Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Africa is renowned for its biodiversity and endemicity, yet little is
known about the factors shaping them across the continent. African Agama
lizards (45 species) have a pan-continental distribution, making them an
ideal model for investigating biogeography. Many species have evolved
conspicuous sexually dimorphic traits, including extravagant breeding
coloration in adult males, large adult male body sizes, and variability in
social systems among colorful versus drab species. We present a
comprehensive time-calibrated species tree for Agama, and their close
relatives, using a hybrid phylogenetic-phylogenomic approach that combines
traditional Sanger sequence data from five loci for 57 species (146
samples) with anchored phylogenomic data from 215 nuclear genes for 23
species. The Sanger data are analyzed using coalescent-based species tree
inference using *BEAST, and the resulting posterior distribution of
species trees is attenuated using the phylogenomic tree as a backbone
constraint. The result is a time-calibrated species tree for Agama that
includes 95% of all species, multiple samples for most species, strong
support for the major clades, and strong support for most of the initial
divergence events. Diversification within Agama began approximately 23
million years ago (Ma), and separate radiations in Southern, East, West,
and Northern Africa have been diversifying for > 10 Myr. A suite of
traits (morphological, coloration, and sociality) are tightly correlated
and show a strong signal of high morphological disparity within clades,
whereby the subsequent evolution of convergent phenotypes has accompanied
diversification into new biogeographic areas.