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Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: Theory and applications.

Authors :
Richards A
Kubatko L
Source :
Journal of theoretical biology [J Theor Biol] 2022 Jun 07; Vol. 542, pp. 111078. Date of Electronic Publication: 2022 Mar 10.
Publication Year :
2022

Abstract

The first step in statistical inference of the evolutionary histories of species is developing a probability model that describes the mutation process as accurately and realistically as possible. A major complication of this inference is that different loci on the genome can have histories that diverge from the common species history and each other. The multispecies coalescent process is commonly used to model one source of this divergence, incomplete lineage sorting, or ILS. In Chifman and Kubatko (2015), the authors computed the site pattern probabilities for four taxa under a full probability model based on the Jukes-Cantor substitution model when the molecular clock holds. This paper generalizes that work to a relaxed clock model, allowing for mutation rates to differ among species. This will enable better phylogentic inference in cases where the molecular clock does not hold.<br />Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.<br /> (Copyright © 2022. Published by Elsevier Ltd.)

Details

Language :
English
ISSN :
1095-8541
Volume :
542
Database :
MEDLINE
Journal :
Journal of theoretical biology
Publication Type :
Academic Journal
Accession number :
35278472
Full Text :
https://doi.org/10.1016/j.jtbi.2022.111078