Inferring phylogeny from sequence variation Flashcards
What are the two types of tree
Phenograms and phylogentic trees
What does ultrametric mean
A tree with equal root to tip path lengths for all lineages
What are cladograms
Y axis has no meaning
What are additive trees
Y axis tells us about the amount of evolutionary change
Whats a fully bifurcated tree
Assumes all speciation events involve one thing splitting into two
What are mutlifurcated trees
Node splits into more than two species, could be rapid speciation event
Why do we construct phylogenies
To know how species are related to eachother
How do we add a root to a tree
Add information for an outgroup
Whats an outgroup
A taxon that we believe to be more distantly related to the focal species than they are to one another
All trees to consider
Taxa, unrooted, rooted
How do we estimate genetic distance
K = porportion of nucleotide sites that are different
Whats an UPGMA
unweighted pair group method with arithmetic mean
Whats the jukes cantor distance correlation
The more evolutionary distance there is, the more likely there’s more hits
Whats the Jukes cantor equation
Kjc = -(3/4)ln[1-(4/3)k]
Examples of when phylogenies are useful
Flying mammals, did they evolve once or twice
Limitations to phylogenetic trees
Trees are hypotheses
Scoring characters is hard
Homoplasy
Ancient events are hard to infer
Some lineages might be adapting too rapidly
Hybridisation may be a problem
