W2 L1 phylogenetic M

Question 1

What is phylogenetic

Answer 1

• Estimating the evolutionary relationships among species (or genes, or both) from molecular sequences

Question 2

how to make a phylogenetic tree whent some animal are already extinct

Answer 2

• Data are available only for extant species (genes)
• What happened in the evolutionary past must be inferred (estimated) statistically

Question 3

Working sequences of extinct species

Answer 3

• fossil give us an estimate date, useful for calibration
• phylogenic analysis and node age reconstruction
• diversification analysis and ancestral state reconstruction

Question 4

Phylogenetic terminology

Answer 4

Closely related species are called sister species

Question 5

Rooted and unrooted trees

Answer 5

Rooting gives directionality to a tree
* Without a root you cannot speak of ancestors, descendents, etc.

Question 6

Stylistic vs. meaningful differences

Answer 6

In phylogeny, the length represents the changes

Question 7

Different between branch and tree

Answer 7

Question 8

Resolution of a tree

Answer 8

Polytonal is where two or more species emerges

Question 9

Hard vs. soft polytomy

Answer 9

Hard polytomy occur when speciation while soft polytomy is when we don’t have enough data

Question 10

Step in building a phylogeny

Answer 10

• start from sequence alignment, the idea of having a common ancestor
  Method involve are
  Distance trees
• Counting changes: maximum parsimony
• Modeling evolution: maximum likelihood
• Searching tree space
• Bayesian inference

Question 11

Distance trees

Answer 11

• Conceptual framework:
• Convert character data to distance matrix
• Use distance matrix to construct dendrogram
• Interpretation as evolutionary trees?
• Fast (no evaluation of many trees)
• UPGMA gives rooted, ultrametric trees
  (assumes molecular clock)
• NJ gives unrooted trees

Question 12

Counting changes, maximum parsimony

Answer 12

The simplest explanation requiring the fewest assumptions should be preferred over more complicated hypotheses.
Translated towards phylogeny
The MP phylogeny is the one that requires the fewest evolutionary steps.

Question 13

Modeling evolution: maximum likelihood

Answer 13

Model describes mathematically how molecular sequences evolve
Why likelihood?
* Mathematically explicit: no hidden assumptions
* Results expressed in terms of probability
* Superior performance in phylogenetics

Question 14

Markov models

Answer 14

Simple stochastic process in which the distribution of future states depends only on the present state
* Simplest case: binary character with states 0 and 1

Question 15

Why is maximum likelihood favored over other model

Answer 15

• different base frequency
• different substitution rate
  -reversion and multiple changes

Question 16

Basic elements of General Time Reversible (GTR) model

Answer 16

• we assume that the rate of change and the reversal rate are the same as each other
  -5 model parameter instead of 12
  Base frequencies
• 4 base frequencies
• 3 model parameters
  [ ] F = p A p C p G p T
  €
  πT =1−(π A + πC + πG )

Question 17

Among site variation

Answer 17

• different site have different mutation rate from each other, this can be taken account by the model

Question 18

Likelihood computation

Answer 18

The likelihood L is the probability of the data given the model.
* The data consist of an alignment of sequences.
* The model is a hypothesis of how the data were generated.
* contain topology, branch lengths and other model parameters (base frequencies, rate matrix, gamma shape, …)
* Different topologies are evaluated one at a time.
* Each time, branch lengths and other parameter are optimized.
* Each site has a likelihood, the total likelihood is the product of all site likelihoods.
* The ML tree is the topology corresponding to the model that yielded the highest overall likelihood.
* Likelihoods are reported on a logarithmic scale for mathematical convenience: ln L