Comparative phylogeography of phrynosomatid lizards in Baja California: Asynchronous divergences and expansion of <em>Callisaurus draconoides</em> across the North American deserts

This dataset comprises eleven archives containing processed genomic data, analysis inputs/outputs, and supporting files from double-digest RAD sequencing (ddRAD) and target sequence capture (TSC). Data span four genera (Callisaurus, Petrosaurus, Sceloporus, and Urosaurus) and include pyRAD assemblies, Admixture clustering, RAxML phylogenies, BPP coalescent-with-migration models, phyluce TSC assemblies, BEAST2 and StarBEAST2 species trees, and ecoevolity divergence-time inferences across Baja California biogeographic breaks. Files are organized by analysis and genus, with configuration files, job scripts, summary statistics, and outputs in formats such as VCF, structure/geno, Phylip/Nexus alignments, phased allele sequences, etc. Geographic coordinates are provided at reduced precision (0.01°) to limit exact locality disclosure. These data are suitable for reuse in comparative phylogeography, population genomics, and phylogenetic method development, enabling replication of published analyses or testing of alternative models and pipelines. Collection and use of specimens were conducted under relevant permits and institutional animal care protocols (see publication for details), and downstream use should continue to respect applicable legal and ethical standards.