The complex geological history of California has played a major role in shaping the evolutionary history of the coachwhip snake, Masticophis flagellum, within the region. Specifically, mountain building and strike-slip movement along major faults during the Pliocene and Pleistocene produced the geographical patterns of genetic structure present within M. flagellum in California. Using mtDNA sequence data we identified five genetically distinct lineages of M. flagellum occurring within areas of the San Joaquin Valley, Western Mojave, Western Riverside County, California deserts, and Baja California. The timing of molecular divergence of these lineages coupled with their present geographical distribution suggests the uprising of the Sierra Nevada, formation and isolation of Baja California, and the uprising of the Transverse and Peninsular Ranges are the major geological events that initially isolated the previously contiguous M. flagellum populations.

Using restriction fragment length polymorphisms (RFLPs) data we identified multiple contact zones between M. flagellum lineages in coastal Southern California. Our data suggests contact between the lineages is secondary in nature and presumably follows the partial erosion of geographical barriers initially responsible for isolating the different lineages. The narrowness of the contact zones suggests the lineages are, to a degree, reproductively isolated from one another. We presume this incompatibility is a consequence of the long periods of isolation endured by the lineages. Given the lineages experienced variable conditions and amounts of time in isolation, we believe comparisons of the extent that each is reproductively isolated form the other should provide significant insight into the process of speciation.

The conservation implications of this work are significant. Much of the newly discovered diversity within M. flagellum is threatened by development within California. Knowledge of the spatial distribution of this diversity allows us to prioritize conservation efforts for this species in this state. Additionally, through describing the phylogeographic patterns of M. flagellum we are aiding in the discovery of areas of endemism within the region. The protection of these areas is critical to the success of any regional conservation plan.