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Updated: Oct 1, 2025

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Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues.

Hélène Morlon¹, Stéphane Robin², Florian Hartig³

¹Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.

Trends in Ecology & Evolution

|March 5, 2022

Summary

This summary is machine-generated.

Phylogenetic diversification analysis using birth-death models can be unreliable due to unidentifiable histories. However, combining phylogenies with prior hypotheses and regularization techniques can still reveal past speciation and extinction dynamics.

Keywords:

diversification extinction model congruency parameter identifiability phylogenies speciation

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Area of Science:

Evolutionary Biology
Phylogenetics
Computational Biology

Background:

Diversification dynamics are often inferred using birth-death models applied to phylogenies of extant species.
The reliability of these phylogenetic diversification analyses is frequently debated.
Identifiability issues arise, where multiple diversification histories are indistinguishable from extant data alone.

Purpose of the Study:

To review the identifiability of birth-death processes in phylogenetic diversification analysis.
To discuss methods for addressing identifiability limitations.
To assess the utility of extant phylogenies for inferring past speciation and extinction.

Main Methods:

Review of existing literature on birth-death process identifiability.
Discussion of statistical regularization techniques.
Analysis of how prior hypotheses impact diversification inference.

Main Results:

Vast sets of congruent, alternative diversification histories are often unidentifiable from extant phylogenies.
Identifiability issues pose significant challenges to reconstructing past speciation and extinction events.
Appropriate prior information and regularization can mitigate some identifiability problems.

Conclusions:

Extant phylogenies, despite limitations, remain valuable for studying diversification dynamics.
Combining phylogenies with well-defined prior hypotheses and regularization is crucial.
Reliable inference of speciation and extinction requires careful consideration of identifiability.