Reduced representation genomics reveals species level phylogeny of Gila spp. from the Colorado River Basin

Authors: Chafin, Tyler K.*, Douglas, Marlis R., Douglas, Michael E.

Year: 2015 (xlvii)

Abstract

The Colorado River Basin (CRB) is the most threatened riverine system in North America, due largely to persistent drought and anthropogenic modifications. Historically, its isolation and harsh environment have provided a theater for diversification for several unique groups of fishes, such that distinctive local adaptations arose over time to cope with these abrasive and erratic conditions. However, the effectiveness of these adaptations has been truncated by human habitat modifications, and by a prolific introduction of non-native competitors to a system with already depauperate levels of intraspecific diversity. Unique adaptations are most apparent within the Gila spp. (Cyprinidae) assemblage, manifested as multiple ecologically and morphologically distinct species, yet phylogenetic discordance and reticulation suggests a history of gene flow and blurred species boundaries. Here, using next-generation sequencing of reduced genomic samples (ddRAD), we present a phylogeny of Colorado River Gila informed by genomic insights, investigate historical interspecific introgression, and characterize species-level structure and admixture among the Gila robusta complex of the lower Colorado River Basin.