W4L1 Inferring phylogeny.pdf

Why are characters 142 192 not parsimony informative

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- Why are characters 142 & 192 not parsimony informative? - Note that many characters are not variable - The “X” means “we don’t know” (bad data). Usually this is denoted with either “?” or “N” Informative & uninformative characters using parsimony Take home question 296 1 2 3 4 5 A C A G C G B C T A C A C C A A T G D A T A T A WHICH OF THESE TREES IS THE MOST PARSIMONIOUS?
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Outline Parsimony Maximum Likelihood Bootstrapping Bayesian Inference 297 Maximum Likelihood 298 L(tree) = P (data | tree topology, branch lengths, model of sequence evolution) To infer phylogeny using maximum likelihood - For every tree, calculate the likelihood of the tree - This likelihood is the probability of the data given a tree topology, branch lengths, and a model of evolution - The model of evolution = a statistical description of the evolutionary process - Choose the tree with the highest likelihood - ML is similar to parsimony in that it uses an optimality criterion How to calculate a likelihood 299 Fig. 4.26 ambiguous data L(tree) = P (data | tree topology, branch lengths, model of sequence evolution)
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300 Fig. 4.26 How to calculate a likelihood 301 Fig. 4.29 - The numbers next to the nodes on the tree indicate support for that node. - These are called “bootstrap support” values. - 100 is a maximum, and 70 is considered pretty good. How to estimate clade support Bootstrapping 302 How to estimate clade support Bootstrapping To build replicate data sets, sample with replacement from the original data set. This is called “bootstrapping.” We have made 5 bootstrap replicates above Fig. 4.28 Original data set for 3 taxa and 1 outgroup
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303 Fig. 4.28 How to estimate clade support Bootstrapping Build a tree from each replicate data set Original data set for 3 taxa and 1 outgroup 304 Fig. 4.28 How to estimate clade support Bootstrapping The percentage of time a clade is recovered is it’s bootstrap support 305 Fig. 4.29 - To calculate the BS support for a clade, find the percentage of BS replicates that recover that clade in a phylogenetic analysis - Clades with lots of
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  • Spring '18
  • MORRIS
  • outgroup, tree making

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