How reliably can we infer diversity-dependent diversification from phylogenies?

Rampal S. Etienne*, Alex L. Pigot, Albert B. Phillimore

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

23 Citations (Scopus)
244 Downloads (Pure)

Abstract

Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings - on survival of the birth-death process given the crown age, on tree size (N) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the (2) likelihood ratio test. Parameter estimate accuracy: Conditioning on survival given the crown age yields a severe bias of the carrying capacity K towards N and an upward bias of the speciation rate, particularly in clades where diversity-dependent feedbacks are still weak (N

Original languageEnglish
Pages (from-to)1092-1099
Number of pages8
JournalMethods in ecology and evolution
Volume7
Issue number9
DOIs
Publication statusPublished - Sep-2016

Keywords

  • Birth-death model
  • conditioning
  • diversity dependence
  • extinction
  • parametric bootstrap
  • simulations
  • RECONSTRUCTED PHYLOGENIES
  • MOLECULAR PHYLOGENIES
  • EVOLUTIONARY MODELS
  • SPECIES-DIVERSITY
  • SPECIATION
  • EXPLAIN
  • NICHE
  • TREES
  • EXTINCTION
  • RADIATIONS

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