Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos

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.

Figure 1

‘Fully-sampled’ maximum likelihood phylogeny of Cyrtodactylus as inferred from mitochondrial locus COI, including novel sequences contributed by this study (51) indicated by asterisks. Circles at nodes indicate BSS values of ≥70: grey indicate intraspecific sampling and black interspecific sampling. Bolded names indicate samples also included in the ‘Standardized ND2’ phylogeny (Fig. 2). Sample numbers are included to aid in determining relationships in cases where more than 2 samples were used for a given species, or species are reconstructed as paraphyletic. Cyrtodactylus pubisulcus image drawn by IGB from photograph courtesy of Ben Karin.

Figure 2

‘Standardized ND2’ Maximum likelihood genealogy of ND2 including only taxa for which COI sequence data also exist. Circles at nodes indicate clade congruence between ND2 and COI loci, with BSS values of ≥70: blue indicate species groups, black interspecific sampling. Asterisks indicate new ND2 sequences contributed by this study. Upper map shows the geopolitical distribution of samples included in this phylogeny, and colored circles associated with tree tips correspond to this map. Lower map highlights the Indochinese region, and boxes represent generalized sampling localities of species groups (IM, IA, IB, IC, TM, WM, EW, VA, VB; denoted by blue circles at nodes). Sampled country localities indicated by colored circles at the tree tips highlight the interdigitated nature of geographic relationships within phylogenetic species groups. Maps drawn and adapted by IGB in Adobe Illustrator CS6 from public domain image provided by Wikimedia Commons (https://commons.wikimedia.org/wiki/File:Location_Map_Asia.svg).