Code from: Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation

Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in the vgll3, but with early maturation in the six6 locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in the six6 locus, and by both parents’ genoty..., , , Data and codes to reproduce the results in the MS titled

Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation

https://doi.org/10.5061/dryad.866t1g1xk

Data files:

FRY_data_dryad: Data frame (in R object form) that contains information on survived individuals including six6 and vgll3 genotypes, stream ID, stream type (high vs low nutrient),

FAMS_dryad: Data frame (in R object form) that contains information on the family ID, family level MMR/SMR data and maternal egg mass, as well as parental six6 and vgll3 genotypes.

parent_LW_dryad: Data frame (in R object form) that contains parental length and weight information.

concord_dryad: Data frame (in R object form) that contains information on the parental six6 and vgll3 genotypes, expected and observed number six6 and vgll3 genotypes in the offspring cohort,

genoSIM_list: An R list that contains 1000 dataset with simulated genotyped of missing (dead or emigrated) individu...