10.5061/DRYAD.2532D
Galván-Femenía, Iván
University of Girona
Graffelman, Jan
University of Washington
Barceló-i-Vidal, Carles
University of Girona
Data from: Graphics for relatedness research
Dryad
dataset
2017
relatedness
isometric log-ratio
ternary diagram
compositional data analysis
identical by state/descent
2017-04-20T16:48:45Z
2017-04-20T16:48:45Z
en
https://doi.org/10.1111/1755-0998.12674
9550 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 is 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.
graphics_for_relatedness_research_R_codeR code for making the graphics of
this paper