RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

Höhna, Sebastian; Landis, Michael J.; Heath, Tracy A.; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R.; Huelsenbeck, John P.; Ronquist, Fredrik

doi:10.1093/sysbio/syw021

Cited by 594 publications

(662 citation statements)

References 79 publications

(92 reference statements)

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“…Our RevBayes (Hoehna et al 2016) relaxed‐clock chronogram (data not shown) was very similar to Fig. 2c.…”

Section: Resultssupporting

confidence: 76%

“…The age of the most recent common ancestor (MRCA) of D. suzukii and D. subpulchrella was set at 1, as an arbitrary scaling of relative ages. To test the robustness of our relative divergence‐time estimates for the host species, we also estimated the chronogram using a relaxed‐clock model in RevBayes (Hoehna et al., 2016). This analysis also partitioned the data by gene and codon position and used the GTR+Γ model, but it assumed uncorrelated lognormal rate variation across branches.…”

Section: Methodsmentioning

confidence: 99%

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Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

Conner

Blaxter

Anfora

et al. 2017

Ecology and Evolution

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Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full‐length copies of 703 of the 734 single‐copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%–0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar—by at least a factor of 100—to be plausible candidates for cladogenic transmission. These three wRi‐like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachia.

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“…Our RevBayes (Hoehna et al 2016) relaxed‐clock chronogram (data not shown) was very similar to Fig. 2c.…”

Section: Resultssupporting

confidence: 76%

Section: Methodsmentioning

confidence: 99%

Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

Conner

Blaxter

Anfora

et al. 2017

Ecology and Evolution

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show abstract

“…study (5). To this end, we first estimated the posterior probability distribution of the speciation and extinction rates for the whale tree under a constant-rate birthdeath model using RevBayes (13). Each tree was simulated under speciation and extinction rates that were independently sampled from the corresponding marginal posterior probability distributions that were previously estimated from the empirical tree.…”

Section: Methodsmentioning

confidence: 99%

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

Moore

Höhna

May

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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278

306

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Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversificationrate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM.volutionary biologists have long sought to detect patterns and understand the causes of variation in rates of lineage diversification (speciation − extinction). This has motivated the development of several statistical methods for detecting whether (and where) diversification rates have changed across the branches of a phylogeny (1-4). A recent approach-Bayesian analysis of macroevolutionary mixtures (BAMM) (5)-promises to greatly enhance our ability to study this problem.This important new method offers several key advantages. (i) BAMM is based on an explicit model that describes how diversification rates shift across the branches of a tree. (ii) The underlying branching process is more complex (and presumably more realistic) than those used in previous methods. Specifically, BAMM not only includes parameters for the rate of speciation and extinction, but also accommodates possible time-dependent effects (where the age of a lineage may affect its diversification rate). This is intended to approximate the phenomenon of diversity-dependent diversification (where the number of species in a lineage may affect its diversification rate), which is believed to be a prevalent feature of empirical phylogenies (6). (iii) By virtue of developing this method in a Bayesian statistical framework, BAMM allows us to gauge the uncertainty in our inferences by providing marginal posterior probability densities rather than point estimates of parameters. (iv) By averaging inferences over any number of diversification-rate shifts, BAMM both accommodates uncertainty in the choice of model and avoids potential complications associated with model selection.BAMM provides estimates of the number and location of diversification-rate shifts across the branches of a tree and also estimates the diversification-rate parameters-speciation, extinction, and time dependence-on each branch of the tree. ...

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“…The episodic birth‐death model (EBD) was implemented in a Bayesian framework using the software RevBayes v1.0.2 (Höhna et al. 2016). …”

Section: Methodsmentioning

confidence: 99%

Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

et al. 2018

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Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ∼53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (∼34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (∼26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (∼14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

Cited by 594 publications

References 79 publications

Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

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