Full-factorial breeding experiment with lake char (Lake Geneva, winter 2017/2018)

We sampled 16 wild lake char (Salvelinus umbla) and used their gametes to
investigate the genetic consequences of different mating scenarios. A
full-factorial breeding was used to separate additive genetic from
maternal environmental effects, and embryos were raised singly after
sublethal exposures to a pathogen, a common pollutant, or water only. In
all treatment groups, embryo development was strongly reduced with
increased genetic relatedness between the parents. Contrary to predictions
of ‘good genes’ sexual selection, pathogen tolerance of offspring declined
with increasing coloration of their fathers. Determination of inbreeding
and kinship coefficients: All 10 males and 4 of the 6 females were used in
a parallel study that included sperm competition experiments (Nusbaumer et
a. 2021). These 14 parents had been prepared in one library for ddRAD
sequencing on 2 lanes on an Illumina HIseq 2500 (see de Guttry et al. 2022
for the corresponding 14 gzipped .fastq of these individuals). The
remaining 2 females were later genotyped in a different library but again
on an Illumina HIseq 2500. After demultiplexing, the 16 individuals were
processed together using stacks 2.53, and with the resulting filtered VCF
file estimations of kinship and inbreeding have been done. For each
individual, the fastq files of the 2 sequencings lanes (2018/2019), or of
the replicates within the same library (2021), were merged after
demultiplexing using process_radtags (Stacks 2.53). The
bash and R scripts are provided. There are no legal or ethical
considerations regarding the above-mentioned data.