BEAST and *BEAST analyses

We utilized a Bayesian strategy that relied on external fossil calibrations in the perciform fish clade Centrarchidae to time-calibrate the mtDNA phylogeny, individual gene trees inferred from each of the ten nuclear genes and a phylogeny inferred from the concatenation of ten nuclear genes, and a phylogeny inferred from the concatenation of ten nuclear and two mitochondrial genes in BEAST. We also calibrated divergence times on a nuclear species tree using *BEAST, excluding the mitochondrial genes to avoid incongruence among gene trees resulting from mitochondrial replacement via introgressive hybridization that is common among species of Ceasia. The xml files were generated in BEAUti, however the species tree divergence time xml file were also changed by hand. All samples were collected in the field and accession numbers for each gene accompany this dryad submission