Genetic diversity is an often ignored but important issue in the design of Marine Protected Areas (MPA), especially in facing the threats of a changing environment. This study found no positive relationship of genetic diversity for two scleractinian corals within an MPA compared to the surrounding area in the Southern Gulf of California. Pocillopora Type 1, a branching and broadcast-spawner, and Porites panamensis, a massive brooding coral, were found to have contrasting patterns of populations structure and genetic diversity. The sites were grouped with a cluster analysis and compared with an analysis of molecular variance (AMOVA). Pocillopora differentiated in clusters (PhiRT=0.088, p=0.007) reflecting the intermediate disturbance hypothesis pattern. The highly disturbed site, due to being highly touristic and predated, grouped with low disturbed sites, the no-take zones. Isolation by environment was not appropriate for this species when comparing the ecosystem heterogeneity and benthic assemblages of sites within clusters. Therefore, isolation by disturbance was proposed to define the pattern of differentiation. Porites clusters differentiated in a geographical pattern (PhiRT=0.122, p=0.002) and was found to follow isolation by distance (r=0.483, p=0.012). Our results indicate that MPA planning should consider the early life-history of the target species to manage genetic diversity effectively.
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