1. The natural seasonal drying and flooding of southern California streams have been altered over the past century by activities related to agriculture, flood control, and reservoir construction. The genetic structure and diversity of aquatic invertebrates inhabiting these environments is largely unexplored, and may be important for conservation.
2. We sampled two species of aquatic invertebrates with different dispersal abilities to assess genetic structure and diversity, and make inferences about the evolutionary processes that underlie these genetic patterns. The mayfly Fallceon quilleri, which has a winged terrestrial stage, was sampled from perennial and intermittent streams from three catchments across San Diego County. The amphipod Hyalella azteca was sampled from streams (perennial and intermittent) and reservoirs in a single catchment (San Dieguito). Because it is obligately aquatic throughout its life-cycle, H. azteca was assumed to disperse less than F. quilleri.
3. Intrapopulation and overall genetic diversity was higher in F. quilleri than in H. azteca. In F. quilleri there was very little genetic divergence among populations, and most of the genetic differentiation that was observed could be attributed to a single population. In H. azteca, populations were markedly differentiated between the upper and lower segments of the San Dieguito basin, which are separated by a c. 10 km section of stream that rarely has surface flow. Within both segments, genetic divergence between sites connected by reservoirs and perennial streams was not significantly different.
4. Our results suggest that F. quilleri disperses widely and thus avoids genetic bottlenecks and marked levels of population differentiation that may be expected from frequent extinctions and recolonizations. In contrast, restricted dispersal in H. azteca is associated with relatively low genetic diversity and high genetic divergence across a portion of the catchment in which surface flow is rare.