Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

Context Lates calcarifer is a widespread Indo-Pacific fish that is important in aquaculture, recreational and commercial fisheries. Genetic divergences from different data sources and sampling schemes have been reported. Aims To conduct phylogenetic and population genetic analyses from a geographically and phylogenetically representative data set to identify hierarchical divisions within L. calcarifer. We further test the evolutionary significance of genetic units in terms of signatures of adaptation. Methods Using a whole-genome sequence data set of 61 fish, including an outgroup, we conducted phylogenetic and population genetic analyses. We also generated measures of fixation index (Fst), nucleotide diversity (π) and Tajima’s D (D). Key results We identified three main lineages of L. calcarifer, corresponding to the Indian subcontinent, South-east Asia and Australasia. Subdivision within each of the three main lineages was also identified and characterised. Adaptively significant differences are indicated within and among the three main lineages. Conclusions L. calcarifer exhibits genetic divergences at different levels that originate before and during the Pleistocene. These divergences are associated with adaptive divergence but unclear phenotypic changes. Implications This study has highlighted the need for comprehensive sampling and integrative study of genotypes and phenotypes across the range of L. calcarifer.