Phylogeographic structure of false clownfish, Amphiprion ocellaris, explained by sea level changes on the Sunda shelf

The phylogenetic structure of the anemonefish Amphiprion ocellaris was established based on sequence data generated for the 5' end of the cytochrome b (cytb) gene at 11 sites throughout Southeast Asia. Considerable genetic structuring was observed throughout the range of A. ocellaris. The region has a complex geography, with the Sunda shelf having been exposed during the lower sea levels associated with periods of glaciation. The direction of subsequent flooding of the Sunda shelf, as a direct consequence of the retreating glacial sheets, can be predicted based on the major river drainage systems in the region. Much of the phylogeographic structure, including levels of intra-site genetic variation, can be explained in terms of the seeding of sites on the Sunda shelf, by those on the shelf rim, as sea levels rose. We often found surface ocean currents in the region, which should influence larval dispersal, to be poorly correlated with phylogeographic structure. Several geographically close sites, which appear to be connected by surface currents, showed significant genetic stratification. We hypothesise that the phylogeographic structure of A. ocellaris is more reminiscent of the Pleistocene sea level changes than surface currents. The high contribution of sea level changes to the phylogeographic structure was also supported by several missing haplotypes in the generated spanning network. Cytb DNA sequences generated for recently recruited A. ocellaris individuals sampled from Singapore indicate that, on a local scale, there is a directional inflow of recruits, which is dependent on the monsoon seasons. The nature of dispersal and genetic structure of reef fish species found on the Sunda shelf is clearly complex, and should take into consideration past phylogeographic events.