DNA barcoding the floras of biodiversity hotspots

Abstract

DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes. Going beyond previous plant studies, we assessed to what extent a "DNA barcoding gap" is present between intra- and interspecific variations, using multiple accessions per species. Given its adequate rate of variation, easy amplification, and alignment, we identified a portion of the plastid matK gene as a universal DNA barcode for flowering plants. Critically, we further demonstrate the applicability of DNA barcoding for biodiversity inventories. In addition, analyzing >1,000 species of Mesoamerican orchids, DNA barcoding with matK alone reveals cryptic species and proves useful in identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes.

Fig. 1.

Relative distribution of interspecific divergence between con-generic species (yellow) and intraspecific distances (with best fit-model; red) for eight loci. (A) accD. (B) rpoC1. (C) rpoB. (D) ndhJ. (E) ycf5. (F) rbcL. (G) matK reduced matrix. (H) trnH-psbA. (I) matK expanded Mesoamerican orchids matrix. x axis, increments of 0.001; y axis, number of occurrences. Barcoding gaps were assessed with Median tests and Wilcoxon two-samples tests, and all were highly significant (P < 0.0001).