I'm not sure of any particular methods that do this, but one preliminary
approach that you could try is combining the two traits into a single trait
(00, 01, 10, and 11) which you could then analyze with any of the standard
methods. You could then look for whether any of the states have higher or
lower diversification rates.

Another approach, particularly easy for large trees, is to calculate the
equal splits metric for your tips (evol.distinct in picante) and then
perform a t-test or other statistical test using your trait data. Come to
think of it, you could actually keep your original two traits and perform
an ANOVA on the equal splits measurements, which would allow you to test
for a significant relationship between either of your traits and the
diversification rate and whether there's a significant interaction between
your two traits which produces higher or lower div. rates.

Best,
Will

On Mon, Jun 18, 2018, 4:46 PM Elizabeth Christina Miller <
ecmil...@email.arizona.edu> wrote:

> Hello,
>
> I am wondering what comparative method(s) is appropriate for testing if
> diversification rates are highest when two traits are present together,
> rather than one alone? Specifically, if I have two binary traits, let's say
> freshwater/marine and temperate/tropical, what is the best way to test if
> diversification rates are highest in tropical+freshwater groups, as opposed
> to tropical+marine or temperate+freshwater? I think MuSSE can do this, but
> my tree is large so I want to avoid issues associated with rate
> heterogeneity. Are there any alternatives?
>
>
>
> --
> Elizabeth Miller
> PhD Candidate: Wiens Lab
> Ecology and Evolutionary Biology
> University of Arizona
>
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>
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