front 1 Main impetus behind development of Bayesian analysis? | back 1 Faster way to do models of evolution and use statistical approaches, past was computationally intense(?) Discrete data, clustering Not a true optimality method optimizing models of evolution and parameters |
front 2 Advantages of bayesian analyses | back 2 faster than a maximum likelihood approach not only a result but also an estimate on how certain I am, able to put a probability score on a node has become primary method of figuring out phylogenetic relationships parsimony eventually find wrong tree long branch attraction ^: tends to cluster two branches together than evolve rapidly |
front 3 L= Prob (Hypothesis|Data) | back 3 Our hypothesis is the tree and the data is analyzed. Start w/ initial hypothesis Initial understanding is is going to influence guess. |
front 4 Accuracy | back 4 how close is it to the true tree? |
front 5 Precision | back 5 how certain are you? How narrow is our range on our true and correct tree? |
front 6 How can we know if our methods are accurately determining historical phylogenetic relationships? | back 6 We can never be sure we are entirely accurate. Simulated data sets that methods are able to recover can help us be sure and confident in accuracy of results + as well as known phylogenies like bacteria. congruence between trees |
front 7 Prior Probability | back 7 if I go into an analysis with some information then I have more power to help inform my subsequent analyses. |
front 8 Posterior Probability | back 8 after initial test, becomes prior probability for new rounds of analyses. |
front 9 Burn- in period | back 9 analyses eventually reaches a plateau red ones, getting results out, stepping stones for getting better estimates |
front 10 MCMC | back 10 short cut to speed up all estimations we have to do, aka when too complex. Quick way to simulate a complex search space. using elevation to figure out if a good solution or a bad solution. allow to sample search topography, might end up isolated so repeated to find best solution |
front 11 plateau period | back 11 blue one, these trees are saved |
front 12 What is the final outcome of a bayesian analysis and how is this represented in a phylogeny? | back 12 results in lots of trees from the plateau phase, consensus tree / majority rule tree created, does the estimation faster than maximum likelihood method, but also gives us a number to show how often those relationships were there / how certain we are of those relationships. "support values" ^^ |
front 13 Neighbor joining | back 13 starting point (?) |
front 14 Posterior probability values | back 14 ??? |
front 15 Congruence | back 15 do two phylogenies match? |
front 16 What is the best method to find the phylogenetic relationships of a group and what does congruence have to do with this? | back 16 Congruence of methods shows accurate representation of analysis. when bayesian analysis is done, part of process gives us support values can be confident in results when compiled with parsimony and maximum likelihood analyses when unsure, taxon sampling or increase data set! |
front 17 Taxon sampling | back 17 what species do I choose to put into my analysis? best strategy is - what group are we working with? |