W2 L2 Phylogenetic p2 W Flashcards
Searching tree space
-When the number of species increase, the amount of three that connect species increase
-The selection of tree is based on heuristic search
BAsic principle of heuristics
-Getting a start tree
-modifying the start tree and evaluating the choices
- many algorithm can be used
Getting a start tree
- stepwise: adding one new member at a time
-star decomposition: using likelihood to create polytomy from an uprooted tree - distance method
Branch swapping
NNI: nearest neighbor interchange, evaluate the change and compare it to the original. The better one is then kept SPR: sub tree pruning and regrafiting, a branch is moved into a new position
TBR: tree bisection & reconnection. Separate and reconnect in a different configuration
why must we carryout Heuristic search many time
Hill climbing algorithms will not always climb the tallest hill (when only used once)
Software will differ in how likely they are to find the optimal tree
* Use multiple start trees to start hill climbing process
Why use different model
- different result based on different model
-Maximum likelihood is Favor over MP when two set of data are contradicting
Advantages of likelihood-based methods
- Deals better than MP with differences in rates between lineages (be cautious of long branches clustering together)
- ML handles this better because it takes the possibility of homoplasies into consideration (parallel, convergent and back substitutions)
- Major advantage that different types of substitutions (and different sites) carry a more realistic weight thanks to use of models
- Reasonably robust against different types of model violations as long as model is a decent approximation of actual process of molecular evolution
- Computationally more expensive
Bayesian phylogenetic inference
Enriching interpritation
-taking the data, letting the branch length to associate with a factor (time/ amount of evolution)
Dating trees for richer interpretaion
- Interpret branching times with earth history
- Localise key events in time (e.g. genome duplication, radiation of gene family)
- Interpret biogeographic scenarios
- When did characters originate?
- Calculate rates of speciation
Molecular clock and phylogeny
- The “molecular clock” ticks at a constant rate
- Seldom true à relax that assumption by modelling rate variation
Relaxing the molecular clock
-take into account autocorrelation: rates are hereditary due to these hereditary element:
* Generation times
* DNA proofreading mechanisms
* Habitat conservatism
* Small rate changes are more likely than large changes
OR sample branch lengths from a distribution
Using fossils to constrain node ages
-look at fossil that is linked to our organism group based on morphology
-Chronogram with node ages and error bars this inform us the age (length of the branch)
question in regard to Trait evolution
- When did a particular character appear in the history of a group and how does this match up with earth history?
- How frequently do changes in that character happen over evolutionary time?
- Are different evolutionary changes equally likely to happen?
- Do some organisms evolve faster than others?
- What’s the role of directional selection in shaping organisms’ traits?
Macroevolutionary inference
-From fossil record: observe when characters appear and disappear
-relationship unclear
From phylogenies
l relationships clear
l infer when characters appear and disappear
