What are the differences between trees?
Branch lengths have different meanings.
What is a Cladogram?
Branch length has no special meaning. Focuses only on the order of branching — who is related to whom. Used when we just care about the pattern of ancestry.
It’s like a simple family tree.
What is a Phylogram?
Branch length represents the amount of evolutionary change. The longer the branch, the more mutations or character changes have occurred. Often built from genetic distance data.
The tree now shows both relationships and evolutionary differences.
What is a Chronogram?
Branch length represents time — calibrated with fossil records or molecular clocks. Assumes a mutation rate per time unit (e.g., 1 mutation per million years). All species living today should line up evenly at the tips (same “present” time).
A chronogram shows both who descended from whom and how long ago they split.
What are the 3 types of trees?
Cladogram, Phylogram, Chronogram.
What does LUCA stand for?
The Last Universal Common Ancestor.
What is LUCA?
The most recent organism from which all life on Earth descended.
How was LUCA characterized?
Scientists believe LUCA lived around 3.5 to 3.8 billion years ago and was: A cellular organism with a lipid bilayer (a real cell structure), using DNA, RNA, and proteins. The ancestor of all three domains of life: Bacteria, Archaea, Eukarya. LUCA is not the first life form ever, but rather the last ancestor before life diversified into the major branches we see today.
What are the shapes of trees?
Polytomy, Bifurcation.
What is a Polytomy?
A node with more than two branches splitting out of it. Means we don’t know the exact order of branching — uncertain relationships.
Example: one ancestor gives rise to A, B, and C at once (but we can’t tell which came first).
What is a Bifurcating tree?
Every node splits into exactly two branches. Called fully resolved because all relationships are clear and unambiguous. Scientists aim for bifurcating trees but often start with polytomies when data are uncertain.
What is important to note about phylogenetic trees?
A phylogenetic tree is a hypothesis, not a confirmed fact. No loops allowed: Trees don’t model hybridization or horizontal gene transfer (those require “networks”).
What are the main assumptions about phylogenetic trees?
All taxa share a common ancestor. Mutations accumulate gradually over time. If two species (A and B) are more similar to each other than to C, then: C likely split off earlier from the common ancestor.
What does the tree interpretation indicate?
(root) | |—— C | └——┬—— A └—— B A and B share a recent ancestor, while C diverged earlier.
What are the groups of trees based on how species relate to their common ancestors?
Monophyletic, Paraphyletic, Polyphyletic Groups.
What is a Monophyletic Group?
Includes a common ancestor and all of its descendants. This is the “ideal” grouping in modern biology.
Example: All mammals (including humans, whales, bats) share a single ancestor → monophyletic.
What is a Paraphyletic Group?
Includes a common ancestor and some, but not all, descendants. Leaves out one or more subgroups.
Example: Reptiles are paraphyletic because birds evolved from reptiles but are excluded from “Reptilia” in the traditional sense.
What is a Polyphyletic Group?
Includes species that don’t share an immediate common ancestor. Grouped together based on similar traits that evolved independently — a case of convergent evolution (homoplasy).
Example: Bats and birds both have wings, but their last common ancestor didn’t. So, “flying animals” as a group is polyphyletic.
What do phylogenetic trees depend on?
Phylogenetic trees depend on which characters you analyze: Morphological features (e.g., color, shape), Genetic sequences (DNA), Behavioral traits.
Why can different datasets produce different trees?
Some traits evolve faster than others. Some similarities arise independently (convergent evolution).
Example scenario: Organism A: uppercase black, Organism B: lowercase black, Organism C: lowercase red, Organism D: uppercase red. If you build a tree based on color, you’ll group black vs. red. If you build it based on letter case, you’ll group uppercase vs. lowercase. Thus, different features tell different evolutionary stories. Scientists usually combine multiple data types to get a more reliable tree.
Why might different characters give different trees?
A phylogenetic tree is an inference: we use observed characters (DNA letters, protein differences, morphological traits) to reconstruct history. Different characters can tell different stories because: Homoplasy / convergent evolution, Multiple changes at the same site (double or back mutations), Mistakes in calling the ancestral state.
What is Homoplasy / convergent evolution?
Two species may look or have sequences that are similar not because they inherited that feature from a recent common ancestor, but because they evolved the same feature independently.
Example: wings in bats and birds — both fly but their wing structures evolved separately.
What are multiple changes at the same site?
A nucleotide can mutate A → G then later G → A (back mutation), or mutate A → G in two independent lineages (parallel mutation). These events hide true history and make unrelated taxa look similar or related taxa look different.
What are mistakes in calling the ancestral state?
When we infer which character state was ancestral, we can be wrong—this leads to incorrect placement of splits.
