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Updated: May 8, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
The influence of gene flow on species tree estimation: a simulation study
Adam D Leaché1, Rebecca B Harris, Bruce Rannala
1Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195 USA;
Systematic Biology
|August 16, 2013
Summary
Gene flow and incomplete lineage sorting (ILS) create gene tree discordance, hindering species tree estimation. Our simulations show gene flow can distort species tree size and divergence times, emphasizing careful sampling for accurate phylogeography.
Area of Science:
- Evolutionary biology
- Phylogenetics
- Population genetics
Background:
- Gene tree discordance arises from gene flow and incomplete lineage sorting (ILS).
- ILS impacts on species tree inference are well-studied, but gene flow's effects are less understood.
- Accurate species tree estimation is crucial for understanding evolutionary history.
Purpose of the Study:
- To simulate and analyze multilocus sequence data to quantify the impacts of gene flow and ILS on species tree inference.
- To investigate various gene flow models, including isolation-migration, n-island, and allelic introgression.
- To assess these impacts across different species tree sizes, time scales, and migration rates.
Main Methods:
- Multilocus sequence data simulation incorporating ILS and diverse gene flow models.
- Species tree estimation using the multispecies coalescent model with Bayesian methods (BEST, *BEAST).
- Application of a summary statistic approach (MPEST) for phylogenomic-scale analysis.
Main Results:
- Gene flow can lead to species tree dilation (overestimated population sizes) and compression (underestimated divergence times), even with accurate topology.
- Signatures of migration events are detectable in gene tree coalescent times.
- Identification of loci that have crossed species boundaries is possible with sufficient data.
Conclusions:
- Gene flow significantly biases species tree topology and parameter estimates (population size, divergence time).
- Phylogeographic and species delimitation studies require careful sampling to mitigate biases from gene flow and introgression.
- Understanding gene flow's impact is essential for robust evolutionary inference.
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