ABSTRACT
Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.
ABSTRACT
El término -Código de Barras de ADN- se basa en el uso de una región de ADN estandarizada, la cual sirve como una etiqueta para la identificación rápida y de especies. El propósito de un sistema de identificación más eficaz es facilitar la conservación, conocimiento y uso sustentable de la biodiversidad. Después de ocho años de discusión y producción en la literatura científica, el tema sigue generando controversia, debido en parte a la falta de homogeneidad en la definición y el alcance del método entre los autores. En este artículo enfatizamos la definición y metodología de los códigos de barra de ADN, así como su uso para contestar preguntas nuevas en los campos de la ecología, la evolución y la conservación.
DNA barcode of life is a global initiative to populate a database of short, standardized DNA fragments from most eukaryotic species to facilitate the identification of whole or fragmented biological samples. Increasing the ability of non-experts to indentify unknown samples should improve our collective understanding and management of the world s biodiversity. In the eight years following its proposal, DNA barcoding remains controversial in the scientific literature due, in part, to a lack of consensus on how DNA barcoding is defined and what activities are included under this rubric. In the present paper we review the definition, methods and goals of DNA barcoding, highlighting how the massive data sets generated by various DNA barcode of life campaigns may be applied to fundamental and novel questions in ecology, evolution and conservation.