Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.

Raquel Vasconcelos,Roberto Sindaco,Salvador Carranza,Mauro Fasola,Marc Simó-Riudalbas,Xavier Santos,Gustavo Llorente,Edoardo Razzetti,Santiago Montero-Mendieta

doi:10.1371/journal.pone.0149985

Abstract

Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra’s most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8–54.4%. This has implications in the species’ ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

Highlights

The accuracy of delimiting species is fundamental in specimen identification and species discovery
As DNA barcoding has proven to be an invaluable tool for specimen identification and preliminary species discovery for many taxa, it can greatly reduce problems that arise from morphological taxonomy approaches, while facilitating biologically-sound conservation planning [16]
While in the ML tree H. pumilio formed a clade with H. inintellectus, H. dracaenacolus and H. granti, in the NJ and Bayesian inference (BI) trees, it emerged as sister group to a clade formed by H. flaviviridis, H. robustus, H. forbesii, H. oxyrhinus, and H. homoeolepis

Summary

Introduction

The accuracy of delimiting species is fundamental in specimen identification and species discovery. As DNA barcoding has proven to be an invaluable tool for specimen identification and preliminary species discovery for many taxa, it can greatly reduce problems that arise from morphological taxonomy approaches, while facilitating biologically-sound conservation planning [16] This is especially important in under-sampled, and biodiversity hotspot areas such as islands. The specific aims were to: i) generate a DNA reference barcode library for the reptiles of the Socotra Archipelago, ii) test the effectiveness of the library for future specimen identification purposes using different distance-based and tree-based techniques, iii) explore previously unrecognized diversity by applying species delimitation methods, and iv) test the robustness of phylogenetic inference and species delimitation using COI compared with previous marker studies

Ethics statements

Results

Discussion