Bayesian Inference of Phylogenetics Revisited: Developments and Concerns

Question 1

What is the title of the Journal Article?

Answer 1

Bayesian Interference of Phylogenetics revisited: Developments and Concerns

Question 2

Who are the authors of the journal?

Answer 2

• Christopher P. Randle
• Mark E. Mort
• Daniel J. Crawford

Question 3

has become prominent in phylogenetic studies utilizing molecular evidence

Answer 3

Bayesian Methodology

Question 4

What is the program most often used in Bayesian inference of Phylogenetics?

Answer 4

Mr. Bayes

Question 5

How many times is MrBayes cited?

Answer 5

833 times

Question 6

algorithm used in Bayesian methodology

Answer 6

Markov Chain Monte Carlo (MCMC)

Question 7

Why does the upgrade in computational speed occurs during the MCMC process?

Answer 7

because clade support can be estimated during the MCMC process, necessary for bootstrap and jackknife estimates.

Question 8

It is prohibitively intensive for even moderately sized datasets

Answer 8

Likelihood bootstrapping

Question 9

According to Reed & al (2002) a likelihood bootstrap of 60 taxa lasted for how many days?

Answer 9

80 days of CPU time

Question 10

Bayesian inference results in the estimation of the

Answer 10

posterior probability distribution

Question 11

posterior probability of any parameter value may be determined from?

Answer 11

posterior probability distribution

Question 12

may be interpreted as the probability of an hypothesis given the data, model, and a set of prior probabilities.

Answer 12

posterior probability

Question 13

is a more direct assessment of hypotheses than is the likelihood function

Answer 13

posterior probability

Question 14

probability of the data given an hypothesis and process model

Answer 14

likelihood function

Question 15

In Bayesian phylogenetics, ________, are all treated as parameters, and, therefore, posterior probabilities may be determined for any of these

Answer 15

tree topology
branch lengths
elements of the process model

Question 16

allows for the testing of hypotheses other than monophyly, including the inference of ancestral character states, the estimation of branching times when rates are not homogeneous acorss branches, and the role of selection in determining codon composition

Answer 16

Bayesian Phylogenetics

Question 17

issues of Bayesian Phylogenetics according to Archibald & al (2003)

Answer 17

model choice
effect of prior probability distributions on posterior probability

Question 18

A Markov chain is said to have converged if it obtains the posterior distribution that would have been obtained by the exact calculation of Bayes theorem

Answer 18

Convergence

Question 19

increase in the ‘temperature’of a Markov Chain

Answer 19

Heating

Question 20

the process by which parameter values are altered more drastically at each proposed step of the chain

Answer 20

Heating

Question 21

This allows for a more rapid sampling of a broad parameter space

Answer 21

Heating

Question 22

The process by which the posterior distribution of parameters is sampled in Bayesian phyloegenetics

Answer 22

Markov Chain Monte Carlo

Question 23

the process begins with a topology, branch lengths and other process parameter vales, drawn from the prior

Answer 23

Markov Chain Monte Carlo

Question 24

In MCMC, at each step, one or more parameter value is altered resulting in a new tree proposal to be evaluated against the inital hypothesis according to the ____________.

Answer 24

Metropolis-Hastings algorithm

Question 25

Markov chains that visit many islands of parameter space efficiently are said to mix well

Answer 25

mixing

Question 26

The probability of a hypothesis not conditional on the data at hand

Answer 26

Prior probability

Question 27

the outcome of Bayesian analysis

Answer 27

Posterior Probability

Question 28

probability of an hypothesis conditional on the data, the likelihood of the data as estimated using a process model, and prior probability of the hypothesis

Answer 28

Posterior Probability

Question 29

In statistical-based methods of phylogenetic inference, a ____ must be incorporated for any assessment of probability to take place, because a phylogeny itself implies nothing about the probability of data.

Answer 29

process model

Question 30

composed of parameters

Answer 30

process model

Question 31

specified ways that character states may change according to a continuous-time Markov chain

Answer 31

process model

Question 32

the simplest model for nucleotide data, which allows a single probability of nucleotide substitution

Answer 32

Jukes-Cantor 69