Abstract
Aim To review the histories of the Colorado River and North American monsoon system to ascertain their effects on the genetic divergence of desert‐adapted animals. Location Lower Colorado River region, including Mojave and Sonoran deserts, United States. Methods We synthesized recent geological literature to summarize initiation phases of lower Colorado River evolution, their discrepancies, and potential for post‐vicariance dispersal of animals across the river. We simulated data under geological models and performed a meta‐analysis of published and unpublished genetic data including population diversity metrics, relatedness and historical migration rates to assess alternative divergence hypotheses. Results The two models for arrival of the Colorado River into the Gulf of California impose east‐west divergence ages of 5.3 and 4.8 Ma, respectively. We found quantifiable river‐associated differentiation in the lower Colorado River region in reptiles, arachnids and mammals relative to flying insects. However, topological statistics, historical migration rates and cross‐river extralimital populations suggest that the river should be considered a leaky barrier that filters, rather than prevents, gene flow. Most markers violated neutrality tests. Differential adaptation to monsoon‐based precipitation differences may contribute to divergence between Mojave and Sonoran populations and should be tested. Main Conclusions Rivers are dynamic features that can both limit and facilitate gene flow through time, the impacts of which are mitigated by species‐specific life history and dispersal traits. The Southwest is a geo‐climatically complex region with the potential to produce pseudocongruent patterns of genetic divergence, offering a good setting to evaluate intermediate levels of geological‐biological (geobiological) complexity.