DOI: 10.5061/dryad.j0zpc86hj
title: Data from: Full-factorial breeding experiment with lake char (lake Geneva, winter 2018/2019)

description: 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
 3,000 embryos in either a stress- or non-stress environment (stress
 induced by microbes). Again, paternal coloration did not predict offspring
 performance, while offspring growth was reduced with higher kinship
 between the parents. We conclude that, in lake char, the genetic benefits
 of mate choice would be strongest if females could recognize and avoid
 genetically related males, while male breeding colors may be more relevant
 in intra-sexual selection.
description: See methods in Garaud et al.
 (Heredity 2024) "Parental kinship coefficient but not paternal
 coloration predicts early offspring growth in lake
 char".
description: 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.
description: # 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 &gt; 3 SD from the overall mean ID_24_well_plate "ID of the fertilized egg (first number = number of 24-well plate, letter and 2nd number = position within the plate)" Dam ID of the dam Length_dam Length of the dam in cm F_dam Inbreeding coefficient of the dam Sire ID of the sire Length_sire Length of the sire in cm Yellow_sire Intensity of the yellow coloration of the sire F_sire "Inbreeding coefficient of the sire; ""n/a"" = inbreeding coefficient was not determined" Sibgroup ID of the sibgroup Kinship "Kinship coefficient between parents; ""n/a"" = kinship coefficient was not determined" fertilized 1 = embryo visible at 35 dpf (days past fertilization); 0 = no embryo visible at 35 dpf Treatment """aero"" = exposed to Aeromononas salmonicida; ""water"" = sham exposed" DeadAtDayOfHatching "1 = dead before hatching or at day of hatching; 0 = alive hatching at day of hatching; ""n/a"" = no embryo" Hatching_dpf "Day of hatching in dpf (days past fertilization); ""n/a"" = no embryo" Length_d0 "Measured length of larva (in mm) at day of hatching; ""n/a"" = length was not determined" YSVolume_d0 "Measured yolk sac volume of larva (in mm^3) at day of hatching; ""n/a"" = volume was not determined" Length_d14 "Measured length of larva (in mm) 14 days after hatching; ""n/a"" = length was not determined" Length_d28 "Measured length of larva (in mm) 28 days after hatching; ""n/a"" = length was not determined" Length_d42 "Measured length of larva (in mm) 42 days after hatching; ""n/a"" = length was not determined" YSVolume_d42 "Measured yolk sac volume of larva (in mm^3) 42 days after hatching; ""n/a"" = volume was not determined" Length_130dpf "Reconstructed length of larva (in mm) 130 days after fertilization; ""n/a"" = length was not determined" YSVolume_130dpf "Reconstructed yolk sac volume of larva (in mm^3) 130 days after fertilization; ""n/a"" = volume was not determined"