High similarity of genetic population structure in the false clown anemonefish (<Emphasis Type="Italic">Amphiprion ocellaris</Emphasis>) found in microsatellite and mitochondrial control region analysis

Many studies, using various marker systems, have been conducted on the genetic population structure of marine organisms to reveal connectivity among locations and dispersal capabilities. Although mitochondrial sequence markers are widely used, their accuracy is controversially discussed in the context of small scale population genetic discrimination. In the present study, the genetic population structure of the False Clown Anemonefish (Amphiprion ocellaris) in the Indo-Malay Archipelago was revealed by screening six microsatellite loci. Results were congruent to previous mitochondrial control region results, with three major genetic breaks within the Indo-Malay Archipelago. Similar to the mitochondrial DNA (mtDNA) analysis, microsatellite data showed a correlation of genetic structure to historical ocean basin separation during Pleistocene sea level low stands, geographic distance, and dominant current patterns. However, microsatellite divergences are not as deep as the mtDNA divergence, suggesting either that admixture of mtDNA lineages is slower than that of nuclear microsatellites, providing a rather historic picture of separation, or the stronger differentiation signal is due to lower effective population sizes presented by mtDNA. As well, the microsatellite analysis did not give a better resolution on the small scale as expected. This study showed that depending on the genetic markers used, different stages of population separation might be illuminated.