Data from: Adaptation via pleiotropy and linkage: association mapping reveals a complex genetic architecture within the stickleback Eda locus

Genomic mapping of the loci associated with phenotypic evolution has
revealed genomic “hotspots”, or regions of the genome that control
multiple phenotypic traits. This clustering of loci has important
implications for the speed and maintenance of adaptation and could be due
to pleiotropic effects of a single mutation or tight genetic linkage of
multiple causative mutations affecting different traits. The threespine
stickleback (Gasterosteus aculeatus) is a powerful model for the study of
adaptive evolution because the marine ecotype has repeatedly adapted to
freshwater environments across the northern hemisphere in the last 12,000
years. Freshwater ecotypes have repeatedly fixed a 16 kilobase haplotype
on chromosome IV that contains Ectodysplasin (Eda), a gene known to affect
multiple traits, including defensive armor plates, lateral line sensory
hair cells, and schooling behavior. Many additional traits have previously
been mapped to a larger region of chromosome IV that encompasses the Eda
freshwater haplotype. To identify which of these traits specifically map
to this adaptive haplotype, we made crosses of rare marine fish
heterozygous for the freshwater haplotype in an otherwise marine genetic
background. Further, we performed fine-scale association mapping in a
fully interbreeding, polymorphic population of freshwater stickleback to
disentangle the effects of pleiotropy and linkage on the phenotypes
affected by this haplotype. Although we find evidence that linked
mutations have small effects on a few phenotypes, a small 1.4 kb region
within the first intron of Eda has large effects on three phenotypic
traits: lateral plate count, and both the number and patterning of the
posterior lateral line neuromasts. Thus, the Eda haplotype is a hotspot of
adaptation in stickleback due to both a small, pleiotropic region
affecting multiple traits as well as multiple linked mutations affecting
additional traits.