In dinaIssakova/rgenesconverged: A Package for Estimating Probability of Convergent Evolution from Genomic Data

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rgenesconverged

Sequence convergence is a type of convergent evolution that results in similarity between orthologous genetic sequences. However, this can be difficult to evaluate statistically given classical paradigms for convergent evolution, which rest on the assumption that convergent phenotypes are achieved by unrelated genetic mechanisms. While sophisticated models exist to model this process and to evaluate the probability of this explanation of genetic similarity across two different species, no tool has currently been implemented in R to carry out these analyses. Here we present rgenesconverged, an R package allowing the exploration of sequence convergence hypotheses in a given phylogeny.

This package implements and extends the model for sequence convergence given by Zhang and Kumar:

J. Zhang and S. Kumar, “Detection of convergent and parallel evolution at the amino acidsequence level,” Mol. Biol. Evol., vol. 14, no. 5, pp. 527–536, 1997.

For more information or to use rgenesconverged in a publication, please consult/cite:

Issakova, D. 2019. rgenesconverged: An R Package for the Exploration of Molecular Convergent Evolution. bioRxiv doi: https://doi.org/10.1101/858076

Installation

You can install the current version of rgenesconverged from github with:

library(devtools)
install_github("dinaIssakova/rgenesconverged")
library(rgenesconverged)

And run the Shiny app by:

shinyRgenesconverged()

Overview

browseVignettes(rgenesconverged)

The inputs required to rgenesconverged are an R phydat object containing alignment information for the selected species and an R tree object - in the RShiny app, only the alignment is asked for and the tree is built from that. The user selects a species of interest for comparison to which the other species in the tree are compared. Sequences are aligned by ClustalOmega to the reference sequence; the position at which convergence is to be evaluated corresponds to that position in the reference sequence, and corresponding positions in the alignment. Two possible 'paths' exist in this package for phylogenetic analysis. The first is a direct implementation of Zhang and Kumar's model, which is a well-established and commonly used model for sequence convergence; the second is a natural extension allowing for a more nuanced and exploratory analysis, but less statistical rigor. An R plot is also available, which finds species that are convergent at the particular position specified to the reference species, and highlights them in a phylogram. While designed for use in an R environment, an RShiny UI is available with the package for users unfamiliar with R programming.

For more information, please see the vignettes for this package, or

Issakova, D. 2019. rgenesconverged: An R Package for the Exploration of Molecular Convergent Evolution. bioRxiv doi: https://doi.org/10.1101/858076

Contributions

rlibrary("rgenesconverged")
lsf.str("package:rgenesconverged")

The author of the package is Dina Issakova. The functions available within this package include:

• getBranchLength
• getMostRecentCommonAncestor
• mapLetters
• areCondSatisfied
• probOfChange
• probOfSiteConfig
• probOfNSitesByChance
• getConvergent
• convSiteData
• rgenesconvergedPlot
• shinyRgenesconverged

All functions above were authored by Dina Issakova. Examples and help files make use of datasets available from phangorn R package and subsets of these datasets. PAM matrix included in dataset is manually copied from:

Dayhoff, M.O. et al. (1978) A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure. p. 345-352

The getMostRecentCommonAncestor function makes use of commonly known algorithms for finding the deepest ancestor of two leaves in a binary tree. The areCondSatisfied and probOfSiteConfig functions make use of the phangorn R package function ancestral.pars to predict ancestral states of amino acid sequences based on branch length and mutation probabilities. The areCondSatisfied, probOfChange and probOfSiteConfig functions make use of the Biostrings R package to translate amino acid sequences using the standard genetic code and access standard lists of amino acids. The probOfChange function makes use of the package foreach for parallelizing.

The areCondSatisfied, probOfChange, probOfSiteConfig, probOfNSitesByChance, getConvergent and convSiteData implement mathematical models of genomic convergent evolution described in :

Zhang, J. and Kumar, S. (1997) Detection of Convergent and Parallel Evolution at the Amino Acid Sequence Level. Mol. Biol. Evol. 14(5):527-536.

The rgenesconvergedPlot was authored by Dina Issakova and makes use of the package ggtree and ggplot to plot the phylogenetic tree.

Specifically, Dina Issakova's contribution was 1) implementing the mathematical model described by Zhang and Kumar above and 2) extending the model by adding a score-based exploratory function.

Walkthrough

For walkthrough, please see vignettes.

dinaIssakova/rgenesconverged documentation built on Jan. 7, 2020, 4:25 p.m.