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A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants
Author(s) -
Radice Rosalba
Publication year - 2012
Publication title -
australian and new zealand journal of statistics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.434
H-Index - 41
eISSN - 1467-842X
pISSN - 1369-1473
DOI - 10.1111/j.1467-842x.2012.00686.x
Subject(s) - phylogenetic tree , phylogenetic network , inference , set (abstract data type) , tree (set theory) , bayesian probability , taxon , bayesian inference , phylogenetics , variety (cybernetics) , bayesian network , biology , evolutionary biology , directed acyclic graph , computer science , computational biology , artificial intelligence , mathematics , algorithm , gene , genetics , ecology , combinatorics , programming language
Summary Traditional phylogenetic inference assumes that the history of a set of taxa can be explained by a tree. This assumption is often violated as some biological entities can exchange genetic material giving rise to non‐treelike events often called reticulations. Failure to consider these events might result in incorrectly inferred phylogenies. Phylogenetic networks provide a flexible tool which allows researchers to model the evolutionary history of a set of organisms in the presence of reticulation events. In recent years, a number of methods addressing phylogenetic network parameter estimation have been introduced. Some of them are based on the idea that a phylogenetic network can be defined as a directed acyclic graph. Based on this definition, we propose a Bayesian approach to the estimation of phylogenetic network parameters which allows for different phylogenies to be inferred at different parts of a multiple DNA alignment. The algorithm is tested on simulated data and applied to the ribosomal protein gene rps 11 data from five flowering plants, where reticulation events are suspected to be present. The proposed approach can be applied to a wide variety of problems which aim at exploring the possibility of reticulation events in the history of a set of taxa.