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Dispersal distance of planktonic larvae of coral reef organisms is influenced by their ecological characteristics and environmental factors such as current flow and physical structure of reefs. This study reviews the degree and pattern of genetic differentiation in scleractinian corals in the Ryukyu Archipelago, compared with other regions. Small-scale genetic heterogeneity, but broad-scale homogeneity, was detected in some species, including brooders and spawners in the Ryukyus. Comparison with other regions indicated that limited gene flow on a small spatial scale (i.e., self-recruitment) seemed to occur in many regions. However, the degree of gene flow over larger distances was complex and species-dependent. With an implication for conservation in the Ryukyus, the larval source hypothesis, which states that coral larvae were recruited from the Kerama Islands to the Okinawa Islands, was consistent with results illustrating high gene flow in some species. Thus, conservation of corals in the Kerama Islands is high priority. Detection of genetic breaks between the southern and central Ryukyus was not common among species. The genetic structure observed in corals is highly variable and depends on both species and spatial scale in the Ryukyus. In addition, the complex genetic structures of corals may be related to coral-specific destructive events, such as bleaching, outbreaks of crown-of-thorns starfish, and disease. Further studies will provide new insights and a more detailed view of the genetic structure of corals by using different markers (e.g., microsatellites) and approaches (assignment tests and clustering analysis), which will provide useful information for coral reef conservation.