B. Diversity of Living Things · Diversity of Living Things

Phylogeny: Reading and Building Cladograms

B3.1 B2.1 A1.10 A1.12About 70 minutes

Learning goals

I can explain what a phylogeny is and identify the root, nodes, branches, tips and clades of a phylogenetic tree.
I can decide which organisms on a tree are most closely related by finding their most recent common ancestor.
I can build a cladogram from a table of shared derived characteristics.
I can describe the evidence used to infer phylogeny, including morphology and DNA.

Words to know

phylogeny
The evolutionary history and relationships of a group of organisms.

phylogenetic tree
A branching diagram showing a hypothesis about how organisms are related through common ancestors.

cladogram
A phylogenetic tree built from shared derived characteristics; it shows branching order, not exact time.

node
A branching point on a tree; it represents the most recent common ancestor of the lineages that branch from it.

clade
A group made of one ancestor and ALL of its descendants (also called a monophyletic group).

shared derived characteristic
A trait that appeared in a common ancestor and is shared by its descendants, but not by more distant groups (e.g. hair in mammals).

outgroup
A related organism outside the group being studied, used to show which traits are ancestral.

homologous structures
Structures in different species that share an origin from a common ancestor, even if they now have different functions (e.g. a human arm and a bat wing).

A family tree for every living thing

You may have seen a family tree: you, your parents, your grandparents, and cousins who share grandparents with you. Biologists draw the same kind of tree for species. A phylogeny is the evolutionary history of a group of organisms, and a phylogenetic tree is a diagram of it.

In the last lesson you saw that the grey wolf and coyote share a genus. Today's question is why: because they share a recent common ancestor. Modern taxonomy tries to make every named group match the branches of the tree of life.

Parts of a phylogenetic tree

The root is the common ancestor of everything on the tree.
Branches are lineages evolving through time.
Each node (branch point) is the most recent common ancestor of the lineages that split there.
The tips are the species (or groups) being compared, usually living today.
A clade is an ancestor plus all of its descendants. You can "cut" any clade off the tree with one snip of a branch.

How to read relatedness: two organisms are more closely related if their most recent common ancestor is more recent (closer to the tips). Do not judge by which names sit next to each other: a tree's branches can be rotated around any node, like a mobile hanging from the ceiling, without changing any relationships.

The wolf and coyote share the most recent common ancestor (rightmost node), so they are the closest relatives. Together with the lynx they form a clade, the order Carnivora. The beaver branched off earlier.

Shared derived characteristics

How do biologists work out the branching order? They look for shared derived characteristics: new traits that first appeared in one ancestor and were passed to all its descendants.

Hair is a derived trait shared by all mammals. It tells us mammals form a clade.
Having a backbone is shared by fish, frogs, lizards and mammals, so it marks a larger, older clade (vertebrates).

A trait shared by every organism in the study (like having cells) tells you nothing about branching order. That is why biologists include an outgroup: a related organism that lacks the derived traits being studied. Traits present in the outgroup are ancestral; traits absent from it are derived.

Worked example

Let's build a cladogram from a trait table

Build a cladogram for six chordates. The traits each animal has are listed below.

Lancelet: none of the five traits
Lamprey: vertebrae
Trout: vertebrae, jaws
Frog: vertebrae, jaws, four limbs
Lizard: vertebrae, jaws, four limbs, amniotic egg
Mouse: vertebrae, jaws, four limbs, amniotic egg, hair

Find the outgroup: the lancelet has none of the traits, so it branches off first. (It is a small marine chordate with a notochord but no true backbone.)
Count traits for each animal: lamprey 1, trout 2, frog 3, lizard 4, mouse 5. The more derived traits an animal shares with the mouse, the later it branches off.
Order the branches: lancelet, then lamprey, trout, frog, lizard, and mouse at the end.
Place each trait as a hash mark on the main line just before the first branch that has it. For example, "jaws" goes after the lamprey's branch and before the trout's, because the trout and everything after it have jaws.
Check: every animal above a hash mark has that trait; every animal below it does not.

See the cladogram below. Each hash mark is a shared derived characteristic; every group to the right of a mark forms a clade with that trait (for example, lizard + mouse = the amniotes).

The cladogram from the worked example. Each hash mark shows where a new trait appeared. Every animal branching off after a mark has that trait: frog, lizard and mouse have four limbs, but trout and lamprey do not.

Evidence used to build trees

Morphology. Homologous structures have the same basic bone pattern because they came from a shared ancestor: the arm of a human, the flipper of a whale, the wing of a bat and the front leg of a cat all have one upper bone, two lower bones, wrist bones and digits.
Fossils show when traits first appeared and what extinct relatives looked like.
Embryology. Related animals often look alike as early embryos. For example, all vertebrate embryos have pharyngeal pouches at an early stage.
Molecular evidence (DNA and proteins). Species that split from a common ancestor more recently have had less time to build up differences, so their DNA sequences are more similar. Today most trees are built from DNA, checked against morphology and fossils.

A tree is a hypothesis. When new evidence appears, biologists redraw it. You will study the processes that create these branches, including natural selection and speciation, in the Evolution unit.

Worked example

Let's use DNA to find relationships

Four species have these stretches of the same gene (short, made-up sequences for practice):

A: ATGCCGTAAGCT
B: ATGCCGTAAGTT
C: ATGACGTTAGTT
D: TTGACCTTCGTT

Count the differences between each pair and decide the branching order.

Compare letter by letter. A vs B: they differ only at position 11 (C vs T) → 1 difference.
A vs C: positions 4, 8, 11 → 3. B vs C: positions 4, 8 → 2.
A vs D: positions 1, 4, 6, 8, 9, 11 → 6. B vs D: 5. C vs D: positions 1, 6, 9 → 3.
Fewest differences = most recent common ancestor. A and B (1) are closest and join first. C is closer to the A–B pair (2 or 3) than D is (5 or 6), so C joins next. D branches off first.
Tree in words: D splits first, then C, then A and B split from each other most recently.

Branching order: D, then C, then A and B. Written as nested groups: (D, (C, (A, B))).

Just for fun

Here is a cladogram surprise: DNA evidence shows that fungi are more closely related to animals than to plants. So the mushroom on your pizza is a closer cousin of yours than the spinach sitting next to it.

Hands-on activity

Invent and trace a family of "creatures"

You need: 8 index cards or paper squares, a pencil, and a family member or friend.

On card 1, draw a simple "ancestor" creature: an oval body with two eyes.
Make a lineage. On card 2 copy the ancestor and add one new trait (e.g. a tail). On card 3, copy card 2 and add another trait (e.g. spots). Branch off sometimes: card 4 can copy card 2 and add a different trait (e.g. antennae) instead of spots.
Keep going until you have 6 or 7 "species." On a separate sheet, secretly record the true tree you made.
Shuffle the cards (remove the ancestor, which is your outgroup clue). Give them to your partner. They make a trait table (✓ for each trait) and build a cladogram.
Compare their cladogram with your secret tree.

What to look for: if every new trait was kept by all descendants, the partner's tree should match yours exactly. Discuss what would happen if a trait were lost in one lineage, or if two lineages evolved the same trait separately (like wings in bats and birds). These cases are why biologists use many traits and DNA, not just one or two traits.

Your turn

What does a node on a phylogenetic tree represent?

Define a clade.

In the vertebrate cladogram, which traits does a frog have?

In the same cladogram, is the lizard more closely related to the mouse or to the frog? Explain.

Why is an outgroup included when building a cladogram?

Two species' DNA differs at 4 of 100 positions. Two other species differ at 25 of 100. Which pair probably shared a common ancestor more recently?

Why can't you judge relatedness by which tips are drawn next to each other?

More practice: warm-up

What is phylogeny?

Give an example of a shared derived characteristic of mammals.

What are homologous structures?

Name two kinds of evidence used to build phylogenetic trees.

In the vertebrate cladogram, which animal is the outgroup?

More practice: on your own

Is "fish" (lamprey + trout) a clade on the vertebrate cladogram? Explain.

A new animal has vertebrae, jaws and four limbs, but lays eggs without an amnion (shell-less eggs in water). Where does it branch on the cladogram?

Bats and birds both have wings, but bats are mammals. Explain why wings are not a shared derived characteristic linking bats and birds.

Using the DNA example, how many differences separate B and D? What does that number suggest?

Why is a phylogenetic tree called a hypothesis?

Challenge

Build a cladogram (describe it in words or nested brackets) for: moss, fern, pine, maple. Traits: vascular tissue (fern, pine, maple); seeds (pine, maple); flowers (maple). Use green alga as the outgroup.

Snakes have no limbs, yet they are placed in the clade of four-limbed vertebrates, next to lizards. Explain how this can be correct.

Explain why DNA evidence can separate two species that look almost the same, and give one reason DNA is especially useful for bacteria.

Check your understanding

Quiz

On a phylogenetic tree, two species are most closely related if they:

A clade includes:

Which is a shared derived characteristic of birds within the vertebrates?

Species P and Q differ at 3 DNA positions; P and R differ at 18; Q and R differ at 17. Which pair is most closely related?

A human arm and a whale flipper have the same pattern of bones. These are:

Why is an outgroup used?

For parents and teachers

Big idea (B3.1): phylogeny is the evolutionary history behind classification. Students read and build cladograms from trait tables and DNA comparisons, and justify conclusions from evidence (A1.10) using correct diagrams (A1.12).

How to help: The invented-creatures activity works well with a sibling or parent. Ask your teen to "prove" a grouping by pointing to the trait mark that unites it.

Common difficulties:

Reading relatedness from left-to-right order. Always trace back to the shared node.
Thinking species at the tips evolved from each other ("humans came from mice"). Tips are cousins that share ancestors; none is the ancestor of another.
Placing hash marks after the wrong branch. A trait mark must sit just before the first lineage that has it.

Sources: vertebrate trait pattern and homologous limbs are standard textbook evidence; the DNA sequences in Example 2 are invented for practice; fungi-animal relationship from molecular phylogenetics.