reconstructing phylogenetic trees

Question 1

remember that trees are hypotheses

Answer 1

they are inferred from the similarities that are observed among taxa

Question 2

understand the components of a taxon-by-character data matrix

Question 3

distinguish between rooted and unrooted trees

Question 4

recall the basic procedure for finding/searching for the most parsimonious tree(s)

Answer 4

1. ignore parsimony-uninformative characters (initially)
2. consider possible trees
3. for each informative character, count the minimum number of steps required on each tree
4. sum over all characters to get the “score” (number of steps) for each tree. add the count for the parsimony-uninformative characters (which is the same for all trees)
5. the most parsimonious tree(s) is/are the one(s) with the lowest score
6. root the tree along the branch leading to the outgroup (if known)

Question 5

run through examples with taxon-character matrices and be sure that you are comfortable with the procedure

Question 6

how do model-based approaches to phylogenetic inference differ from parsimony?

Question 7

a common alternative to parsimony is maximum likelihood

Answer 7

in which we develop a probabilistic model of character evolution and search for most likely tree (ML tree) under that model

Question 8

today phylogenies are often based on DNA sequence data. what are some features of DNA sequence evolution that might be incorporated into a model?

Answer 8

-differences in the frequency of transitions vs transversions
-differences in frequency of synonymous vs non-synonymous substitutions
-variation in rates of change among characters (and among taxa)