Model inadequacy and mistaken inferences of trait-dependent speciation

Daniel L. Rabosky, Emma E. Goldberg

Research output: Contribution to journalArticlepeer-review

349 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)340-355
Number of pages16
JournalSystematic Biology
Issue number2
StatePublished - Mar 1 2015

Bibliographical note

Funding Information:
FUNDING This work was carried out in part using computing resources at the University of Minnesota Supercomputing Institute and was supported in part by National Science Foundation [DEB-1256330 to D.L.R.].

Publisher Copyright:
© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.


  • Character evolution
  • Extinction
  • Macroevolution
  • Speciation
  • Statistics


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