ArticleMolecular biology and evolution2020
Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Phylogenomic assessment of the role of hybridization and introgression in trait evolution.PLoS genetics · 2021Article
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3 authors.
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Abstract
Species tree inference from multilocus data has emerged as a powerful paradigm in the postgenomic era, both in terms of the accuracy of the species tree it produces as well as in terms of elucidating the processes that shaped the evolutionary history. Bayesian methods for species tree inference are desirable in this area as they have been shown not only to yield accurate estimates, but also to naturally provide measures of confidence in those estimates. However, the heavy computational requirements of Bayesian inference have limited the applicability of such methods to very small data sets. In this article, we show that the computational efficiency of Bayesian inference under the multispecies coalescent can be improved in practice by restricting the space of the gene trees explored during the random walk, without sacrificing accuracy as measured by various metrics. The idea is to first infer constraints on the trees of the individual loci in the form of unresolved gene trees, and then to restrict the sampler to consider only resolutions of the constrained trees. We demonstrate the improvements gained by such an approach on both simulated and biological data.
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