Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

Abstract

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.