Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia

Analyzing DNA sequence data from multiple unlinked nuclear loci in a coalescent Isolation-with-Migration (IM) model is a statistically powerful method for estimating population divergence times, effective population sizes, and gene flow. This approach was used to reconstruct the evolutionary history of the Mojave fringe-toed Lizard, Uma scoparia, which is restricted to windblown sand habitats in the Mojave and Colorado Deserts of southern California and western Arizona, a region that is thought to have undergone dramatic climatic change during and since the Pleistocene epoch. To shed light on the origin of this species, I analyzed 15 nuclear loci (621,694 total bp) representing twenty localities of U. scoparia and four localities from its sister species to the south, U. notata. I found a latitudinal gradient in heterozygous SNPs and indels, low nucleotide diversity in U. scoparia (π = 0.148%, SD = 0.167%), particularly relative to U. notata (π = 0.469%, SD = 0.366%), and reciprocal monophyly in 3/15 gene trees. Using the IM model, I estimated with 95% confidence that U. scoparia and U. notata speciated in the Pleistocene epoch (~1 – 1.4 mya, 95% CI ~0.7 mya – 2.1 mya) without significant gene flow (2Nm 1), an estimate that is robust to violations of the no-recombination assumption. I also found that U. notata has 2-5 times the effective population size of U. scoparia. These findings suggest that U. scoparia originated in the Pleistocene epoch and was confined to a Colorado Desert refuge during glacial maxima; northern populations represent a recent range expansion.