#### A relatively traditional view of terrestrial vertebrate classes (the position of turtles is not very certain) and the dates are very approximate
#### Hugall, A.F., Foster, R., Lee, M.S.Y. (2007) Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst. Biol. 56(04):543–563. DOI: 10.1080/10635150701477825


library(ape)
library(phytools)


vert_orders<-read.tree(text="((tuatara, (lizards, snakes),(turtles, (crocodiles, (birds, non.avian_dinosaurs)))));")
plot(vert_orders)
plotTree(vert_orders)
nodelabels()

## add an extra pair of parentheses around the squamate group to force the root
vert_orders<-read.tree(text="(((tuatara, (lizards, snakes)),(turtles, (crocodiles, (birds, non.avian_dinosaurs)))));")
plot(vert_orders)


###adding the extra clades
vert_tree_extras<-read.tree(text="(((tuatara, (lizards, snakes))), (turtles,(crocodiles, (ornithischian_dinosaurs,(birds, saurischian_dinosaurs)))));")
plot(vert_tree_extras)

### NEW
par(mfrow=c(2,1))
vert_orders<-read.tree(text="((tuatara,(lizards, snakes)), (turtles,(crocodiles, (birds, non.avian_dinosaurs))));")
plot(unroot(vert_orders))
vert_orders<-read.tree(text="(((tuatara,(lizards, snakes))), (turtles,(crocodiles, (birds, non.avian_dinosaurs))));")
plot(vert_orders)


par(mfrow=c(1,1))
vert_tree_extras<-read.tree(text="(((tuatara,(lizards, snakes))), (turtles,(crocodiles, (birds, non.avian_dinosaurs))));")
plot(vert_tree_extras)



vert_tree_extras<-read.tree(text="(((tuatara,(lizards, snakes))), (turtles,(crocodiles, (ornithischian_dinosaurs,(birds, saurischian_dinosaurs)))));")
plot(vert_tree_extras)

#now adding dates

vert_tree_dates<-read.tree(text="(((tuatara:240,(lizards:220,snakes:220):20):43):0, (turtles:270,(crocodiles:245,(ornithischian_dinosaurs:230,(birds:160,saurischian_dinosaurs:160):70):15):25):13);")
plot(vert_tree_dates)

add.scale.bar(vert_tree_dates,col="red",lcol="red",lwd=3)