Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree

JOURNAL OF THEORETICAL BIOLOGY

卷:461

Article

Tahir, Daniah¹  Glemin, Sylvain^2,3  Lascoux, Martin²  Kaj, Ingemar¹ 

[1] Uppsala Univ, Dept Math, Box 480, SE-75106 Uppsala, Sweden

[2] Uppsala Univ, Dept Plant Ecol & Evolut, Norbyvagen 18D, SE-75236 Uppsala, Sweden

[3] Univ Montpellier, CNRS, IRD, EPHE,ISEM,UMR 5554, FR-34095 Montpellier 5, France

关键词: Branching processes;    Irreversible transitions;    Binary traits;    Phylogenetic trees;    Mutation rates;   

DOI  :  10.1016/j.jtbi.2018.10.032

来源: Elsevier

【 摘 要 】

Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. In this work, we present a probabilistic modeling framework for binary trait, random species trees, in which the number of species and their traits are represented by an asymmetric, two-type, continuous time Markov branching process. The model involves a number of different parameters describing both character and molecular evolution on the so-called 'reduced' tree, consisting of only extant species at the time of observation. We expand our model by considering the impact of binary traits on dN/dS, the normalized ratio of nonsynonymous to synonymous substitutions. We also develop mechanisms which enable us to understand the substitution rates on a phylogenetic tree with regards to the observed traits. The properties obtained from the model are illustrated with a phylogeny of outcrossing and selfing plant species, which allows us to investigate not only the branching tree rates, but also the molecular rates and the intensity of selection. (C) 2018 Elsevier Ltd. All rights reserved.

【 授权许可】

Free