Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

Multi-locus nuclear DNA data were used to delimit species of fringe-toed
lizards of the Uma notata complex, which are specialized for living in
wind-blown sand habitats in the deserts of southwestern North America, and
to infer whether Quaternary glacial cycles or Tertiary geological events
were important in shaping the historical biogeography of this group. We
analyzed ten nuclear loci collected using Sanger sequencing and
genome-wide sequence and single-nucleotide polymorphism (SNP) data
collected using restriction-associated DNA (RAD) sequencing. A combination
of species discovery methods (concatenated phylogenies, parametric and
non-parametric clustering algorithms) and species validation approaches
(coalescent-based species tree/isolation-with-migration models) were used
to delimit species, infer phylogenetic relationships, and to estimate
effective population sizes, migration rates, and speciation times. Uma
notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk
Dunes, Arizona (U. sp.) were supported as distinct in the concatenated
analyses and by clustering algorithms, and all operational taxonomic units
were decisively supported as distinct species by ranking hierarchical
nested speciation models with Bayes factors based on coalescent-based
species tree methods. However, significant unidirectional gene flow (2NM
>1) from U. cowlesi and U. notata into U. rufopunctata was detected
under the isolation-with-migration model. Therefore, we conservatively
delimit four species-level lineages within this complex (U. inornata, U.
notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid
population (U. notata x cowlesi). Both concatenated and coalescent-based
estimates of speciation times support the hypotheses that speciation
within the complex occurred during the late Pleistocene, and that the
geological evolution of the Colorado River delta during this period was an
important process shaping the observed phylogeographic patterns.