Dorsal spine reduction in acidic-adapted threespine stickleback

The repeated evolution of reduced skeletal armor in threespine stickleback provides a powerful model for understanding the genetic basis of morphological change. We investigated the genetic and developmental mechanisms underlying the loss of the second dorsal spine in a freshwater stickleback population from North Uist, Scotland. Crosses between spineless freshwater and fully spined marine individuals confirmed a genetic basis for the trait, with inheritance patterns inconsistent with simple Mendelian expectations. A bulk segregant analysis of F3 hybrids revealed a strong genomic signal on chromosome VI, overlapping the hoxdb cluster. Developmental staining and bulk RNA sequencing showed delayed and incomplete cartilage formation and altered gene expression during critical stages of dorsal development in spineless fish, notably of the hoxdb genes. Our findings indicate that while the loss of dorsal spines has evolved repeatedly, it may involve distinct genetic mechanisms across populations, with chromosome VI playing a central role in this case.