Populations of Symbiodinium muscatinei show strong biogeographic structuring in the intertidal anemone Anthopleura elegantissima.

Among temperate cnidarian symbioses, the partnership between the intertidal anemone Anthopleura elegantissima and its dinoflagellate and chlorophyte symbionts is one of the most well characterized. Biogeographic, reciprocal transplant, and physiological studies have convincingly demonstrated a relationship between environmental factors such as temperature and irradiance and the distribution of symbionts from both algal phyla. However, little is known about the fine-scale diversity or biogeographic distribution within symbiont lineages of this anemone. We used sequence information from the mitochondrial cytochrome b and chloroplast 23S ribosomal genes and restriction fragment length polymorphism data from the 18S nuclear ribosomal gene to characterize the Symbiodinium populations in tentacles clipped from 105 anemones at 14 sites along the entire California coast, spanning about 1200 km. Our results show the presence of at least three primary biogeographic regions with breaks around Cape Mendocino and Monterey Bay, each dominated by a different Symbiodinium muscatinei genotype. Sharp clines suggest limited gene flow between adjacent regions. Few sampling locations or individual anemones showed symbiont diversity at either organellar locus within the limits of our detection method, while sequence analysis of cloned nr18S polymerase chain reaction product suggests that nuclear pseudogenes may underlie intra-host diversity observed at that locus.