Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral–algal symbioses. The fine-scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intracolony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in the Gulf of California. The genetic diversity and allelic frequencies in reef populations of S. glynni remained stable over 3 years. Common clone genotypes persisted over this period, and no temporal population subdivision (ΦPT = 0.021 and −0.003) was detected. Collections from circular plots showed no statistical correlation between related Pocillopora individuals and their associations with particular S. glynni genotypes, with no spatial structuring or clonal aggregation across a reef for the symbiont. From permanent linear transects, samples were analysed from multiple locations within a colony and some were resampled approximately 1 year later. Many of these multisampled colonies (approximately 53%) were dominated by a single S. glynni genotype and tended to associate with the same symbiont genotype(s) over time, while colony ramets often possessed unrelated symbiont genotypes. In contrast to the species level, associations between genotypes of Pocillopora and S. glynni are apparently more flexible over space and time. The abundance of sexually recombinant genotypes of S. glynni combined with greater flexibility might provide adaptive mechanisms for these symbioses to evolve rapidly to changes in environmental conditions and allow particular symbiont genotypes to spread through a host population.
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