Genetic Dissection of a Supergene Implicates in Craniofacial Evolution of Threespine Sticklebacks.

In nature, multiple adaptive phenotypes often coevolve and can be controlled by tightly linked genetic loci known as supergenes. Dissecting the genetic basis of these linked phenotypes is a major challenge in evolutionary genetics. Multiple freshwater populations of threespine stickleback fish () have convergently evolved two constructive craniofacial traits, longer branchial bones and increased pharyngeal tooth number, likely as adaptations to dietary differences between marine and freshwater environments. Prior QTL mapping showed that both traits are partially controlled by overlapping genomic regions on chromosome 21 and that a regulatory change in likely underlies the tooth number QTL. Here, we mapped the branchial bone length QTL to a 155 kb, eight-gene interval tightly linked to, but excluding the coding regions of and containing the candidate gene Further recombinant mapping revealed this bone length QTL is separable into at least two loci. During embryonic and larval development, was expressed in the branchial bone primordia, where allele specific expression assays revealed the freshwater allele of was expressed at lower levels relative to the marine allele in hybrid fish. Induced loss-of-function mutations in revealed an essential role in stickleback craniofacial development and show that bone length is sensitive to dosage in heterozygotes. Combined, these results suggest that closely linked but genetically separable changes in and contribute to a supergene underlying evolved skeletal gain in multiple freshwater stickleback populations.