Lab9_Distance - Integrative Biology 200A "PRINCIPLES...

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Integrative Biology 200A University of California, Berkeley "PRINCIPLES OF PHYLOGENETICS" Spring 2006 Distance Methods Due at the end of class: - Distance matrices and trees for two different distance measures - Tree from one extra distance-based tree building method - Parsimony reference tree Today we’re going to use PAUP* to generate trees using distance methods. We’ve discussed distance methods in class, and you have learned that they are not the most theoretically justified of methods for inferring phylogenies, although clustering methods do have some uses in other areas of statistics. For several reasons, it is important that you learn how to utilize them. First, you should use them as one of the analyses in your final project, as a comparison to other methods. They will almost always give a different tree than the other optimality criteria, since they are searching for total similarity, and not distinguishing between synapomorphy, symplesiomorphy, and homoplasy. Second, some workers people do feel that they are a good way to infer phylogenies. Finally, they are by far the fastest way to find a tree. Whereas parsimony and likelihood methods have to search through tree space and compare the optimization of the character matrix on many trees, most distance methods use an algorithm to directly generate a tree from the distance matrix. This speed makes it very useful for genomics, where it is often necessary to generate tens of thousands of trees, but getting the exact tree each time is not as important as getting the right tree the vast majority of the time. Distance analysis have two main components: the formulas used to calculate the distances (a.k.a. distance measures) and the algorithms used to compute a tree from the distances. Get Sequences, Generate a Reference Tree First, download the cephalopod nexus file from the syllabus page on the 200A website. You may have to right-click on the link and choose save as to download it rather than open it in your browser. Save it to the desktop, or to a folder you create for yourself on the desktop, and open it in PAUP*. Generate a parsimony tree for comparison to the other trees you will make during this lab: set criterion = parsimony; hs; The search will retain only one tree. Look at the tree, then save it: showtree; savetree file=ceph_COI_parsimony.tre; Print out this tree and save it to turn in.
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Distance Measures: ways to measure how different things are Phenetic methods start by measuring how “different” taxa are from one another. They look at the total similarity across many different characters, and analyze these in a statistical framework to come up a measure of the “distance” between each pair of taxa. This works a lot like those timetables that tell you the distance between two cities – like the example at left. Notice that the distance method can only compare two cities at a time – the same is true for
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Lab9_Distance - Integrative Biology 200A "PRINCIPLES...

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