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rvosa authored Oct 26, 2017
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Expand Up @@ -42,18 +42,20 @@ vascular plants ([_Tracheophyta_](http://eol.org/pages/4077/overview)).
group, and so do hornworts and vascular plants (A,T), resulting in:
`((Marchantiophyta,Bryophyta),(Anthocerotophyta,Tracheophyta));`
**In the manuscript, this is considered the preferred rooting, which we will explore
in more depth than the others.**
in more depth than the others. Earlier versions of the analyses also explored MBasal,
so there may be reference to that here and there.**

For each of these rootings, we performed a BEAST analysis to date the trees. The results
of these analysis are part of a separate (too-large-for-github) submission available at
For each of the rootings, we performed a BEAST dating analysis. The results of these
analyses are part of a separate (too-large-for-github) submission available at
[10.5281/zenodo.1037548](http://doi.org/10.5281/zenodo.1037548).

## Comparative analysis

Using the consensus trees, we performed phylogenetic comparative `multistate` analyses
with the program [BayesTraits](http://www.evolution.rdg.ac.uk/BayesTraits.html), in which
each state change is a transition that is modeled in a Q matrix, which is amenable to
parameter restriction so that various hypotheses can be tested using Bayes Factors.
Using consensus over the BEAST trees, we performed phylogenetic comparative `multistate`
analyses with the program [BayesTraits](http://www.evolution.rdg.ac.uk/BayesTraits.html),
in which each state change is a transition that is modeled in a Q matrix, which is
amenable to parameter restriction so that various hypotheses can be tested using Bayes
Factors.

Because different higher taxa among the mycorrhiza can associate with land plants in
[a variety of observed combinations](results/legend.pdf) there is potentially a very
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