Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales)

Abstract

Background and aims: 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.

Materials and 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.

Conclusion: 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.

Keywords::

• DNA barcoding
• character-based methods
• psbK-I
• Zamia
• population level
• Megamexico

Acknowledgements

The authors thank Raúl Jiménez-Rosenberg and Martha Gual for their support during the planning stages of the project. They also acknowledge Alejandro Espinosa de los Monteros and Eduardo Ruíz for data analysis support, and Julia Hernández Villa and Janet Nolasco Soto for technical assistance in the laboratory. Finally, the authors are grateful to the staff at the JBC (Xalapa, Veracruz, Mexico) for access to living specimens in their cycad collections, and to the Montgomery Botanical Center, Miami, FL for supplying samples of some species.

This research project was supported by Mexican Comisión Nacional para el Uso y Conservación de la Biodiversidad (CONABIO) Grant GE004, and US NSF Grants BSR-8607049 and EF-0629817 (to D.W.S).

Declarations of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.