inbreedR: inbreedR: Workflows for analysing variance in inbreeding and HFCs based on SNP or microsatellite markers.

Description

inbreedR contains the following functions:

g2_microsats g2_snps convert_raw check_data r2_hf r2_Wf HHC sMLH MLH simulate_g2 simulate_r2_hf plot.inbreed print.inbreed

Arguments

Details

A correlation between heterozygosity (h) and fitness (W) requires a simultaneous effect of inbreeding level (f) on both of them. A heterozygosity-fitness correlation (HFC) thus is the product of two correlations, which can be summarized in the following equation:

$$r(W, h) = r(W, f)r(h, f)$$

Estimating these parameters and their sensitivity towards the number and type of genetic markers used is the central framework of the inbreedR package. At the heart of measuring inbreeding based on genetic markers is the g2 statistic, which estimates the correlation of heterozygosity across markers, called identity disequilibrium (ID). ID is a proxy for inbreeding.

The package has three main goals:

Assessing identity disequilibria and the potential to detect heterozygosity-fitness correlations
Providing insights on the sensitivity of these measures based on the number/type of molecular markers used
Implementing computationally efficient functions in a flexible environment for analysing inbreeding and HFC`s with both small and large datasets.

For a short introduction to inbreedR start with the vignette: browseVignettes(package = "inbreedR")

References

Slate, J., David, P., Dodds, K. G., Veenvliet, B. A., Glass, B. C., Broad, T. E., & McEwan, J. C. (2004). Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity, 93(3), 255-265.

Szulkin, M., Bierne, N., & David, P. (2010). HETEROZYGOSITY-FITNESS CORRELATIONS: A TIME FOR REAPPRAISAL. Evolution, 64(5), 1202-1217.

David, P., Pujol, B., Viard, F., Castella, V. and Goudet, J. (2007), Reliable selfing rate estimates from imperfect population genetic data. Molecular Ecology, 16: 2474

Hoffman, J.I., Simpson, F., David, P., Rijks, J.M., Kuiken, T., Thorne, M.A.S., Lacey, R.C. & Dasmahapatra, K.K. (2014) High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America, 111: 3775-3780.