Adaptation via pleiotropy and linkage: Association mapping reveals a complex genetic architecture within the sticklebackEdalocus

Abstract

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.

Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus)

“…About half of the F0 fish used in our crosses carried the marine allele at this gene, meaning that the effects of genotypes at Gjb1 and Eda were unlinked in our experiment (Archambeault et al. 2020). Consistent with a locus other than Eda conferring a growth advantage, selection on Eda in a freshwater pond experiment (Barrett et al.…”

“…Wild marine stickleback were collected in Puget Sound, WA, USA in the summers of 2015 and 2016 as previously described (Archambeault et al. 2020). In 2015, fish were collected at the surface during a multiday trawling survey conducted in water that was at least 30 m deep in the Whidbey Basin and Bellingham Bay areas.…”

“…Wild‐caught and F1 fish were housed in freshwater conditions (3.5 parts per thousand [ppt] saltwater), as previously described (Archambeault et al. 2020). F2 crosses were made as described above (see F2 EXPERIMENTAL CROSS SETUP) and housed in either full (35 ppt) saltwater or reduced (3.5 ppt) saltwater conditions (referred to as saltwater and freshwater, respectively, from here on).…”

“…2007) as previously described (Archambeault et al. 2020). Wild‐caught fish were genotyped at markers listed in Table S2.…”

“…2019; Archambeault et al. 2020). Lateral plate number is the most intensively studied of these phenotypes and is one of many bony armor traits that are reduced or lost in freshwater (Bell and Foster 1994).…”