title: Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species.
abstract: Four 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.
  
  
  
  All 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.
  
  
  
  Our 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.
authors.affiliation: Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques & University of Geneva, Chemin de l'Impératrice, 1, 1292, Chambésy, Geneva, Switzerland.|SwissBOL, University of Geneva, Department of Genetics and Evolution, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland.
authors.forename: Sofia
authors.initials: S
authors.lastname: Caetano Wyler
authors.affiliation: Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques & University of Geneva, Chemin de l'Impératrice, 1, 1292, Chambésy, Geneva, Switzerland. Yamama.Naciri@ville-ge.ch.
authors.forename: Yamama
authors.initials: Y
authors.lastname: Naciri
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D019684:Magnoliopsida / Q000235:genetics*; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D014197:Trees / Q000235:genetics
chemical_list: D018744:DNA, Plant
keywords: Acer; Adenostyles; Chloroplast capture; Gentiana; Geranium; Incomplete lineage sorting; Interspecific hybridization; Lonicera; Salix; Veronica