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

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.

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

“…Despite the fact that more sequence data can be obtained easily, a currently limiting factor in the analysis of this data is the restriction to available diatom reference sequences in GenBank. A more secure identification could be gained by establishing reference libraries, which specifically contain species collected from the sampling localities (Sønstebø et al 2010). Our study indicates a very high diversity within the Staurosira/ Fig.…”

Next-generation hybridization and introgression

“…In pooled amplicon sequencing, PCR products of target regions are mixed and sequenced using an NGS platform. The most basic application of this method is for mixed environmental samples where only a single PCR primer pair and DNA sample are used, such as sequencing the P6 loop (chloroplast trnL intron) to identify plant families in an ice core using 454 pyrosequencing (Sønstebø et al, 2010). More complex applications, required in many population genetic and phylogenetic studies, require the ligation of a specific barcode to each sample so that the reads from pooled genetic data can be traced to the individual of interest.…”

Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA

“…Polymerase chain reaction (PCR) amplifications of the trnL fragment with the g and h primers [2] were performed at Uppsala University, in a clean aDNA room, physically separated from modern DNA laboratories. The length of the trnL fragment varies from 13 to 158 base pairs (bp) in the Arctic database [42]. We followed established aDNA methodologies during amplification from aDNA extracts [38] and standard procedures for cloning and sequencing [14].…”

“…Briefly, trimmed sequences were aligned using BIOEDIT v. 7.1.3.0 [40] to identify errors owing to base call mis-identifications and post-mortem DNA damage [41]. We constructed a database that included a subset of the trnL sequences from the Arctic database [42] and all trnL sequences available in GenBank for known Table 1. Sediment samples used for palaeoecological and barcoding analyses at Kaarreoja (NF) and Seida (NER) study sites, with summary of the results obtained after PCR amplifications of the trnL fragment (g/h).…”