Data from: Use of continuous traits can improve morphological phylogenetics

The recent surge in enthusiasm for simultaneously inferring relationships
from extinct and extant species has reinvigorated interest in statistical
approaches for modelling morphological evolution. Current statistical
methods use the Mk model to describe substitutions between discrete
character states. Although representing a significant step forward, the Mk
model presents challenges in biological interpretation, and its adequacy
in modelling morphological evolution has not been well explored. Another
major hurdle in morphological phylogenetics concerns the process of
character coding of discrete characters. The often subjective nature of
discrete character coding can generate discordant results that are rooted
in individual researchers' subjective interpretations. Employing
continuous measurements to infer phylogenies may alleviate some of these
issues. Although not widely used in the inference of topology, models
describing the evolution of continuous characters have been well examined,
and their statistical behaviour is well understood. Also, continuous
measurements avoid the substantial ambiguity often associated with the
assignment of discrete characters to states. I present a set of
simulations to determine whether use of continuous characters is a
feasible alternative or supplement to discrete characters for inferring
phylogeny. I compare relative reconstruction accuracy by inferring
phylogenies from simulated continuous and discrete characters. These tests
demonstrate significant promise for continuous traits by demonstrating
their higher overall accuracy as compared to reconstruction from discrete
characters under Mk when simulated under unbounded Brownian motion, and
equal performance when simulated under an Ornstein-Uhlenbeck model.
Continuous characters also perform reasonably well in the presence of
covariance between sites. I argue that inferring phylogenies directly from
continuous traits may be benefit efforts to maximise phylogenetic
information in morphological datasets by preserving larger variation in
state space compared to many discretisation schemes. I also suggest that
the use of continuous trait models in phylogenetic reconstruction may
alleviate potential concerns of discrete character model adequacy, while
identifying areas that require further study in this area. This study
provides an initial controlled demonstration of the efficacy of continuous
characters in phylogenetic inference.