Adding new tips randomly to different specific position in a phylogenetic tree

Question

I am building a phylogenetic tree, and now I have several species only identified to genus level only. However, I want to keep them and bind to the tree for futher analysis.

The package I am using now is phytools and following Liam's toturials.

Solution1

Initially, let's assume we have a phylogenetic tree like this.

Now, I want to add a set of species to the corresponding genus by using the function add.species.to.genus .

#add a set of species in a vector
species <- c("Genus1_sp2", "Genus2_sp3", "Genus3_sp2", "Genus4_sp7", "Genus4_sp8", "Genus5_sp3")
for(i in 1:length(species)) tree<-add.species.to.genus(tree,species[i],where="random")
plotTree(tree)

The outcome will be like this.

However, as you guys see here, one name only is binded to one tip.

Solution2

# get a pseudo-tree
tree<-pbtree(n=26,tip.label=LETTERS)
plotTree(tree)
nodelabels()

#set a node we want to add a tip randomly
node<-45
tt<-splitTree(tree,split=list(node=node,
    bp=tree$edge.length[which(tree$edge[,2]==node)]))
tt[[2]]<-add.random(tt[[2]],tips="tip to add")
new.tree<-paste.tree(tt[[1]],tt[[2]])
plotTree(new.tree)

#replicate times
foo<-function(tree,node){
    tt<-splitTree(tree,split=list(node=node,
        bp=tree$edge.length[which(tree$edge[,2]==node)]))
    tt[[2]]<-add.random(tt[[2]],tips="tip to add")
    paste.tree(tt[[1]],tt[[2]])
}
new.trees<-replicate(9,foo(tree,node),simplify=FALSE)
class(new.trees)<-"multiPhylo"
# add colour
nulo<-sapply(new.trees,function(x) plot(paintSubTree(x,45,"2"),
    colors=setNames(c("black","blue"),1:2),fsize=0.6))

Here, one name randomly binded to different tips' position.

In sum, I would like to ask:

For solution 1, how can I do replicate for the binding? I mean that one name/species can be binded to more tips, eg Genus 5_sp3 can be added to Genus 5_sp1 .

For solution 2, how can I do add more than a tip to pre-specified clades.

General question : How can I add new tips randomly repeatly to different clades in a tree?

Does anyone know how to do this or have any experiences for this case? It would be appreciative if anyone could give a solution for this.

Note : The codes and images I used from the Liam's website.

Above codes provided by Liam from his website http://blog.phytools.org/2017/10/adding-tip-at-random-to-pre-specified.html and http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html

Answer 1

updated Hi guys,

I dont know my answer is correct or not but it seems to go on the right way.

#I find the node of clade that I want to add.
node = 193
tt <- list()
class(tt) <- "multiPhylo"

fun<-function(sample_1,node){
  tt<-splitTree(sample_1,split=list(node=node,
                                bp=sample_1$edge.length[which(sample_1$edge[,2]==node)]))
  tt[[2]]<-add.random(tt[[2]], tips = "Pycnonotus sp.01")
  paste.tree(tt[[1]],tt[[2]])
}

new.trees<-replicate(20,fun(sample_1,node),simplify=FALSE)
plotTree(new.trees[[1]])

# Then, I will use the saving tree for the next round of adding another species. 
#sp2
node1 = 194

tt1 <- lapply(seq_along(new.trees), function(i)
  splitTree(new.trees[[i]], split = list(node = node1,
                                         bp = new.trees[[i]]$edge.length[which(new.trees[[i]]$edge[,2]==node1)])))

new.trees.1 <- list()
new.trees.1 <- lapply(seq_along(tt1), function(i){
  tt1[[i]][[2]] <- add.random(tt1[[i]][[2]], tips = "Pycnonotus sp.02");
  new.trees.1[[i]] <- paste.tree(tt1[[i]][[1]], tt1[[i]][[2]])})

# I would like to do the same thing for adding more species

What do you think about my solution? Does it make sense?