title: Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales).
abstract: OBJECTIVE
  With the recent proposal of matK and rbcL as core plant DNA barcoding regions by the Consortium for the Barcoding of Life Plant Working Group, the construction of reference libraries in the botanical DNA barcoding initiative has entered a new phase. However, in a recent DNA barcoding study in the three Mexican genera of the gymnosperm order Cycadales, we found that neither matK nor rbcL allow high levels of molecular identification of previously established species.
  
  
  METHODS
  Our data analysis in that study rested on the "Characteristic Attributes Organization System" (CAOS), a character-based algorithm for the definition of "DNA diagnostics." Here, we use CAOS to analyze a population-level molecular data set in Zamia, one of the three cycad genera occurring in Mexico, whose populations display contrasting biogeographic patterns. Our population-level study, which includes all species in the region formally known as Megamexico, is restricted to the genome region, which showed the best single-locus molecular identification performance in our previous study-namely, the noncoding intergenic chloroplast spacer psbK-I.
  
  
  RESULTS
  Our comparison of single-individual vs. population-level psbK-I datasets in Zamia indicates that CAOS analyses are sensitive to slight alignment changes, which in turn derive from the different amounts of molecular variation present in each matrix type.
  
  
  CONCLUSIONS
  We, therefore, suggest that character-based studies that involve population-level data should contemplate this type of comparison between data matrices, before a set of DNA diagnostics in a given DNA barcoding reference library is considered definitive.
authors.affiliation: Laboratorio de Genética de Poblaciones, Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico. f_nicolalde@yahoo.com
authors.forename: Fernando
authors.initials: F
authors.lastname: Nicolalde-Morejón
authors.forename: Francisco
authors.initials: F
authors.lastname: Vergara-Silva
authors.forename: Jorge
authors.initials: J
authors.lastname: González-Astorga
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods; D018742:DNA, Chloroplast / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D017343:Genes, Plant; D008800:Mexico; D008969:Molecular Sequence Data; D010802:Phylogeny; D013045:Species Specificity; D032481:Zamiaceae / Q000145:classification* / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast; D021901:DNA, Intergenic; D018744:DNA, Plant