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N G Yoccoz,
K A Bråthen,
L Gielly,
J Haile,
M E Edwards,
T Goslar,
H Von Stedingk, A K Brysting,
E Coissac,
F Pompanon, [......],
W Thuiller,
P Wincker,
C Cruaud,
F Gavory,
M Rasmussen,
M T P Gilbert,
L Orlando,
C Brochmann,
E Willerslev,
P Taberlet
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ABSTRACT: Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.
Molecular Ecology 04/2012; 21(15):3647-55. · 5.52 Impact Factor
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J H Sønstebø,
L Gielly, A K Brysting,
R Elven,
M Edwards,
J Haile,
E Willerslev,
E Coissac,
D Rioux,
J Sannier,
P Taberlet,
C Brochmann
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ABSTRACT: Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13-158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.
Molecular Ecology Resources 11/2010; 10(6):1009-1018. · 3.06 Impact Factor
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ABSTRACT: Morphometric and isozyme data were used to test the hypothesis that the pseudoviviparous Poa jemtlandica has originated as a hybrid between the sexual P flexuosa and the facultative apomict P alpina. Plants were sampled from three localities in southern Norway. In addition, some Icelandic plants were included. Both morphometric and isozyme data clearly support the hybrid hypothesis. Poa jemtlandica was morphologically intermediate between its supposed parents in several individual characters as well as in a discriminant analysis. Seven enzyme systems were analysed. Eight areas of activity were interpreted as “loci”, each of which certainly represented several duplicated genes in these plants which all are polyploid. A total of 27 different multilocus phenotypes was observed: ten phenotypes in P alpina var. vivipara, eight phenotypes in I. alpina var. alpina, seven phenotypes in P jemtlandica, and three phenotypes in P flexuosa. The phenotype of Icelandic P jemtlandica was identical to that of P. jemtlandica from one of the Norwegian localities. Additive electrophoretic patterns were observed for P jemtlandica at four individual “loci”. At the remaining “loci” some phenotypes of P. jemtlandica were most similar to P. flexuosa, others to P alpina. The data also suggest that P jemtlandica has originated several times, but there is no indication of frequent or recent hybridization where the species coccur today.
Nordic Journal of Botany 06/2008; 17(2):199 - 214. · 0.55 Impact Factor
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ABSTRACT: The Arctic is an excellent model system for the study of polyploidy. It is one the Earth's most polyploid-rich areas, in particular of high-level and recently evolved polyploids. Here we re-address previous hypotheses on arctic polyploidy based on a new analysis of the circumarctic flora, and review recent molecular, cytological and reproductive studies. The frequency and level of polyploidy strongly increase northwards within the Arctic. We found no clear-cut association between polyploidy and the degree of glaciation for the arctic flora as a whole, which contains many widespread species. However, for 'arctic specialist' taxa with restricted distributions, the frequency of diploids is much higher in the Beringian area, which remained largely unglaciated during the last ice age, than in the heavily glaciated Atlantic area. This result supports the hypothesis that polyploids are more successful than diploids in colonizing after deglaciation. There is abundant molecular evidence for recurrent formation of arctic polyploids at different scales in time and space. Examples are given of low-level polyploids formed after the last glaciation and of repeated and successively more high-level polyploidizations throughout the Quaternary. Recurrent polyploid origins, followed by interbreeding within and across ploidal levels, provide a major explanation for the taxonomic complexity of the arctic flora. In the well-studied, recently deglaciated archipelago of Svalbard, most species are mainly self-fertilizing or clonal. All Svalbard polyploids examined so far are genetic allopolyploids with fixed heterozygosity at isozyme loci. The level of heterozygosity in 65 taxa increases dramatically from diploids to high-level polyploids. In the circumarctic area, there is evidence for numerous recently evolved sibling species within diploid taxonomic species. Rapid evolution of crossing barriers at the diploid level promotes further diversification after expansion from different refugia, and may provide new raw materials for allopolyploid formation. We conclude that the evolutionary success of polyploids in the Arctic may be based on their fixed-heterozygous genomes, which buffer against inbreeding and genetic drift through periods of dramatic climate change.
Biological Journal of the Linnean Society. 01/2004; 82(4):521-536.
