Lecture 9 Parsimony and Bootstrap Flashcards
What does the parsimony principle tell us?
choose the simplest scientific explanation that fits the evidence.
In terms of tree-building what does the parsimony principle hypothesize?
the best hypothesis is the one that requires the fewest evolutionary changes.
How is the Character Fit done?
The fit of a site to a tree means the smallest number of changes needed to explain how the amino acids, nucleotides or morphologies in the sequences are distributed.
Given a set of Sequences, phylogenetic analysis can be seen as a procedure where
1) The universe of all possible trees for N. sequences is defined (this is the tree space).
2) The score of each tree is calculated (given the data).
3) The best tree is selected.
what is an Exhaustive Search.
the complete tree-space is visited and the length of each possible tree calculated.
Because the tree space is HUGE, when are exhaustive searches feasible?
exhaustive searches are feasible only if the number of sequences (<10) is very small (even with the most powerful supercomputer)
what method is used in Assessing Phylogenetic Hypotheses
The bootstrap method
What Bootstrapping
A statistical technique that uses computer intensive random resampling of data to determine sampling error or confidence intervals for some estimated parameter
What is a measure of support for those groups
bootstrap proportions (BPs)
What do BPs depend on?
the numbers of characters supporting a group
the level of support for incongruent groups
what do BPs provide?
BPs is a way to measure how much support there is for different groups based on the data we have.
High BPs (e.g. >85%) is indicative of…?
strong signal in the data
High BPs are likely to reflect…?
strong phylogenetic signal
What do Low BPs mean?
The relationship is poorly supported
