Lecture 22: Phylogenetics Models And Discussion

Question 1

DNA is composed of 4 nucleic acids (bases)

Answer 1

A, C, T, G, belonging to 2 classes, purines and pyrimidines

Question 2

Nucleotide data

Answer 2

Transitions, transversions, transition/transversion types, base frequencies

Question 3

Models are defined by their structure

Answer 3

Which items are in which categories, not by the specific numerical values

Question 4

3 common models

Answer 4

JC (Jukes-Cantor)
HKY85 (Hasegawa-Kishino-Yano 1985)
GTR (General Time Reversible)

Question 5

JC models

Answer 5

Simplest, all rates equal (1 rate), all base frequencies equal

Question 6

HKY85 model

Answer 6

Transition/transversion ratio (2 rates), base frequencies unequal

Question 7

GTR

Answer 7

Most complex, every nucleotide pair has its own rate (6 rates), base frequencies unequal

Question 8

Protein data

Answer 8

Models exist for proteins, but very complex (20 x 20 for amino acid or 64 x 64 for codon matrices)

Question 9

Among-site Rate Variation

Answer 9

Some sites (characters) evolve consistently at different rates than others

Question 10

Sources of ASRV:

Answer 10

Codon position (1st vs 2nd vs 3rd), functional constraints (important vs unimportant), RNA stem or loop

Question 11

Power of phylogenetics

Answer 11

Is making predictions about the past without direct (fossil) evidence:
WHAT (traits did an ancestor have)?
WHEN (did an event happen)?
WHERE (did it live)?

Question 12

Mapping geography and a trait onto trees (Vicariance biogeography)

Answer 12

Treat areas as if they were characters; allow reconstruction of geologic history

Question 13

Ratite birds

Answer 13

Their common ancestor did fly, explaining why the phylogeny does not match the geographic breakup of Gondwana

Question 14

Transistions

Answer 14

Within a class (change shape)

Question 15

Transversions

Answer 15

Between a class