Xianping Li A learner

Test phylogenetic signal

19 Dec 2015

Phylogenetic signal

Ecological traits of related species always tend to be more similar than species randomly drawn from the same phylogeny. This is called phlogenetic signal[1-3]. It is often interpreted as providing information about the evolutionary process, and is controlled as the statistical nonindependence among species trait values in ecological analysis. There are some posts about how to test phylogenetic signal in R, this, this and this. I would give another example which I was recently involved in.

Steps in R

Let’s take some amphibians with a virtual trait for example.

0. Amphibians with a virtual trait

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species <- read.csv("amphibians.csv", stringsAsFactors = F)

# Some amphibian species. 
# Variable "tip_labels" is the species' name in the phylogenetic tree, 
# while "species_name" is the name I got. 
# They are the synonyms, or they are same. 
# I retain them two for demonstrating 
# how to substitute the tip labels later.

species
##                      species_name                     tip_labels
## 1             Alytes_obstetricans            Alytes_obstetricans
## 2              Ambystoma_tigrinum             Ambystoma_tigrinum
## 3         Amietophrynus_regularis                 Bufo_regularis
## 4             Anaxyrus_americanus                Bufo_americanus
## 5                 Aneides_vagrans                Aneides_vagrans
## 6             Dendrobates_auratus            Dendrobates_auratus
## 7    Desmognathus_quadramaculatus   Desmognathus_quadramaculatus
## 8             Discoglossus_pictus            Discoglossus_pictus
## 9      Duttaphrynus_melanostictus             Bufo_melanostictus
## 10        Eleutherodactylus_coqui        Eleutherodactylus_coqui
## 11   Eleutherodactylus_johnstonei   Eleutherodactylus_johnstonei
## 12 Eleutherodactylus_planirostris Eleutherodactylus_planirostris
## 13              Glandirana_rugosa                    Rana_rugosa
## 14       Hoplobatrachus_rugulosus       Hoplobatrachus_rugulosus
## 15       Hoplobatrachus_tigerinus       Hoplobatrachus_tigerinus

# A virtual variable
set.seed(1234)
species$x <- rnorm(dim(species)[1], mean = 50, sd = 10)

1. Built the phylogenetic tree

Actually prune a built tree from Pyron & Wiens (2011)[4].

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# Load library
library(ape)
supertree <- read.tree("amphibia.tre")

# Remove tips and branches that will not be used
tree_am <- drop.tip(supertree,supertree$tip.label[!(supertree$tip.label 
    %in% species[,"tip_labels"])])

# Substitute the tip labels (tip_labels) with the labels I want (species_name)
matched_labels <- tapply(tree_am$tip.label,
    1:length(tree_am$tip.label),
    function(x) species[which(species$tip_labels == x), "species_name"])

tree_am$tip.label <- as.data.frame(matched_labels)[,1]

# Plot the tree (Fig. 1)
plot(tree_am)

fig1 Figure 1 Amphibian phylogeny.

2. Test phylogenetic signal

Use the indices of Pagel’s lambda and Blomberg’s K. See Pagel (1999)[5] and Blomberg, et al. (2003)[6] for details.

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# Load library
library(phytools)

# Named the variable
x <- species$x
names(x) <- species[,"species_name"]

phylosig(tree_am,x,method="lambda",test=T)
## $lambda
## [1] 6.901966e-05

## $logL
## [1] -53.78967

## $logL0
## [1] -53.78936

## $P
## [1] 1

phylosig(tree_am,x,method="K",test=T)
## $K
## [1] 0.2171225 

## $P
## [1] 0.811

No phylogenetic signal was detected.

References:

[1]: Revell, L.J., Harmon, L.J. & Collar, D.C. (2008) Phylogenetic Signal, Evolutionary Process, and Rate. Systematic Biology, 57, 591-601.
[2]: Hof, C., Rahbek, C. & Araujo, M.B. (2010) Phylogenetic signals in the climatic niches of the world's amphibians. Ecography, 33, 242-250.
[3]: Münkemüller, T., Lavergne, S., Bzeznik, B., Dray, S., Jombart, T., Schiffers, K. & Thuiller, W. (2012) How to measure and test phylogenetic signal. Methods in Ecology and Evolution, 3, 743-756.
[4]: Pyron, R.A. & Wiens, J.J. (2011) A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution, 61, 543-583.
[5]: Pagel, M. (1999) Inferring the historical patterns of biological evolution. Nature, 401, 877-884.
[6]: Blomberg, S.P., Garland, T., Jr. & Ives, A.R. (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717-745.

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