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Output from the Jetz BirdTree is a whole distribution of trees. Right now, I am only using one of those trees to clamp in RevBayes for ACE. Is there a way to incorporate this whole distribution of input trees? Does RB accept a "clamp" of multiple trees? Should I collapse all of the trees into a single consensus tree ahead of time?

Keep time-reversible, but separate STAGE versus CHARACTER versus COLOR transitions, in addition to dependencies.

Need explicit developmental dependencies in ACE from PARAMO. Integrate .Rev file with dependency chart after plumage patch coding method is complete.

Explicitly code STAGES as characters, along with

This reintroduces the tripartite plumage patch dependency:

DPM is dependent on dichromatism: P1 | D (i.e., dichromatism)
Inserted stages are dependent on earlier inserted stages: P2 | P1 for example
Predefinitive plumage characters are dependent on plumage stages: P1-Crown | P1

And, to add a color-type dependency:
P1-Crown-Structural | P1-Crown
P1-Crown-Carotenoid | P1-Crown
P1-Crown-Melanin | P1-Crown

This change to character coding will allow the explicit detection of P-STAGE and P-CHARACTER homologies, as well as the separate transition rates for STAGE changes versus CHARACTER changes versus COLOR changes. Need then PARAMO dependency.