Exercise 14: Diversification analysis with RPANDA
June/2016
RPANDA
RPANDA is another recently developed R package that allows us to fit different models of rate variation through time and select the best fitting model using maximum likelihood analysis.
RPANDA shows basically two main differences from BAMM:
In RPANDA, the user must inform which models are going to be tested, whereas in BAMM the program itself will average among the rates for each clade;
In RPANDA, the user must know a priori which are the clades that might show a particular diversification regime, while BAMM will estimate where rate shifts are positioned using a rjMCMC algorithm.
The package also contains some simuation functions as well as datasets. You can find more details on CRAN.
Model selection
For this exercise, we will test four different scenarios with all combinations of constant and variable speciation and extinction rates as follows (based on Morlon et al. 2011, PNAS)
Read in the whale tree
library(ape)
library(RPANDA)## Loading required package: picante## Loading required package: vegan## Loading required package: permute## Loading required package: lattice## This is vegan 2.4-0## Loading required package: nlmewhales <- read.tree("whaletree.tre")
plot(whales, cex = 0.35)
nodelabels(cex = 0.5)
lambda.cst <- function(x,y){y}
lambda.var <- function(x,y){y[1]*exp(y[2]*x)}
mu.cst <- function(x,y){y}
mu.var <- function(x,y){y[1]*exp(y[2]*x)}The rate variations for the four possible pairwise combinations look like this:
Having decided which models one would like to test, the next step is to extract the clades that most likely share similar diversification regimes. As said previously, RPANDA needs the user to a priori indicate these clades. In this example, we will use the four main cetacean families plus the rest of cetaceans as a fifth clade.
##create a pdf of the tree with the internal nodes labelled
pdf("whale_tree.pdf", width = 4, height =16)
plot(whales, cex = 0.5)
nodelabels(cex = 0.5)
dev.off()## quartz_off_screen
## 2#Use these node numbers to extract clades.
balaenidae.tree <- extract.clade(whales, 90)
balaenopteridae.tree <- extract.clade(whales,95)
delphinidae.tree <- extract.clade(whales, 140)
phocoenidae.tree <- extract.clade(whales, 135)
ziphidae.tree <- extract.clade(whales, 109)
par(mfcol = c(3, 2))
plot(balaenidae.tree, main = "Balaenidae")
plot(balaenopteridae.tree, main = "Balaenopteridae")
plot(delphinidae.tree, main = "Delphinidae")
plot(phocoenidae.tree, main = "Phocoenidae")
plot(ziphidae.tree, main = "Ziphidae")
#We also need to capture the rest of the cetaceans that do not fall into these clades
othercetaceans.tree <- drop.tip(whales,c(balaenopteridae.tree$tip.label,delphinidae.tree$tip.label, phocoenidae.tree$tip.label, ziphidae.tree$tip.label))
plot(othercetaceans.tree, main = "Other cetaceans")
If you do not know the node numbers, you can also extract clades by passing a list of clade names. This block shows how we could use grep to accomplish this.
balaenidae <- c(whales$tip.label[grep("Balaena",whales$tip.label)],whales$tip.label[grep("Eubalaena",whales$tip.label)])
balaenopteridae <- c(whales$tip.label[grep("Balaenoptera",whales$tip.label)],whales$tip.label[grep("Megaptera",whales$tip.label)])
delphinidae <- c(whales$tip.label[grep("Delphinus",whales$tip.label)],whales$tip.label[grep("Cephalorhynchus",whales$tip.label)],whales$tip.label[grep("Feresa",whales$tip.label)],whales$tip.label[grep("Globicephala",whales$tip.label)],whales$tip.label[grep("Lagenodelphis",whales$tip.label)],whales$tip.label[grep("Lagenorhynchus",whales$tip.label)],whales$tip.label[grep("Lissodelphis",whales$tip.label)],whales$tip.label[grep("Orcaella",whales$tip.label)],whales$tip.label[grep("Orcinus",whales$tip.label)],whales$tip.label[grep("Peponocephala",whales$tip.label)],whales$tip.label[grep("Pseudorca",whales$tip.label)],whales$tip.label[grep("Sotalia",whales$tip.label)],whales$tip.label[grep("Sousa",whales$tip.label)],whales$tip.label[grep("Stenella",whales$tip.label)],whales$tip.label[grep("Steno",whales$tip.label)],whales$tip.label[grep("Tursiops",whales$tip.label)],whales$tip.label[grep("Grampus",whales$tip.label)])
phocoenidae <- c(whales$tip.label[grep("Neophocaena",whales$tip.label)],whales$tip.label[grep("Phocoena",whales$tip.label)],whales$tip.label[grep("Phocoenoides",whales$tip.label)])
ziphidae <- c(whales$tip.label[grep("Berardius",whales$tip.label)],whales$tip.label[grep("Hyperoodon",whales$tip.label)],whales$tip.label[grep("Indopacetus",whales$tip.label)],whales$tip.label[grep("Mesoplodon",whales$tip.label)],whales$tip.label[grep("Tasmacetus",whales$tip.label)],whales$tip.label[grep("Ziphius",whales$tip.label)])
balaenidae.tree <- drop.tip(whales,whales$tip.label[-match(balaenidae,whales$tip.label)])balaenopteridae.tree <- drop.tip(whales,whales$tip.label[-match(balaenopteridae,whales$tip.label)])
delphinidae.tree <- drop.tip(whales,whales$tip.label[-match(delphinidae,whales$tip.label)])
phocoenidae.tree <- drop.tip(whales,whales$tip.label[-match(phocoenidae,whales$tip.label)])
ziphidae.tree <- drop.tip(whales,whales$tip.label[-match(ziphidae,whales$tip.label)])
othercetaceans.tree <- drop.tip(whales,c(balaenopteridae,delphinidae, phocoenidae, ziphidae))Lets fit our four models to the tree for the phocoenidae.
#fit a constant rate bd model, bvardcst
fit_bd(phocoenidae.tree, max(branching.times(phocoenidae.tree)), f.lamb=lambda.cst, f.mu=mu.cst, lamb_par=0.4, mu_par=0,cst.lamb=TRUE,cst.mu=TRUE,cond="crown",f=87/89,dt=1e-3)## model :
## [1] "birth death"
##
## LH :
## [1] -11.89603
##
## aicc :
## [1] 31.79207
##
## lamb_par :
## [1] 0.1410234
##
## mu_par :
## [1] -6.012454e-08#how does this compare to the bd fit under ape from this AM?
bd<-function(x){
if(class(x)!="birthdeath") stop("x should be an object of class 'birthdeath'")
b<-x$para[2]/(1-x$para[1])
d<-b-x$para[2]
setNames(c(b,d),c("b","d"))
}
fit.bd<-birthdeath(phocoenidae.tree)
bd(fit.bd)## b d
## 0.1383232 0.0000000# diversitree fit
# library(diversitree)
# pbModel<-make.bd(phocoenidae.tree,sampling.f=87/89)
# bdMLFit<-find.mle(bdModel,c(0.1,0.05),method = "optim",lower = 0)
# bdMLFit
##fit a model where the speciation rate varies through time and the extinction rate is constant, bvardcst
fit_bd(phocoenidae.tree, max(branching.times(phocoenidae.tree)), f.lamb=lambda.var, f.mu=mu.cst, lamb_par= c(0.4,-0.05),mu_par=0,expo.lamb=TRUE,cst.mu=TRUE,cond="crown",f=87/89,dt=1e-3)## model :
## [1] "birth death"
##
## LH :
## [1] -8.066742
##
## aicc :
## [1] 34.13348
##
## lamb_par :
## [1] 0.002377951 1.140276500
##
## mu_par :
## [1] -1.58053e-07This function will help automate the calculation of the likelihood for the RPANDA models.
library(RPANDA)
fit.multi.rpanda <- function(tree,par)
{
bcstdcst <- fit_bd(tree, max(branching.times(tree)), f.lamb=lambda.cst, f.mu=mu.cst, lamb_par=par[[1]][1],mu_par=par[[1]][2],cst.lamb=TRUE,cst.mu=TRUE,cond="crown",f=87/89,dt=1e-3)
bvardcst <- fit_bd(tree, max(branching.times(tree)), f.lamb=lambda.var, f.mu=mu.cst, lamb_par=par[[2]][c(1,2)],mu_par=par[[2]][3],expo.lamb=TRUE,cst.mu=TRUE,cond="crown",f=87/89,dt=1e-3)
bcstdvar <- fit_bd(tree, max(branching.times(tree)), f.lamb=lambda.cst, f.mu=mu.var, lamb_par=par[[3]][1],mu_par=par[[3]][c(2,3)],cst.lamb=TRUE,expo.mu=TRUE,cond="crown",f=87/89,dt=1e-3)
bvardvar <- fit_bd(tree, max(branching.times(tree)), f.lamb=lambda.var, f.mu=mu.var, lamb_par=par[[4]][c(1,2)],mu_par=par[[4]][c(3,4)],expo.lamb=TRUE,expo.mu=TRUE,cond="crown",f=87/89,dt=1e-3)
return(list("bcstdcst"=bcstdcst,"bvardcst"=bvardcst,"bcstdvar"=bcstdvar,"bvardvar"=bvardvar))
}
whales.par <- list(c(0.4,0),c(0.4,-0.05,0),c(0.4,0.1,0.05),c(0.4,-0.05,0.1,0.05)) #we need to supply starting parameter values for optimization to RPANDAEstimation of model parameters
In the posession of all models and clades, we can finally estimate the parameters of all the four models to each of the five clades and create an AICc table in order to select which one is the best model that describes the changes in both diversification rates (speciation and extinction) rates. (This part of the code take a while to complete)
results <- list("balaenopteridae.res"=fit.multi.rpanda(balaenopteridae.tree,whales.par),
"delphinidae.res" = fit.multi.rpanda(delphinidae.tree,whales.par),
"phocoenidae.res" = fit.multi.rpanda(phocoenidae.tree,whales.par),
"ziphidae.res" = fit.multi.rpanda(ziphidae.tree,whales.par),
"othercetaceans.res"= fit.multi.rpanda(othercetaceans.tree,whales.par))aic.table <- matrix(nrow=4,ncol=5,NA)
for(i in 1:5)
{
for(j in 1:4)
{
aic.table[j,i] <- results[[i]][[j]]$aicc
}
}
colnames(aic.table) <- c("Balaenopteridae","Delphinidae","Phocoenidae","Ziphidae","Other Cetaceans")
rownames(aic.table) <- c("bcstdcst","bvardcst","bcstdvar","bvardvar")
aic.table## Balaenopteridae Delphinidae Phocoenidae Ziphidae Other Cetaceans
## bcstdcst 56.73336 171.4150 31.79207 132.6440 119.4690
## bvardcst 58.44456 170.0338 34.13348 130.1843 117.5562
## bcstdvar 58.32515 170.6453 41.79207 127.6094 115.3723
## bvardvar 65.67244 171.3258 64.13348 133.2251 118.9789par.table <- data.frame("Balaenopteridae"=c(results[[1]]$bcstdcst$lamb_par[1:2],results[[1]]$bcstdcst$mu_par[1:2]),"Delphinidae"=c(results[[2]]$bvardcst$lamb_par[1:2],results[[2]]$bvardcst$mu_par[1:2]),"Phocoenidae"=c(results[[3]]$bcstdcst$lamb_par[1:2],results[[3]]$bcstdcst$mu_par[1:2]),"Ziphidae"=c(results[[4]]$bcstdcst$lamb_par[1:2],results[[4]]$bcstdcst$mu_par[1:2]),"Other Cetaceans"=c(results[[5]]$bcstdvar$lamb_par[1:2],results[[5]]$bcstdvar$mu_par[1:2]))
par.table## Balaenopteridae Delphinidae Phocoenidae Ziphidae Other.Cetaceans
## 1 7.343080e-02 1.405102e-01 1.410234e-01 9.485149e-02 0.1857764
## 2 NA 1.257642e-01 NA NA NA
## 3 -6.391602e-10 -1.521115e-07 -6.012454e-08 7.545982e-08 0.8313274
## 4 NA NA NA NA -0.1742352Plotting diversity through time
After selecting which model best fits the trees, we can estimate the diversity trajectory through time for each of the five clades.
# Function to calculate species richness in a given point in time
div.times <- c(max(branching.times(balaenopteridae.tree)),max(branching.times(delphinidae.tree)),max(branching.times(phocoenidae.tree)),max(branching.times(ziphidae.tree)),max(branching.times(othercetaceans.tree)))
# Function modified from plot_dtt from RPANDA package
plotdtt <- function (fit.bd, tot_time, N0, col=1, add=FALSE, div.time, xlim, ylim)
{
if (!inherits(fit.bd, "fit.bd"))
stop("object \"fit.bd\" is not of class \"fit.bd\"")
t <- seq(tot_time-div.time, tot_time, 0.01)
if ("f.mu" %in% attributes(fit.bd)$names) {
r <- function(t) {
-fit.bd$f.lamb(t) + fit.bd$f.mu(t)
}
R <- function(s) {
RPANDA:::.Integrate(Vectorize(r), 0, s)
}
N <- N0 * exp(Vectorize(R)(t))
#dev.new()
if(add==FALSE)
{
plot(-t, N, type = "l", xlab = "time", ylab = "Number of species",
main = "Diversity Through Time", col=col, xlim=xlim, ylim=ylim)
}
else
{
lines(-t, N, type = "l", xlab = "time", ylab = "Number of species",
main = "Diversity Through Time", col=col, xlim=xlim, ylim=ylim)
}
}
else {
r <- function(t) {
-fit.bd$f.lamb(t)
}
R <- function(s) {
RPANDA:::.Integrate(Vectorize(r), 0, s)
}
N <- N0 * exp(Vectorize(R)(t))
#dev.new()
if(add==FALSE)
{
plot(-t, N, type = "l", xlab = "time", ylab = "Number of species",
main = "Diversity Through Time",col=col, xlim=xlim, ylim=ylim)
}
else
{
lines(-t, N, type = "l", xlab = "time", ylab = "Number of species",
main = "Diversity Through Time",col=col, xlim=xlim, ylim=ylim)
}
}
}
plotdtt(results$balaenopteridae$bcstdcst,div.times[1],N0=Ntip(balaenopteridae.tree),xlim=c(-max(div.times),0),ylim=c(0,150),div.time=div.times[1])
plotdtt(results$delphinidae$bvardcst,div.times[2],N0=Ntip(delphinidae.tree),col=6,add=TRUE,xlim=c(-max(div.times),0),ylim=c(0,150),div.time=div.times[2])
plotdtt(results$phocoenidae$bcstdcst,div.times[3],N0=Ntip(phocoenidae.tree),col="goldenrod",add=TRUE,xlim=c(-max(div.times),0),ylim=c(0,150),div.time=div.times[3])
plotdtt(results$ziphidae$bcstdcst,div.times[4],N0=Ntip(ziphidae.tree),col=4,add=TRUE,xlim=c(-max(div.times),0),ylim=c(0,150),div.time=div.times[4])
plotdtt(results$othercetaceans$bcstdvar,div.times[5],N0=Ntip(othercetaceans.tree),col="darkred",add=TRUE,xlim=c(-max(div.times),0),ylim=c(0,150),div.time=div.times[5])
legend("topleft",legend=c("Balaenopteridae","Delphinidae","Phocoenidae","Ziphidae","Other Cetaceans"),text.col=c(1,6,"goldenrod",4,"darkred"))
Challenge
- Fit models using RPANDA for the entire whale phylogeny, and plot its diversity through time using parts of the previous codes chunks.