The same branching tree can be drawn many ways. Learn to see which parts of the drawing carry information and which are just how it happened to be hung.
5-tip tree: shark, tuna, lizard, mouse, human. The mouse and human are sister taxa. The lizard is sister to (mouse, human). The tuna is sister to (lizard, mouse, human). The shark is the outgroup. Rotate any node — the relationships don't change. Only the visual order.
# The two Newick strings below represent the same tree:tree1 <- "(shark,(tuna,(lizard,(mouse,human))));"tree2 <- "((((human,mouse),lizard),tuna),shark);"# ape::all.equal.phylo(read.tree(text=tree1), read.tree(text=tree2)) returns TRUE
The MRCA of two tips is found by tracing each tip back to the root until the two paths meet. The common ancestor is the deepest internal node both tips descend from. Many students try to go forward from one tip to the other — that doesn't work; you have to go back to the join.
library(ape)tr <- read.tree(text="((A,B),(C,D));")getMRCA(tr, c("A","D")) # root node
The instinct is to compare a living organism to humans (or another familiar form) and call the more-different one "primitive." This is wrong. Primitive only means "similar to a common ancestor at a specific trait." For two living taxa, evolution has continued in both for the same elapsed time. Neither is primitive overall.
# Two living species: branch lengths from MRCA to tip are equal under a molecular clock.# Neither is "more primitive" — they've each had the same elapsed time to evolve.
Schematic Anolis tree. Tip color = ecomorph. Look at where the "trunk-ground" lizards sit — are they gathered on one branch, or scattered across the tree? Ask what that would take on each island.
library(ape)tr <- read.tree("data/clean/anolis_tree.nwk")ecomorphs <- read.csv("data/clean/anolis_svl.csv")$ecomorph# Count independent state changes on the tree (parsimony)
Take the same four-tip tree twice. Same topology, same sister relationships. Different branch lengths: in the "shallow" tree, every tip diverged from its sister recently; in the "deep" tree, the same sisters diverged much earlier. Trait values evolve under Brownian motion along each branch — variance accumulates with time.
Watch the trait scatter on the right. Same topology, same sister pairs. How correlated should sister trait values be in each case?
# Brownian motion along branches: trait variance accumulates with branch length.# Sister r ≈ shared / (shared + private), where shared = ancestor-to-MRCA# and private = MRCA-to-tip. Topology alone fixes the pairing; depth scales r.