Conserving Nemo: Genomic insights into the history and status of the endangered anemonefish Amphiprion mccullochi and its sister species Amphiprion akindynos

Abstract Endemic species are often at greater risk of extinction and therefore should be a high priority for conservation. Lord Howe Island is a biodiversity hotspot with numerous endemic species, including the iconic McCulloch’s anemonefish, Amphiprion mccullochi . This study investigates the genetic relationship between A. mccullochi and its closely related sister species, Amphiprion akindynos , to clarify whether these species are genetically distinct; assess historical and contemporary gene flow; and evaluate genomic diversity and effective population sizes. We sampled across the range distribution of both species and used genome-wide Single Nucleotide Polymorphism (SNP) data. Clustering analyses showed a clear partition between A. mccullochi and A. akindynos with no evidence of recent gene flow, while demographic modelling indicated historical unidirectional gene flow from A. akindynos to A. mccullochi . Genetic diversity metrics revealed lower nucleotide diversity ( π ) and effective population size ( Ne ) in A. mccullochi , reflecting its restricted distribution and suggesting heightened extinction risk. Our findings provide genomic context and baseline information for the conservation management of A. mccullochi . Given the current trend of declining A. mccullochi populations, our findings suggest that conservation efforts should emphasize preserving population sizes and genetic diversity and ultimately preventing extinction of this endemic reef fish.