Hello everyone,
Please, I am trying to use the fitMk function in phytools to test different
scenarios for character evolution (equal rates, all-rates-different, and
customized matrices with irreversible states) and getting some unexpected
results.
Specifically, I have a character that has a defined ancestral condition
(established by outgroups not present in the analysis), three different derived
conditions, and taxa which lack this particular structure and have been coded
as "absent". A small group of taxa which is deeply nested in the tree presents
the plesiomorphic condition, and I would like to test if this is a
plesiomorphic retention or a re-gain. In the all-rates-different model, it is
optimized as a re-gain. So I wanted to compare this with a model where re-gains
are impossible, using this custom model:
- "ancestral" can shift to any state-"derived" states can shift to "absent"
only, but not to other derived states, nor reverse to the "ancestral"
condition-"absent" cannot shift to any condition
This gives me a tree in which the character is optimized as a plesiomorphy.
Everything seems fine so far!
However, the exact same optimization is produced if I use a different, less
restrictive model where all transitions are possible except for re-gains from
absent structures (i.e. the model allows for reversals from the derived states
to the ancestral state, and also transitions among derived states). I find this
very strange, because the only difference between this and the ARD model is the
impossibility to reverse from "absent" to other states - but neither of the
trees suggested such an optimization would occur. Thus, I would expect that
this second customized matrix would give results identical to those of ARD --
please, does anyone know why such a result is to be expected?
Many thanks in advance.
Best regards,Ivan
--
Dr. Ivan L. F. Magalhaes
División Aracnología
Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"
Av. Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentinatel +54 11 4982-8370
int. 169
researchgate.net/profile/Ivan_MagalhaesTwitter: @6eyes8legs
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