Uses of phylogenies Yves Desdevises

Computer Lab

If needed, you can download softwares and instructions from the following link: http://desdevises.free.fr/Phylogenetic_reconstruction/Courses_and_Labs.html Create a folder, and subfolders, on your computer to place input and output files, they tend to multiply very rapidly! Of course, you may any other software you are familiar with. Take your time and do not hesitate to use help, example files and manuals from the various programs you will use. 1. Independent contrasts and related methods Softwares: Compare, statistical package -

You need the morphological data in sparmorpho and molecular tree(s) phylomol. You will generate evolutionary scenarios for morphological characters and propose hypotheses for ancestral states

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Compare will be used for quantitative characters (independent contrasts). Mesquite can also be used with the module PDAP o Compare is a java program that run on web browsers like Explorer o You need a quatitative data file corresponding to the hypotheses to test: size, size/body heigth, age, depth, diet, gregarity, … Use for example morphological data and biological data from FishBase (http://www.fishbase.org/search.cfm?lang=French) o Run Compare and choose Main Window o Data are directly copied and pasted in corresponding windows. You can look at the data format by choosing Demo o Select options and run the analysis (select Independent Contrasts in the drop down menu at the bottom right) o You can also recover contrasts to use them in a statistical package, but do not forget to force regression via the origin o Test if Brownian motion is an adequate model (how?). If not, try another method like PGLS

2. Phylogenetic eigenvector regression and variation partitionning Softwares: DistPCoA, Permute!

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3. Discrete characters Softwares: Mesquite o You can test correlation beween binary characters via Analysis ➙ Pairwise Comparison 4. Character mapping Softwares: Mesquite -

Mesquite will be used for discrete characters (mapping via parsimony and ML) o You need a tree in nexus format. If you made you tree in Phylo_win: open phylomol in e.g. TreeView and save it as nexus (name it phylomol.nex) o Run Mesquite. Import sparmorpho o Link the molecular tree phylomol.nex to sparmorpho (File ➙ Link File) and open it (Taxa&Trees ➙ New Tree Window and follow the instructions) o You can modify tree shape via Drawing ➙ Tree Form o Map morphological character on the the molecular phylogeny with the method you choose via Analysis ➙ Trace Character History

+ continuous characters 5. Molecular dating Softwares: BEAST, Tracer, r8s -

You can test correlation beween binary characters via Analysis ➙ Pairwise Comparison

3. Cophylogeny Softwares: TreeMap 2.0, CopyCat, ParaFit, DistPCoA

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