Abstract

   Yellow seabream (Acanthopagrus latus), a species of significant
   economic importance, predominantly inhabits the warm waters of the
   Indo-Western Pacific. While previous studies have explored the genetic
   diversity of A. latus using microsatellites and other nuclear markers,
   a comprehensive understanding of its genetic characteristics and
   adaptive evolution using whole-genome resequencing (WGR) remains
   limited. In this study, we collected 60 individuals from six distinct
   geographic locations and performed WGR, achieving an average sequencing
   depth of 12.59×, which resulted in the identification of 19,488,059
   high-quality single-nucleotide polymorphisms (SNPs). The nucleotide
   polymorphism (π[θ]) across all populations was consistent, ranging from
   0.003042 to 0.003155, indicating low genetic differentiation among
   populations. Comparative analyses revealed that populations other than
   that in Xiamen (XM) have undergone adaptive evolution, potentially
   linked to traits such as growth and development, feeding, immunity, and
   movement. This study explores the population genetics and adaptive
   evolutionary patterns of Acanthopagrus latus at the genomic level,
   providing an essential foundation for the conservation and management
   of this economically important species in the future.

1. Introduction

   Yellow seabream (Acanthopagrus latus), which belongs to Actinopterygii,
   Perciformes, Sparidae, is primarily distributed in the warm waters of
   the Indo-Western Pacific. This species inhabits shallow coastal waters
   and estuaries and does not typically engage in long-distance migration
   [[42]1]. Despite its economic importance, natural populations of A.
   latus have declined due to intense fishing. As a result, it has become
   a significant aquaculture species, with stock enhancement efforts
   underway in order to restore its natural population [[43]2]. In recent
   years, there has been increasing interest in the genetic background of
   this species and in the conservation and utilization of resources
   [[44]3,[45]4,[46]5,[47]6].

   With the discovery of genomes for an increasing number of species,
   whole-genome resequencing technology has developed rapidly [[48]7]. By
   using the known genome sequences as references, we can obtain variation