RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

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

doi:10.1101/2021.05.10.443470

Cited by 19 publications

(18 citation statements)

References 59 publications

(82 reference statements)

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“…Estimated time-calibrated Lampyridae phylogeny under the fossilized birth-death-range process using the high posterior probability of Photinus being monophyletic data subset. The plot was generated using the R package (Tribble et al 2022). The bars around the node show the 95% credible interval of the node ages.…”

Section: Resultsmentioning

confidence: 99%

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

Höhna

Lower

Duchen

et al. 2021

Preprint

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Fireflies (Coleoptera: Lampyridae) consist of over 2,000 described extant species. A well-resolved phylogeny of fireflies is important for the study of their bioluminescence, evolution, and conservation. We used a recently published anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) and state-of-the-art statistical methods (the fossilized birth-death-range process implemented in a Bayesian framework) to estimate a time-calibrated phylogeny of Lampyridae. Unfortunately, estimating calibrated phylogenies using AHE and the latest and most robust time-calibration strategies is not possible because of computational constraints. As a solution, we subset the full dataset and applied three different strategies: using the most complete loci, the most homogeneous loci, and the loci with the highest accuracy to infer the well established Photinus clade. The estimated topology using the three data subsets agreed on almost all major clades and only showed minor discordance with less supported nodes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust as long as the topology inference is robust and any well selected data subset suffices. Additionally, we observed an unexpected amount of gene tree discordance between the 436 AHE loci. Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci which is likely to bias phylogenetic inferences. We performed a simulation study to explore the impact of (a) incomplete lineage sorting, (b) uniformly distributed and systematic missing data, and (c) systematic bias in the position of highly variable and conserved sites. For our simulated data, we observed less gene tree variation and hence the empirically observed amount of gene tree discordance for the AHE dataset is unexpected.

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Section: Resultsmentioning

confidence: 99%

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

Höhna

Lower

Duchen

et al. 2021

Preprint

Self Cite

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“…RevGadgets is hosted on CRAN (https://cran.r-proje ct.org/web/ packa ges/RevGa dgets/ index.html) and available on GitHub (https:// github.com/revba yes/RevGa dgets (Tribble et al, 2021)). All example datasets are freely available on the RevBayes website (https://revba yes.github.io/tutor ials/intro/ revga dgets) and/or are bundled with the R package.…”

Section: Ack N Owled G Em Entsmentioning

confidence: 99%

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

et al. 2021

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Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing and communicating their key results. We present RevGadgets, an R package for creating publication‐quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages). We demonstrate how to use RevGadgets through a set of vignettes that cover the most common use cases that researchers will encounter. RevGadgets is an open‐source, extensible package that will continue to evolve in parallel with RevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses.

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“…We followed the tutorial (https://revba yes.github.io/tutor ials/divra te/ebd.html#Hoehn a2015a) with ρ = 1 and a chain length of 10 × 10 6 generations. We used the R package revgadgets version 1.0 (Tribble et al, 2021) to visualize the rates. For both comet and revbayes, we performed two additional analyses changing the global sampling fraction to ρ = .5 and ρ = .25, considering that we only sampled the 50% and 25% of the total diversity of Cyphoderiidae, respectively.…”

Section: Diversification Analysesmentioning

confidence: 99%

Cyphoderia ampulla(Cyphoderiidae: Rhizaria), a tale of freshwater sailors: The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists

et al. 2022

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The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions have been extensively investigated in animals, the tempo, mode, and outcome of crossing the salinity barrier have been scarcely studied in other eukaryotes. Here, we reconstructed the evolutionary history of the species complex Cyphoderia ampulla (Euglyphida: Cercozoa: Rhizaria) based on DNA sequences from the nuclear SSU rRNA gene and the mitochondrial cytochrome oxidase subunit I gene, obtained from publicly available environmental DNA data (GeneBank, EukBank) and isolated organisms. A tree calibrated with euglyphid fossils showed that four independent transitions towards freshwater systems occurred from the mid‐Miocene onwards, coincident with important fluctuations in sea level. Ancestral trait reconstructions indicated that the whole family Cyphoderiidae had a marine origin and suggest that ancestors of the freshwater forms were euryhaline and lived in environments with fluctuating salinity. Diversification rates did not show any obvious increase concomitant with ecological transitions, but morphometric analyses indicated that species increased in size and homogenized their morphology after colonizing the new environments. This suggests adaptation to changes in selective pressure exerted by life in freshwater sediments.

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RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

Cited by 19 publications

References 59 publications

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

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

Cyphoderia ampulla(Cyphoderiidae: Rhizaria), a tale of freshwater sailors: The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists

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