Data from: Journeys through discrete-character morphospace: synthesising phylogeny, tempo, and disparity

Palaeontologists have long employed discrete categorical data to capture
morphological variation in fossil species, using the resulting
character-taxon matrices to measure evolutionary tempo, infer phylogenies,
and capture morphological disparity. However, to date these have been seen
as separate approaches despite a common goal of understanding
morphological evolution over deep time. Here I argue that there are clear
advantages to considering these three lines of enquiry in a single space:
the phylomorphospace. Conceptually these high-dimensional spaces capture
how a phylogenetic tree explores morphospace and allow us to consider
important process questions around evolutionary rates, constraints,
convergence, and directional trends. Currently the literature contains
fundamentally different approaches used to generate such spaces, with no
direct comparison between them despite the differing evolutionary
histories they imply. Here I directly compare five different
phylomorphospace approaches, three with direct literature equivalents and
two that are novel. I use a single empirical case study of coelurosaurian
theropod dinosaurs (152 taxa, 853 characters) to show that under many
analyses the literature-derived approaches tend to reflect introduced
phylogenetic – rather than the intended morphological – signal. The two
novel approaches, which produce limited ancestral state estimates prior to
ordination, are able to minimise this phylogenetic signal and thus exhibit
more realistic amounts of phylogenetic signal, rate heterogeneity, and
convergent evolution. Palaeontologists are interested in the diversity and
tempo of evolutionary change along the branches of the tree of life, but
these are typically treated as separate numerical analyses. Here I argue
for a statistical technique that allows us to treat these aspects of
evolution simultaneously, allowing a more complete understanding of how
evolution has explored the possibilities of physical form. Specifically, I
compare five different approaches, two novel to this study, showing that
the three pre-existing approaches may contain biases that stem from a
different signal (evolutionary relationships) than we intend to capture
(the exploration of physical form).