(Opening paragraph)
Phylogeography seeks to explain the geographic distribution of genetic lineages. To the extent that organisms are products of their DNA, phylogeography also seeks to explain the distribution of organisms, including variation within and, less commonly, between species. Because genetic variation may take thousands or millions of years to accrue, phylogeography has a strong historical component. Thus, phylogeography is closely allied with biogeography, particularly historical and cladistic biogeography, and can be thought of as opening a window in time through which we can observe the influence of historical factors on modern patterns of biodiversity.

Since its inception (Avise et al., 1987), phylogeography has grown exponentially (Avise, 2000), reflecting its intuitive appeal and perceived success. Although the vast majority of phylogeographic studies still explore patterns within single species, greater access to larger amounts of molecular data is making comparative phylogeography, which compares the genealogies of two or more species with overlapping geographic ranges, increasingly popular and powerful (Avise, 1992, 1994; Riddle et al., 2000a, b, c). Comparative phylogeography has proven particularly useful in revealing common patterns and causes of genetic inhomogeneities within species as well as suggesting links between life-history and genetic structure. The goal of this chapter is to employ the comparative phylogeographic approach to elucidate the factors that have most influenced geographic patterns of genetic variation in California fishes.