Abstract

Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.

Highlights

  • Barcoding initiatives across the tree of life have helped document and describe thousands of species of bony fishes, birds, sharks, and sponges, among many other groups[1,2,3,4,5]

  • Phylogenetic Inference using c oxidase subunit I (COI) and ND2. New sequences and those acquired from GenBank included a total of 63 individuals sampled for both mitochondrial markers

  • As in any field, assessing the appropriateness of the data to resolve the question of interest is paramount. This means addressing the ability of the data to provide phylogenetic information at the evolutionary depth or depths of interest

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Summary

Introduction

Barcoding initiatives across the tree of life have helped document and describe thousands of species of bony fishes, birds, sharks, and sponges, among many other groups[1,2,3,4,5]. Cold Code[6], the barcoding initiative for amphibians and non-avian reptiles, has produced an immense quantity of sequence data for the mitochondrial locus encoding cytochrome c oxidase subunit I (COI). Cold Code instigated barcoding on the grounds of species identification and discovery[8], recent studies have increasingly used barcoding data for phylogenetic inference and to answer phylogeographic questions[9, 10]. This practice is often undertaken without sufficient assessment of the utility of barcoding for the taxonomic group of interest. In narrower phylogenetic contexts, DNA barcoding remains valuable[11]

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