Miller_et_al_RepeatABLE_GWAS_Script

R script for conducting GWAS analyses with the RepeatABLE packag

Miller_et_al_Base_Circ_Typed_IDs_Only_No_Dupes

Phenotype file with only 1 measure per individual for setting "base model" in RepeatABE

Miller_et_al_Animals_with_phenos_transposed

PLINK tfam file for individuals used in GWAS analyse

Miller_et_al_Mass_Typed_IDs_Only

Repeated measures of body mass for sheep used in GWAS analyse

Miller et al VCF SNP genotypes

Miller et al VCF SNP genotype

Miller et al BAM File

Sequence alignments (one .bam file per individual) of Illumnia reads to the domestic sheep genome

Miller_et_al_Base_Circ_Typed_IDs_Only

Repeated measures of horn base circumference for sheep used in GWAS analyse

NBR genotyoes

Microsatellite genotype data for bighorn sheep (Ovis canadensis) from National Bison Range in Montana, USA. Columns A-C contain locus names, linkage group (lg), and position on the linkage group respectively. Subsequent columns are individual genotypes. For individual genotypes row 1 indicates if the individual is an NBR founder (ParentPop1), a transplanted individual (ParentPop2), or a hybrid progeny (Hybrid); row 2 is the individual ID corresponding to the modeling table. Missing data is coded as NA/NA

NBR modeling_table

Data used for analyses of geographic ancestry and individual fitness. Column headings for columns A-G are as follows: ID = individual ID (corresponding to that in genotype data, Gender = sex of the sheep, h.index = hybrid index value as calculated from INTROGRESS analyses, Year_Birth = year of birth or introduction, Longevity = longevity as of 2010, Progeny = number of progeny that individual contributed to the pedigree, Introduced = binary indicator if that sheep was introduced to the population or not. Subsequent columns are genotypes at each locus coded as a factor with three levels (0, 1, or 2) corresponding to the number of alleles predicted to be derived from founders during the INTROGRESS analysis. Missing data is coded as NA

NBR_Data

Microsatellite genotypes for the National Bison Range population