Workshops‎ > ‎

Phylogenetic Analysis

Tuesday, April 26, 2011  14h-16h
Adam Herman & Dr. Jonathan Davies, McGill Department of Biology

Topics

The most elegant way to understand the principle of common ancestry is the phylogenetic tree. Famously, the lone figure in Charles Darwin’s On the Origin of Species was a depiction of such a tree. There is an exceptionally rich body of statistics that has developed around reconstructing the relationships among evolving units, but when it comes to visual representation of those relationships the options are few. Also, inference of a phylogeny answers questions about relationships among units but creates new questions about the larger trends of evolution along a tree. The ape package available in R allows a researcher to create visually attractive trees and employ phylogenetic comparative methods for analysing correlations between species' traits. This workshop will cover those aspects in two parts: Part I will focus on importing and manipulating trees in R with the aim of giving the user maximum control over the visual representation of their tree. Part II will cover methods for correcting for species evolutionary non-independence using phylogenetically independent contrasts (PIC).

Prerequisites

Basic knowledge of R scripting is always helpful. Familiarity with simple graphical manipulation of plot() objects is a big plus. However, as with all previous workshops, we have tried to make the material accessible to participants at any skill level in R.

Basic knowledge of evolutionary biology (e.g. what is a phylogenetic tree?). Chapter 2 of Doug Futuyma’s Evolution text is a great background read.

All topics covered in Part I come from Chapter 4 of Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis (the author of the ape package).   

Packages

install.packages(‘ape’)

install.packages(‘geiger’)

install.packages(‘nlme’)


NB We will NOT be covering the phylogenetic methods for tree reconstruction/search. Though this is an area of very interesting advanced statistics, R is simply not an appropriate environment for such analyses. I (Adam) would be happy to recommend programs for building trees.

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Examplephylogeneticcontrasts.R
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Corey Chivers,
Apr 26, 2011, 8:50 AM
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Corey Chivers,
Apr 26, 2011, 8:47 AM
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Corey Chivers,
Apr 26, 2011, 8:49 AM
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Phylo_plot.R
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Corey Chivers,
Apr 26, 2011, 8:47 AM
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Phylo_plot_ans.R
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Corey Chivers,
Apr 26, 2011, 8:47 AM
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WStree.txt
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Corey Chivers,
Apr 26, 2011, 8:48 AM
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