Data from: Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data

Species divergence is typically thought to occur in the absence of gene
flow, but many empirical studies are discovering that gene flow may be
more pervasive during species formation. Although many examples of
divergence with gene flow have been identified, only few clades have been
investigated in a comparative manner, and fewer have been studied using
genome-wide sequence data. We contrast species divergence genetic
histories across eight triplets of North American Sceloporus lizards using
a maximum likelihood implementation of the isolation–migration (IM) model.
Gene flow at the time of species divergence is modeled indirectly as
variation in species divergence time across the genome or explicitly using
a migration rate parameter. Likelihood ratio tests (LRTs) are used to test
the null model of no gene flow at speciation against these two alternative
gene flow models. We also use the Akaike information criterion to rank the
models. Hundreds of loci are needed for the LRTs to have statistical
power, and we use genome sequencing of reduced representation libraries to
obtain DNA sequence alignments at many loci (between 340 and 3,478; mean
1⁄4 1,678) for each triplet. We find that current species distributions
are a poor predictor of whether a species pair diverged with gene flow.
Interrogating the genome using the triplet method expedites the
comparative study of species divergence history and the estimation of
genetic parameters associated with speciation.