|10 March 2011|
|Example data files|
Assessing Lineage Evolution in the Valerianaceae with SymmeTree
You've been provided with a phylogenetic tree for the plant group Valerianaceae. This tree includes 103 of the 300 known species in Valerianaceae. We're going to run this tree through SymmeTree to assess the degree of among-lineage diversification rate variation and to identify significant shifts in diverfication rates along lineages.
Drag (a copy of) the tree file, Val.tre to the SymmeTREE directory. Open your terminal and navigate to the program directory. Execute the program by typing ./SymmeTREE. When you do this, the main menu for SymmeTree should appear. Type 'c' to navigate to the 'change options' menu. Now type 'o' to rename the output file to 'Val.xls'. The rest of default settings are fine for this tree, so type 'd' to return to the main menu. At the main menu, type 'i' to import the tree file, and at the prompt type 'Val.tre' and hit return.
A pile of output will display to the console, and a file called 'Val.xls' will be generated in the program directory when the analysis is complete. When the run is finished, type 'x' to exit.
Open the output file in a spreadsheet program. There are two main blocks of interest - the frst is a cryptic description of the probabilities fo rate shifts along internal branches (the manual explains how to interpret this output), the other summarizes the estimated degree of among-lineage diversification rate variation for 5 statistics.
What do these results suggest about diversification rates in Valerianaceae? Have rates varied significantly across lineages? What are the implications of these results for other methods (for parameter estimation, for detecting shifts in diversification rate though time, etc.). Along which branches have diversification rates been inferred to experience shifts?