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inbreedR: An R package for the analysis of inbreeding based on genetic markers

Stoffel, MA, Esser, M, Kardos, M, Humble, E, Nichols, HJ, David, P and Hoffman, JI (2016) inbreedR: An R package for the analysis of inbreeding based on genetic markers. Methods in Ecology and Evolution, 7 (11). pp. 1331-1339. ISSN 2041-210X

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1. Heterozygosity fitness correlations (HFCs) have been used extensively to explore the impact of inbreeding on individual fitness. Initially, most studies used small panels of microsatellites, but more recently with the advent of next generation sequencing, large SNP datasets are becoming increasingly available and these provide greater power and precision to quantify the impact of inbreeding on fitness. 2. Despite the popularity of HFC studies, effect sizes tend to be rather small. One reason for this may be a low variation in inbreeding level across individuals. Using genetic markers, it is possible to measure variance in inbreeding through the strength of correlation in heterozygosity across marker loci, termed identity disequilibrium (ID). 3. ID can be quantified using the measure g2 which is also a central parameter in HFC theory that can be used within a wider framework to estimate the direct impact of inbreeding on both marker heterozygosity and fitness. However, no software exists to calculate g2 for large SNP datasets nor to implement this framework. 4. inbreedR is an R package that provides functions to calculate g2 based on microsatellite and SNP markers with associated p-values and confidence intervals. Within the framework of HFC theory, inbreedR also estimates the impact of inbreeding on marker heterozygosity and fitness. Moreover, we implemented easy-to-use simulations to explore the precision and magnitude of estimates based on different numbers of genetic markers. We hope this package will facilitate good practice in the analysis of HFCs and help to deepen our understanding of inbreeding effects in natural populations.

Item Type: Article
Additional Information: This is the accepted version of the following article:inbreedR: An R package for the analysis of inbreeding based on genetic markers, which has been published in final form at http://dx.doi.org/10.1111/2041-210X.12588
Uncontrolled Keywords: 0602 Ecology, 0603 Evolutionary Biology
Subjects: Q Science > QH Natural history
Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Natural Sciences & Psychology (closed 31 Aug 19)
Publisher: Wiley
Date Deposited: 13 May 2016 09:24
Last Modified: 20 Apr 2022 10:03
DOI or ID number: 10.1111/2041-210X.12588
URI: https://researchonline.ljmu.ac.uk/id/eprint/3593
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