Exam 3: 10 Flashcards
What is a model?:
Some representational description of something else.
Can be:
- An image
- An equation
Components of a model
Parameters and relationships
What makes a good model?
Simplicity, predictive ability, and realism
Why parsimony（简约法）is useful
It provides a computationally simple way of determining evolutionary relationships
Problem with parsimony
When there is real homoplasy and real noise, it makes errors. Because homoplasy（非同源相似性）and noise are not parsimonious but they happen in the real world.
What does likelihood represent in a bell curve?
How reasonable a model is given observations.
*Takes parsimony into consideration.
Why is likelihood useful?
It accounts for homoplasy and noise and therefore makes better trees.
*Does this by having a MODEL FOR EVOLUTION that is more complex than simply “characters evolve parsimonioysly”.
Bayes theorem
The (posterior) probability of a model given the data is equal to the likelihood of the data given the model, times the prior probability of the model, divided by the probability of the data.
Why is Bayesian useful?
It provides a statistical framework, AND has a method of incorporating prior information
Assumptions of 1 parameter nucleotide substitution model
- All nucleotides have the same frequency
- All nucleotides are equally likely to be substituted by any other nucleotide.
Parameters: Substitution rate
Assumptions and parameters of 2 parameters nucleotide substitution model
Assumptions:
1. All nucleotides have the same frequency
2. Transitions are more likely than trans versions
Parameters:
1. Transition rate (point mutation: A<->G (purines) or C<->T (pyrimidines))
2. Transversion rate (purines to pyrimidines)
Assumptions and parameters of n parameters nucleotide substitution model
These models can be expanded to include all the information we know about DNA function and evolution.
