ArticleBMC bioinformatics2011
MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- The Effects of Post-Divergence Gene Flow on Simultaneous Divergence Time Testing.Molecular ecology resources · 2026Article
- Mitogenomes reveal the timing and distribution of divergence events among trans-Beringian birds.PeerJ · 2026Article
- Generalizing Bayesian phylogenetics to infer shared evolutionary events.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The genetics of adaptation in freshwater Eurasian shad (Ecology and evolution · 2022Article
- A novelCold Spring Harbor molecular case studies · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
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- Characterization of differential gene expression of broiler chicken to thermal stress in discrete developmental stages.Animal cells and systems · 2022Article
- 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
- Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny.BMC evolutionary biology · 2019Article
- The dual role of Amazonian rivers in the generation and maintenance of avian diversity.Science advances · 2018Article
- Article
- 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
- 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
- Matching loci surveyed to questions asked in phylogeography.Proceedings. Biological sciences · 2016Article
- The aggregate site frequency spectrum for comparative population genomic inference.Molecular ecology · 2015Article
- Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence.Frontiers in genetics · 2015Article
- Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.Molecular biology and evolution · 2014Article
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4 authors.
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Abstract
backgroundMTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs.
resultsSimulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred.
conclusionsTo retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).
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