Given a set of characters and character states, you can reconstruct
a phylogeny
If all characters agree with each other, making a tree is easy -- find
the tree that fits all the characters
Informative vs.uninformative characters in parismony
Synapomorphy
Autapomorphy
Character conflict
Homoplasy - apparent similarity that is not the result of common
descent
Molecular data are inherently prone to homoplasy
Finding a tree that corresponds to the data involves a series of compromises.
The text describes:
Algorithmic methods - a set of rules used to build a tree
Optimality methods - use a criterion to choose among alternative
trees
Compare trees and find the best one
Branch swapping generates trees to be compared
Algorithms
Algorithm - Any mechanical or recursive computational procedure (American
Heritage Dictionary of the English Language. 1981. W. Morris, ed. Houghton
Mifflin Co., Boston).
All modern phylogenetic methods rely on algorithms to evaluate trees, but
algorithmic methods differ from optimality methods in that they define the
"best" tree as that which is found by the algorithm. By contrast,
optimality methods can calculate a score based on some optimality criterion
for any tree. When several candidate trees are compared, the tree that has
the better score under the optimality criterion in use is considered to be
the best tree. Thus with optimality methods the "best" tree is independent
of the algorithm used to find the tree.
Optimality Criteria
Parsimony
Distance
Maximum Likelihood
Maximum Parsimony
Optimality criterion used by cladistic methods
Between two trees, the one that requires the smallest number of changes
is the best
We have access only to the data at the tips of the tree
Want to reconstruct the events that gave rise to the observed data
Postulate
Dichotomously branching tree, and
Changes in the sequences over time
Wagner parsimony - ordered characters; used in first example in book