Insights into the Etheostoma spectabile species complex: Incongruence between mitochondrial and nuclear gene sequence data

Hybridization is recognized as an evolutionary process that can provide a significant source of genetic variation and whose genetic consequences have been investigated across a wide taxonomic range of plants and animals. Darters (Percidae: Etheostomatinae) are a clade with documented interspecific hybridization and many species with a recent evolutionary origin, yet most molecular phylogenetic analyses of darters to date have relied primarily on mitochondrial DNA (mtDNA) sequences. Inferring relationships within and between closely related species using a single locus gene tree is potentially confounded by introgression as well as retention of ancestral polymorphisms. This can lead to incongruence between the gene tree and the species tree, and confound interpretations of phylogeography and species relationships. Considering these limitations, I utilized both mtDNA and six nuclear genes to reconstruct the phylogeny of the E. spectabile species complex, a hypothesized reciprocally monophyletic group with known instances of intergradation and hybridization. My objectives were twofold: 1) to determine if the molecular evidence supported the recent species delimitations based on meristics and breeding male coloration and 2) to determine the phylogenetic utility and congruence of mtDNA and nuclear DNA data to address possible hybridization in the species complex. I found concordance between distinct genetic signals, meristics and geographic distributions that supported many, but not all of the recognized species. I also found that introgression is prevalent throughout the history of the E. spectabile species complex, and confounds the monophyly of the complex, specifically with E. fragi and E. uniporum mtDNA haplotypes grouping outside of the complex. Understanding the prevalence of introgression is crucial for future investigation of the evolution of these fishes.