RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes

Tribble, Carrie M.; Freyman, William A.; Landis, Michael J.; Lim, Jun Ying; Barido‐Sottani, Joëlle; Kopperud, Bjørn Tore; Höhna, Sebastian; May, Michael R.

doi:10.1111/2041-210x.13750

Cited by 47 publications

(40 citation statements)

References 62 publications

(95 reference statements)

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“…The phasing estimates from a homologizer MCMC analysis can be summarized and plotted using the R (R Core Team, 2013) package RevGadgets (Tribble et al, 2020), which displays the joint maximum a posteriori (MAP) phasing assignment across the set of a polyploid's subgenomes for each locus and summarized on a phylogeny. This joint MAP assignment is the highest probability assignment of each gene uniquely to a subgenome.…”

Section: Methodsmentioning

confidence: 99%

“…RevBayes (Höhna et al, 2016) is an open‐source software package available at http://revbayes.com. RevGadgets (Tribble et al, 2020), the R package used for summarizing the output from RevBayes analyses, is also open‐source and is available at https://github.com/revbayes/revgadgets. Further details, including an example analysis and all scripts and data used in this paper, are available at https://github.com/wf8/homologizer and https://doi.org/10.5281/zenodo.7048276.…”

Section: Methodsmentioning

confidence: 99%

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homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

2023

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Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome and thus share an evolutionary history. Here we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into their respective subgenomes. Through the use of simulation tests, we demonstrate that homologizer is robust to a wide range of factors, such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data, by analysing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae. Finally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non‐homologous sequences, such as hidden paralogs or contaminants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

2023

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“…The analyses were carried out with a total of 20,000 generations, with burn-in adjusted in 25% of the samples, and convergence (ESS > 200) was evaluated in Tracer 1.8 [ 76 ]. The resulting tree was then plotted in R 4.2 [ 80 ], using the ggtree [ 81 , 82 , 83 , 84 , 85 ] and Revgadgets [ 86 ] packages. Vertical bars and grouping names were inserted using Adobe Illustrator CS6.…”

Section: Methodsmentioning

confidence: 99%

Karyotype Evolution in Triatominae (Hemiptera, Reduviidae): The Role of Chromosomal Rearrangements in the Diversification of Chagas Disease Vectors

Reis

Oliveira

Madeira

et al. 2023

IJMS

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Several cytogenetic studies have already been performed in Triatominae, such that different karyotypes could be characterized (ranging from 2n = 21 to 25 chromosomes), being the changes in the number of chromosomes related mainly to fusion and fission events. These changes have been associated with reproductive isolation and speciation events in other insect groups. Thus, we evaluated whether different karyotypes could act in the reproductive isolation of triatomines and we analyzed how the events of karyotypic evolution occurred along the diversification of these vectors. For this, experimental crosses were carried out between triatomine species with different karyotypes. Furthermore, based on a phylogeny with 88 triatomine taxa (developed with different molecular markers), a reconstruction of ancestral karyotypes and of anagenetic and cladogenetic events related to karyotypic alterations was performed through the ChromoSSE chromosomal evolution model. All crosses performed did not result in hybrids (prezygotic isolation in both directions). Our modeling results suggest that during Triatominae diversification, at least nine cladogenetic events may be associated with karyotype change. Thus, we emphasize that these alterations in the number of chromosomes can act as a prezygotic barrier in Triatominae (karyotypic isolation), being important evolutionary events during the diversification of the species of Chagas disease vectors.

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“…We assessed convergence by Tracer v.1.7 116 (ESS over 200) and summarized the trees into a single tree and rooted it by FigTree 117 . Then the phasing estimates were plotted by RevGadgets 118 .…”

Section: Methodsmentioning

confidence: 99%

Reticulate evolution in the Pteris fauriei group (Pteridaceae)

Chao

Ebihara

Chiou

et al. 2022

Sci Rep

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The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of the P. fauriei group generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.

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RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes

Cited by 47 publications

References 62 publications

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Karyotype Evolution in Triatominae (Hemiptera, Reduviidae): The Role of Chromosomal Rearrangements in the Diversification of Chagas Disease Vectors

Reticulate evolution in the Pteris fauriei group (Pteridaceae)

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