BiogeographyandTreemap - Integrative Biology 200A...

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Integrative Biology 200A University of California, Berkeley Principals of Phylogenetics Spring 2008 Biogeographic Reconstruction on Phylogenies Today we’re going to be looking at programs that compare trees between two associated groups of objects to deduce their common history. This could be a comparison of host & parasite, organism & gene or area & organism trees. The different relationships can be analogized like this (read down): Host Organism Area P a r a s i t e G e n e O r g a n i s m Host switch Horizontal transfer Dispersal Cospeciation Orthology Vicariance Parasite speciation Gene duplication or Sympatric speciation on one host allelic divergence (kind of) Parasite extinction Gene loss or fixation Extinction In all three cases comparisons can be made between the two trees to see how often dispersal or vicariance (or their analogous events) best explains the situation. We are going to try two different programs that use different criteria to determine the relationship between areas and associated organisms. Treemap COMPONENT by Rod Page is a good program for analyzing and comparing trees and can do some of these comparisons. However, it can only reconcile the trees. To reconcile trees is to add hypothesized extinct taxa to the organism/parasite tree based on the assumption that there is no dispersal/ host switching. Thus all differences between the trees are a consequence of an ancestral area/host having two organisms/parasites one of which has since gone extinct. The reconciled tree adds hypothesized extinct organisms/parasites. There is another program Treemap from Rod Page’s lab. It is only “experimental”, and is not widely used, but it looks cool and allows you to do diverse comparisons of the trees. Both programs are available for free. We are going to use Treemap to explore comparisons between the host-parasite trees that they provide as examples. We will look at host parasite-data, but the same principles apply for biogeography. 1. Go to , and download the program for “A PC running Windows 3.1 or later.” Save on the desktop. 2. Extract Treemap by right clicking and choosing “extract all” to make an unzipped folder, also on the desktop. 3. Open Treemap by double-clicking it, then choose open from the File menu. Open the HAFFNER88.NEX file. This is a file with a phylogeny of gophers and their associated lice. This file contains two trees, one for the host and one for the parasite, and a description of which hosts are associated with which parasites. You will see four windows. The first window is the Tanglegram , which shows the parasite tree on the right, the host tree on the left and arrows
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connecting the associated hosts and parasites. This is basically a graphical representation of the data in the input file. 4.
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BiogeographyandTreemap - Integrative Biology 200A...

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