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New genome sequencing techniques are enabling phylogenetic studies to scale-up from using a handful of loci to hundreds or thousands of loci from throughout the genome. In this study, we use targeted sequence capture (TSC) data from 540 ultraconserved elements and 44 protein-coding genes to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma. Previous molecular phylogenetic analyses of Phrynosoma based on a few nuclear genes, restriction site associated DNA (RAD) sequencing, or mitochondrial DNA (mtDNA) have produced conflicting relationships. Some of these conflicts are likely the result of rapid speciation at the start of Phrynosoma diversification, whereas other examples of gene tree discordance appear to be caused by active and residual traces of hybridization. Concatenation and coalescent-based species tree phylogenetic analyses of these new TSC data support the same topology, and a divergence dating analysis suggests that the Phrynosoma crown group is up to 30 million years old. The new phylogenomic tree supports the recognition of four main dades within Phrynosoma, including Anota (P. mcallii, P. solare, and the P. coronatum complex), Doliosaurus (P. modestum, P. goodei, and P. platyrhinos), Tapaja (P. ditmarsi, P. douglasii, P. hemandesi, and P. orbiculare), and Brevicauda (P. braconnieri, P. sherbrookei, and P. taurus). The phylogeny provides strong support for the relationships among all species of Phrynosoma and provides a robust new framework for conducting comparative analyses.
HORNED lizards (Phrynosoma) are a peculiar group with respect to their morphology and behavior, and they have evolved a number of remarkable adaptations including anti-predator blood squirting, water harvesting, and a wide array of horn armaments (Sherbrooke, 2003). Not surprisingly, horned lizards have been the subjects of diverse research in ecology and evolutionary biology (Hodges, 2004; Meyers et al., 2006; Luxbacher and Knouft, 2009; Bergmann and Berk, 2012). The group currently includes 17 species with a collective distribution extending from Canada to Guatemala with most of the species diversity found in Mexico (Nieto-Montes de Oca et al., 2014). The phylogenetic relationships among Phrynosoma have been difficult to resolve for at least three reasons. First, rapid spéciation events early in the diversification of Phrynosoma have made it difficult to resolve relationships with small amounts of data (Hodges and Zamudio, 2004). Second, hybridization and introgression between species...