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The Effects of Post-Divergence Gene Flow on Simultaneous Divergence Time Testing
Michael A Tofflemire1,2, Kevin J Burns1, Jeet Sukumaran1
1Department of Biology, San Diego State University, San Diego, California, USA.
Molecular Ecology Resources
|July 25, 2026
Summary
Estimating simultaneous divergence using genetic data can be unreliable when gene flow occurs between populations. Researchers found that migration can lead to incorrect support for simultaneous divergence, even when it did not happen.
Area of Science:
- Evolutionary Biology
- Genetics
- Phylogeography
Background:
- Phylogeographical studies often estimate simultaneous divergence times across multiple species using genetic data.
- The reliability of these estimates when post-divergence gene flow is present is frequently overlooked.
Purpose of the Study:
- To assess the robustness of simultaneous divergence time estimates in a full-likelihood Bayesian framework when gene flow assumptions are violated.
- To identify migration rate thresholds that bias divergence time estimations.
Main Methods:
- A simulation-based approach was employed to generate datasets for multiple population pairs with varying migration rates.
- Divergence times were estimated using the Ecoevolity software package under different gene flow scenarios.
- Estimates were compared between populations with and without migration.
Main Results:
- Simultaneous divergence was incorrectly supported across a wide range of parameter space when gene flow assumptions were violated.
- Migration rates were found to bias divergence time estimates, challenging the accuracy of full-likelihood Bayesian methods in complex demographic scenarios.
Conclusions:
- Future phylogeographical studies using simultaneous divergence testing should explicitly account for gene flow.
- Support for simultaneous divergence should be interpreted cautiously, potentially indicating a failure to detect non-simultaneous divergence rather than true simultaneous evolutionary events.
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