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7 results for “BEAST2”
The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2
<p>Bayesian phylogenetic inference requires a tree prior, which models the underlying diversification process which gives rise to the phylogeny. Existing birth-death diversification models include a wide range of features, for instance lineage-specific variations in speciation and extinction rates. While across-lineage variation in speciation and extinction rates is widespread in empirical datasets, few heterogeneous rate models have been implemented as tree priors for Bayesian phylogenetic inference. As a consequence, rate heterogeneity is typically ignored when reconstructing phylogenies, and rate heterogeneity is usually investigated on fixed trees. In this paper, we present a new BEAST2 package implementing the cladogenetic diversification rate shift (ClaDS) model as a tree prior. ClaDS is a birth-death diversification model designed to capture small progressive variations in birth and death rates along a phylogeny. Unlike previous implementations of ClaDS, which were designed to be used with fixed, user-chosen phylogenies, our package is implemented in the BEAST2 framework and thus allows full phylogenetic inference, where the phylogeny and model are co-estimated from a molecular alignment. Our package provides all necessary components of the inference, including a new tree object and operators to propose moves to the MCMC. It also includes a graphical interface through BEAUti. We validate our implementation of the package by comparing the produced distributions to simulated data, and show an empirical example of the full inference, using a cetaceans dataset.</p>
beast2-paper bModelTest files
<p>beast2-paper.xml BEAST 2 XML file + outputs of 4 runs of the XML file.</p> <p>beast2-paper/beast2-paper.xml<br> beast2-paper/run*/yang.log trace log<br> beast2-paper/run*/yang.trees tree log<br> beast2-paper/run*/beast2-paper.xml.state BEAST 2 state file</p>
The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2
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The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for the whole-class multi-gene alignments
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The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for each gene group and region
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Figure 4. Time-calibrated phylogeny from BEAST2 in Origin and evolution of the Haustoriidae (Amphipoda): a eulogy for the Haustoriidira
Figure 4. Time-calibrated phylogeny from BEAST2. Green diamonds represent calibration points: 1, closure of the Okefenokee Trough (1.75 Mya); 2, proposed migration to Europe by H. arenarius (~5 Mya); 3, Pontocaspian gammarid clade radiation (9–83 Mya); 4,Niphargidae–Pseudoniphargidae split (38–215 Mya); 5, Crangonyctidae-Pseudocrangonyctidae split (38–215 Mya).
Fig. 5.—Maximum clade credibility tree obtained with BEAST2 in Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex
Fig. 5.—Maximum clade credibility tree obtained with BEAST2 for species of the Reithrodontomys tenuirostris group using Cytochrome b sequences data. Values above branches represent mean divergence times and below the 95% highest posterior density (HPD) intervals. Dark gray bars represent taxa delimited as species-level by the single-locus methods mPTP and bGMYC with probability values above 0.95, and the multiple-loci method STACEY.
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