Wednesday, December 23, 2015

DTT and the pattern of comparative data

A colleague recently inquired as to how one might go about interpreting the pattern shown by a so-called disparity-through-time (DTT) plot.

A DTT plot shows the mean disparity (effectively, variance) of each subtree compared to the total disparity, and is calculated by taking a time slice at each 'event' (speciation event recorded in the reconstructed phylogeny) of the tree.

DTT plots are interpreted in a variety of ways in the literature - for instance, as evidence that variability accumulates within, rather than between, clades; or that phenotypic diversity has tended to accrue in the early rather than the later stages of a diversification.

I thought it might be nonetheless useful to conduct a 'mini' simulation study in which I examined how, in general, the accumulation of disparity among clades through time may be related to biological process.

To start with, here are a couple of small custom functions that I wrote to facilitate the analyses:

meanDtt<-function(D){
    max.t<-max(sapply(D,function(x) max(x$times)))
    t<-seq(0,1,by=0.01)*max.t
    d<-vector()
    for(i in 1:length(t)){
        d[i]<-0
        for(j in 1:length(D)){
            ii<-max(which(D[[j]]$times<=t[i]))
            d[i]<-d[i]+D[[j]]$dtt[ii]/length(D)
        }
    }
    obj<-list(times=t,dtt=d)
    obj
}
plotDtt<-function(D,main=""){
    max.d<-max(sapply(D,function(x) max(x$dtt)))
    max.t<-max(sapply(D,function(x) max(x$times)))
    plot.new()
    plot.window(xlim=c(0,max.t),ylim=c(0,max.d))
    for(i in 1:length(D)) lines(D[[i]]$times,D[[i]]$dtt,
        col=rgb(0,0,1,0.1),lwd=2,
        type="s")
    axis(1)
    axis(2)
    title(xlab="time",ylab="disparity",main=main)
    obj<-meanDtt(D)
    lines(c(0,obj$times),c(1,obj$dtt),lwd=2)
}   

Next, we can load our packages. DTT calculation is part of the geiger package.

library(phytools)
## Loading required package: ape
## Loading required package: maps
## 
##  # ATTENTION: maps v3.0 has an updated 'world' map.        #
##  # Many country borders and names have changed since 1990. #
##  # Type '?world' or 'news(package="maps")'. See README_v3. #
library(geiger)

OK, now we can simulate some trees:

trees<-pbtree(n=100,scale=1,nsim=200)
trees
## 200 phylogenetic trees

OK, now let's explore the relationship between process & DTT. Our custom function, plotDtt, plots all the DTTs but also overlays the average DTT across simulations.

First, Brownian motion:

## Brownian motion
X<-lapply(trees,fastBM)
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Brownian motion")

plot of chunk unnamed-chunk-4

Now, early-burst evolution:

## early burst
X<-lapply(trees,function(x) fastBM(rescale(x,"EB",a=-4)))
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Early-Burst")

plot of chunk unnamed-chunk-5

Late-burst:

## late burst
X<-lapply(trees,function(x) fastBM(rescale(x,"EB",a=4)))
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Late-Burst")

plot of chunk unnamed-chunk-6

Now, how about the Ornstein-Uhlenbeck model with a single optimum:

## OU
X<-lapply(trees,function(x) fastBM(rescale(x,"OU",alpha=4)))
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Ornstein-Uhlenbeck")

plot of chunk unnamed-chunk-7

In addition, here are a couple of models that we can simulate very easily, but not fit:

## Brownian motion with bounds
X<-lapply(trees,fastBM,bounds=c(-1,1))
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Bounded BM [-1,1]")

plot of chunk unnamed-chunk-8

X<-lapply(trees,fastBM,bounds=c(-0.4,0.4))
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Bounded BM [-0.4,0.4]")

plot of chunk unnamed-chunk-8

X<-lapply(trees,fastBM,bounds=c(-0.2,0.2))
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="Bounded BM [-0.2,0.2]")

plot of chunk unnamed-chunk-8

## Brownian motion with a trend
X<-lapply(trees,fastBM,mu=4)
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,main="BM with a trend")

plot of chunk unnamed-chunk-8

Finally, it is important to keep in mine that DTT plots can be pretty substantially affected by sampling error in the estimation of species means. Here is a demo of the effect of two different levels of sampling error. I have simulated sampling variances from a exponential distribution with rate 1.0, but then multiplied by different values of a constant k, in which larger values imply more sampling error:

## measurement error
sim.error<-function(tree,k=0.1){
    x<-fastBM(tree)
    v<-k*setNames(rexp(n=Ntip(tree)),names(x))
    sampleFrom(x,v,n=rep(1,Ntip(tree)))
}
X<-lapply(trees,sim.error,k=0.01)
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,"BM with sampling error (k=0.01)")

plot of chunk unnamed-chunk-9

X<-lapply(trees,sim.error,k=0.05)
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,"BM with sampling error (k=0.05)")

plot of chunk unnamed-chunk-9

X<-lapply(trees,sim.error,k=0.2)
D<-mapply(dtt,trees,X,MoreArgs=list(plot=FALSE),SIMPLIFY=FALSE)
plotDtt(D,"BM with sampling error (k=0.2)")

plot of chunk unnamed-chunk-9

That's really all I have.

4 comments:

  1. Dear Liam, thanks for these simulations. I wonder whether "dtt" performs well also when one has multiple samples per species or whether this method is not appropriate for such datasets.
    Best,
    Martin

    ReplyDelete
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