Maybe someone has some insight here...
I am coming up against the problem, when it comes to phylogenetic analysis.
Basically I want to conduct a parsimony (or other phylogenetic) analysis
where "inapplicable" scores are treated as separate states *for each taxon*
I.e. I want to hypothesize shared ancestry for taxa scored with one state
(let's say state 0), but not hypothesize shared ancestry for the other
taxa. However, I still want to penalize a change in state from and to state
There are three approaches which I have thought about, but none seems to
fit the bill:
-Score all taxa not showing state 0 as separate states. This should do what
I want, but the problem here is the limit on the number of states in most
-Scoring binary presence/absence. The problem is here that it could end up
being parsimonious to group the "absence" state together, when there is no
reason to infer homology within (i.e. for taxa scored with) this state.
-Score as 0 and inapplicable. The problem is this does not penalize a
change from 0 to inapplicable.
A real life example, is the shape of the ilium in crocodiles. I want to say
that it is likely that a particular curve in the dorsal margin of the ilium
in crocodile-line crocodilians is homologous, but I don't want to
hypothesize homology of those taxa "lacking" this state. They are all
equally far from each other.
Thanks very much indeed
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