The genomic complexity of invasion: cryptic lineages, founder effects, and polygenic sex determination in armored catfish

Genetic biocontrol approaches offer promising tools for managing invasive species. However, their success depends on species identity, demographic history, and the genomic architecture of sex determination, which remain poorly resolved for many non-model taxa. We integrated high-quality genome assembly, whole-genome resequencing, and population genomics to evaluate biocontrol feasibility in invasive suckermouth armored catfish (Loricariidae) in Texas. Mitochondrial phylogenies and genome-wide SNPs revealed cryptic diversity, with distinct lineages from at least two genera ( Hypostomus and Pterygoplichthys ) exhibiting strong drainage-level genetic differentiation. Effective population size estimates were exceptionally low, consistent with founder effects and moderate inbreeding. Genome-wide association analyses detected no large-effect loci for sex in either genus, despite high statistical power in Hypostomus , suggesting that sex determination is polygenic and/or environmentally influenced. These results identify key biological constraints for sex-ratio-based biocontrol and underscore the importance of genomic assessments prior to management interventions. More broadly, our study highlights how integrating genomic resources, demographic inference, and evolutionary context can guide invasive species control strategies.