Lab 8 Phylogenetics I: creating and analysing a data matrix

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1 G44 Geobiology Fall 23 Name Lab 8 Phylogenetics I: creating and analysing a data matrix For this lab and the next you will need to download and install the Mesquite and PHYLIP packages: Mesquite. Mesquite has tools for creating and modifying phylogenetic data matrices, as well as tools for displaying trees and doing certain kinds of analysis on phylogenetic data. It does not, however, do an exhaustive parsimony analysis. Mesquite s documentation can be found by opening the file documentation.html in your web browser. PHYLIP. PHYLIP (Phylogenetic Inference Package) has modules for estimating phylogenetic trees from data and for displaying the trees. We will use the Penny module, which calculates a parsimony tree from binary data, and the onsense module, which calculates a consensus tree (average) when more than one tree is found by Penny. PHYLIP s documentation can be found in the folder docs where you stored the PHYLIP package on your computer.. Tree lengths and the most parsimonious tree The objective of a parsimony analysis is to find the cladogram that has the most synapomorphies and the fewest homoplasies for a given data set. Parsimony, or Occam s razor, is the scientific principle that when there are competing hypotheses for a set of data, it is the one that makes the fewest assumptions that is preferred, all else being equal. In phylogenetic analysis the branching structure of the tree is the hypothesis and the characters are the data. The parsimony criterion assumes that a derived character state found in more than one taxon arose once from a common ancestor based on principles of evolution. Instances of homoplasy are assumptions that are to be avoided if necessary. Parsimony therefore looks for the tree that minimizes the number of homoplasies and maximizes the number of synapomorphies. To understand what this means, consider the following data set in which taxa,, and have one character whose plesiomorphic state is and whose apomorphic state is :

2 Three taxa can be related in four possible ways: If is the plesiomorphic state, it was found at the root of the tree. If we map our character onto these four trees we obtain the following: 2 changes (homoplasy) Tree length = 2.I. =.5 change (synapomorphy) Tree length =.I. =. 2 changes (homoplasy) Tree length = 2.I. =.5 2 changes (homoplasy) Tree length = 2.I. =.5 The second tree is preferred by the parsimony method because it requires only one evolutionary change and has no homoplasy. ll the other trees require at least two evolutionary changes and, thus, more assumptions that characters evolved separately instead of being inherited from their ancestor. Parsimony computer algorithms try all possible trees and find the one with the shortest tree length, which is also the one with most synapomorphies and the highest consistency index (I). n important aspect of parsimony is that many characters are used to calculate a tree, each of which provides one piece of evidence about relationships. Some combinations of characters are contradictory and require that the best tree have at least some homoplasy. onsider the following two-character data set: If we map these onto the four possible trees we get the following:,,,,,,,,,,,, Tree length = 3.I. =.67 Tree length = 3.I. =.67 Tree length = 4.I. =.5 Tree length = 4.I. =.5 The first two trees are equally parsimonious, each with one synapomorphy and one homoplasy. Parsimony considers both trees to be equally plausible given the data. We would need additional characters to resolve the relationships among these taxa. 2

3 2. Scoring characters For parsimony analysis, characters must be scored. Scoring includes two steps: () defining characters and their states; and (2) tabulating the state of each character for every taxon in the analysis. Scoring is one of the most critical steps in phylogeny reconstruction. It can be done well or it can be done badly. If it is done badly, then the outcome of the analysis will be bad: garbage in, garbage out. The key to successful scoring involves understanding the morphology. good character is one that evolves independently of others, can be recognized by scientists other than yourself, has genetic underpinnings (e.g., the feature is inherited and not the result of pathology or individual life history), and evolves at an appropriate rate (e.g., the character changes slowly enough so that it has changed a few times at most among the group of interest). Similarly the divisions between character states should be crisp enough that scoring is obvious for all the taxa in the analysis. Most of the scientific debate about the accuracy of a particular phylogenetic tree is about the character scoring. Here is an example of typical character definitions and scorings for them: (Polly, 996) ssignment: Using the data you collected in the first labs, write formal character and character state descriptions. Things to consider: identifying characters and dividing them into states can be very subjective because there is no right way to do it. For scientific rigor it is important to be as objective as possible. Normally one considers characters that other scientists have used (e.g., the presence and absence of temporal fenestra) but one also systematically examines the organism from tip to tail, so to speak, to look for new characters that vary between taxa. lso one should be excruciatingly honest in scoring the characters. If you can t see a feature, score it as absent even if you think it should be there (e.g., if you think an animal is an 3

4 archosaur but you can see no evidence of an anteorbital fenestra, score the fenestra as being absent perhaps the animal is not an archosaur after all). 3. Polarizing characters Scoring involves more then just description. haracters must be polarized, meaning the ancestral state of each character must be determined. The ancestral state is scored as and derived states are scored with a. If there is more than one derived states, then higher integers are used. ssignment: Use the outgroup method to polarize your characters. You may use the information learned in class about the ancestral state of characters among vertebrates for this task. 4. reating a data matrix in Mesquite ssignment: Use Mesquite to create a data file for your data dd a fourth taxon at the beginning of the matrix named Outgroup and give it a for each of the characters. To do this, start Mequite. From the File menu choose New. Specify the number of taxa and tick the box to make a character matrix. We are using standard categorical data (=discrete characters, =meristic characters). Note that you can give names to the characters if you want. Remember to save your file. Make a screen capture of your data matrix to turn in with this lab. 5. nalyzing the data matrix in PHYLIP ssignment: Use PHYLIP to find a parsimony tree for your data. To do this, export your data from Mesquite in PHYLIP format. While your data matrix is showing on the screen, choose Export from the File menu. hoose the Phylip (categorical data) option and accept the default values in the save window (taxon names = characters, end of line current system default). PHYLIP is a simple program and always reads data from a file named infile that is located in the PHYLIP folder. opy the file you exported from Mesquite to the PHYLIP folder named exe. If there is currently a file named infile then delete it. Rename your file as infile (remove the extension.phy). The Penny module does a parsimony analysis. Double click on the Penny icon to start the program. It should read your data file automatically if you have performed the above steps correctly. 4

5 The user interface of Penny in the PHYLIP package. PHYLIP is a simple program and you change settings by typing the letter or number in the left column. You can use the defaults, but it may be interesting to change item 4 and 5 so that the program reports the steps for each character (the number of changes in that character on the tree) and the states of at the nodes of the tree. Type Y to run the program after you have chosen your options. PHYLIP is a simple program and it sends its results to text files that are automatically saved in the exe folder. The main results are in a text file named outfile and the most parsimonious tree(s) is in the file named outtree. oth of these are text files and you can open them in Word or a text editing program. The outfile shows a text picture of the most parsimonious tree, reports the tree length in the line that begins requires a total of.. (the number is the number of steps on the tree, which is the tree length). If you chose options 4 and 5 you will also see the number of steps in each character and the states at each node on the tree (numbered using the same numbering system as in the picture of the tree). The outtree file contains the tree written using the parenthesis notation that was presented in lecture. This file can be displayed using the drawtree or drawgram modules of PHYLIP or in Mesquite. 6. Plotting trees in Mesquite ssignment: Plot the PHYLIP tree in Mesquite. To do this, copy the outtree file to another folder and rename it appropriately. dd the extension.tre. Using the Taxa&Tree menu, choose Import file with trees with the Include contents option. Select your file and open, choosing the Phylip (trees) option when 5

6 prompted. You can view the tree by clicking on View Trees in the Imported tree pane at the left of the main window. Make a screen capture of your tree to turn in with this lab. 6