Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico

A new species of leaf-toed gecko (Phyllodactylidae, Phyllodactylus) from María Cleofas Island, Nayarit, Mexico

“…Our field observations were conducted during the day from 09:00 to 17:00 h, and at night from 21:00 to 04:00 h. All captured lizards were taken to the María Cleofas Research Boat for sampling and data collection (see below for morphological analyses). We captured 36 individuals of the genus Phyllodactylus during fieldwork under collecting permits SGPA/DGVS/01208/17 and SGPA/ DGVS/010144/18, of which tissue samples of two specimens were used for molecular analyses (Ramírez-Reyes et al 2020), and 11 specimens were used for the present morphological description. We only sacrificed nine individuals (the type series) by injection of sodium pentobarbital, following the animal ethics guidelines of UNAM.…”

“…We elaborated a species tree in SVDquartets Kubatko 2014, 2015) implemented in PAUP* v. 4 (Swofford 2003) with the 14,271 binary SNPs. The individual samples (n = 13) from the VCF file were assigned to seven species, based upon previous studies about evolution and candidate species in the saxatilis clade (Ramírez-Reyes et al 2020;Ramírez-Reyes et al unpublished data). We performed a species tree search using exhaustive quartet sampling (289 quartets) and used the QFM assembly algorithm to assemble the species tree.…”

“…Phyllodactylus is among the 10 gecko genera with the highest number of species (Uetz et al 2020). Within this diverse genus, particularly in Mexico, recent studies incorporating genomic data indicate a need for taxonomic changes and the description of new species that have remained undetected (or weakly differentiated) on the basis of morphological data alone (Ramírez-Reyes et al 2020).…”

“…Recently, Ramírez-Reyes et al (2020) showed that the gecko population from María Cleofas Island was isolated and had differentiated from mainland lineages during the early Pliocene. Later, Ramírez-Reyes et al (unpublished data) found that Phyllodactylus tuberculosus is a polyphyletic taxon and that none of the three subspecies studied (P. t. tuberculosus, P. t. magnus and P. t. saxatilis) share an exclusive more recent common ancestor with each other (i.e.…”

“…However, there is uncertainty about the phylogenetic relationships of the insular lineage with respect to the continental lineages of the saxatilis clade. According to phylogenetic approximations (ML and Bayesian) based on the supermatrix (or supergene) of genomic data, the insular lineage of the saxatilis clade is related to Phyllodactylus lineages from Sinaloa (Ramírez-Reyes et al 2020;Ramírez-Reyes et al unpublished data). A species tree approach with coalescence methods could provide greater certainty about the phylogenetic relationships of lineages and species within the saxatilis clade.…”