Introduction/Modeling Molecular Evolution
Type of inference methods commonly used when speed of analysis is more important that phylogenetic precision
What are methods based on evolutionary distances?
The calculation of the proportion of traits that differ between a set of taxa
What is pairwise distance?
The probability that the present data would have arisen under the given hypothesis
What is likelihood?
Bayesian inference judges trees based on their _______ ________, the probability the tree is true, given the data, the models of evolution, and any prior beliefs
posterior probability
University of California - Berkeley
Who is Natasha Stepanova?
All models in widespread use in Phylogenetics are continuous-time ______ ______, meaning they describe a process in which the probability of an event happening is dependent only on the state at that time and independent of how it came to be in that state
What is a Markov model?
This algorithm is widely used in situations where we need a quick, approximate estimate of a true phylogenetic tree
What is the neighbor-joining (NJ) algorithm?
The difference between maximum likelihood and maximum parsimony (chapter 7)? MP seeks to find the tree topology that requires the fewest changes in character states to produce characters of tip species, while ML seeks to find the tree topology that confers the ______ ________ on the observed characters of tip species.
What is the highest probability?
Pr(H|D) = Pr(D|H) x Pr(H) / Pr(D)
What is Bayes' Theorem?
California State University
Who is Sam Borstein?
How far apart two taxa are from each other; (in terms of DNA sequence data) the average number of substitutions that have occurred at each nucleotide position
What is the evolutionary distance?
This distance method involves choosing the optimal branch lengths for a given tree topology using the least-squares method and results in a tree topology on which total branch length is minimized
What is the minimum evolution method?
Maximum Likelihood relies on a comparison of likelihoods of two competing hypotheses. This comparison is called the ______ ______ and is usually presented as a natural logarithm. It is a measure of support for one hypothesis vs another
What is the likelihood ratio?
A type of analysis used in Bayesian Phylogenetics that calculates relative posteriors of different trees, because calculating actual posterior is not easily done
What is the Markov chain Monte Carlo (MCMC) analysis?
California Polytechnic State University
Who is Hayley Crowell
This type of model assumes all four nucleotide bases occur at equal frequency, each substitution occurs at equal rate, and substitution rate is that same for all nucleotide positions
What is the Jukes-Cantor model of molecular evolution?
The minimum evolution tree in Figure 8.14 (page 238) gives branch lengths based on this quality, rather than average number of substitutions per site as seen in a neighbor-joining tree.
What is the average number of character state changes per character?
When making trees using ML, branch length is determined by these two components (which are difficult to disentangle) and represented by the product: "ut"
What is the branch duration and the branch's rate of evolution?
The numbers written on the branches in figure 8.26, pg 257 represent the fraction of trees in the posterior sample that contain the clade in question. These are used when building this specific type of tree.
What is a Bayesian majority-rule consensus tree?
University of California, Santa Cruz
Who is Alison Davis-Rabosky?