Molecular data reveal spatial and temporal patterns of diversification and a cryptic new species of lowland Stenocercus Duméril & Bibron, 1837 (Squamata: Tropiduridae)

[Display omitted] •We include previously understudied lowland species in a new phylogeny of Stenocercus.•We infer divergence times, ancestral distributions, and environmental space occupancy.•Stenocercus began to diversify in the South American Midwest by the late Oligocene.•Dispersal, landscape shifts and ecological differentiation have shaped species ranges.•Based on phylogenetic and morphological data, we describe a new Stenocercus species. Phylogenetic studies have uncovered biogeographic patterns and the associated diversification processes of Neotropical wet forest taxa, yet the extensive open and drier biomes have received much less attention. In the Stenocercus lizard radiation, restricted sampling and phylogenetic information have limited inferences about the timing, spatial context, and environmental drivers of diversification in the open and dry lowland settings of eastern and southern South America. Based on new DNA sequence data of previously unsampled species, we provide an updated historical biogeographic hypothesis of Stenocercus. We infer phylogenetic relationships, estimate divergence times, and track ancestral distributions, asking whether cladogenetic events within the genus correlate to reported shifts in South American landscapes during the past 30millionyears, focusing in the open and drier areas. To examine correlations between genetic and ecological divergence, we extracted environmental data from occurrence records and estimated climatic envelopes occupied by lowland taxa. Our results suggest that Stenocercus began to diversify around the South American Midwest by the late Oligocene. We recovered two main lowland and two main Andean clades within the genus; within both Andean clades, most cladogenetic events date back to the Miocene, synchronously with the most intense phase of Andean uplift. In the western clade of lowland Stenocercus, species ranges and divergence times are consistent with major landscape shifts at the upper Guaporé and Paraguay River basins as a result of Andean orogeny, suggesting vicariant speciation. By contrast, in the ‘horned’ lowland clade, we find evidence that dispersal and ecological differentiation have shaped species divergences and current ranges in the Brazilian Cerrado, Caatinga, Pampas and Atlantic Forest, possibly under a vanishing refuge scenario. Lastly, our phylogenetic results indicate two divergent clades within the formerly recognized taxon S. sinesaccus, and further evaluation of morpholo