Abstract
Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article was to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS‐ and IBD‐based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log‐ratios of IBS and IBD probabilities. We illustrate all graphical tools with genetic data from the HGDP‐CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel. We enhance all graphics with convex hulls obtained by simulation and use these to confirm the documented relationships. The proposed compositional graphics are shown to be useful in relatedness research, as they also single out the most prominent related pairs. The ternary diagram is advocated for its ability to display all three allele sharing probabilities simultaneously. The log‐ratio plots are advocated as an attempt to overcome the problems with the Euclidean distance interpretation in the classical graphics.
Highlights
Statistical methods for the analysis of the genetic relationships between individuals of a population are of great relevance for molecular ecology (Blouin, 2003)
We propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log-ratios of IBS and IBD probabilities
We illustrate all graphical tools with genetic data from the HGDP-CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel
Summary
Statistical methods for the analysis of the genetic relationships between individuals of a population are of great relevance for molecular ecology (Blouin, 2003). Relatedness estimation is important for conservation programmes, and the performance of several estimators has been compared in that context (Oliehoek, Windig, van Arendonk, & Bijma, 2006). It plays an important role in structuring societies with fusion–fission dynamics (Croft et al, 2012; Snyder-Mackler, Alberts, & Bergman, 2014; Spencer et al, 2015), can bias estimates of allele frequencies (Hansen, Nielsen, & Mensberg, 1997) and violates the assumption of independent individuals in trait-gene association studies (Foulkes, 2009). Statistical methods that can verify documented or uncover undocumented family relationships in the database are important tools in molecular ecology
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