Comparative Phylogeography of Phrynosomatid Lizards in Baja California: Asynchronous Divergences and Expansion of <i>Callisaurus draconoides</i> Across the North American Deserts

ABSTRACT Aim We tested whether co‐distributed phrynosomatid lizards in the Baja California Peninsula (BCP) share synchronous phylogeographic discontinuities, as predicted by the “peninsular archipelago” hypothesis, and examined the diversification of Callisaurus draconoides throughout its range. Location The BCP and the Great Basin, Mojave and Sonoran Deserts of southwestern North America. Taxa Five co‐distributed species complexes representing four genera within Phrynosomatidae: Callisaurus , Petrosaurus , Urosaurus and Sceloporus . Methods Double‐digest restriction‐associated‐DNA (ddRAD) sequencing was used to collect genome‐wide sequence data for 309 lizards. We used phylogenetic analyses of concatenated loci and population admixture analysis of unlinked SNPs to identify lineages. To infer a species tree, we collected target sequence capture (TSC) data. Migration between adjacent peninsular lineages was estimated using the multispecies coalescent with migration (MSC‐M) in BPP. A full‐likelihood Bayesian comparative phylogeographic approach (ecoevolity) was used to test the simultaneous divergence hypothesis for the Isthmus of La Paz and Vizcaíno Desert. Results We identified 24 potential lineages within the five co‐distributed complexes. Contact zones between lineages were observed at the Isthmus of La Paz in four of the five complexes, and in all five within the Vizcaíno Desert. The time‐calibrated species tree indicates that within each complex, divergences at the Isthmus of La Paz predate those across the Vizcaíno Desert. We found strong support for at least three independent divergence events at the Isthmus of La Paz and the Vizcaíno Desert, thereby rejecting the simultaneous divergence hypothesis. Inferred migration rates between adjacent peninsular populations were generally low (M &lt;&lt; 1) to absent. Zebra‐tailed lizards ( Callisaurus ), in which the earliest diverging lineages are endemic to the southern BCP, exhibit a clear pattern of Pleistocene range expansion from the BCP into the deserts of the western United States and mainland Mexico. The most deeply nested populations in Callisaurus occur at the northern, eastern and southeastern range limits in temperate, subtropical and tropical biomes, respectively. Main Conclusions These results support the BCP's tectonic isolation as a driver of peninsular endemism and a contributing factor to lineage diversification more broadly in the region. Taxonomic adjustments, including resurrecting Urosaurus microscutatus , are proposed to better reflect evolutionary history in taxonomy.