Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada

Abstract

Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.

Metabarcoding a diverse arthropod mock community

“…As in other metabarcoding studies (Vivien et al, ; Ficetola et al, ; Brandon‐Mong et al, ; Port et al, ), false positives were also encountered, likely reflecting eDNA associated with specimens or contamination during sample processing (Port et al ) or NUMTs (Song et al, ). Their impact can be reduced by employing curated reference libraries to discriminate sequences that derive from known species versus those that represent pseudogenes (Bergsten et al, ; Braukmann, Kuzmina, Sills, Zakharov, & Hebert, ; Hebert et al, ; Landi et al, ; Zimmerman et al, ). As well, negative controls make it possible to identify reads that derive from contamination events during sample processing (Port et al ).…”

Revealing the Complexities of Metabarcoding with a Diverse Arthropod Mock Community

“…As in other metabarcoding studies (Vivien et al 2016; Ficetola et al 2014; Brandon-Mong et al 2015; Port et al 2015), false positives were also encountered, likely reflecting eDNA associated with specimens, contamination during sample processing (Port et al 2015) or NUMTs (Song et al 2008). Their impact can be reduced by employing curated reference libraries to both recognize sequences derived from known species and to exclude paralogs and pseudogenes (Hebert et al 2003; Landi et al 2014; Zimmerman et al 2014; Braukmann et al 2017; Bergsten et al 2014). In addition, the use of negative controls is an effective way to evaluate the incidence of contaminants introduced during sample processing (Port et al 2015).…”

Approaches to integrating genetic data into ecological networks

“…Identification to known taxa is more complex as the different regions provide resolution at different taxonomic depths in different taxa. For example, rbc L typically provides generic level resolution (CBOL plant working group, ) (occasionally to species level), whereas the mat K and trn H‐ psb A regions can provide resolution to species in ~60%–90% of cases (depending on the taxa and geographic scope) (Braukmann, Kuzmina, Sills, Zakharov, & Hebert, ; Burgess et al, ; Lahaye et al, ). Due to incompleteness of the reference sequence databases for the flora, many sequences did not show 100% identity to any species in the reference database.…”