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Related Experiment Video

Updated: Nov 29, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent

Théo Pannetier^1,2, César Martinez¹, Lynsey Bunnefeld²

¹Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands.

Evolution; International Journal of Organic Evolution

|November 18, 2020

Summary

Macroevolutionary biology struggles to distinguish diversity-dependent diversification from time-dependent patterns. Phylogenetic branching patterns alone lack sufficient information to identify the true diversification mode, necessitating additional data.

Keywords:

Birth-death models diversity dependence macroevolution maximum likelihood simulations time dependence

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Area of Science:

Macroevolutionary biology
Phylogenetic analysis
Diversification modeling

Background:

Macroevolutionary biology aims to explain long-term diversity patterns and their relationship to lower-scale processes.
Reconstructed phylogenies often exhibit decelerated lineage accumulation, frequently attributed to diversity-dependent (DD) diversification via niche filling.
Alternative explanations, such as time dependence without diversity dependence, can also yield similar patterns.

Purpose of the Study:

To determine if phylogenetic branching patterns can differentiate between diversity-dependent and time-dependent diversification mechanisms.
To assess the efficacy of likelihood methods in recovering the true diversification mode from simulated phylogenies.

Main Methods:

Formulated a time-dependent, diversity-independent model mimicking the expected diversity-through-time of a DD model.
Simulated phylogenies under both diversity-dependent and the formulated time-dependent models.
Employed likelihood methods and a bootstrap correction approach to analyze simulated data and assess model recovery.

Main Results:

Standard model selection criteria consistently favored diversity dependence, even when absent in simulations.
A bootstrap correction method revealed that neither the diversity-dependent nor the time-dependent model was decisively supported.
Phylogenetic branching patterns alone appear insufficient to reliably detect or exclude diversity dependence.

Conclusions:

The branching patterns within reconstructed phylogenies contain limited information for distinguishing diversity dependence from time dependence.
Additional data, such as species traits or geographic range distributions, are crucial for robustly evaluating the role of diversity in macroevolutionary trends.
Future research should integrate diverse data types to better understand the drivers of macroevolutionary diversification.