Climate change has already led to substantial modification in the composition of Arctic plant communities as reflected by shifting ranges and genetic differentiation. Many arctic plant species are likely to lose genetic diversity due to their limited dispersal capacity, and consequent range reduction, making them particularly vulnerable to climate change. Identifying the impacts of climate change on the composition of plant communities is currently the focus of many studies in the Arctic which employ two main approaches. The first examines the impact of manipulations in light, temperature and nutrient regimes on species composition and richness[4–7]. The second approach involves direct examination of plant community composition to identify species that are particularly effective predictors of shifts in vegetation in response to climate change. Both approaches require rapid and accurate identification of plants, many of which lack diagnostic floral or fruit characters at the time of their collection.
DNA barcoding employs sequence diversity in short, standardized gene region(s) to facilitate species identification. Two gene regions from the chloroplast genome, rbc L and mat K, have been adopted as the standard barcodes for land plants. Both of these genes have played a very important role in phylogenetic reconstructions for land plants due to their strong phylogenetic signal[11–14]. Their capacity to resolve species in local floras has now been tested in many settings, particularly in species-rich tropical communities. As well, numerous studies have tested the additional discrimination provided by supplemental chloroplast (trn H-psb A, atp B-atp H, rpo C1) and nuclear (ITS) markers[15–19]. All prior studies have reported 100% success in generic-level assignments, while success in species-level assignment has ranged from 50 – 92% for the two-locus barcode (rbc L & mat K), and from 70 – 98% with one or more supplementary markers. However, in all analyzed cases DNA barcoding has proven an efficient approach for the evaluation of hyper-diverse floras.
The nuclear ribosomal DNA region ITS and its two components, ITS1 and ITS2, have been extensively utilized for studies on the molecular systematics of plants because of their high rate of nucleotide substitution and relative ease of amplification, sequencing and alignment. Among the varied supplemental barcode markers, ITS2 shows particular promise because its short length (160-320 bp) and the availability of universal primers make it easy to recover. Although it has been suggested that ITS2 exhibits too much paralogy, and is too susceptible to fungal contamination to be adopted as a DNA barcode marker[21, 22], it delivered 92.7% discrimination in a recent study on 4800 species of medicinal plants. Given this high performance, ITS2 merits serious consideration as a standard marker for plant barcoding.
Although plant communities in temperate and arctic regions are much less diverse than those in the tropics, they may not be easier targets for DNA barcode analysis because rates of molecular evolution in both plastid and nuclear genomes appear lower in groups of flowering plants with low diversity and in plant species from high latitudes. However, there is some evidence that arctic plant communities have experienced more rapid speciation, due to intense processes of hybridization, refugial isolation and range shifts. The question of how this affects the performance of DNA barcoding for the identification of plant species has seen little investigation. However, a recent study of the flora at a temperate site in Canada revealed 93% success in species identification with rbc L & mat K, while the addition of the trn H-psb A intergenic spacer raised resolution to 95%.
The present study tests the effectiveness of DNA barcoding for the identification of species in the flora at Churchill, Manitoba, Canada. Our decision to work at this locality reflects an ongoing effort to assemble a comprehensive DNA barcode library for all animal and plant species at Churchill. Sequence information was collected for three gene regions (rbc L, mat K, ITS2) from 312 of the 354 species of vascular plants known from this locale[28, 29]. Since herbarium collections can aid the rapid creation of comprehensive DNA barcode libraries, we compared the success of barcode recovery from herbarium and freshly collected specimens preserved in silica gel. We also investigated factors affecting sequence recovery for these three gene regions in a high-throughput barcoding setting, and adjusted protocols to enhance success. Finally, we compared the success of species identification in this arctic flora with those reported for temperate and tropical floras.