A novel dataset to identify the endemic herpetofauna of the New Caledonia biodiversity hotspot with DNA barcodes

Abstract

New Caledonia is the smallest global biodiversity hotspot, yet has one of the highest levels of endemism for an insular region of its size. Lizards are the dominant vertebrate fauna, and, while ecologically important, can be difficult to identify and many are in decline due to anthropogenic threats. As an aid to facilitate identification, we generated a near-complete DNA barcode dataset for New Caledonian lizards, consisting of 601 mitochondrial CO1 sequences of 100 of the 107 described lizards, and a number of yet undescribed species. We use this dataset to assess the performance of CO1 in delimiting species recognised by other, more extensive data and in recovering phylogenetic signal. Most species had intraspecific genetic distances ≤3.7%. Most comparisons between described species were at least ~5% divergent, with the exception of three pairwise species comparisons showing interspecific distances > 2.5%. Maximum likelihood CO1 trees of the six most speciose genera recovered each as monophyletic and, although discordant with previously published ND2 trees using quantitative topology tests, showed similar patterns of intraspecific and interspecific divergence, supporting the utility of CO1 in taxonomic identification and species delimitation. Some species showed overlap between intra- and interspecific pairwise distances, suggesting cryptic taxa, a finding also supported by species delimitation analyses using GMYC and mPTP. This dataset not only provides the basis for economical and reliable identification of New Caledonian lizards encountered during biodiversity assessments, but also provides a potential tool for investigating the identity of native lizards and their ecosystem interactions, even from partial remains.