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...

性选择的“优质基因”假说（"good genes" hypotheses）预测，雌性会偏好具有醒目装饰特征的雄性，因为这类雄性健康且活力充沛，能够承担装饰结构所需的代谢成本。该假说的核心假设为：雄性的健康状况与活力可有效反映其遗传质量，进而影响后代的生存与生长表现。我们以野生捕获的湖红点鲑（Salvelinus umbla）为研究对象验证了这一预测，已知该物种的繁殖体色可体现雄性的健康状态。我们首先重新分析了精子竞争试验的结果——该试验中，已知亲本信息的胚胎被单独饲养于应激或非应激环境中。结果显示，父本体色与后代的各项表现指标均无相关性。但亲本间的亲缘系数越高，后代的生长速度越慢。为验证这一初步发现的稳健性，我们采集了新的野生雌雄个体样本，通过全因子体外繁殖实验利用其配子开展繁育，并单独饲养了约……详细实验方法参见Garaud等人发表于《Heredity》2024年的论文"亲本亲缘系数而非父本体色可预测湖红点鲑的早期后代生长"。

本研究共对33尾湖红点鲑（Salvelinus umbla）进行了ddRAD测序（ddRADsequencing），测序在Illumina HiSeq 2500的一个测序通道上完成。数据集包含33个经STACKS 2.53处理生成的压缩.fastq文件，以及包含亲缘系数和近交系数估算值的最终数据集。我们还提供了实验中使用的bash与R脚本。

仅需按照提供的脚本流程操作，即可从.fastq文件出发复现全部实验结果。基因组数据的处理基于bash环境完成，亲缘系数与近交系数的估算则通过R包Hierfstat实现。

# 数据来源：湖红点鲑全因子繁殖实验（日内瓦湖，2018/2019年冬季）
[https://doi.org/10.5061/dryad.j0zpc86hj](https://doi.org/10.5061/dryad.j0zpc86hj)

## 数据与文件结构说明
本研究共对33尾湖红点鲑（Salvelinus umbla）进行了ddRAD测序（ddRADsequencing），测序在Illumina HiSeq 2500的一个测序通道上完成。数据集包含33个经STACKS 2.53处理生成的压缩.fastq文件，以及包含亲缘系数和近交系数估算值的最终数据集。我们还提供了实验中使用的bash与R脚本。
仅需按照提供的脚本流程操作，即可从.fastq文件出发复现全部实验结果。基因组数据的处理基于bash环境完成，亲缘系数与近交系数的估算则通过R包Hierfstat实现。

变量 说明
Select 1 = 纳入统计分析；0 = 排除，排除原因为父本无法完成基因分型，或其近交系数与总体均值的偏差超过3个标准差
ID_24_well_plate "受精卵的ID（首段数字为……"