Data from: Distinguishing punctuated and continuous-time models of character evolution for discrete characters and its implications for macroevolutionary theory

The recent proliferation of quantitative models for assessing anatomical
character evolution all assume that character change happens continuously
through time. However, the punctuated equilibrium model posits that
character change should be coincide with cladogenetic events, and thus
should be tied to origination rates. Rates of cladogenesis are important
to quantitative phylogenetics, but typically only for establishing prior
probabilities in the tree model component of phylogenetic analyses. Here,
we modify existing character-likelihood models to use the local
cladogenesis rates from Bayesian analyses to generate amounts of character
change over time dependent on origination rates, as expected under the
punctuated equilibrium model. In the case of strophomenoid brachiopods
from the Ordovician, Bayesian analyses strongly favor punctuated models
over continuous-time models, with elevated rates of cladogenesis early in
the clade’s history inducing frequencies of change despite constant rates
of change per speciation event. This corroborates prior work proposing
that the early burst in strophomenoid disparity simply reflects elevated
speciation rates, which in turn has implications for seemingly unrelated
macroevolutionary theory about whether early bursts reflect shifts in
intrinsic constraints or empty ecospace. Future development of punctuated
character evolution models should account for the full durations of
species, which will provide a test of continuous change rates. Ultimately,
continuous change versus punctuated change should become part of
phylogenetic paleobiology in the same way that we currently test other
models of character evolution.