Demerelate: calculating interindividual relatedness for kinship analysis based on codominant diploid genetic markers using R

Abstract

The Demerelate package offers algorithms to calculate different interindividual relatedness measurements. Three different allele sharing indices, five pairwise weighted estimates of relatedness and four pairwise weighted estimates with sample size correction are implemented to analyse kinship structures within populations. Statistics are based on randomization tests; modelling relatedness coefficients by logistic regression, modelling relatedness with geographic distance by mantel correlation and comparing mean relatedness between populations using pairwise t-tests. Demerelate provides an advance on previous software packages by including some estimators not available in R to date, along with F_IS , as well as combining analysis of relatedness and spatial structuring. An UPGMA tree visualizes genetic relatedness among individuals. Additionally, Demerelate summarizes information on data sets (allele vs. genotype frequencies; heterozygosity; F_IS values). Demerelate is - to our knowledge - the first R package implementing basic allele sharing indices such as Blouin's M_xy relatedness, the estimator of Wang corrected for sample size (wang_xy ), estimators based on Morans I adapted to genetic relatedness as well as combining all estimators with geographic information. The R environment enables users to better understand relatedness within populations due to the flexibility of Demerelate of accepting different data sets as empirical data, reference data, geographical data and by providing intermediate results. Each statistic and tool can be used separately, which helps to understand the suitability of the data for relatedness analysis, and can be easily implemented in custom pipelines.

Keywords: allele sharing; genotype sharing; heterozygosity; mantel test.