Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realization from the phenotype distribution of that individual. If all individua...

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Main Authors: Ansari, M. Azim, Didelot, Xavier
Format: Online
Language:English
Published: Genetics Society of America 2016
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012407/
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spelling pubmed-50124072016-09-07 Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree Ansari, M. Azim Didelot, Xavier Investigations The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realization from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is, however, often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated data sets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen and the other studying host range distribution in a lineage of Salmonella enterica, and we discuss many other potential applications. Genetics Society of America 2016-09 2016-07-11 /pmc/articles/PMC5012407/ /pubmed/27412711 http://dx.doi.org/10.1534/genetics.116.190496 Text en Copyright © 2016 Ansari and Didelot Available freely online through the author-supported open access option. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Ansari, M. Azim
Didelot, Xavier
spellingShingle Ansari, M. Azim
Didelot, Xavier
Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
author_facet Ansari, M. Azim
Didelot, Xavier
author_sort Ansari, M. Azim
title Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
title_short Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
title_full Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
title_fullStr Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
title_full_unstemmed Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
title_sort bayesian inference of the evolution of a phenotype distribution on a phylogenetic tree
description The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realization from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is, however, often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated data sets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen and the other studying host range distribution in a lineage of Salmonella enterica, and we discuss many other potential applications.
publisher Genetics Society of America
publishDate 2016
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012407/
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