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Updated: Jun 17, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Extinction rates should not be estimated from molecular phylogenies
1Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA. drabosky@berkeley.edu
Evolution; International Journal of Organic Evolution
|December 25, 2009
Summary
Estimating extinction rates from molecular phylogenies is unreliable when diversification rates vary. Fossil data is crucial for accurate extinction rate estimation in such cases.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Diversification Analysis
Background:
- Molecular phylogenies offer insights into species diversification over time.
- Extinction events leave detectable patterns in phylogenetic tree shapes.
- Current methods often infer extinction rates using only extant taxa data, especially when fossil records are unavailable.
Purpose of the Study:
- To investigate the impact of violating a key assumption in phylogenetic extinction rate estimation.
- To assess the accuracy of simple birth-death process estimators when diversification rates differ among lineages.
Main Methods:
- Exploration of simulation or theoretical models examining phylogenetic tree shapes.
- Analysis of the consequences of rate variation on standard extinction rate estimators.
- Comparison of results for complete taxon sampling versus clades with known age and richness.
Main Results:
- Simple birth-death process estimators fail to accurately recover true extinction rates when diversification rates vary across lineages.
- This inaccuracy persists regardless of whether phylogenetic trees have complete taxon sampling or represent clades with known age and species richness.
- The study highlights a significant limitation in inferring extinction from molecular phylogenies under realistic evolutionary scenarios.
Conclusions:
- The assumption of uniform diversification rates is often violated in nature.
- Estimating extinction rates from molecular phylogenies without considering rate variation can lead to substantial errors.
- Fossil data is essential for robust extinction rate estimation, particularly when diversification rates are heterogeneous.
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