Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

Matthew A. Campbell; Joy A. Becker

doi:10.1071/MF24227

RESEARCH ARTICLE (Open Access)

Previous Contents Vol 75(18)

Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

Matthew A. Campbell

^A ^* and Joy A. Becker ^A

+ Author Affiliations

- Author Affiliations

^A The University of Sydney, School of Life and Environmental Sciences, 380 Werombi Road, Brownlow Hill, NSW 2570, Australia.

^* Correspondence to: m.campbell@sydney.edu.au

Handling Editor: Peter Unmack

Marine and Freshwater Research 75, MF24227 https://doi.org/10.1071/MF24227

Submitted: 14 October 2024 Accepted: 5 November 2024 Published: 2 December 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

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 (F_st), 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.

Keywords: adaptive genetic variation, aquaculture, Asian sea bass, barramundi, conservation genetics, Latidae, phylogenetics, population genetics, recreational fisheries.

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