Abstract
Plant DNA barcoding currently relies on the application of a two-locus combination, matK + rbcL. Despite the universality of these two gene regions across plants, it is suspected that this combination might not have sufficient variation to discriminate closely related species. In this study, we tested the performance of this two-locus plant barcode along with the additional plastid regions trnH-psbA, rpoC1 and rpoB and the nuclear region internal transcribed spacer (nrITS) in a group of 38 species of Lotus from the Macaronesian region. The group has radiated into the five archipelagos within this region from mid-Miocene to early Pleistocene, and thus provides both early divergent and recent radiations that pose a particularly difficult challenge for barcoding. The group also has 10 species considered under different levels of conservation concern. We found different levels of species discrimination depending on the age of the lineages. We obtained 100 % of the species identification from mainland Africa and Cape Verde when all six regions were combined. These lineages radiated >4.5 Mya; however, in the most recent radiations from the end of the Pliocene to the mid-Pleistocene (3.5-1.5 Mya), only 30 % of the species were identified. Of the regions examined, the intergenic region trnH-psbA was the most variable and had the greatest discriminatory power (18 %) of the plastid regions when analysed alone. The nrITS region was the best region when analysed alone with a discriminatory power of 26 % of the species. Overall, we identified 52 % of the species and 30 % of the endangered or threatened species within this group when all six regions were combined. Our results are consistent with those of other studies that indicate that additional approaches to barcoding will be needed in recently evolved groups, such as the inclusion of faster evolving regions from the nuclear genome.
Highlights
DNA barcoding is a procedure that uses universal DNA sequences to assign species names to sampled individuals
Species discrimination was greatly reduced on the lineages that diverged at the end of the Pliocene and beginning of the Pleistocene (3.5 to 2 Mya) within the Canary Islands, Madeira and the Salvages
Plant DNA barcoding of phylogenetically diverse assemblages has proven successful with high levels of species discrimination, e.g. Panamanian trees with 98 % of species identification (Kress et al 2009) and Mesoamerican orchids with .90 % of species identification (Lahaye et al 2008), but the success of species discrimination tends to decrease as the number of species within families or genera is increased (Gonzalez et al 2009; Xiang et al 2011; Yesson et al 2011; Zhang et al 2011; Arca et al 2012; Maia et al 2012; Saarela et al 2013)
Summary
DNA barcoding is a procedure that uses universal DNA sequences to assign species names to sampled individuals (http://www.barcodeoflife.org/). Many of the studies that have tested regions as barcodes in plants have focused on large data sets that span a wide range of land plants, or at least angiosperms (Kress and Erickson 2007; Fazekas et al 2008; Lahaye et al 2008; CBOL Plant Working Group 2009; Ford et al 2009). Their purpose has been the assessment of the universal applicability of the regions in species discrimination. It has been argued that the success in species discrimination of DNA barcodes will drop in (i) some groups with complex biology and (ii) closely related species within the same genus (or in recently evolved groups) (Pillon et al 2013)
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