Inbreeding and kinship coefficients of parents of sperm competition experiment with lake char (Lake Geneva 2017/18)
Cite this dataset
de Guttry, Christian et al. (2022). Inbreeding and kinship coefficients of parents of sperm competition experiment with lake char (Lake Geneva 2017/18) [Dataset]. Dryad. https://doi.org/10.5061/dryad.rn8pk0pct
Abstract
A total of 14 lake char (Salvelinus umbla) were genotyped in the same library using ddRADsequencing. The data includes 14 gzipped .fastq files generated using 2 lanes of sequencing on an Illumina HIseq 2500 and the final dataset with the final estimates of kinship and inbreeding. For each individual, the fastq files of the 2 sequencings lanes were merged after demultiplexing using process_radtags (Stacks 1.48). We provide the bash and R scripts that we used. There are no legal or ethical considerations regarding the above-mentioned data.
Methods
See Nusbaumer et al., 2021
Nusbaumer D., Garaud L., de Guttry C., Ançay L., Wedekind C. 2021 Sperm of more colorful males are better adapted to ovarian fluids in lake char (Salmonidae). bioRxiv. (doi: https://doi.org/10.1101/2021.10.02.462848).
Usage notes
Starting from the .fastq files it is possible to reproduce the result by following the provided scripts. Genomic data processing was done on bash together with MLH estimates. Kinship and inbreeding coefficients were estimated using R package Hierfstat.
Funding
Swiss National Science Foundation, Award: 31003A_182265