The Evolutionary History of Dragon Lizards (Squamata: Agamidae) Revealed by Phylogenomics

Dragon lizards (Squamata: Agamidae) are a species-rich, ecologically, and morphologically diverse group that is broadly distributed across the eastern hemisphere. Here, we present a phylogenomic study of this major clade of lizards to elucidate their biogeographic history, understand how dispersal and vicariance generated modern species distributions, and examine whether ecological opportunities encountered during agamid evolutionary history shaped speciation rates. We generated genome-wide sequence data for 42 species representing 40 genera to infer the evolutionary relationships and timescale of dragon lizards. The phylogeny was largely concordant across several different types of genetic loci, but rapidly evolving long exons had better support values across gene and species trees compared with other data sets. We also inferred a supermatrix tree and timetree for 433 (72% of described species) species to perform taxonomically well-sampled biogeographic and macroevolutionary analyses. These analyses inferred that agamids originated during the Late Cretaceous and in Laurasia, and that Southeast Asia has been a major source of agamid diversity. Rate analyses found that neither individual biogeographic and cladogenetic events nor ecological opportunities appear to have resulted in structured variation in speciation rates when considering all agamid lizards. Our study refutes supercontinental vicariance as a driving mechanism for speciation in Agamidae and provides a case of a broadly distributed and diverse clade with weak evidence for variation in speciation rates.