Matrix-analytic methods for the evolution of species trees, gene trees, and their reconciliation

We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the species tree, a subfunctionalisation model for the evolution of...

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Main Authors Soewongsono, Albert C, Diao, Jiahao, Stark, Tristan, Wilson, Amanda E, Liberles, David A, Holland, Barbara R, O'Reilly, Malgorzata M
Format Journal Article
LanguageEnglish
Published 11.09.2023
Subjects
Mathematics - Probability
Quantitative Biology - Populations and Evolution
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Summary:We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the species tree, a subfunctionalisation model for the evolution of the gene tree, and provide an algorithm to compute the likelihood of the reconciliation. We derive our results using the theory of matrix-analytic methods and describe efficient algorithms for the computation of a range of useful metrics. We illustrate the theory with examples and provide the physical interpretations of the discussed quantities, with a focus on the practical applications of the theory to incomplete data.
DOI:10.48550/arxiv.2309.06447