geomorph (version 3.0.2)

compare.evol.rates: Comparing rates of shape evolution on phylogenies

Description

Function calculates rates of shape evolution for two or more groups of species on a phylogeny from a set of Procrustes-aligned specimens

Usage

compare.evol.rates(A, phy, gp, iter = 999, print.progress = TRUE)

Arguments

A

A 3D array (p x k x n) containing GPA-aligned coordinates for all specimens, or a matrix (n x variables)

phy

A phylogenetic tree of class phylo - see read.tree in library ape

gp

A factor array designating group membership

iter

Number of iterations for significance testing

print.progress

A logical value to indicate whether a progress bar should be printed to the screen. This is helpful for long-running analyses.

Value

An object of class "evolrate" returns a list with the following components:

sigma.d.ratio

The ratio of maximum to minimum evolutionary rates.

P.value

The significance level of the observed ratio.

sigma.d.gp

The phylogenetic evolutionary rate for each group of species on the phylogeny.

random.sigma

The sigma values found in random permutations of the resampling procedure.

permutations

The number of random permutations used.

Details

The function compares rates of morphological evolution for two or more groups of species on a phylogeny, under a Brownian motion model of evolution. It is assumed that the landmarks have previously been aligned using Generalized Procrustes Analysis (GPA) [e.g., with gpagen]. The approach is based on the distances between species in morphospace after phylogenetic transformation (Adams 2014). From the data the rate of shape evolution for each group is calculated, and a ratio of rates is obtained. If three or more groups of species are used, the ratio of the maximum to minimum rate is used as a test statistic (see Adams 2014). Significance testing is accomplished by phylogenetic simulation in which tips data are obtained under Brownian motion using a common evolutionary rate pattern for all species on the phylogeny. Specifically, the common evolutionary rate matrix for all species is used, with the multi-dimensional rate used along the diagonal elements (see Denton and Adams 2015). This procedure is more general than the original simulation procedure, and retains the desirable statistical properties of earlier methods, and under a wider array of data types. If three or more groups of species are used, pairwise p-values are also calculated. The function can be used to obtain a rate for the whole dataset of species by using a dummy group factor assigning all species to one group. This function can be used with univariate data (i.e. centroid size) if imported as matrix with rownames giving the taxa names. The generic functions, print, summary, and plot all work with compare.evol.rates. The generic function, plot, produces a histogram of random rate-ratios associated with the resampling procedure.

Notes for geomorph 3.0 Compared to older versions of geomorph, the order of input variables has changed, so that it is consistent with other functions in the program. Additionally, for 3 or more groups, the pairwise p-values are found in the output object.

References

Adams, D.C. 2014. Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data. Syst. Biol. 63:166-177.

Denton, J.S.S., and D.C. Adams. 2015. A new phylogenetic test for comparing multiple high-dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae). Evolution. 69:2425-2440.

Examples

data(plethspecies) 
Y.gpa<-gpagen(plethspecies$land)    #GPA-alignment    
 gp.end<-factor(c(0,0,1,0,0,1,1,0,0))  #endangered species vs. rest
 names(gp.end)<-plethspecies$phy$tip

ER<-compare.evol.rates(A=Y.gpa$coords, phy=plethspecies$phy,gp=gp.end,iter=999)
summary(ER)
plot(ER)