Holistic Species Delimitation Supports Recognition of Multiple Lineages in the Gila robusta Complex of the American Southwest

Challenges associated with species delimitation of the Gila robusta species complex in the Gila River basin arise because of convergence of multiple evolutionary processes that result in perplexing patterns of morphological, genetic, and ecological variation. As currently recognized, the complex comprises three nominal species: Gila robusta, Gila intermedia, and Gila nigra, each with overlapping traits and disjunct geographic distributions. Key challenges for delimitation include limited morphological divergence, strong local genetic differentiation that obscures broader patterns of lineage diversification, interspersed geographic distributions of nominal taxa, and phylogenetic analyses complicated by admixture. We review and synthesize ecological, morphological, geological, and genetic data to infer evolutionary processes that shaped diversity in the complex. Historical events, including tectonically-driven drainage isolation and integration and cyclic climatic fluctuations strongly influenced the distribution and diversification of Gila. Morphological analyses revealed overlap among traits traditionally used for species identification, while genetic studies indicated strong population-level differentiation with limited gene flow. Independent phylogenomic analyses yielded conflicting interpretations that hinge upon methodologies employed. To reconcile these complexities, we advocate a holistic approach that integrates evolutionary processes, geologic history, and contemporary morphological and genetic patterns. We suggest these, in tandem, argue against a single polytypic species and support instead the presence of two (possibly three) distinct evolutionary lineages. Importantly, our review underscores the importance of integrating diverse data sources to evaluate taxonomic ambiguities in cryptic species complexes, especially those that evolved in highly dynamic geological and climatic settings.