Phylogenetic Analysis Tutorial

Tutorial 1: Comparing gene trees and species trees.

Among three species of fungi in the Class Sordariomycetes, there are three possible species trees (including an outgroup).  In this tutorial, we will construct three gene trees and compare them to the species trees.  We will use the gene trees to determine which of the species trees is correct.

There are three data sets:

1.  Open the web site and select “One Click” under the Phylogeny Analysis menu.

2.  Copy and Paste one of the three sequence data sets into the web page and click the submit button.

3.  Compare the gene tree to the species trees in the figure.  Which of the three species trees does it match?

Tutorial 2: Find gene duplications and speciations in a tree; Find the root of  a tree using a gene duplication.

Construct a phylogenetic tree for each of the following three gene families.  Each gene family contains one or more gene duplications.  Compare the tree to the correct species tree that you determined in Tutorial 1 and try to identify which internal nodes represent gene duplication events and which nodes represent speciation events.  Can you find the root of the tree using a gene duplication?

Note: In these sequence files the species are indicated by the first two letters of the sequence ID: NC = Neurospora crassa, AN = Aspergillus nidulans, FG = Fusarium graminearum, MG = Magnaporthe grisea.

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