Phenotypic crypticity despite strong phylogenetic divergence: diversification dynamics in a species complex of...

Absence of phenotypic differentiation can challenge the study of diversification by concealing evolutionary divergence through morphological similarity. Such cryptic species diversity is found particularly often in extreme environments, including arid mountain ranges. In the Hajar Mountains of southeastern Arabia, the Pristurus rupestris species complex comprises divergent lineages with notable phenotypic variation. Here, we investigate the evolutionary dynamics of this radiation by integrating geometric morphometric analyses with whole-genome sequencing and phylogenomic reconstructions. We analyzed five species-P. ali, P. assareen, P. feulneri, P. omanensis, and P. rupestris-including all previously identified genetic lineages within those species, and generated a new reference genome for an Old World sphaerodactylid gecko (P. rupestris sensu stricto). Morphometric analyses of comprehensive two- and three-dimensional morphological datasets indicate strong overlap in both body and head shape. Despite considerable phenotypic similarities, our results reveal deep interspecific divergences exceeding 16 million years and contrasting demographic histories. While we detected introgression restricted to specific lineage pairs, phenotypic crypticity persists across the entire complex, suggesting stabilizing selection in harsh environments. Our study highlights the P. rupestris species complex as an ideal model for investigating the role of environmental constraints in limiting morphological divergence and shaping diversification dynamics in arid mountain ecosystems.