Sympatric species of coral trout (Plectropomus) show contrasting patterns of genomic structure across isolated atoll reefs

Understanding patterns of connectivity across remote atoll reefs is important for managing fishery target species, as they often have small population sizes and limited options for replenishment in the event of localised decline. In this study, we used a comprehensive hierarchical sampling design combined with reduced representation genotyping to compare the population genomics of two sympatric species of coral trout ( Plectropomus ) within and between three isolated offshore atoll reef systems in north-western Australia. The blue spot coral trout, Plectropomus laevis (8979 single nucleotide polymorphisms—SNPs, 223 individuals, 25 sites) and the passionfruit coral trout, P. areolatus (3702 SNPs, 452 individuals, 20 sites) showed high levels of connectivity within reef systems and restricted connectivity between reef systems, indicating that biological stocks primarily occur at the scale of each reef system. Despite being closely related and co-managed species, inter-specific variation in the magnitude of genetic structure was notable. Plectropomus areolatus at the southern-most reef system display modest genetic structure with populations ~ 450 km to the north, whilst P. laevis at the same location show a level of genetic divergence that reflects deep historical isolation. Our results provide the most comprehensive assessment of genetic connectivity across these remote atoll reefs, facilitating management advice that reflect empirically determined population dynamics for these species. We identify contrasting patterns of genetic connectivity among closely related sympatric species, and highlight the role of extrinsic (e.g., geography/environment) and intrinsic (e.g., life history) factors in shaping population dynamics.