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.