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Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. University of Montpellier, CNRS, IRD, EPHE, ISEM, UMR 5554, Montpellier 5, France.ORCID iD: 0000-0001-7260-4573
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Probability Theory.ORCID iD: 0000-0002-7672-190X
2019 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 461, p. 189-203Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2019. Vol. 461, p. 189-203
Keywords [en]
Branching processes, Irreversible transitions, Binary traits, Phylogenetic trees, Mutation rates
National Category
Evolutionary Biology Probability Theory and Statistics
Identifiers
URN: urn:nbn:se:uu:diva-372749DOI: 10.1016/j.jtbi.2018.10.032ISI: 000452245900018PubMedID: 30340056OAI: oai:DiVA.org:uu-372749DiVA, id: diva2:1278988
Available from: 2019-01-15 Created: 2019-01-15 Last updated: 2019-04-25
In thesis
1. Multi-trait Branching Models with Applications to Species Evolution
Open this publication in new window or tab >>Multi-trait Branching Models with Applications to Species Evolution
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis provides an analysis of the evolution of discrete traits and their effect on the birth and survival of species using the theory of supercritical, continuous time Markov branching processes. We present a branching modeling framework that incorporates multi-trait diversification processes associated with the emergence of new species, death of existing species, and transition of species carrying one type of a trait to another. The trait-dependent speciation, extinction, and transition help in interpreting the relationships between traits on one hand, and linking together the diversification process with molecular evolution on the other. Various multitype species branching models are applied in order to examine the evolutionary patterns in known data sets, such as the impact of outcrossing and selfing mating systems on the diversification rates of species, and the analysis of virulent behavior of pathogenic bacterial strains in different environments. Stochastic equations and limit theorems for branching processes help scrutinize the long time asymptotics of the models under an asymmetry in change of types, and under various schemes of rescaling. In addition, we explore diversity-dependent processes in which, instead of allowing supercritical growth of population sizes, the increase in species numbers is regulated by modifying the species branching rates. The use of probabilistic methods in a setting of population genetics leads to an analogy between biallelic frequency models and binary trait species tree models. To obtain an approximation for a Markov branching process of species evolution over a long geological time scale, we methodically utilize the theory of diffusion processes. Overall, our results show that branching models can be effectively used to seek to comprehend the diversification patterns in species during the process of evolution.

Place, publisher, year, edition, pages
Uppsala: Department of Mathematics, 2019. p. 55
Series
Uppsala Dissertations in Mathematics, ISSN 1401-2049 ; 115
Keywords
Markov models, branching processes, density dependence, discrete traits, species trees, diversification rates, diffusion approximation
National Category
Mathematics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-380975 (URN)978-91-506-2765-7 (ISBN)
Public defence
2019-06-14, Room 80101, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2019-05-23 Created: 2019-04-25 Last updated: 2019-05-23

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Publisher's full textPubMedhttps://www.sciencedirect.com/science/article/pii/S0022519318305083

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Tahir, DaniahGlemin, SylvainLascoux, MartinKaj, Ingemar

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