Data from: Model inadequacy and mistaken inferences of trait-dependent speciation

Species richness varies widely across the tree of life, and there is great
interest in identifying ecological, geographic, and other factors that
affect rates of species proliferation. Recent methods for explicitly
modeling the relationships among character states, speciation rates, and
extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related
models - have been widely used to test hypotheses about character
state-dependent diversification rates. Here, we document the disconcerting
ease with which neutral traits are inferred to have statistically
significant associations with speciation rate. We first demonstrate this
unfortunate effect for a known model assumption violation: shifts in
speciation rate associated with a character not included in the model. We
further show that for many empirical phylogenies, characters simulated in
the absence of state-dependent diversification exhibit an even higher Type
I error rate, indicating that the method is susceptible to additional,
unknown model inadequacies. For traits that evolve slowly, the root cause
appears to be a statistical framework that does not require replicated
shifts in character state and diversification. However, spurious
associations between character state and speciation rate arise even for
traits that lack phylogenetic signal, suggesting that phylogenetic
pseudoreplication alone cannot fully explain the problem. The surprising
severity of this phenomenon suggests that many trait-diversification
relationships reported in the literature may not be real. More generally,
we highlight the need for diagnosing and understanding the consequences of
model inadequacy in phylogenetic comparative methods.