DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (<i>rbcL</i> + <i>matK</i>) for 490 Vascular Plant Species

<div><p>Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (<i>rbcL</i> and <i>matK</i>) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for <i>rbcL</i> than <i>matK</i> (93% and 81%), and <i>rbcL</i> was easier to recover than <i>matK</i> from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined <i>rbcL</i> + <i>matK</i> data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (<i>Carex</i>, <i>Draba</i>, <i>Festuca</i>, <i>Pedicularis</i>, <i>Poa</i>, <i>Potentilla</i>, <i>Puccinellia</i>, <i>Ranunculus, Salix</i>, and <i>Saxifraga</i>) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in <i>Salix</i> to 85% in <i>Carex</i>. Haplotype variation in multiple genera does not correspond to species boundaries, including <i>Taraxacum</i>, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of <i>Poa glauca</i> plastid DNA into multiple individuals of <i>P. hartzii</i> is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (<i>psbA–trnH</i>, <i>psbK–psbI</i>, <i>atpF–atpH</i>) collected for a subset of <i>Poa</i> and <i>Puccinellia</i> species, only <i>atpF–atpH</i> improved discrimination in <i>Puccinellia</i>, compared with <i>rbcL</i> and <i>matK</i>. Variation in <i>matK</i> in <i>Vaccinium uliginosum</i> and <i>rbcL</i> in <i>Saxifraga oppositifolia</i> corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.</p> </div

Scatterplots of the number of species sampled in each genus against the percentage of species resolved in each genus with <i>rbcL</i>, <i>matK</i>, and <i>rbcL</i> + <i>matK</i>.

<p>A. rbcL-175 genera (Pearson correlation coefficient r = 0.4180, n = 175, P < 0.0001), R² = 0.1747. B. matK-159 genera (Pearson correlation coefficient r = 0.3685, n = 159, P < 0.0001), R² = 0.1358. C. rbcL + matK-153 genera (Pearson correlation coefficient r = 0.3636, n = 153, P < 0.0001), R² = 0.1322. Species resolution was scored in neighbour joining trees generated from uncorrected <i>p</i>-distances calculated from single-family alignments.</p

Resolution (%) of genera, species, and additional infraspecific taxa for <i>rbcL</i>, <i>matK</i>, and <i>rbcL</i> + <i>matK</i> in neighbour joining trees and BLAST searches.

<p>Neighbour joining trees were generated from single-family alignments using uncorrected <i>p</i>-distances. Numbers in parentheses are the numbers of genera or species sampled in each data set. BLAST searches were not conducted for the combined <i>rbcL</i> + <i>matK</i> data.</p

Percentage of specimens, families, genera, species, additional infraspecific taxa, and unnamed hybrids in the data set from which <i>rbcL</i> and <i>matK</i> barcodes were recovered.

<p>Numbers in parentheses are the total number of individuals (specimens, unnamed hybrids) and taxa (families, genera, species, additional infraspecific taxa) in each category in the data set.</p

Frequency distribution of infraspecific and congeneric interspecific genetic divergences of <i>rbcL</i> and <i>matK</i>.

<p>Numbers in parentheses are the total number of comparisons for each category. Divergences were calculated using uncorrected <i>p</i>-distances. </p

Species resolution (%) per family for <i>rbcL</i>, <i>matK</i>, and <i>rbcL</i> + <i>matK</i>.

<p>Numbers in parentheses refer to the numbers of species for which barcode data were recovered for <i>rbcL</i>, <i>matK</i>, and <i>rbcL</i> + <i>matK</i>, respectively. Families with a single genus and species sampled are excluded. Dashes (-) indicate that no sequences were recovered.</p

Relationship between herbarium specimen age and sequence recovery (%) for <i>rbcL</i> and <i>matK</i>.

<p>Material was sampled from 1169 herbarium specimens collected between 1950–2010. These were divided into seven age classes and a Spearman rank correlation was used to test for a relationship between age class and percent recovery of <i>rbcL</i> (Spearman's rho 0.306, p = 0.50079) and <i>matK</i> (Spearman's rho 0.893, p = 0.012302). The <i>matK</i> analysis excluded Dryopteridaceae, Equisetaceae, Juncaceae, Polypodiaceae, and Lycopodiaceae, which failed for all samples for this marker due to primer mismatch. Numbers in parentheses are the total number of herbarium specimens sampled from each age class for <i>rbcL</i> and <i>matK</i>, respectively.</p

Species resolution (%) in ten genera with the greatest number of species sampled.

<p>Numbers in parentheses refer to the number of species sampled for <i>rbcL</i>, <i>matK</i>, and <i>rbcL</i> + <i>matK</i>, respectively. </p