ArticleBMC evolutionary biology2014
An improved approximate-Bayesian model-choice method for estimating shared evolutionary history.
Article in BMC evolutionary biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- The Effects of Post-Divergence Gene Flow on Simultaneous Divergence Time Testing.Molecular ecology resources · 2026Article
- Generalizing Bayesian phylogenetics to infer shared evolutionary events.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Evolution of Comparative Phylogeography: Putting the Geography (and More) into Comparative Population Genomics.Genome biology and evolution · 2022Review
- The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago.Evolution; international journal of organic evolution · 2019Article
- Full Bayesian Comparative Phylogeography from Genomic Data.Systematic biology · 2019Article
- Conserved community structure and simultaneous divergence events in the fig wasps associated with Ficus benjamina in Australia and China.BMC ecology · 2018Article
- multi-dice: r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes.Molecular ecology resources · 2017Article
- Strategies for improving approximate Bayesian computation tests for synchronous diversification.BMC evolutionary biology · 2017Article
- Phenotypes in phylogeography: Species' traits, environmental variation, and vertebrate diversification.Proceedings of the National Academy of Sciences of the United States of America · 2016Review
- Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- The aggregate site frequency spectrum for comparative population genomic inference.Molecular ecology · 2015Article
- Deep and wide valleys drive nested phylogeographic patterns across a montane bird community.Proceedings. Biological sciences · 2015Article
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Abstract
backgroundTo understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences times, a pattern that can be estimated using genetic data from co-distributed species. I introduce a new approximate-Bayesian method for comparative phylogeographical model-choice that estimates the temporal distribution of divergences across taxa from multi-locus DNA sequence data. The model is an extension of that implemented in msBayes.
resultsBy reparameterizing the model, introducing more flexible priors on demographic and divergence-time parameters, and implementing a non-parametric Dirichlet-process prior over divergence models, I improved the robustness, accuracy, and power of the method for estimating shared evolutionary history across taxa.
conclusionsThe results demonstrate the improved performance of the new method is due to (1) more appropriate priors on divergence-time and demographic parameters that avoid prohibitively small marginal likelihoods for models with more divergence events, and (2) the Dirichlet-process providing a flexible prior on divergence histories that does not strongly disfavor models with intermediate numbers of divergence events. The new method yields more robust estimates of posterior uncertainty, and thus greatly reduces the tendency to incorrectly estimate models of shared evolutionary history with strong support.
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