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Parducci L, Väliranta M, Salonen JS, Ronkainen T, Matetovici I, Fontana SL, Eskola T, Sarala P, Suyama Y. Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130382. [PMID: 25487333 DOI: 10.1098/rstb.2013.0382] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ØsterVoldgade 5-7, 1350 Copenhagen, Denmark
| | - Minna Väliranta
- Department of Environmental Sciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - J Sakari Salonen
- Department of Geosciences and Geography, University of Helsinki, PO Box 64, 00014 Helsinki, Finland
| | - Tiina Ronkainen
- Department of Environmental Sciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Irina Matetovici
- Molecular Biology Centre, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babes-Bolyai-University ClujNapoca, 42 TreboniuLaurian Street, 400271 Cluj-Napoca, Romania
| | - Sonia L Fontana
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, UK
| | - Tiina Eskola
- Department of Geosciences, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Pertti Sarala
- Geological Survey of Finland, PO Box 77, 96101 Rovaniemi, Finland
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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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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Parducci L, Edwards ME, Bennett KD, Alm T, Elverland E, Tollefsrud MM, Jørgensen T, Houmark-Nielsen M, Larsen NK, Kjær KH, Fontana SL, Alsos IG, Willerslev E. Response to Comment on “Glacial Survival of Boreal Trees in Northern Scandinavia”. Science 2012; 338:742; author reply 742. [DOI: 10.1126/science.1225476] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
| | - Mary E. Edwards
- Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - K. D. Bennett
- School of Geography, Archaeology and Palaeoecology, Queen’s University Belfast, University Road, Belfast BT7 1NN, Northern Ireland
| | - Torbjørn Alm
- Tromsø University Museum, NO-9037 Tromsø, Norway
| | | | | | - Tina Jørgensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
- Tromsø University Museum, NO-9037 Tromsø, Norway
| | - Michael Houmark-Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
| | - Nicolaj Krog Larsen
- Department of Geoscience, Aarhus University, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
| | - Kurt H. Kjær
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
| | - Sonia L. Fontana
- Department of Palynology and Climate Dynamics, University of Göttingen, Untere Karspüle 2,37073 Göttingen, Germany
| | | | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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