Cryptic Ancestral Diversity and Recent Bottlenecks Shape the Genetic Landscape of Farmed Largemouth Black Bass in China

Largemouth black bass (<i>Micropterus salmoides</i>) is a cornerstone of China's freshwater aquaculture, but its sustainable development is threatened by germplasm degradation and widespread admixture. To provide a genomic foundation for effective management, we employed an integrated phylogenomic approach using 746 orthologous groups (OGs) reconstructed from whole-genome sequencing data of 140 individuals across six major cultivated populations, including newly generated genomic data from 30 individuals. Our analyses revealed a fundamental genetic structure that differentiates a phylogenetically basal group (Anhui-WL, Panzhihua-PL, Zhejiang-ZL) from a complex of more derived populations, which is itself substructured into a highly admixed, selectively-bred cluster (Jiadefeng-JDF, Youlu-YL) and a distinct regional population (Taiwan-TWL). Demographic reconstruction uncovered a key finding: the introduced stock was not genetically homogeneous but instead comprised at least three cryptic ancestral lineages with deeply divergent ancient histories. Furthermore, a comparison of long-term and contemporary effective population size estimates revealed a sharp, recent decline in the number of effective breeders across all populations, highlighting the impacts of hatchery practices. Our dual selection scans identified distinct evolutionary patterns: seven candidate genes under long-term balancing selection, enriched in functions related to environmental sensing and physiological regulation, and several genes under recent positive selection in the JDF-bred line, including those involved in olfaction and neuronal excitability. This study unravels the complex genetic background of China's farmed Largemouth black bass, providing an essential genomic toolkit for defining management units, preserving cryptic ancestral diversity, and designing informed breeding strategies to ensure the long-term sustainability of this vital aquaculture industry.