Cytonuclear Discordance, Cryptic Diversity, Complex Histories, and Conservation Needs in Vietnamese Bent-toed Geckos of the Cyrtodactylus irregularis Species Complex

Abstract

Examples of cytonuclear discordance (CD), i.e. differing branching patterns from mitochondrial and nuclear DNA data, are increasing. This raises concerns about combining data from the two genomes for the purpose of reconstructing phyletic history. Because of this, we explore the efficacy of DNA barcoding based on the gene cytochrome c oxidase subunit I ( COI ; Entrez COX1 ) from the perspective of two nuclear DNA (nDNA) loci: RPL35 and RAG1 . Our analyses use 164 samples of Vietnamese bent-toed geckos of the Cyrtodactylus irregularis species complex (Reptilia: Gekkonidae) collected from 24 localities and 306 new sequences. DNA barcoding infers the presence of ten described species and identifies at least 11 unknown lineages from different areas. K2P genetic distances between sites average 16.6 ± 4.6%. Phylogenetic analyses of nuclear DNA data resolve two strongly supported main clades that correspond with northern and southern groups of geckos and presence or absence of enlarged fermoral scale rows. The matrilineal genealogy and nDNA phylogeny are concordant in resolving major lineages, yet trees derived from the two sets of data, and a combined mtDNA-nDNA dataset, are significantly incompatible (AU test: p < 0.01). The extent of CD precludes combining the two genomes for a single analysis. Analyses of both genomes suggest the presence of at least five undescribed cryptic species. Geckos at one site, Ta Kou Mountain, have a complex history involving the unification of two divergent matrilines (K2P = 10.2%). Analyses of nDNA markers alone does not recover this event because gene flow has erased the historical signal. Finally, the independent and geographically isolated lineages face a battle for survival owing to continued habitat destruction. Urgent conservation planning and implementation is necessary for many sites.