convrat {convevol}

Quantifies convergent evolution using the C1, C2, C3, and C4 measures as described by Stayton (2015).

Description

Calculates the current phenotypic distance (Euclidean) between two taxa. Then uses ancestral state reconstruction under a BM model to calculate the maximum phenotypic distance at any time between lineages leading from the most recent common ancestor of those two taxa to the tips. Also calculate the total amount of phenotypic evolution in the clade defined by the most recent common ancestor of those lineages, and the total amount of phenotypic evolution in the input tree. These quantities are used to calcualte C1-C4: C1 = 1-(current distance / maximum ancestral distance); C2 = maximum ancestral distance - current distance; C3=C2/(total phenotypic evolution in the clade defined by the two taxa); C4 = C2/(total amount of phenotypic evolution in the entire tree). If more than two convergent taxa are input, then C1-C4 are calculated for all possible pairs of taxa, and averaged.

Usage

convrat(phyl, phendata, convtips)

Arguments

phyl

The phylogeny of interest in phylo format

phendata

Phenotypic data for all tips

convtips

A list consisting of the names of all convergent taxa

Details

None

Value

Four numbers - C1, C2, C3, C4.

References

Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K.(2013). cluster: Cluster Analysis Basics and Extensions. R package version 1.14.4.

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R langauge. Bioinformatics, 20, 289-290.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3 217-223.

Stayton, C.T. (2015). The definition, recognition, and interpretation of convergent evolution, and two new measure for quantifying and assessing the significance of convergence. Evolution 69:2140-2153.

Examples

phyl<-rtree(10)
phendata<-fastBM(phyl,nsim=2)
convtips<-c("t1","t2","t3")
answer<-convrat(phyl,phendata,convtips)