| Summary: | Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there
is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these
heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards
in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and
provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum
likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported
nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography
and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking
speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We
detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of
north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further
advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old
divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.
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