A genomic and morphological reassessment of angle-headed dragons (Agamidae: Gonocephalus ) in the Philippines elucidates over a century of taxonomic uncertainties

Abstract

Defining species boundaries challenges taxonomists, particularly for groups with multiple, conflicting, or alternative names. An example is the taxonomy of forest agamid lizards (Gonocephalus) in the Philippines, which have not been comprehensively studied until a multilocus molecular study by Welton et al. (2017) identified 12 distinct lineages. However, the relation of these lineages to known species remains unclear, raising questions about biologically meaningful species-level diversity. Here, we tested the occurrence of 12 lineages using new genomic and morphological data. We recovered a phylogenomic tree similar to that of Welton et al. with at least 12 lineages embedded within two highly supported clades: the northern-central Philippines and the southern Philippines. Species delimitation analyses revealed widespread discordance among lineages within clades, characterised by minimal genomic divergence and high levels of shared ancestry, but no discordance was observed between the two clades. Concordant with phylogenomic results, our morphological analyses consistently identified two diagnosable groups. Examination of name-bearing type specimens clarifies the appropriate assignment of two names (among three available) to the two species delimited here. Our study demonstrates that a long-standing taxonomic issue can be addressed by rigorously integrating all available data and modern tools to support or overturn species hypotheses.