Adaptive diversification of the Mstnb locus drives genomic architecture of growth in Thai clariid catfish

The production of clariid catfish in Thai aquaculture depends on culture of the native species (Clarias macrocephalus and C. batrachus) and introduced African catfish (C. gariepinus). Particularly, hybridization with C. gariepinus has improved productivity but raised significant conservation concerns. These lineages show distinct growth variations; however, the underlying genetic factors remain uncharacterized. We performed a comprehensive genomic assessment of the myostatin-b (Mstnb) gene in 535 individuals comprising 19 Thai populations. The study design involved a novel integration of high-throughput sequencing, structural modeling, and multi-locus analysis. We identified eight novel alleles defined by 19 variable sites within exon 1. The observed diversity challenges the paradigm of extreme sequence conservation that typically occurs in vertebrate Myostatin. Although Bayesian phylogenetics showed intermingled allelic lineages, an integrated “growth-gene pool” approach that combined Mstnb and GH1 polymorphisms resolved a robust species-level split (K = 2) and hierarchical sub-structuring (K = 6). Selection analyses identified significant adaptive diversification (ω = 1.857). Codon-level models highlighted Site 95 as a primary target of pervasive diversifying selection. Moreover, a nonsense mutation that resulted in a premature stop codon was identified as the mechanism underlying the functional modulation of growth traits. These findings provide a high-resolution molecular toolkit for marker-assisted selection and invasive species monitoring, which would enhance the sustainability of clariid aquaculture and protect native biodiversity against the risks of anthropogenic hybridization.