Flashcards in Oct 16 Deck (25):
How are timescales determined in a tree?
In the tree containing foxes, wolves, dogs, and bear, why is the dog group polyphyletic?
Descendants of most recent common ancestor of dogs are not all dogs
How do cluster methods work? Does order matter?
add taxa sequentially
What are the 2 steps of optimality criteria?
a) model to explain changes between taxa
b) evaluate each tree
Which is a quicker tree building method, cluster methods or optimality criteria?
What are 3 considerations for evaluating tree building methods?
1) efficient- will it break my computer?
2) power/consistency- minimum amount of data
needed to arrive at the correct tree all the time
3) robustness/falsifiability- how do violations of the assumptions impact outcomes and can it ‘report’ those effects
Parsimony is sensitive to what type of species?
What is long-branch attraction?
dissimilar species are drawn together due to having more changes than their sister taxa
How do distance methods work?
quantify pairwise differences to yield a ‘distance score'
What are the 3 steps of a DNA sequence alignment?
1) look for regions of homology
2) identify insertions and deletions (indels)
3) identify substitutions
Multiple pairwise distances yield a...
How do sister taxa look in the tree representation?
lines form a triangle NOT a trapezoid
What are DNA substitution models of evolution?
General Time-Reversible + Gamma +1
What does the Jukes-Cantor model assume?
equal probability of character (base-pair) change
What does the Kimura Two-Parameter model assume?
pur->pur changes more likely than pur->pyr
What does the General Time-Reversible + Gamma +1 assume?
accounts for diff. probabilities of substitutions/time; sites that remain unchanged; rates of change...at each site
What does maximum likelihood predict?
probability that the given tree explains the collected data
What are 2 assumptions of maximum likelihood?
1) characters evolve independently
2) substitution rate is constant
Statistical confidence provides
level of certainty about how well the data supports monophyletic clades and the overall phylogeny
What does bootstrap analysis do?
‘resampling with replacement’ to evaluate how data randomization affects tree topology; reorders character traits and duplicates some
What are the steps of bootstrap analysis?
1) create many reordered character matrices with randomly replaced traits
2) trees are generated from each matrix
3) frequency of clade recovery is evaluated
What does odds ratio testing do?
compares the best tree with clade X vs. the best tree lacking clade X and reports a significance statistic
What is phylogeography?
Linking phylogeny and geological evidence to help explain migration/dispersal or adaptive radiation/speciation/extinction events
What does comparative analysis do?
Establishing evolutionary relationships to aid in making hypotheses about specific trait dynamics ie. association btw habitat and activity, testes size increases/decreases w/ age