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Maximum parsimony of Veronica AFLP dataset
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1. PAUP provides two basic classes of methods for searching for optimal trees; exact, branch&bound and heuristic. Which are the main differences among these methods ? We selected the heuristic search. Why do you think this is the best option for using with this dataset? *
2. Which algorithm are we using to obtain the trees? *
3. Which algorithm are we using to reorganize the trees? Can you explain how does this algorith work? *
4. Why it is recommended to root the tree? *
5. Which differences do you observe between the two obtained consensus trees? What do the values observed in the majorityRule50 consensus tree are indicating? *
6. What do bootstrap values mean? *
7. Look and compare the „majorityRule50.consensus tree and the „bootstrap.consensus tree“. Why bootstrap values are different to the values obtained in the majority rule consensus tree? *
8. According to these analyses, which species do you consider that are well-supported within Veronica Pentasepalae ? Why? *
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