Full-factorial breeding experiment with lake char (lake Geneva, winter 2018/2019)

The ‘good genes’ hypotheses of sexual selection predict that females prefer males with strong ornaments because they are in good health and vigor and can afford the costs of the ornaments. A key assumption of this concept is that male health and vigor are useful predictors of genetic quality and hence offspring performance. We tested this prediction in wild-caught lake char (Salvelinus umbla) whose breeding coloration is known to reveal aspects of male health. We first reanalyzed results from sperm competition trials in which embryos of known parenthood had been raised singly in either a stress- or non-stress environment. Paternal coloration did not correlate with any measures of offspring performance. However, offspring growth was reduced with higher kinship coefficients between the parents. To test the robustness of these first observations, we collected a new sample of wild males and females, used their gametes in a full-factorial in vitro breeding experiment, and singly raised about..., See methods in Garaud et al. (Heredity 2024) \"Parental kinship coefficient but not paternal coloration predicts early offspring growth in lake char\"., A total of 33 lake char (Salvelinus umbla) were genotyped using ddRADsequencing on one lane of Illumina HIseq 2500. The data includes 33 gzipped .fastq files generated using STACKS 2.53  and the final datasets with the estimates of kinship and inbreeding. We provide the bash and R scripts that we used.
Starting from the .fastq files it is possible to reproduce the result by following the provided scripts. Genomic data processing was done on bash. Kinship and inbreeding coefficients were estimated using the R package Hierfstat., # Data from: Full-factorial breeding experiment with lake char (lake Geneva, winter 2018/2019)

[https://doi.org/10.5061/dryad.j0zpc86hj](https://doi.org/10.5061/dryad.j0zpc86hj)

## Description of the data and file structure

A total of 33 lake char (Salvelinus umbla) were genotyped using ddRADsequencing on one lane of Illumina HIseq 2500. The data includes 33 gzipped .fastq files generated using STACKS 2.53  and the final datasets with the estimates of kinship and inbreeding. We provide the bash and R scripts that we used.

Starting from the .fastq files it is possible to reproduce the result by following the provided scripts. Genomic data processing was done on bash. Kinship and inbreeding coefficients were estimated using the R package Hierfstat.

Variable Explanation

Select 1 = include in statistics ; 0 = exclude because the sire could not be genotyped or its inbreeding coefficient is > 3 SD from the overall mean

ID_24_well_plate \"ID of the fertilized egg (first number = numbe...