Molecular markers have contributed much to our understanding of evolution in recent years, but the origins of evolutionary patterns in the marine environment generally still are poorly known. Here, I describe the patterns of molecular variation in mitochondrial (mt) or nuclear DNA of three coastal marine animals: the California halibut (Paralichthys californicus), the tidewater goby (Eucyclogobius newberryi), and the moon jellyfish (Aurelia aurita).

DNA sequence data reveal considerable genetic variation (*5.8% sequence divergence in the mtDNA control region) within P. californicus, but there is little geographic structure to this variation. In contrast, a similar amount of genetic variation in E. newberryi (~4.9% divergence in the mtDNA control region and cytochrome b) is geographically highly structured and includes a deep divergence within the California Transition Zone, the interface between Oregonian and Californian biogeographic provinces. Even greater differentiation is apparent within A. aurita, in which 14.0-30.9% sequence divergence in mitochondrial Cytochrome Oxidase c subunit I and 16.0-23.9% divergence in nuclear Internal Transcribed Spacer One distinguish six putative cryptic species, including one north and one south of the California Transition Zone. The modern phylogeographies of these species likely have been influenced variously by Cenozoic (Aurelia) to Quaternary and Holocene (all species) changes in climate, sea-level, geography, and oceanography, as well as different life-histories and habitats, and historical human activity.

I draw on these studies and others published previously to discuss the relationship between intra-specific phylogeography and supra-specific biogeography and its implications for our understanding of the processes and patterns of evolution in coastal marine taxa. Contrary to previous studies of coastal California taxa, I find that phylogeographic gaps are approximately concordant with the Oregonian-Californian biogeographic boundary, which is described appropriately as the California Transition Zone. More specifically, I find highly concordant intra-specific phylogeographic gaps and supra-specific biogeographic ‘breaks’ in the vicinity of Los Angeles and Monterey Bay. Coupled with the distribution of ‘one-degree endemic species’, which likely inhabit regions of steep environmental gradients, these data suggest that parapatric or allopatric speciation across ecotones may be an important source of intra-specific and supra-specific diversity in coastal marine taxa.