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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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2
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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Díaz FP, Latorre C, Carrasco-Puga G, Wood JR, Wilmshurst JM, Soto DC, Cole TL, Gutiérrez RA. Multiscale climate change impacts on plant diversity in the Atacama Desert. GLOBAL CHANGE BIOLOGY 2019; 25:1733-1745. [PMID: 30706600 DOI: 10.1111/gcb.14583] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo-informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.
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Affiliation(s)
- Francisca P Díaz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Claudio Latorre
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Ñuñoa, Santiago, Chile
| | - Gabriela Carrasco-Puga
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jamie R Wood
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | - Janet M Wilmshurst
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- School of Environment, The University of Auckland, Auckland, New Zealand
| | - Daniela C Soto
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Theresa L Cole
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. PLANTA 2017; 246:1165-1176. [PMID: 28825134 DOI: 10.1007/s00425-017-2758-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.
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Affiliation(s)
- Min Yu
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Juan Guo
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaomei Jiang
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Birks HJB, Birks HH. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? THE NEW PHYTOLOGIST 2016; 209:499-506. [PMID: 26402315 DOI: 10.1111/nph.13657] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/03/2015] [Indexed: 06/05/2023]
Abstract
499 I. 499 II. 500 III. 500 IV. 500 V. 500 VI. 501 VII. 502 VIII. 504 504 References 505 SUMMARY: Ancient DNA (aDNA) from lake sediments, peats, permafrost soils, preserved megafaunal gut contents and coprolites has been used to reconstruct late-Quaternary floras. aDNA is either used alone for floristic reconstruction or compared with pollen and/or macrofossil results. In comparative studies, aDNA may complement pollen and macrofossil analyses by increasing the number of taxa found. We discuss the relative contributions of each fossil group to taxon richness and the number of unique taxa found, and situations in which aDNA has refined pollen identifications. Pressing problems in aDNA studies are contamination and ignorance about taphonomy (transportation, incorporation, and preservation in sediments). Progress requires that these problems are reduced to allow aDNA to reach its full potential contribution to reconstructions of Quaternary floras.
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Affiliation(s)
- H John B Birks
- Department of Biology, University of Bergen, and Bjerknes Centre for Climate Research, Postbox 7803, N-5020, Bergen, Norway
- Environmental Change Research Centre, University College London, Gower Street, London, WC1E 6BT, UK
| | - Hilary H Birks
- Department of Biology, University of Bergen, and Bjerknes Centre for Climate Research, Postbox 7803, N-5020, Bergen, Norway
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Pedersen MW, Overballe-Petersen S, Ermini L, Sarkissian CD, Haile J, Hellstrom M, Spens J, Thomsen PF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AMZ, Gilbert MTP, Hansen AJ, Orlando L, Willerslev E. Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130383. [PMID: 25487334 PMCID: PMC4275890 DOI: 10.1098/rstb.2013.0383] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Affiliation(s)
- Mikkel Winther Pedersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Søren Overballe-Petersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - James Haile
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Trace and Environmental DNA Laboratory, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
| | - Micaela Hellstrom
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Johan Spens
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Department of Wildlife, Fish and Environmental Studies, SLU, Umeå S-901 83, Sweden
| | - Philip Francis Thomsen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Kristine Bohmann
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Enrico Cappellini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ida Bærholm Schnell
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nathan A Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Astrid M Z Schmidt
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
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Liu H, Tian X, Zhang Y, Wang C, Jiang H. The discovery of Artemisia annua L. in the Shengjindian cemetery, Xinjiang, China and its implications for early uses of traditional Chinese herbal medicine qinghao. JOURNAL OF ETHNOPHARMACOLOGY 2013; 146:278-86. [PMID: 23295167 DOI: 10.1016/j.jep.2012.12.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 12/02/2012] [Accepted: 12/08/2012] [Indexed: 05/26/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Artemisia annua L., with the ancient name of qinghao, is a traditional Chinese herbal medicine. It has appeared in many ancient Chinese medical manuscripts, which describe its uses to include treatment of wounds, alleviating intermittent fevers, as well as enhancing the brightness of eyes and even improving longevity. MATERIALS AND METHODS A sheaf of plant remains, including stalks and inflorescence intentionally placed in the corner of a tomb, have been recovered from the Shengjindian cemetery (about 2400-2000 BP on the basis of (14)C dating), Turpan, Xinjiang, China. The morphology of these materials was examined using a stereomicroscope and a scanning electron microscope. Ancient DNA was also extracted from these remains. RESULTS By comparing the morphological and DNA characteristics with modern specimens, these plant remains were identified to belong to Artemisia annua L. Owing to its strong fragrance, these plant remains are suggested as serving to disguise the odor of the deceased. CONCLUSIONS This is the first material archaeological evidence to date despite numerous records of A. annua in ancient Chinese texts as herbal medicine qinghao, though it seems to have been employed as odor suppressant, not for medical purpose.
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Affiliation(s)
- Huan Liu
- The Laboratory of Human Evolution, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
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Gismondi A, Leonardi D, Enei F, Canini A. Identification of Plant Remains in Underwater Archaeological Areas by Morphological Analysis and DNA Barcoding. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aa.2013.34034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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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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11
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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] [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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