Evolution: Estimating rate of speciation and extinction in a tropical plant

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Background: Estimating how fast species are appearing and disappearing through time and what are the factors influencing this rate, is an important aspect of evolutionary biology. This is becoming even more important given the current loss of biodiversity. Available dated phylogenetic trees of Morea, a very species-rich tropical plant genus, will be used to illustrate this type of analyses.

Goal: The goal of the project is to estimate the rate of speciation and extinction through time from Morea phylogenetic tree using a stochastic process called birth and death to model these two parameters.

Mathematical tools: The tool of choice for this project will be Maximum Likelihood estimation of model parameters. The student will use divergence time of Morea species to find the optimum rate of speciation and extinction using existing computer based analytical tools.

Biological or Medical aspects: The “biology supervisor” will provide background of the evolutionary theory of speciation and phylogenetic analysis.

Supervisor: Nicolas Salamin

Presentation: Media:Nicholas.pdf


T. G. Barraclough and S. Nee. (2001). Phylogenetics and speciation, Trends in Ecology and Evolution, 16(7): 391-399.

F. Bokma. (2003). Testing for equal rates of cladogeneis in diverse taxa, Evolution, 57(11): 2469-2474.

S. Nee, E. C. Home, R. M. May and P. H. Harvey. (1994). Extinction rates can be estimated from molecular phylogenies, Philosophical Transactions of the Royal Society of London, Serie B, 349:25-31.

E. Paradis. (2004). Can extinction rates be estimated without fossils?, Journal of Theoretical Biology, 229(1): 19-30.

Student's "workspace"

At the moment, we are three biology students working on this subject (Anna Lisa Mascitti, Linda Müller and Vincent Sonnay).

Now we have arrived at he end of our project. In the following document, you can found a summary of the work that we have done and some explanations about the process we have used to obtain our results:

Media:Compte rendu.pdf

An important part of our work was realised with R software. This document contains the principal R orders we have used:

Media:Script R.pdf

Finaly, we are very pleased to have taken part in this course and we are delighted to see you on Friday, May 29th to present the work we realized during this half-year. In this last document, you can find the Powerpoint we are going to use in this occasion:

Media:Présentation du 29 mai 09.ppt

(Project in Course: "Solving Biological Problems that require Math".)