R23 Phylogenetics (building trees) Flashcards
What does ‘Taxonomic ranks are arbitrary” mean ?
Made by one person
Molecular phylogeny is much more resolved rather than arbitrary
What do these components of a tree mean:
- Direction arrow
- branches
- nodes
- clades
Direction arrow shows time, from older to modern species
branches are the edges
root node are the most recent common ancestors and leaf nodes are the tips, the modern species we are sampling
clade: everything stemming from one node
How many types of trees are there to show the exact same phylogenies ?
4
What data can phylogenies show ?
trait data, morphological data, molecular data
What is an example of clustering algorithms ?
UPGMA (unweighted pair group method with arithmetic mean)
Clustering using pair wise similarities, then the difference between the other cluster is the distance in the branch
What is the problem with parsimony reconstructions ?
Not all changes are equally likely, different mutation rates and substitution rates
We need to check a large number of trees to be sure we found the best one
What are the solutions to parsimony reconstruction?
A substitution model shows the maximum likelihood tress using probability
Only look at plausible trees, use efficient algorithms, subtree prune and regrafts
What do trees do ?
Trees reflect inheritance, flow of genes through time, allow a model for evolutionary changes through time
What is parsimony ?
The easiest, most simplest hypothesis is correct
How can we root an unrooted tree ?
Place the line in different locations and make that the root
Multiple trees may be correct
UPGMA will give a different topology to than rooting an unrooted tree. How ?
Species that are closest together will be placed on the tree with the most recent common ancestor
The path with lowest mutations is taken as the shortest branch
What is midpoint rooting ?
When we place the root at the centre of the unrooted tree
What is a tree called when the branch length information is not present ?
Cladograms
If two species diverted but have different length branches with different number of mutation events how do we work out how long ago they diverted?
Work out an average between both branches
Why do phylogenetic branches differ in length ?
- Substitution rates vary between branches
- Samples differ in age
- Mutations are random, so some branches accumulate more by chance.
