11.2

Question 1

LTT

Answer 1

plot of # of ancestral lineages of contemporary spp as a function of time; needs ultrametric tree

Question 2

Waiting time and cladogenesis

Answer 2

• sister clade comparison method
• test whether evolutionary history of candidate trait is associated with shorter waiting times btwn cladogenesis events
• good for unique events, recently evolved innovations, and traits that exhibit homoplasy

Question 3

Issues with “key innovation” hypotheses

Answer 3

• each ancestral branch may have more than one apomorphic trait-> can’t know which is the “key”
• more than one trait may be acting in combo
• if trait arose only once in clade, how do you test if it confers advantage in all cases

Question 4

key innovation

Answer 4

biological trait that promotes lineage diversification by inc rate of speciation or dec rate of extinction

Question 5

Detecting Unexpectedly Large/Small clades

Answer 5

• test every node in phylogeny; make Bonferroni correction to estimate p-values
• likelihood tests involving birth-death process; estimate speciation/extinction rates for entire clade and then use values to calculate prob of each clade being as large as it is
• likelihood ratio tests

Question 6

Mean path length

Answer 6

• measure of clade imbalance

- sum of # of nodes below each tip; total length from root to tip (species)

Question 7

Colless’s I

Answer 7

• measure of clade imbalance

- sum of absolute values of the difference between the # of taxa in every pair of sister clades

Question 8

How to measure imbalance of clade? (general)

Answer 8

multiple trees of same size are simulated from null distribution and imbalance of clade is compared to generate a p-value

Question 9

Yule process

Answer 9

• aka uniform speciation, pure birth
• mod of birth-death process where extinction rate is assumed to be 0
• easier for calcs

Question 10

Birth-Death Model Equation

Answer 10

Noe^(rt)
r = speciation rate - extinction
No = # of spp at time 0
t = time
e = natural log ish

Question 11

Equiprobable Trees

Answer 11

• null model of character evolution; generates trees randomly so each possible labelled topology is equally likely; produces particularly imbalanced trees
• if actual observations fall far outside of expected distribution-> null may be rejected

Question 12

Random Branching/Random Joining

Answer 12

null model of character evolution; assumes each branch has equal chance of splitting; unexpectedly imbalanced; only concerned with probability of a topology

Question 13

What 3 things is the rate of evolution dependent on?

Answer 13

1) rate of mutation
2) rates of selection
3) rate of environmental change

Question 14

Limits of molecular clocks

Answer 14

• changing generation times
• population size
• species-specific differences (metabolism, ecology, ect)
• change in function of protein used
• changes in intensity of natural selection

Question 15

Challenges for molecular clock at short/long timescales

Answer 15

long: saturation

very short: differences do not represent fixation for diff pops

Question 16

Rates of molecular change assuming a molecular clock

Answer 16

D =2rt
D-> proportion of base pairs that differ btwb 2 sequences
r-> rate of divergence per bp per Myr
t-> time in Myr since common ancestor
2-> 2 diverging lineages

Question 17

BEAST

Answer 17

• accounts for uncertainty

- does not require any nodes/ages to be fixed

Question 18

shortcomings of Thorne’s Bayesian Relaxed Clock

Answer 18

• requires root prior

- uncertainty in phylogeny not accounted for