| Summary: | The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using Isolation-with-Migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia, and define this species as a single evolutionarily significant unit for conservation purposes. DNA Sequence Data Diploid nuclear DNA sequence data in fasta format. Sequences.zip PHASE Input and output files for PHASE v2.1. RAxML Input, output, and gene tree files from RAxML v7.3.0. MrBayes Input, output, and gene tree files from MrBayes v3.2.2. Structurama Input and output files for Structurama v2.0. Geneland Input files and R script for Geneland v4.0.3. IM and IMa Input and output files for IM and IMa. IM.zip Coalescent Simulations Tree files simulated with Mesquite v2.75 and chi-square test. CoalescentSimulations.zip BEAST Input and output from the Extended Bayesian Skyline Plot implemented in BEAST v1.7.5.
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