Review and Interpretation of Trends in DNA Barcoding

Rob Desalle,Paul Goldstein

doi:10.3389/fevo.2019.00302

Abstract

Interpretations and analytical practices surrounding DNA barcoding are reviewed from a compilation of 3,756 papers (as of December 31, 2018) with “DNA Barcode” in the title since 2004. By examining the practice of DNA barcoding in natural history and biodiversity science over this period, we explore the extent to which its purposes, premises, rationale and application have evolved. The number of studies involving identification, taxonomic decisions and the discovery of cryptic species has driven the publication of DNA barcode studies overall. Forensic studies and papers on biological conservation involving DNA barcodes have tracked the ensemble number of studies but rose sharply in 2017. Although neighbor-joining and graphic (tree-based) criteria for species delimitation have been preeminent, analytical paradigms have diversified slightly following the growing availability of tools in the Barcode of Life Database (BoLD). We conclude that the paradigms of DNA barcoding data are likely to persist and, in groups such as Lepidoptera, DNA barcoding has become a widely used tool in taxonomic science. The degree to which systematists will avail themselves of tools for extracting diagnostic data from barcodes remains to be seen.

Highlights

Heralded as a revolutionary taxonomic discovery tool, DNA barcoding represents perhaps the most reliable framework available for organizing specimens and specimen-based data for systematic research
Recognizing the potential bearing of cryptic species on each of these fields, Figure 1H illustrates that the study of cryptic species has consistently played a focal role in a range of fields over the 15-year period we examined, with explicit mention of conservation and taxonomy appearing with less frequent emphasis, followed by “forensic” and “biodiversity.”
In the context of phylogenetic inference, clustering operations based on phenetic similarity have for several decades been rejected by systematists for empirical and statistical reasons, not the least of which is that since they combine available character data into a single ensemble metric, they cannot test or summarize specific character homologies that would otherwise contribute to a diagnosis (Ferguson, 2002; DeSalle, 2007; Little and Stevenson, 2007)

Summary

INTRODUCTION

Heralded as a revolutionary taxonomic discovery tool, DNA barcoding represents perhaps the most reliable framework available for organizing specimens and specimen-based data for systematic research. To the extent controversy emerged around barcode data, it was generally associated with the taxonomic interpretation and applicability of their analyses These included the uniformity and generalizability of criteria for circumscribing species, the phylogenetic implications of dendrograms, and the proliferation of informal specific epithets in reference to species that were discovered through DNA barcodes but which remained undescribed. DNA barcoding engendered a democratization of molecular data (or at least metadata) by automating analytical steps that might otherwise have deterred may some practicing taxonomists This quickened the pace of alpha taxonomy by enabling the rapid and unambiguous discovery of new species in many groups. To the extent they have not, we highlight those considerations at the empirical intersection of DNA barcoding, taxonomy and phylogenetics that are not semantic

A CONCEPTUAL FRAMEWORK FOR EXAMINING THE ONTOLOGY OF DNA BARCODING

DISCUSSION