Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape

Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analyzed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and Salton Sea. We recommend additional lands in the U.S. and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy (RMS). We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change and other long-term impacts.

Methods
A ddRADseq dataset was collected for 45 lizards (including outgroups). Sequencing occurred on an Illumina NextSeq. Raw sequence data were processed (including mapping to the P. platyrhinos reference genome) using iPyrad. After filtering with VCFtools, the data were analyzed with the software packages adegenet (DAPC), Admixture, splitstree, IQTree, EEMS, and moments. Inputs, outputs, jobscripts, and other metadata for these analyses are included in this data package. Full methods are detailed in the paper.