I want to reconstruct ancestral states of morphological characters on a
phylogenetic tree. However, these are 'complex' and I am not sure how best
to appropriately code these characters and do the mapping.
Specifically, I have developmental data where three adjacent cell layers
(A,B,C) can contribute to a particular developing tissue, either singly or
in combination. However, layer C can in principle not contribute singly,
and combinations can only comprise adjacent layers (so AB, BC, and ABC are
possible but AC is not).
A solution would be to code everything as a single character with a total
of 5 states (A,B,AB,BC,ABC). But this would require a matrix that would
appropriately set the rates of change between all these states. Given that
I do not have many observations I fear that this would result in
overparameterization (also I have many more than three dependent characters
that I ignored for the sake of clarity). Moreover, reconstruction as a
single character would not give much insight in the underlying processes at
the level of cell layers.
Ideally, therefore, I would code the three layers separately so that all
three ancestral states can be reconstructed. But that would require
specifying character combinations that are not allowed. But I am not sure
if that is possible and if there are packages that would be able to do such
Any advice would be greatly appreciated!
Robin van Velzen
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