title: Graphics for relatedness research.
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.
authors.affiliation: Department of Computer Science, Applied Mathematics and Statistics, Universitat de Girona, Girona, Spain.|Disease Genomics-GCAT Group, Germans Trias Health Research Institute (IGTP)-Program of Predictive and Personalized Medicine of Cancer (PMPPC), Can Ruti Campus, Badalona, Barcelona, Spain.
authors.forename: Iván
authors.initials: I
authors.lastname: Galván-Femenía
authors.affiliation: Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.|Department of Biostatistics, University of Washington, Seattle, WA, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Graffelman
authors.affiliation: Department of Computer Science, Applied Mathematics and Statistics, Universitat de Girona, Girona, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Barceló-I-Vidal
mesh_terms: D000483:Alleles; D003196:Computer Graphics; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans
keywords: compositional data analysis; identical by state/descent; isometric log-ratio; microsatellite; relatedness; ternary diagram