DOI: 10.5061/dryad.05qfttf0j
title: Data from: Adaptation via pleiotropy and linkage: association mapping reveals a complex genetic architecture within the stickleback Eda locus

description: 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.
description: Description of datasets: This work includes association mapping
 of multiple phenotypes to genetic markers within the Eda locus for three
 different sets of stickleback collections: (1) lab crosses of Puget Sound
 marine stickleback heterozygous for the freshwater Eda haplotype; (2) lab
 crosses of Puget Sound marine stickleback heterozygous for the
 freshwater NAKA SNP; and (3) wild-caught stickleback from the polymorphic,
 freshwater Lake Washington population.  Please see the
 associated manuscript for sample processing, phenotypic trait measurements
 and genotyping details. Genotypes: Genotypes for the
 Lake Washington wild-caught fish are presented in three versions: raw,
 trimmed, and filled. Raw genotypes are the collected genotypes and
 therefore contain missing information as not all fish were successfully
 genotyped at every marker. The trimmed and filled genotype files have been
 processed to remove missing data in two different ways as described in the
 manuscript. The results in the manuscript are based on the trimmed Lake
 Washington genotype file, but the filled genotype file gives qualitatively
 similar results. There were relatively few missing genotypes for the NAKA
 and Puget Sound datasets, so the raw genotypes are uploaded and used in
 the analysis. Trait values & outliers: The
 trait values are uploaded in the unedited form as well as the trimmed
 form, where outliers have been removed. Outliers were considered values
 &gt; 4 SD from the mean of the sample. Please see the manuscript for
 descriptions of additional removed outliers such as rare wild-caught fish
 that were outside the age class of the fish caught in the fall. The
 trimmed dataset is used in the uploaded analysis script.
description: Follow the instructions in the
 "calculating.LODs.and.p-vals.R" script to run the analyses of
 the three mapping datasets.