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

Albert C. Soewongsono; Jiahao Diao; Tristan Stark; Amanda E. Wilson; David A. Liberles; Barbara R. Holland; Malgorzata M. O'Reilly

arXiv · 2309.06447

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

Albert C. Soewongsono·Jiahao Diao·Tristan Stark·Amanda E. Wilson·David A. Liberles·Barbara R. Holland·Malgorzata M. O'Reilly

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Abstract

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.

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Albert C. Soewongsono, Jiahao Diao, Tristan Stark, Amanda E. Wilson, David A. Liberles, Barbara R. Holland, Malgorzata M. O'Reilly. 2023-09-12. Matrix-analytic methods for the evolution of species trees, gene trees, and their reconciliation. https://arxiv.org/abs/2309.06447

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