Lecture 8

Question 1

What happens if you have more than one “best tree”?

Answer 1

create a consensus tree

Question 2

majority-rule consensus tree

Answer 2

includes clades only present in specified number of “best” trees, with the % scores at each node

Question 3

Confidence in phylogenetic inferences can be thought of in 2 ways:

Answer 3

1) dtmn if there is meaningful signal in dataset

2) assess confidence in particular clades/topological conclusions

Question 4

detecting nonrandomness in a set:

Answer 4

look at extent to which characters within a matrix contradict each other

Question 5

Permutation Tail Prob (PTP) Test

Answer 5

• using any method that assigns score to individual tree (pars, ME, ML)
• compares score of shortest optimal tree to scores of trees found with random permuted data sets

Question 6

parsimony PTP test

Answer 6

if length of shortest optimal tree is shorter than all/nearly all random trees-> data has more phylogenetic structure than would be expected from random

Question 7

permutation

Answer 7

character states of each character independently shuffled among taxa

Question 8

point estimate of phylogeny

Answer 8

pars, distance, and likliehood

Question 9

decay index (Bremer Support)

Answer 9

• difference in tree length between the optimal tree and the optimal tree lacking the clade in question
• higher number means stronger support
• for likelihood: diff in log-likleihood scores (ratios)

Question 10

bootstrap (general)

Answer 10

• assesses the chances of recovering a particular clade again if we were able to sample from a new set of characters
• simulates other possible datasets by randomly drawing from data
• informs on consistency of branching patterns

Question 11

nonparametric bootstrap

Answer 11

• sampling with replacement (pseudoreplicate)
• tree search performed on pseudoreplicate datasets and resulting tree(s) added to optimals
• proportion of bootstrap trees with a given clade is the score
• usually presented in a bootstrap consensus tree

Question 12

jackknife

Answer 12

same as bootstrap but sampling WITHOUT replacement

Question 13

parametric bootstraping

Answer 13

• generates new data sets by simulating them with evolutionary model
• used mostly in ML analyses to test specific hypotheses, not clade support (ie controversial placing of sister clades)
• random seq conforming to models assumptions placed at base of tree and then allowed to evolve along branches-> repeat for all positions in seq and all branches in tree

Question 14

Bayesian posterior distribution

Answer 14

• Bayesian not point estimate

- distribution has sample of trees ranked by prob that each is the true tree

Question 15

Bayesian posterior probability (BPP)

Answer 15

• majority-rule of topology examined
• prob that tree is correct, assuming model is correct
• clade-credibility values (0.0-1.0)
• can be sensitive to model misspecification, use most complex model, faster

Question 16

Partition homogeneity test (PHT)

Answer 16

• evaluates data set conflicts
• randomly assigns characters to partitions many times and then conducts a phylogenetic analysis of random partitions
• pars, ME, or ML
• similar to PTP (smaller is better)

Question 17

Species tree

Answer 17

the relationships among spp when contrasted with gene trees; most assume gene-to-gene discordance due to incomplete lineage sorting

Question 18

Minimizing deep coalescence (MDC)

Answer 18

• parsimony based
• search among spp trees to find topology that minimizes the total # of deep coalescence events
• shortcoming: fails to use branch length estimates from individual gene trees

Question 19

Multi-species coalescent

Answer 19

• assumes gene coalescence always predates spp divergence
• likelihood of gene tree given a spp tree is function of gene data/spp tree, including branch lengths and widths
• L of a spp tree given set of genes is function of the summed gene likelihoods

Question 20

Bayesian concordance factor (BCA)

Answer 20

• estimates the extent of gene discordance without assuming any one source
• measure of the prior prob of gene-to-gene discordance to estimate the prop of genome for which any clade is true (concordance factor)
• scores on tree