Phylogenomics and species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq...

The Lepidophyma sylvaticum complex occurs from west-central Nuevo León to the Sierra de Chiconquiaco in central Veracruz, Mexico. Morphological studies have revealed population groups that are "moderately divergent from each other" within the complex. In addition, a molecular phylogenetic study found L. sylvaticum to be strongly structured and paraphyletic with respect to L. micropholis. We used ddRADseq and morphological data to evaluate the phylogenetic relationships and species boundaries within the complex. Phylogenetic analyses performed using both concatenation and coalescent methods estimated the same well-supported tree, composed of five allopatric, strongly supported lineages of L. sylvaticum (from Nuevo León [NL]; Sierra de Álvarez, San Luis Potosí [ASLP]; southeastern San Luis Potosí, Querétaro, Hidalgo, and northwestern Veracruz [HSQV]; Tamaulipas [T]; and Puebla and northern Veracruz [PV]) branching off (in that order) from the base of the tree, with L. micropholis as the sister taxon to the last of them. A population genetics analysis revealed one pattern of genetic structure in L. micropholis and three in L. sylvaticum: one in the L. sylvaticum NL and ASLP lineages, another in the L. sylvaticum HSQV and T lineages, and a third in the L. sylvaticum PV lineage. The six lineages identified were genetically distinctive across our phylogenetic and population genetics analyses, and congruent with geography. Species tree and phylogenetic network analyses, considering the six lineages as potentially independent, inferred trees identical to the concatenated tree. Additionally, the phylogenetic network analysis detected a recent introgression event from the L. sylvaticum T lineage into L. micropholis. A time-calibrated tree indicated that the diversification of the complex began in the late Miocene and continued into the Pleistocene. A species delimitation analysis, based on the genealogical divergence index, suggested that the L. sylvaticum NL, ASLP, and PV lineages are independent evolutionary lineages. A morphological analysis showed that L. micropholis and the L. sylvaticum NL and ASLP lineages were distinguishable from each other and from the remaining L. sylvaticum lineages. We conclude that the L. sylvaticum NL and ASLP lineages, the two oldest in the complex, represent independent evolutionary lineages, and propose recognizing the other four lineages as subspecies (historical sublineages) of L. sylvaticum sensu stricto.