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Graphics for relatedness research

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...

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Autores principales: Galván‐Femenía, Iván, Graffelman, Jan, Barceló‐i‐Vidal, Carles
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624821/
https://www.ncbi.nlm.nih.gov/pubmed/28374569
http://dx.doi.org/10.1111/1755-0998.12674
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author Galván‐Femenía, Iván
Graffelman, Jan
Barceló‐i‐Vidal, Carles
author_facet Galván‐Femenía, Iván
Graffelman, Jan
Barceló‐i‐Vidal, Carles
author_sort Galván‐Femenía, Iván
collection PubMed
description 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.
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spelling pubmed-56248212017-12-12 Graphics for relatedness research Galván‐Femenía, Iván Graffelman, Jan Barceló‐i‐Vidal, Carles Mol Ecol Resour RESOURCE ARTICLES 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. John Wiley and Sons Inc. 2017-05-12 2017-11 /pmc/articles/PMC5624821/ /pubmed/28374569 http://dx.doi.org/10.1111/1755-0998.12674 Text en © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle RESOURCE ARTICLES
Galván‐Femenía, Iván
Graffelman, Jan
Barceló‐i‐Vidal, Carles
Graphics for relatedness research
title Graphics for relatedness research
title_full Graphics for relatedness research
title_fullStr Graphics for relatedness research
title_full_unstemmed Graphics for relatedness research
title_short Graphics for relatedness research
title_sort graphics for relatedness research
topic RESOURCE ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624821/
https://www.ncbi.nlm.nih.gov/pubmed/28374569
http://dx.doi.org/10.1111/1755-0998.12674
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