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Reading tree leaves: inferring speciation anfd extinction processes using phylogenies.

Bruce Rannala1, Ziheng Yang2

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Summary
This summary is machine-generated.

The generalized birth-death process (GBDP) for phylogenetic trees is often non-identifiable. However, a specific version with constant rates is identifiable, aiding evolutionary inference.

Keywords:
Yule processgeneralized birth–death processidentifiabilityphylogenetic treesstatistical inference

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Area of Science:

  • Evolutionary biology
  • Phylogenetics
  • Mathematical modeling

Background:

  • The birth-death process (BDP) is a fundamental model in evolutionary biology for phylogenetic tree generation.
  • The generalized birth-death process (GBDP) extends BDP by allowing time-varying speciation and extinction rates.
  • Understanding the identifiability of these models is crucial for accurate evolutionary inference.

Purpose of the Study:

  • To review the probability theory of the GBDP for cladogenesis.
  • To discuss recent findings on the identifiability of GBDP models.
  • To explore implications for inferring evolutionary tempo and mode from phylogenetic trees.

Main Methods:

  • Review of probability theory for generalized birth-death processes.
  • Analysis of identifiability for continuous and piecewise-constant rate functions.
  • Illustration using simple examples.

Main Results:

  • The GBDP with arbitrary continuous rate functions is non-identifiable from lineage-through-time data, even with infinite phylogenies.
  • A restricted class of BDPs with piecewise-constant rates is identifiable.
  • Identifiability is crucial for parameter estimation in phylogenetic models.

Conclusions:

  • The non-identifiability of continuous-rate GBDPs poses challenges for evolutionary inference.
  • Piecewise-constant rate models offer a tractable and identifiable alternative for phylogenetic analysis.
  • These findings impact the interpretation of phylogenetic trees and the study of macroevolutionary dynamics.