaeologists and anthropologists with innovative, scientific and accurate data to study and understand the past. In this work, ancient seeds, found in the "Mora Cavorso" archaeological site (Latium, Central Italy), were analyzed to increase information about Italian Neolithic populations (plant use, agriculture, diet, trades, customs and ecology). We performed morphological and genetic techniques to identify fossil botanical species. In particular, this study also suggests and emphasizes the use of DNA barcode method for ancient plant sample analysis. Scanning electron microscope (SEM) observations showed seed compact structure and irregular surface but they did not permit a precise nor empirical classification: so, a molecular approach was necessary. DNA was extracted from ancient seeds and then it was used, as template, for PCR amplifications of standardized barcode genes. Although aDNA could be highly degraded by the time, successful PCR products were obtained, sequenced and compared to nucleotide sequence databases. Positive outcomes (supported by morphological comparison with modern seeds, geographical distribution and historical data) indicated that seeds could be identified as belonging to two plant species: Olea europaea L. and Cornus mas L.
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Affiliation(s)
- Angelo Gismondi
- Department of biology, university of Rome "Tor Vergata", Italy.
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Parducci L, Jorgensen T, Tollefsrud MM, Elverland E, Alm T, Fontana SL, Bennett KD, Haile J, Matetovici I, Suyama Y, Edwards ME, Andersen K, Rasmussen M, Boessenkool S, Coissac E, Brochmann C, Taberlet P, Houmark-Nielsen M, Larsen NK, Orlando L, Gilbert MTP, Kjaer KH, Alsos IG, Willerslev E. Glacial Survival of Boreal Trees in Northern Scandinavia. Science 2012; 335:1083-6. [DOI: 10.1126/science.1216043] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Brewer S, Jackson ST, Williams JW. Paleoecoinformatics: applying geohistorical data to ecological questions. Trends Ecol Evol 2012; 27:104-12. [DOI: 10.1016/j.tree.2011.09.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/01/2011] [Accepted: 09/14/2011] [Indexed: 11/16/2022]
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Abstract
A variety of protocols for DNA extraction from archaeological and paleobotanical plant specimens have been proposed. This is not surprising given the range of taxa and tissue types that may be preserved and the variety of conditions in which that preservation may take place. Commercially available DNA extraction kits can be used to recover ancient plant DNA, but modifications to standard approaches are often necessary to improve yield. In this chapter, I describe two protocols for extracting DNA from small amounts of ancient plant tissue. The CTAB protocol, which I recommend for use with single seeds, utilizes an incubation period in extraction buffer and subsequent chloroform extraction followed by DNA purification and suspension. The PTB protocol, which I recommend for use with gourd rind and similar tissues, utilizes an overnight incubation of pulverized tissue in extraction buffer, removal of the tissue by centrifugation, and DNA extraction from the buffer using commercial plant DNA extraction kits.
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35
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Palmer SA, Smith O, Allaby RG. The blossoming of plant archaeogenetics. Ann Anat 2012; 194:146-56. [DOI: 10.1016/j.aanat.2011.03.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 03/25/2011] [Accepted: 03/25/2011] [Indexed: 11/19/2022]
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Boere AC, Rijpstra WIC, De Lange GJ, Sinninghe Damsté JS, Coolen MJL. Preservation potential of ancient plankton DNA in Pleistocene marine sediments. Geobiology 2011; 9:377-393. [PMID: 21884361 DOI: 10.1111/j.1472-4669.2011.00290.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent studies have shown that ancient plankton DNA can be recovered from Holocene lacustrine and marine sediments, including from species that do not leave diagnostic microscopic fossils in the sediment record. Therefore, the analysis of this so-called fossil plankton DNA is a promising approach for refining paleoecological and paleoenvironmental information. However, further studies are needed to reveal whether DNA of past plankton is preserved beyond the Holocene. Here, we identified past eukaryotic plankton members based on 18S rRNA gene profiling in eastern Mediterranean Holocene and Pleistocene sapropels S1 (~9 ka), S3 (~80 ka), S4 (~105 ka), and S5 (~125 ka). The majority of preserved ~400- to 500-bp-long 18S rDNA fragments of microalgae that were studied in detail (i.e. from haptophyte algae and dinoflagellates) were found in the youngest sapropel S1, whereas their specific lipid biomarkers (long-chain alkenones and dinosterol) were also abundant in sediments deposited between 80 and 124 ka BP. The late-Pleistocene sediments mainly contained eukaryotic DNA of marine fungi and from terrestrial plants, which could have been introduced via the river Nile at the time of deposition and preserved in pollen grains. A parallel analysis of Branched and Isoprenoid Tetraethers (i.e. BIT index) showed that most of the organic matter in the eastern Mediterranean sediment record was of marine (e.g. pelagic) origin. Therefore, the predominance of terrestrial plant DNA over plankton DNA in older sapropels suggests a preferential degradation of marine plankton DNA.
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Affiliation(s)
- A C Boere
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
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Magyari EK, Major A, Bálint M, Nédli J, Braun M, Rácz I, Parducci L. Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses. BMC Evol Biol 2011; 11:66. [PMID: 21392386 PMCID: PMC3068097 DOI: 10.1186/1471-2148-11-66] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 03/10/2011] [Indexed: 12/04/2022] Open
Abstract
Background Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. Results We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Conclusion Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect. This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.
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Affiliation(s)
- Eniko K Magyari
- MTA-MTM Research Group for Paleontology, 1476 Budapest, P, O, Box 222, Hungary.
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Anderson-Carpenter LL, McLachlan JS, Jackson ST, Kuch M, Lumibao CY, Poinar HN. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evol Biol 2011; 11:30. [PMID: 21272315 PMCID: PMC3041685 DOI: 10.1186/1471-2148-11-30] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes. Results We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments. Conclusions An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.
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Abstract
Long-distance dispersal (LDD) theory requires a method for marking live LDD pollen. Such a method must complement more intensive sampling methods inclusive of molecular cytogenetics, proteomics and genomics. We developed a new method for marking live Pinus taeda pollen using two dyes, rhodamine 123 and aniline blue, dissolved in a sucrose solution. Marked and unmarked pollen were compared with respect to in vitro germination, storage, terminal velocity, and in vivo pollen tube penetration of ovules. We found that: (1) both types of marked pollen retained their capacity for germination, (2) both types of marked pollen had similar aerodynamic properties when compared to unmarked pollen controls, (3) marked pollen retained its germination capacity for 48 h, and (4) of the marked pollen, only the aniline-marked pollen penetrated ovules during pollination. Germination declined rapidly for both types of marked pollen after 48 h and before 37 days at -20°C storage, while unmarked pollen lots retained 93% germination at all stages. This method for marking live P. taeda pollen is feasible for tracing LDD pollen only if released and deposited within 48 h of dye treatment.
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Tsumura Y, Kado T, Yoshida K, Abe H, Ohtani M, Taguchi Y, Fukue Y, Tani N, Ueno S, Yoshimura K, Kamiya K, Harada K, Takeuchi Y, Diway B, Finkeldey R, Na'iem M, Indrioko S, Ng KKS, Muhammad N, Lee SL. Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products. J Plant Res 2011; 124:35-48. [PMID: 20473629 PMCID: PMC3388261 DOI: 10.1007/s10265-010-0348-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 04/04/2010] [Indexed: 05/29/2023]
Abstract
The extent of tropical forest has been declining, due to over-exploitation and illegal logging activities. Large quantities of unlawfully extracted timber and other wood products have been exported, mainly to developed countries. As part of the export monitoring effort, we have developed methods for extracting and analyzing DNA from wood products, such as veneers and sawn timbers made from dipterocarps, in order to identify the species from which they originated. We have also developed a chloroplast DNA database for classifying Shorea species, which are both ecologically and commercially important canopy tree species in the forests of Southeast Asia. We are able to determine the candidate species of wood samples, based on DNA sequences and anatomical data. The methods for analyzing DNA from dipterocarp wood products may have strong deterrent effects on international trade of illegitimate dipterocarp products. However, the method for analyzing DNA from wood is not perfect for all wood products and need for more improvement, especially for plywood sample. Consequently, there may be benefits for the conservation of tropical forests in Southeast Asia.
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Affiliation(s)
- Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan.
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Williams CG, von Aderkas P. Marking live conifer pollen for long-distance dispersal experiments. Oecologia 2010; 165:249-54. [DOI: 10.1007/s00442-010-1817-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 10/08/2010] [Indexed: 10/18/2022]
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Rotherham D, Harbison SA. Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay. Forensic Sci Int 2011; 207:193-7. [PMID: 21036496 DOI: 10.1016/j.forsciint.2010.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 09/20/2010] [Accepted: 10/05/2010] [Indexed: 11/24/2022]
Abstract
Cannabis sativa is both an illegal drug and a legitimate crop. The differentiation of illegal drug Cannabis from non-drug forms of Cannabis is relevant in the context of the growth of fibre and seed oil varieties of Cannabis for commercial purposes. This differentiation is currently determined based on the levels of tetrahydrocannabinol (THC) in adult plants. DNA based methods have the potential to assay Cannabis material unsuitable for analysis using conventional means including seeds, pollen and severely degraded material. The purpose of this research was to develop a single nucleotide polymorphism (SNP) assay for the differentiation of "drug" and "non-drug"Cannabis plants. An assay was developed based on four polymorphisms within a 399 bp fragment of the tetrahydrocannabinolic acid (THCA) synthase gene, utilising the snapshot multiplex kit. This SNP assay was tested on 94 Cannabis plants, which included 10 blind samples, and was able to differentiate between "drug" and "non-drug"Cannabis in all cases, while also differentiating between Cannabis and other species. Non-drug plants were found to be homozygous at the four sites assayed while drug Cannabis plants were either homozygous or heterozygous.
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WILSON ERINE, SIDHU CSHEENA, LeVAN KATHERINEE, HOLWAY DAVIDA. Pollen foraging behaviour of solitary Hawaiian bees revealed through molecular pollen analysis. Mol Ecol 2010; 19:4823-9. [PMID: 20958818 DOI: 10.1111/j.1365-294x.2010.04849.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ERIN E. WILSON
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, Mail Code 0116, La Jolla, CA 92093, USA
| | - C. SHEENA SIDHU
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA 16802, USA
| | - KATHERINE E. LeVAN
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, Mail Code 0116, La Jolla, CA 92093, USA
| | - DAVID A. HOLWAY
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, Mail Code 0116, La Jolla, CA 92093, USA
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Hasegawa Y, Suyama Y, Seiwa K. Pollen donor composition during the early phases of reproduction revealed by DNA genotyping of pollen grains and seeds of Castanea crenata. New Phytol 2009; 182:994-1002. [PMID: 19383107 DOI: 10.1111/j.1469-8137.2009.02806.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In plants, pollen donor composition can differ during the early phases of reproduction through various selection mechanisms favouring self, related or nonrelated pollen donors, but such differences have not been examined under natural conditions because paternity is difficult to analyse in a natural setting. Here, we performed paternity analyses based on microsatellite genotyping of individual pollen grains deposited on female flowers (n = 773) and seeds (n = 304) to evaluate pollen donor composition from three individuals of the insect-pollinated monoecious tree Castanea crenata in a natural forest. Spatial genetic structure was also investigated. A mean self-pollen rate of 90.2% was observed at the pollination stage, but a low selfing rate of 0.3% was observed at the seed stage. In outcross events, however, pairwise distance and relatedness between maternal and paternal parents were not different between pollination and seed stages. We also observed significant positive relatedness, based on clear fine-scale genetic structure of individual trees within 80 m of one another, and 71% of seeds were derived using pollen grains of related trees within 80 m. The results suggest that the mechanism of self-incompatibility strongly avoids self-pollen before seed production. However, the avoidance of biparental inbreeding was not obvious between pollination and seed stages.
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Affiliation(s)
- Yoichi Hasegawa
- Laboratory of Forest Ecology, Graduate School of Agricultural Science, Tohoku University, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Yoshihisa Suyama
- Laboratory of Forest Ecology, Graduate School of Agricultural Science, Tohoku University, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Kenji Seiwa
- Laboratory of Forest Ecology, Graduate School of Agricultural Science, Tohoku University, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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Ito M, Suyama Y, Ohsawa TA, Watano Y. Airborne-pollen pool and mating pattern in a hybrid zone between Pinus pumila and P. parviflora var. pentaphylla. Mol Ecol 2009; 17:5092-103. [PMID: 19120991 DOI: 10.1111/j.1365-294x.2008.03966.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reproductive isolation barriers and the mating patterns among Pinus pumila, P. parviflora var. pentaphylla and their hybrids were examined by flowering phenology and genetic assays of three life stages: airborne-pollen grains, adults and seeds, in a hybrid zone on Mount Apoi, Hokkaido, Japan. Chloroplast DNA composition of the airborne-pollen was determined by single-pollen polymerase chain reaction. Mating patterns were analysed by estimating the molecular hybrid index of the seed parent, their seed embryos and pollen parents. The observation of flowering phenology showed that the flowering of P. pumila precedes that of P. parviflora var. pentaphylla by about 6 to 10 days within the same altitudinal ranges. Although this prezygotic isolation barrier is effective, the genetic assay of airborne-pollen showed that the two pine species, particularly P. pumila, still have chances to form F(1) hybrid seeds. Both parental species showed a strong assortative mating pattern; F(1) seeds were found in only 1.4% of seeds from P. pumila mother trees and not at all in P. parviflora var. pentaphylla. The assortative mating was concluded as the combined result of flowering time differentiation and cross-incompatibility. In contrast to the parental species, hybrids were fertilized evenly by the two parental species and themselves. The breakdown of prezygotic barriers (intermediate flowering phenology) and cross-incompatibility may account for the unselective mating. It is suggested that introgression is ongoing on Mount Apoi through backcrossing between hybrids and parental species, despite strong isolation barriers between the parental species.
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Affiliation(s)
- Megumi Ito
- Department of Biology, Graduate School of Science, Chiba University, Yayoi, Inage, Chiba 263-8522, Japan
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Abstract
Single pollen grain polymerase chain reaction (PCR) has succeeded in several species, however only limited numbers of pollen grains were involved due to difficulties in pollen isolation and lysis. This has limited its application in genetic analysis and mapping studies in plants. A high-throughput (HT) procedure for collecting and detecting genetic variation in a large number of individual pollen grains by PCR is reported. The HT procedure involved the collection of individual pollen grains by a pair of special forceps and the lysis of pollen grains in a heated alkali/detergent solution followed by neutralization with a tris-ethylenediamine tetraacetic acid (TE) buffer. These resulting template solutions yielded PCR reactions involving the 5S ribosomal RNA intergenic spacers, randomly amplified polymorphic DNA, and simple sequence repeats markers. Using this procedure, one person with experience could collect and process up to 288 single pollen grain PCR reactions per day. The method worked well on sugarcane, corn, Miscanthus spp., snap bean, sorghum, and tomato. The ability to collect and conduct PCR on individual pollen grains on a large scale offers a new approach to genetic analyses and mapping studies in an easily controllable environment with a considerable cost reduction. The method will also significantly benefit studies in species that are difficult subjects for classical genetic research.
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Affiliation(s)
- Ping-Hua Chen
- USDA-ARS, Southern Regional Research Center, Sugarcane Research Laboratory, Houma, LA 70360, USA
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Paffetti D, Vettori C, Caramelli D, Vernesi C, Lari M, Paganelli A, Paule L, Giannini R. Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon. BMC Evol Biol 2007; 7 Suppl 2:S6. [PMID: 17767734 PMCID: PMC1963477 DOI: 10.1186/1471-2148-7-s2-s6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogeographic analyses on the Western Euroasiatic Fagus taxa (F. orientalis, F. sylvatica, F. taurica and F. moesiaca) is available, however, the subdivision of Fagus spp. is unresolved and there is no consensus on the phylogeny and on the identification (both with morphological than molecular markers) of Fagus Eurasiatic taxa. For the first time molecular analyses of ancient pollen, dated at least 45,000 years ago, were used in combination with the phylogeny analysis on current species, to identify the Fagus spp. present during the Last Interglacial period in Italy. In this work we aim at testing if the trnL-trnF chloroplast DNA (cpDNA) region, that has been previously proved efficient in discriminating different Quercus taxa, can be employed in distinguishing the Fagus species and in identifying the ancient pollen. RESULTS 86 populations from 4 Western Euroasistic taxa were sampled, and sequenced for the trnL-trnF region to verify the efficiency of this cpDNA region in identifying the Fagus spp.. Furthermore, Fagus crenata (2 populations), Fagus grandifolia (2 populations), Fagus japonica, Fagus hayatae, Quercus species and Castanea species were analysed to better resolve the phylogenetic inference. Our results show that this cpDNA region harbour some informative sites that allow to infer relationships among the species within the Fagaceae family. In particular, few specific and fixed mutations were able to discriminate and identify all the different Fagus species. Considering a short fragment of 176 base pairs within the trnL intron, 2 transversions were found able in distinguishing the F. orientalis complex taxa (F. orientalis, F. taurica and F. moesiaca) from the remaining Fagus spp. (F. sylvatica, F. japonica, F. hayataea, F. crenata and F. grandifolia). This permits to analyse this fragment also in ancient samples, where DNA is usually highly degraded. The sequences data indicate that the DNA recovered from ancient pollen belongs to the F. orientalis complex since it displays the informative sites characteristic of this complex. CONCLUSION The ancient DNA sequences demonstrate for the first time that, in contrast to current knowledge based on palynological and macrofossil data, the F. orientalis complex was already present during the Tyrrhenian period in what is now the Venice lagoon (Italy). This is a new and important insight considering that nowadays West Europe is not the natural area of Fagus orientalis complex, and up to now nobody has hypothesized the presence during the Last Interglacial period of F. orientalis complex in Italy.
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Affiliation(s)
- Donatella Paffetti
- Department of Environmental and Forestry Technologies and Sciences, University of Florence, Via San Bonaventura 13, 50145 Florence, Italy
| | - Cristina Vettori
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | - David Caramelli
- Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, University of Florence, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Cristiano Vernesi
- Centro Ecologia Alpina, Viote del Monte Bondone, 38040 Trento, Italy
| | - Martina Lari
- Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, University of Florence, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Arturo Paganelli
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35121, Padova, Italy
| | - Ladislav Paule
- Faculty of Forestry, Technical University, SK-96053 Zvolen, Slovakia
| | - Raffaello Giannini
- Department of Environmental and Forestry Technologies and Sciences, University of Florence, Via San Bonaventura 13, 50145 Florence, Italy
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
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Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, Johnsen S, Steffensen JP, Bennike O, Schwenninger JL, Nathan R, Armitage S, de Hoog CJ, Alfimov V, Christl M, Beer J, Muscheler R, Barker J, Sharp M, Penkman KEH, Haile J, Taberlet P, Gilbert MTP, Casoli A, Campani E, Collins MJ. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 2007; 317:111-4. [PMID: 17615355 PMCID: PMC2694912 DOI: 10.1126/science.1141758] [Citation(s) in RCA: 333] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.
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Affiliation(s)
- Eske Willerslev
- Centre for Ancient Genetics, University of Copenhagen, Denmark.
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