An evaluation of the poorly understood Cenozoic hydrologic history of the American Southwest using combined geological and biological data yields new insights with implications for tectonic evolution. The Mesozoic Cordilleran orogen next to the continental margin of southwestern North America probably formed the continental divide. Mountain building migrated eastward to cause uplift of the Rocky Mountains during the Late Cretaceous to early Tertiary Laramide orogeny. Closed drainage basins that developed between the two mountain belts trapped lake waters containing fish of Atlantic affinity. Oligocene-Miocene tectonic extension fragmented the western mountain belt and created abundant closed basins that gradually filled with sediments and became conduits for dispersal of fishes of both Pacific and Atlantic affinity. Abrupt arrival of the modern Colorado River to the Mojave-Sonora Desert region at ca. 5 Ma provided a new conduit for fish dispersal. Great dissimilarities in modern fish fauna, including differences in their mitochondrial deoxyribonucleic acid (DNA), indicate that late Miocene runoff from the Colorado Plateau did not flow down the Platte or Rio Grande, or through the Lake Bonneville Basin. Fossil fishes from the upper Miocene part of the Bidahochi Formation on the Colorado Plateau have characteristics that reflect a habitat of large, swift-moving waters, and they are closely related to fossil fishes associated with the Snake and Sacramento Rivers. This evidence suggests that influx of fishes from the ancestral Snake River involved a major drainage, not merely small headwater transfers.

We estimated the timing of paleodrainage connections in the Colorado River Basin using mitochondrial deoxyribonucleic acid (DNA) sequence divergences among populations of the speckled dace, Rhinichthys osculus . Cytochrome b and ND4L sequences were analyzed by maximum likelihood methods to estimate phylogenetic branch lengths, which were calibrated to geological time with a fossil age estimate. We assume that heterogeneity in rate of evolution of mitochondrial DNA is caused in part by differences in body size, temperature, and correlated life-history traits; therefore, branch lengths are used directly to calculate rates of nucleotide substitution and ages of nodes on the phylogenetic tree. Rhinichthys osculus is estimated (by the corrected age of the oldest fossil) to have diverged from its sister species at 6.3 Ma. We estimate that speckled dace have been in the Colorado drainage for 3.6 m.y., and they have dispersed through the drainage and to former connectives, such as the Los Angeles Basin, in the past 1.9 m.y. Divergence among lineages of the upper and lower Colorado River drainages (above and below Grand Canyon) is estimated to have occurred ca. 1.9–1.3 Ma. Genetic divergence of allopatric lineages in the lower Colorado River drainage was accompanied by morphological adaptations to different stream gradients, but small genetic distances among these forms indicate recent gene flow and lack of reproductive isolation.