10.5061/DRYAD.08HC4
Waters, Charles D.
University of Washington
Hard, Jeffrey J.
Northwest Fisheries Science Center
Brieuc, Marine S.O.
University of Washington
Fast, David E.
University of Washington
Warheit, Kenneth I.
Washington Department of Fish and Wildlife
Knudsen, Curtis M.
Oncorh Consulting; Olympia WA USA
Bosch, William J.
Yakama Nation Fisheries; Toppenish WA USA
Naish, Kerry A.
University of Washington
Brieuc, Marine S. O.
University of Washington
University of Oslo
Data from: Genomewide association analyses of fitness traits in
captive-reared Chinook salmon: applications in evaluating conservation
strategies
Dryad
dataset
2018
Captive Populations
Genomics/Proteomics
Oncorhynchus tshawytscha
2018-01-12T16:22:16Z
2018-01-12T16:22:16Z
en
https://doi.org/10.1111/eva.12599
297471760 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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