Dear all, 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 reconstructions? Any advice would be greatly appreciated! Robin van Velzen [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/