Evolution of polymorphism in plants

Evolution of polymorphism in plants

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Background:

Understanding modes of species evolution is the major questions to the current evolutionary biology. As more DNA data become available, an increasing number of researchers is now switching to phylogeny-based stochastic models. Therefore, the key challenge today is to develop and test algorithms which can adequately describe evolution of phenotypes.

Goal:

The goal of this project is to develop MCMC optimization of Ornstein-Uhlenbeck process with group-specific variance and then use it in phylogenetic comparative analysis to test for signal of directional/divergent selection in a group of plants

Mathematical tools:

Statistics (stochastic models and MCMC) and programming. The students will learn how to use R to implement stochastic models and develop optimization procedures of the model parameters

Biological or Medical aspects:

This kind of analysis allow to estimate the most probable way of evolution, and permit to answer a lot of question like phenotypic evolution, comparative analysis between species and more other.

Supervisors:

Anna Kostikova & Nicolas Salamin

Students:

Rémy Morier-Genoud

Presentation on Brownian Motion:

Media:Slides_BrownianMotion.pptx

Implementation of Brownian Motion in Python: Code & Input examples:

Media:Polymorphism.zip, Media:dated_tree.zip, Media:frogs_bio10.zip

Report: Project Summary & Code explanations

Media:Report_BrownianMotion.pdf‎ Media:Report_Hoffman.pdf‎

References:

A Butler, A A King 2004 "Phylogenetic comparative analysis: A modeling approach for adaptive evolution" American Naturalist: 164(6): 683-695

Back to UNIL BSc course: "Solving Biological Problems that require Math 2012"