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Fossils improve extinction-rate estimates under state-dependent diversification models.

Bruno do Rosario Petrucci1, Michael R May2, Tracy A Heath1

  • 1Department of Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|February 20, 2025
PubMed
Summary
This summary is machine-generated.

Including fossil data improves extinction rate estimates in evolutionary biology models. However, even with fossils, models may still incorrectly link neutral traits to diversification rates.

Keywords:
Bayesian inferencefossilized birth–death processmacroevolutionpalaeobiologysimulationstate-dependent speciation and extinction

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Area of Science:

  • Evolutionary biology
  • Palaeontology
  • Macroevolutionary studies

Background:

  • State-dependent speciation and extinction (SSE) models are widely used in evolutionary biology.
  • These models predominantly utilize phylogenetic trees of extant species, limiting extinction rate estimation accuracy.
  • SSE models can falsely associate neutral traits with diversification rates if the true trait is unobserved.

Purpose of the Study:

  • To investigate the impact of incorporating fossil data into the binary-state speciation and extinction (BiSSE) model.
  • To assess improvements in parameter estimation accuracy, particularly for extinction rates.
  • To evaluate the effect on speciation and state transition rate estimates.

Main Methods:

  • Combined SSE models with the fossilized birth-death process.
  • Applied Bayesian inference within the BiSSE model framework.
  • Compared parameter estimates from analyses including fossil data versus those using only extant taxa.

Main Results:

  • Inclusion of fossil data significantly enhanced the accuracy of extinction rate estimates.
  • Speciation and state transition rate estimates remained accurate and were not negatively impacted by fossil data inclusion.
  • The BiSSE model, even with fossil data, continued to incorrectly infer correlations between diversification rates and neutral traits.

Conclusions:

  • Fossil data integration enhances the reliability of extinction rate estimations in phylogenetic analyses.
  • While improving extinction estimates, fossil data does not resolve issues with neutral trait correlations in BiSSE models.
  • Future research should address the persistent challenge of accurately identifying trait-diversification rate associations.