Lecture 22

Question 1

transitions

Answer 1

a mutation within the same nucleotide class (C <–> T) or (A <–> G)

Question 2

transversions

Answer 2

a mutation that is between different nucleotide classes (A,G <–> C,T)

Question 3

This model is the simplest, with all mutation rates remaining the same

Answer 3

JC (Jukes-Cantor) Model

Question 4

This model is slightly more complex than the JC model, and is defined by two different rates of mutation depending on whether there is a transition (alpha) or transversion (beta)

Answer 4

HKY85 Model

Question 5

This is the most complex model, where each nucleotide mutation rate is different depending on what it is mutated to (6 different rates). Also exists for AAs and Proteins

Answer 5

General Time Reversible (GTR)

Question 6

some sites evolve consistently at different rates than others

Answer 6

Among-Site Rate Variation (ASRV)

Question 7

Sources of ASRV

Answer 7

1. codon positioning
2. functional constraints (important vs unimportant)
3. RNA stem vs loop

Question 8

Assumes that some sites dont evolve at all

Answer 8

Invariable sites

Question 9

used to model model site rate and homogeneity, gives an alpha value that coordinates with the model that best fits your data

Answer 9

Gamma-distribution

Question 10

Define Saturation

Answer 10

When there is an observed mutation rate less than expected due to mutliple mutations that “cancel out.” These are not seen as the level of mutations becomes saturated.

Question 11

Variance biogeography

Answer 11

mapping geography and a trait onto trees