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.
What is the use of a molecular clock ?
allow substitution rates to differ between branches
What is topology ?
The branching pattern of a tree, what it looks like
How do you fill in a pairwise distance matrix to build a tree?
find the smallest distance, those 2 species are now a cluster in the following matrix
find out the distance from that cluster to the other species and fill in a new matrix. Distance to the other species is calculated by: d(A,B)= d(A,X)+d(B,X) / 2
A and B are the newly merged cluster and X is another specie
then repeat with the next smallest distance and another matrix until all species are clustered
The last specie to be clustered is the one that diverts first, then the second last to be clustered diverts second and so on, the branch length they diverted by will be in the matrix
What assumptions is UPGMA making ?
rate of evolution is constant across all lineages
pairwise distance is additive, no evidence of unequal mutations or horizontal gene transfer
What determines the steepness of a lineage through time plot, which measures the (log) number of species against time?
the ratio of the speciation and extinction rate S/E
the carrying capacity for the clade
the difference between the rate of speciation and the rate of extinction, i.e. S -E
the amount of incomplete lineage sorting for the clade
the difference between the rate of speciation and the rate of extinction, i.e. S -E
What is the the “pull of the present”?
a speed-up in the recent past in the rate of lineage diversification inferred from a dated phylogeny
the expected increase in the (log) number of lineages for a clade with non-zero extinction rate
the artefactual upturn in the (log) number of lineages in the recent past if we include both extinct and extant taxa
the effect of niche filling on the change of the (log) number of lineages in the recent past
the expected increase in the (log) number of lineages for a clade with non-zero extinction rate
When might a phylogeny reconstructed using UPGMA be incorrect?
the principle of maximum parsimony is violated
we have specified the wrong root
we have assumed the wrong substitution model
rates of evolution vary drastically between taxa
rates of evolution vary drastically between taxa
