Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

TY - JOUR

T1 - Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

AU - Sønstebø, J. H.

AU - Gielly, L.

AU - Brysting, A. K.

AU - Elven, R.

AU - Edwards, M.

AU - Haile, James Seymour

AU - Willerslev, Eske

AU - Coissac, E.

AU - Rioux, D.

AU - Sannier, J.

AU - Taberlet, P.

AU - Brochmann, C.

N1 - © 2010 Blackwell Publishing Ltd.

PY - 2010/11

Y1 - 2010/11

N2 - 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.

AB - 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.

U2 - 10.1111/j.1755-0998.2010.02855.x

DO - 10.1111/j.1755-0998.2010.02855.x

M3 - Journal article

C2 - 21565110

SN - 1755-098X

VL - 10

SP - 1009

EP - 1018

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - 6

ER -