Cryptic Ancestral Lineages and Hatchery Bottlenecks Shape the Genetic Landscape of Introduced Largemouth Bass in China

Biological invasions and global translocations of economically important species provide unintentional evolutionary experiments shaped by founder events, admixture, and rapid adaptation. The largemouth bass (Micropterus nigricans; historically referred to as M. salmoides in aquaculture) is a prominent example and now a cornerstone of China's freshwater aquaculture, where germplasm degradation and widespread broodstock exchange raise concerns for breeding efficiency and feral establishment. We analysed 140 genomes spanning six cultivated strains by combining 110 public genomes with 30 newly sequenced individuals from under-represented populations. To reduce sensitivities of standard reference-based SNP callsets to ascertainment/reference bias and filtering-dependent shifts in inference, we applied a phylogenomics-guided framework based on 746 orthologous groups (OGs) and complemented it with allele-frequency summaries. We detected a hierarchical structure separating a phylogenetically basal group (Anhui-WL, Panzhihua-PL, Zhejiang-ZL) from derived populations that split into a highly admixed, selectively bred cluster (Jiadefeng-JDF, Youlu-YL) and a distinct regional population (Taiwan-TWL). Demographic reconstruction indicates that introduced germplasm comprised at least three cryptic ancestral lineages with deeply divergent histories, followed by layered admixture. Contrasting long-term versus contemporary effective population size estimates reveals a sharp recent decline in effective breeders across all strains, consistent with hatchery-driven bottlenecks. Dual selection scans highlight candidate loci consistent with long-term balancing selection (environmental sensing and physiological regulation) and recent artificial selection in the JDF breeding line (including olfaction and neuronal excitability). Together, these results define management units, motivate preservation of cryptic ancestral diversity, and inform broodstock redesign to reduce bottlenecks, supporting sustainable aquaculture and risk assessment of feral establishment.