An ordered (additive) character can be rewritten as a mathematically
equivalent hierarchy of binary neomorphic characters
Farris1970TreeTools.
Two reasons to prefer the latter approach are:
It makes explicit the evolutionary assumptions underlying an ordered
character, whether the underlying ordering is linear, reticulate or
branched Mabee1989TreeTools.
It avoids having to identify characters requiring special treatment to
phylogenetic software, which requires the maintenance of an up-to-date
log of which characters are treated as additive and which sequence their
states occur in, a step that may be overlooked by re-users of the data.
Careful consideration is warranted when evaluating whether a group of
related characteristics ought to be treated as ordered
Wilkinson1992TreeTools.
On the one hand, the 'principle of indifference' states that we should treat
all transformations as equally probable (/ surprising / informative);
ordered characters fail this test, as larger changes are treated as less
probable than smaller ones.
On the other hand, ordered characters allow more opportunities for homology
of different character states, and might thus be defended under the auspices
of Hennig’s Auxiliary Principle Wilkinson1992TreeTools.
For a case study of how ordering phylogenetic characters can affect
phylogenetic outcomes in practice, see
Brady2024;textualTreeTools.