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Updated: Jun 4, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting
1Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA. ychung@stat.wisc.edu
Systematic Biology
|March 4, 2011
Summary
Bayesian estimation of species trees (BEST) and BUCKy methods were compared for gene tree discordance. BUCKy accurately reconstructed species trees with horizontal gene transfer (HGT), while BEST performed similarly otherwise, though BUCKy underestimated uncertainty.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Genetics
Background:
- Gene tree/species tree reconciliation methods are crucial for understanding evolutionary history.
- Discordance between gene genealogies can arise from incomplete lineage sorting (ILS) and horizontal gene transfer (HGT).
- Bayesian estimation of species trees (BEST) and BUCKy are two prominent methods for inferring species trees.
Purpose of the Study:
- To compare the performance of BEST and BUCKy in reconstructing species trees under simulated ILS and HGT.
- To assess the accuracy of each method given different patterns and sources of gene tree discordance.
Main Methods:
- Simulated DNA alignments incorporating ILS and HGT scenarios.
- Applied Bayesian estimation of species trees (BEST) assuming only ILS.
- Utilized BUCKy with a nonparametric approach to gene tree discordance and estimated concordance factors (CFs).
Main Results:
- BUKy demonstrated higher accuracy in species tree reconstruction when HGT was present and unevenly distributed.
- BEST and BUCKy showed similar performance under strong ILS and evenly distributed HGT.
- BUKy tended to underestimate uncertainty in concordance factor estimation.
Conclusions:
- BUKy is more robust to HGT than BEST, particularly when HGT events are unevenly distributed.
- The concordance pattern estimated by BUCKy can be compared to ILS signatures, enabling tests for coalescent model adequacy.
- BUKy provides a powerful test for discordance sources, especially when HGT is a major factor.
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