Endemic species on islands are considered at risk of extinction for several reasons, including limited dispersal abilities, small population sizes, and low genetic diversity. We used mitochondrial DNA (D-Loop) and 17 microsatellite loci to explore the evolutionary relationship between an endemic anemonefish, Amphiprion mccullochi (restricted to isolated locations in subtropical eastern Australia) and its more widespread sister species, A. akindynos. A mitochondrial DNA (mtDNA) phylogram showed reciprocal monophyly was lacking for the two species, with two supported groups, each containing representatives of both species, but no shared haplotypes and up to 12 species, but not location-specific management units (MUs). Population genetic analyses suggested evolutionary connectivity among samples of each species (mtDNA), while ecological connectivity was only evident among populations of the endemic, A. mccullochi. This suggests higher dispersal between endemic anemonefish populations at both evolutionary and ecological timeframes, despite separation by hundreds of kilometers. The complex mtDNA structure results from historical hybridization and introgression in the evolutionary past of these species, validated by msat analyses (NEWHYBRIDS, STRUCTURE, and DAPC). Both species had high genetic diversities (mtDNA h > 0.90, π = 4.0%; msat genetic diversity, gd > 0.670). While high gd and connectivity reduce extinction risk, identifying and protecting populations implicated in generating reticulate structure among these species should be a conservation priority.

Marine protected areas (MPAs) are increasingly being advocated and implemented to protect biodiversity on coral reefs. Networks of appropriately sized and spaced reserves can capture a high proportion of species diversity, with gene flow among reserves presumed to promote long term resilience of populations to spatially variable threats. However, numerically rare small range species distributed among isolated locations appear to be at particular risk of extinction and the likely benefits of MPA networks are uncertain. Here we use mitochondrial and microsatellite data to infer evolutionary and contemporary gene flow among isolated locations as well as levels of self-replenishment within locations of the endemic anemonefish Amphiprion mccullochi, restricted to three MPA offshore reefs in subtropical East Australia. We infer high levels of gene flow and genetic diversity among locations over evolutionary time, but limited contemporary gene flow amongst locations and high levels of self-replenishment (68 to 84%) within locations over contemporary time. While long distance dispersal explained the species’ integrity in the past, high levels of self-replenishment suggest locations are predominantly maintained by local replenishment. Should local extinction occur, contemporary rescue effects through large scale connectivity are unlikely. For isolated islands with large numbers of endemic species, and high local replenishment, there is a high premium on local species-specific management actions.

Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long-term persistence of these species following local extinction. This study explored population connectivity in the ecologically-specialized endemic three-striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self-replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self-replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self-replenishment (95%), and low contemporary abundance.