Stress-induced reductions in the world’s coral populations are, in many locations, giving way to an increase in macroalgae, for example the common brown macroalgal genus Lobophora. While many ecological studies report a single species (Lobophora variegata), DNA-based identification methods have recently shown that Lobophora is a highly diverse genus with over 100 reported species. Here, we aim to identify possible ecological differences among Lobophora species by investigating environmental drivers of Lobophora assemblages. We sampled Lobophora thalli from 12 reefs around Palau (Micronesia) at varying depths, wave exposure, and herbivore biomass. Using one mitochondrial marker (cox3) and two chloroplast markers (psbA, rbcL), we uncovered a striking cryptic diversity of 15 species, including 8 undescribed taxa. Associations between potential drivers and Lobophora assemblages varied at two spatial scales. At the larger scale of both island coastlines only a single variable—wave exposure—was found to be important. On a smaller geographic scale, confined to the east coast, all factors—wave exposure, depth and herbivory—were associated with assemblages of Lobophora. Widespread sampling indicates the presence of generalist species, which were found in most sampled habitats, and specialists, which occupy specific habitats. Such high levels of cryptic diversity have important implications for ecological studies. Given that species inhabit different environments, have a variable growth form, and have a threefold difference in thallus thickness, it seems likely that species differ in their function. If these differences manifest in competitive strengths, these results have broad implications for our understanding of coral reef recovery following perturbation.
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