3
|
Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
Collapse
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
| |
Collapse
|
4
|
Smith O, Momber G, Bates R, Garwood P, Fitch S, Pallen M, Gaffney V, Allaby RG. Response to Comment on “Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago”. Science 2015. [DOI: 10.1126/science.aab2062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bennett questions the rigor of the dating of our sample from which sedimentary ancient DNA was obtained and the reliability of the taxonomic identification of wheat. We present a further radiocarbon date from S308 that confirms the lateral consistency of the palaeosol age. The suggestion of taxonomic false positives in our data illustrates a misinterpretation of the phylogenetic intersection analysis.
Collapse
Affiliation(s)
- Oliver Smith
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Garry Momber
- Maritime Archaeology Trust, Room W1/95, National Oceanography Centre, Empress Dock, Southampton SO14 3ZH, UK
| | - Richard Bates
- Department of Earth Sciences University of St. Andrews, St. Andrews, Fife, KY16 9AL, Scotland
| | - Paul Garwood
- Department of Classics, Ancient History and Archaeology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Simon Fitch
- School of History and Cultures, University of Birmingham, IBM VISTA ERI building, Pritchatts Road, Birmingham, B15 2TT, UK
| | - Mark Pallen
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Vincent Gaffney
- Division of Archaeological, Geographical, and Environmental Sciences, University of Bradford, Bradford, West Yorkshire BD7 1DP, UK
| | - Robin G. Allaby
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|