Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species

Abstract

BackgroundFour plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range.ResultsAll possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture.ConclusionsOur results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64 % success and Salix, 86 % failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0678-0) contains supplementary material, which is available to authorized users.

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

“…As a consequence, the use of multiple barcode markers consistently improves taxonomic resolution because a particular marker can compensate for the deficits in resolution of its counterparts [7; 9; 10; 15; 17; 18; 19; 20; 21; 22; 23; 24; 25; 26]. This complementarity supports the use of specific barcodes that optimize species resolution for different groups [58; 59]. …”

“…However, the same lack of resolution was observed with our ITS2 data and in a more detailed analysis of 22 species [26], indicating that the lack of divergence extends into the nuclear genome. This difficulty in differentiating Salix species using molecular markers may reflect hybridization, introgression, recent speciation, allele surfing via range expansion, and low rates of molecular evolution [52; 59; 67; 68; 69]. More extensive phylogenetic studies targeting nuclear markers or whole plastid genomes are necessary to clarify the processes driving the unusually low divergences in Salix .…”

Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia

“…was estimated to have diversified from only 3.9 (HPD values: 2.1–6.0) million years onwards [ 40 ]. Incomplete lineage-sorting and interspecific hybridisation events may also contribute to the failure of DNA barcodes to accurately resolve taxa that have only recently diverged [ 55 ]. Additional resolution may be achieved from concatenation of multiple markers [ 56 ], however, this may not always be the case.…”

“…Determination accuracy was lower based on our combined (rbcL+matK+ITS) dataset than that of our ITS datasets ( Table 3 ). Other studies that also have found that the concatenation of loci does not always improve resolution power [ 55 ].…”

Phylogenetic Relationship among the Wild Rice (Oryza Nivara) and Intraspecies of Rice Genotypes Belonging to Chhattisgarh Revealed by Chloroplast Dna Regions psbA-trnH

“…DNA barcoding is a technique, which provides quick identification of species without involving the morphological indication and physiological conditions, of the plant species chosen for study [2]. The plant DNA barcoding studies were initially restricted to the chloroplast genome to understand the variation of its gene sequences of coding matK, rbcL and rpoC1 and non-coding ITS and psbA-trnH [1], team together tested the ability of rpoB,rpoC1,matK and psbA-trnH regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). In the study nucleotide variation at chloroplast (Cp) region, loci psbA-trnH and phylogenetic diversity among 24 rice genotypes belonging to Chhattisgarh was analyzed.…”