ancestral state reconstruction on a single fixed tree

[Joseph Ryan]

Hello,

I am trying to perform ancestral state reconstruction of a single trait on a single fixed tree. I have tried, without luck, to adapt the excellent revbayes tutorials to this task. (I understand the utility of using a tree distribution, but this is not an option in our case).  Would it be possible to get some advice from you all on how to do this? 

While I'm here, I would also appreciate any advice on any key parameters that we should explore in our analyses. For example, Ekman et al., 2008 (http://goo.gl/2Vl8CH) explored a range of models in BayesTraits (e.g., reversible-jump MCMC unrestricted with uniform prior distribution and uniform(0,10) hyperpriors,  reversible-jump MCMC on a single-rate model with uniform prior distribution and uniform(0,10) hyperpriors, fixed gamma-distributed prior on transformation rates). Any advice here I realize would be above and beyond software support, but would be greatly appreciated.

Best wishes,

Joseph Ryan

[Sebastian Höhna]

Hi Ryan,

if I understand you correctly, then you want to fix the tree to an estimated phylogeny from some other analyses.Then you want to estimate ancestral states for a single trait, right?

In the tutorial from Will Freyman, he is reading in a tree as a starting tree (starting_tree <- readBranchLengthTrees("data/matK_starting_tree.nwk")[1]). You could simply use this tree variable instead of specifying a prior distribution and estimating it. You could have a look into the morphology tutorials (https://github.com/revbayes/revbayes_tutorial/tree/master/RB_Morphology_Tutorial) were we do this.

I haven't looked into the paper by Ekman et al. When I get the time I'll send you some advice on it. I hope this helps you to get going for now.

Best,

Sebastian

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