Complex evolutionary history and possible unrecognized diversity in Philippine waterside skinks (Squamata: Scincidae: Tropidophorus) inferred from molecular and morphological evidence

We present the first robust geographical characterization of variation and phylogeographic population structure in Philippine Tropidophorus (spiny waterside skinks), based on extensive sampling from throughout the archipelago and a combined focus on genetic and morphometric variation. Last revised more than 40 years ago, the Philippine Tropidophorus have never been the subject of an integrative study to evaluate their evolutionary relationships, genetic diversity, population structure, and species boundaries. Our best-supported phylogenetic estimate, based on mitochondrial ND2, 12S, and 16S genes, confirms earlier studies suggesting that Philippine species do not form a single clade. We focus on five broadly delimited groups, corresponding to three currently recognized species ( T. grayi , T. davaoensis , T. partelloi ), and two deep lineages within the taxon T. misaminius , suggesting that T. misaminius may represent a species complex. Estimated divergence times were approximately 8.3 Mya between T. grayi and the Sulawesi lineage ( T. baconi ), and 11.4 Mya between T. micropus and the lineage comprising T. davaoensis , T. partelloi , T. misaminius , and some Bornean taxa ( T. brookei , T. sebi , and T. beccarii ). An unrooted phylogenetic network revealed no haplotype sharing among the four currently recognized Philippine species, which also exhibited high interspecific genetic distances (0.141–0.278), providing further evidence for the taxonomic validity of these nominal species. However, the available single-locus species delimitation frameworks (ABGD and ASAP) and the evaluation of morphological variation all provide strong support for the possible existence of a fifth species, which should be the focus of future analyses of genomic variation and the characterization of the occurrence and/or cessation of gene flow throughout the southern Philippines and Bornean populations.