geomorph (version 1.1-6)

physignal: Assessing phylogenetic signal in morphometric data

Description

Function calculates the degree of phylogenetic signal from a set of Procrustes-aligned specimens

Usage

physignal(phy, A, iter = 249)

Arguments

phy

A phylogenetic tree of type 'phylo'

A

An array (p x k x n) containing GPA-aligned coordinates for a set of specimens

iter

Number of iterations for significance testing

Value

• Function returns a list with the following components:
• phy.signal
  The estimate of phylogenetic signal
• pvalue
  The significance level of the observed signal

Details

The function estimates the degree of phylogenetic signal present in shape data for a given phylogeny based on 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]. To assess phylogenetic signal under alternative models, first consider branch-length transformations of the phylogeny. Phylogenetic signal is estimated as the sum of squared changes (SSC) in shape along all branches of the phylogeny (Klingenberg and Gidaszewski 2010). Significance testing is found by permuting the shape data among the tips of the phylogeny. A plot of the specimens in tangent space with the phylogeny superimposed is included, and ancestral states are returned. Note that the method can be slow as ancestral states must be estimated for every iteration.

References

Klingenberg, C. P., and N. A. Gidaszewski. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst. Biol. 59:245-261.

Examples

data(plethspecies)
Y.gpa<-gpagen(plethspecies$land)    #GPA-alignment

physignal(plethspecies$phy,Y.gpa$coords,iter=5)