search algorithm allows for a collection of posterior ... · 10/29/2018 · beast - bayesian...
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Search algorithm allows for a collection of posterior trees that can be both used in subsequent analyses and help interpret the phylogenetic result
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Sampling through time. E.g. Tracing the spread of Salmonella resistance
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Careful not to treat it like a black box.
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Model testing can be done within Beast (path sampling).
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Broom vs bush trees
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Really need some sort of hard bound on a node: many studies will use a maximum
age of the group
C volcanic emergence : uniform prior with hard upper limit : equal prob after the
event.
F fossil: lognormal: most of distribution around the age of the fossil but a tail that lets
the node age be older.
J1-4: breakup (beginning and late) of land: normal broad priors around the age that is
known
M2-2:opening up of a straight: exponential
We are
going to set M = 1:78 and S = 0:085 which will specify a distribution centred
at about 6 million years with a standard deviation of about 0.5 million years.
This will give a central 95% probability range covering 5-7 Mya.
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Yule: birth only (probably only reasonable for closely related organisms) BD: includes extinction in the model
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