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Updated: Nov 4, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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Why extinction estimates from extant phylogenies are so often zero.

Stilianos Louca1, Matthew W Pennell2

  • 1Department of Biology, University of Oregon, 1210 University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR 97403, USA.

Current Biology : CB
|May 21, 2021
PubMed
Summary
This summary is machine-generated.

Phylogenetic studies often report zero extinction rates due to congruent diversification scenarios. This mathematical artifact, not biological reality, explains why extinction rate estimates are zero-inflated in phylogenetic analyses.

Keywords:
birth-death modelcongruentextinctionfossil recordidentifiabilitymacroevolutionphylogenetic trees

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Computational Biology

Background:

  • Time-calibrated phylogenies (extant timetrees) are used to estimate speciation and extinction rates via birth-death models.
  • Previous studies often report zero extinction, contradicting fossil records and the high historical extinction rates.

Purpose of the Study:

  • To provide a novel explanation for the "zero-inflated" extinction rate estimates in phylogenetic studies.
  • To resolve the long-standing discrepancy between phylogenetic estimates and fossil-based extinction rates.

Main Methods:

  • Investigated the impact of congruent diversification scenarios on birth-death model fitting.
  • Analyzed simulated phylogenetic trees and 121 empirical trees to test predictions.

Main Results:

  • Identified "congruent" diversification scenarios that are statistically indistinguishable from true scenarios using extant timetrees.
  • Demonstrated that estimation methods can converge to biologically unrealistic scenarios with negative extinction rates, leading to zero-inflated estimates.
  • Confirmed predictions using both simulated and empirical phylogenetic data.

Conclusions:

  • Model congruencies, not necessarily model violations, explain zero-inflated extinction rate estimates in phylogenetics.
  • This finding resolves a major controversy in estimating historical extinction rates from extant timetrees.
  • Highlights the practical consequences of model congruencies in phylogenetic inference.