BIO 202, Spring 2026, draft v1. The horizontal order of tips means nothing. Only the depth of splits means anything.
Rotate nodes to see the same tree differently. Find common ancestors. Disprove "more primitive." End at the Anolis tree.
Click a node to flip its children. The tree's topology doesn't change. The list of tip names changes order.
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
Five trees. For each, click the node that is the MRCA of the two highlighted tips. Track score.
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
Given two living organisms, which is more primitive? Correct answer: neither. Both have been evolving for the same amount of time. Five rounds.
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.
Anolis lizards on Caribbean islands have repeatedly evolved the same ecomorphs (trunk-ground, twig, grass-bush, ...). Each ecomorph evolved independently on each island. The tree reveals this — similar-looking lizards are not sister taxa.
Schematic Anolis tree. Tip color = ecomorph. Notice that all "trunk-ground" lizards are not on the same branch — they're scattered. Each Caribbean radiation independently produced this body plan.
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)
Topology answers "who is whose closest relative?". Branch length answers "how similar should they be?". Lesson 19 builds on this.
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.