Data from: The fundamental role of character coding in Bayesian morphological phylogenetics

Phylogenetic trees establish a historical context for the study of
organismal form and function. Most phylogenetic trees are estimated using
a model of evolution. For molecular data, modeling evolution is often
based on biochemical observations about changes between character states.
For example, there are four nucleotides, and we can make assumptions about
the probability of transitions between them. By contrast, for
morphological characters, we may not know a priori how many character
states there are per character, as both extant sampling and the fossil
record may be highly incomplete, which leads to an observer bias. For a
given character, the state space may be larger than what has been observed
in the sample of taxa collected by the researcher. In this case, how many
evolutionary rates are needed to even describe transitions between
morphological character states may not be clear, potentially leading to
model misspecification. To explore the impact of this model
misspecification, we simulated character data with varying numbers of
character states per character. We then used the data to estimate
phylogenetic trees using models of evolution with the correct number of
character states and an incorrect number of character states. The results
of this study indicate that this observer bias may lead to phylogenetic
error, particularly in the branch lengths of trees. If the state space is
wrongly assumed to be too large, then we underestimate the branch lengths,
and the opposite occurs when the state space is wrongly assumed to be too
small.