I have now posted development
for a fossil version of the phytools function
This function uses ML to place a single fossil tip into a tree based on
continuous character data. It allows the user to impose a
time.constraint, in the form of a time range for the fossil. If
the age of the fossil is known precisely, this can just be a single numeric
value; and if the user wants to supply it (rather than as a height above the
root) as a time before present, this should be given as a negative scalar.
time.constraint constrains only the height of the tip,
and not at all the height of the attachment of the terminal edge to the tree -
except inasmuch as this must precede in time the height of the tip of course!
The user can also supply an
edge.constraint which constrains the
edges of the tree to which the tip can attach. Obviously, these must be
time.constraint or the function will not work.
Here's a demo of estimation using simulated data:
library(phytools) library(mnormt) ## here is our true tree (normally unknown) plotTree(true.tree,ftype="i",fsize=0.8)
## simulate data X<-fastBM(true.tree,nsim=20) ## drop tip to recreate the empirical backbone tree tree<-drop.tip(true.tree,"fossil") plotTree(tree,ftype="i",fsize=0.8)
## now let's make an age constraint based on the real (known) age of ## the fossil lineage: h<-nodeHeights(true.tree)[true.tree$edge[,2]==which(true.tree$tip.label=="fossil"),2] max(nodeHeights(tree))-h
##  30.14439
##  64.85561 74.85561
## load source code for locate.fossil source("locate.fossil.R") mltree<-locate.fossil(tree,X,time.constraint=age.range,plot=FALSE)
## Optimizing the phylogenetic position of fossil using ML. Please wait.... ## Done.
## plot the result plotTree(mltree,mar=c(2.1,0.1,3.1,0.1),ftype="i",fsize=0.8) axis(1) obj<-lapply(age.range,function(x,tree) lines(rep(x,2), c(0,Ntip(tree)+1),col="red",lty="dashed"),tree=tree) title(paste("Optimized position of taxon \"",setdiff(rownames(X),tree$tip.label), "\"",sep=""))
The function also contains an option to plot the progress of the likelihood
search. This is somewhat difficult to illustrate on the web. (I attempted to use
saveGIF from the 'animation' package, but was having trouble for
some unknown reason.)
That's it for now.
A few queries:ReplyDelete
1) What's the minimum size of the branch the fossil taxon attaches to the tree with? Do you allow for zero-length branches? (A ZLB would essentially mean its a direct ancestor of an extant lineage...)
2) Would it be possible to constrain the search to only consider scenarios where the taxon is connected by a ZLB? Then one could compare the likelihood scores (using an LRT, I think) to test if a fossil specimen was likely to be a direct ancestor or not (which is a feasible hypothesis and an pertinent question in some cases...).
1) Yes, zero.ReplyDelete
2) Not presently, but theoretically straightforward.
This is a prototype function right now - it computes the likelihood correctly, but I don't know about optimization and/or constraints on the optimization. I will be working on it more.
Ah, well, cool function nonetheless!ReplyDelete