DOI: 10.5061/dryad.08hc4
title: Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies

description: A novel application of genome-wide association analyses is to use
 trait-associated loci to monitor the effects of conservation strategies on
 potentially adaptive genetic variation. Comparisons of fitness between
 captive- and wild-origin individuals, for example, do not reveal how
 captive rearing affects genetic variation underlying fitness traits or
 which traits are most susceptible to domestication selection. Here, we
 used data collected across four generations to identify loci associated
 with six traits in adult Chinook salmon (Oncorhynchus tshawytscha), and
 then determined how two alternative management approaches for captive
 rearing affected variation at these loci. Loci associated with date of
 return to freshwater spawning grounds (return timing), length and weight
 at return, age at maturity, spawn timing, and daily growth coefficient
 were identified using 9108 restriction site-associated markers and Random
 Forest, an approach suitable for polygenic traits. Mapping of
 trait-associated loci, gene annotations, and integration of results across
 multiple studies revealed candidate regions involved in several
 fitness-related traits. Genotypes at trait-associated loci were then
 compared between two hatchery populations that were derived from the same
 source but are now managed as separate lines, one integrated with and one
 segregated from the wild population. While no broad scale change was
 detected across four generations, there were numerous regions where
 trait-associated loci overlapped with signatures of adaptive divergence
 previously identified in the two lines. Many regions, primarily with loci
 linked to return and spawn timing, were either unique to, or more
 divergent in, the segregated line, suggesting that these traits may be
 responding to domestication selection. This study is one of the first to
 utilize genomic approaches to demonstrate the effectiveness of a
 conservation strategy, managed gene flow, on trait-associated – and
 potentially adaptive – loci. The results will promote the development of
 trait-specific tools to better monitor genetic change in captive and wild
 populations.
description: Input files for Random
 Forest analysesThis file contains the
 original phenotypes and imputed genotypes for individuals prior to Random
 Forest analyses, along with the corrected phenotypes and genotypes that
 were analyzed by Random Forest for each of the six fitness
 traits.Random_forest_traits_input_files.xlsxCode to correct phenotypes and genotypes for confounding factorsThis is the R script that was used to correct the phenotypes and imputed genotypes for possible confounding factors prior to conducting Random Forest analysesCode_correct_for_covariates_before_RF.RR script for Random Forest analyses of six fitness traitsR code for conducting Random Forest analyses on the six fitness traitsPhenotype comparisons for 2010R code to quantify phenotypic differences between fish from the integrated and segregated hatchery lines in 2010Phenotype_comparisons_2010.R