Dynamic genomes uncover opposite sex determination in the invasive quagga and zebra mussels

Sex determination (SD) in zebra and quagga mussels, two globally invasive freshwater bivalves responsible for major ecological and economic impacts, has remained unexplored. Using chromosome-scale genomes and whole-genome resequencing of 80 individuals, we uncover strikingly different SD architectures: zebra mussels exhibit a polygenic ZZ ZW system, with FoxL2 among the prominent female-associated candidates. In contrast, quagga mussels carry a highly localized ∼800 kb XX XY SD region containing FoxL2-Y, a novel candidate male-determining locus that arose through duplication and divergence of FoxL2. K-mer analyses and staged embryonic transcriptomes reveal rare but specific FoxL2-Y expression consistent with an early regulatory role in male determination. The quagga mussel SD region is also enriched for C-lectins, a gene family implicated in gamete-interaction processes, supporting a model in which haploid selection facilitated SD turnover. These findings reveal unexpected SD divergence between closely related species and illuminate mechanisms enabling rapid evolution of reproductive systems in invasive taxa.