Phylogenetics & Classification
Phylogenetics is the study of how organisms are related through evolution. This guide takes you from reading a phylogenetic tree and the different ways trees are drawn, through homologous and analogous structures, to the molecular methods — comparing DNA and proteins — that corrected the old classification and split the five Kingdoms into three Domains.
Reading a phylogenetic tree
Phylogeny is the study of the evolutionary relationships between organisms. Those relationships are drawn as a phylogenetic tree. Before anything else, you need to be able to read one — and the single most important rule is: read the branch points, not the order of the tips.
Read the branch points, not the order of the tips. Two descendants are more closely related the more recent the common ancestor they share.
How to interpret it
- Tips = organisms living today. Here they are descendants 1, 2, 3 and 4. All of them evolved from a shared common ancestor at the base, which lived in the past.
- Branch points = common ancestors. Ancestor A is the oldest (most distant); C is the most recent. So C is more recent than B, which is more recent than A.
- Relatedness = the most recent common ancestor two organisms share. Descendants 3 and 4 are very closely related because they share the recent ancestor C. Descendant 2 is less related to them because it joins further back, at B.
- An outlier branches off on its own lineage near the base. Descendant 1 splits away at the oldest ancestor A, so it has little relatedness to the others. A lineage is a continuous line of descent from a common ancestor.
Being drawn next to each other at the top does not mean two organisms are closely related. What matters is how recently their lineages meet at a branch point.
Different ways of representing a tree
The same evolutionary relationships can be drawn in several different styles. They look different but mean exactly the same thing — which is why you must always read the branch points, not the picture’s shape or the order of the tips.
Rectangular, diagonal, or with branches rotated — same tree, same meaning.
Try it: switch the style, watch the branch points stay put
Switch styles — the branch points (where the lines meet) stay in the same place. That is why both drawings mean the same thing.
Rectangular vs diagonal
A rectangular tree uses right-angled branches, which makes the branch points (the common ancestors) easy to spot. A diagonal tree uses slanted lines and looks more like a fan. They carry identical information — the exam may show either.
Rooted trees & the time axis
Most trees are rooted: a single common ancestor sits at the base and time runs from the past (base) to the present (tips). The root tells you the direction of evolution and where everything started.
You can rotate the two branches at any branch point — flipping which side each descendant is drawn on — and the tree still means exactly the same thing. So never decide relatedness from whether two tips are drawn side by side. Trace them back to the branch point they share.
A worked tree: the tetrapods
Here is a fuller tree for the tetrapods (four-limbed vertebrates) within the phylum Chordata. The red bars mark key evolutionary developments — a new feature that appears once and is then inherited by every group above it. Reading these bars tells you the order in which features evolved and how the groups are related.
Each red bar is a new shared feature inherited by everything above it.
- The first key development is the vertebrae (backbone) — the feature that defines the phylum Chordata.
- The shark is the outlier: it branches off before “bony skeleton” because it has a cartilaginous skeleton. It is the least related to the other chordates.
- Everything above the “4 limbs” bar is a tetrapod. Everything above “amniote egg” lays (or descends from) an egg with a protective membrane.
- Hair marks the branch leading to the mammals (primates + rabbits); scales marks the reptiles and birds.
A second example: the apes
The same rules read any tree. On this tree of the apes, the Old World monkeys are the outlier — they branch off first, about 25 million years ago. Humans and chimpanzees share the most recent common ancestor (8–6 million years ago), so they are the most closely related pair.
The monkey lineage is the outlier; humans and chimpanzees are the most closely related.
Homologous vs analogous structures
One way to work out relatedness is to compare body structures (morphology). But this only works if you can tell two kinds of similarity apart — because one is real evidence of ancestry and the other is a trap.
The pentadactyl limb — the limb built on a five-digit ground plan found in mammals, birds, reptiles and amphibians. The human arm, whale flipper, bird wing and bat wing all share the same underlying bone structure (humerus → radius and ulna → wrist → digits), even though they perform completely different functions.
✔ Real evidence of a common ancestor
Because this bone structure was inherited from a shared ancestor that already had that limb, the similarity genuinely shows relatedness. It is a homologous structure, produced by divergent evolution — one ancestral structure evolving to perform different functions under different conditions.
A bird wing vs an insect wing (or a bird wing vs a bat wing). Both perform the same function — flight — but the flight surfaces are built differently and evolved separately: feathers on a bird, a bare membrane on an insect, skin stretched over long finger bones on a bat.
✘ The wing surface is NOT evidence of a common ancestor
Same function but a different structure and a separate origin = an analogous structure, produced by convergent evolution: organisms facing the same conditions evolve similar features independently. Analogous structures can make organisms look more related than they are — the weakness of using morphology alone.
Careful — birds and bats show both at once. Their forelimb bones are homologous (both are pentadactyl limbs inherited from a shared tetrapod ancestor — the bird’s is a reduced version with three functional digits). But their wings, as flight surfaces, are analogous: feathers versus skin, evolved separately. Same limb, separately-evolved wings.
Same colour = same bone. The bat, bird, whale and human forelimbs share the same underlying bone structure — humerus, then radius and ulna, then the wrist (carpals) and finger bones (metacarpals and phalanges) — inherited from a shared tetrapod ancestor. The bird’s is a reduced pentadactyl limb (fused and reduced digits) and the whale’s is a flipper, but the bones are still homologous. That is a homologous structure, produced by divergent evolution. The insect wing (E) does the same job — flight — but has no bones: it is an analogous structure that evolved independently.
Diagram © Biology Education.
Bat wings are skin stretched over long finger bones; bird wings are feathers along the arm. The arm bones are homologous (a shared tetrapod inheritance), but the wings themselves — the flight surfaces — are analogous: they evolved separately, so they are not evidence of a common winged ancestor. Same job, built two different ways.
Diagram © Biology Education.
Molecular methods: comparing DNA and proteins
Because morphology can be misled by convergent evolution, biologists now compare the genetic blueprint itself. This is molecular phylogeny, and it can correct mistakes made by comparing body structures. The logic is always the same: over time, DNA accumulates mutations, so fewer differences means fewer mutations since two species diverged — and therefore a more recent common ancestor.
1 · Comparing DNA base sequences
Compare the same region of the same gene across each species (different regions have different sequences, so they must match). The gene should code for a protein that all the organisms have — haemoglobin works for mammals, and cytochrome C is often used because all eukaryotes have it (it is used in respiration). Count the base differences: the fewer the differences, the more closely related.
The chosen gene must be present in every organism being compared, and you must always analyse the same region of it — otherwise the comparison is meaningless.
2 · Comparing amino-acid sequences
A gene’s base sequence codes for the order of amino acids in a protein’s primary structure, so the amino-acid sequence of a protein can be compared in exactly the same way. Fewer amino-acid differences means the organisms are more closely related. You can practise reading a difference table for this in the interactive table below.
3 · DNA hybridisation
This measures overall DNA similarity by how tightly two species’ DNA strands bind to a human strand. Try it below: pick a species to hybridise with human DNA, then press Hybridise & heat. The strands zip together, and the more matching base pairs form, the higher the temperature needed to pull them apart again.
Strands are combined and heated until the hydrogen bonds break. More base pairs = more hydrogen bonds = a higher separation temperature (near 86 °C) = more closely related. Fewer base pairs separate at a lower temperature = less related, a more distant common ancestor.
4 · The antibody (immunological) method
Relatedness can also be measured using proteins such as albumin. The more similar a species’ albumin is to human albumin, the better the human antibodies bind to it, and the more precipitate forms. Watch the method run:
Press play to run the immunology method.
Interactive: reading a difference table
When you compare a protein’s amino-acid sequence across several organisms, the results are often written as a difference table — a triangular grid counting how many amino acids differ between each pair. This one uses a protein found in six organisms. Tap any number: the highlight sweeps left to its row organism and up to its column organism, so you can see exactly which pair it compares. Fewer differences = more closely related.
Why is half the grid empty? You never compare an organism to itself (that is always 0), so the diagonal is struck out. And “Human vs Yeast” gives the same answer as “Yeast vs Human”, so the top-right triangle would just repeat the bottom-left. Only the lower triangle is filled in — read every cell by sliding left to its row and up to its column.
Turning the differences into a tree
Once you know how different every pair is, you group the most-similar organisms closest together and the most-different furthest apart:
- Human, Tomato, Yeast, Protoctista cluster tightly (only 1–3 differences apart) — these are the eukaryotes.
- Archaea sits a short step outside that cluster (4–6 from the eukaryotes).
- Eubacteria is far from everything else (10–11).
Notice that archaea is closer to the eukaryote cluster than eubacteria is to anything. This is the clue that led to the three-Domain system — covered next.
Another worked example: the hippo and the whales
The same skill answers a famous puzzle. Whales and dolphins (the cetaceans) look nothing like land mammals — so which land mammal are they most closely related to? The table below shows the number of differences in the DNA of the gene for the milk protein casein. Tap a cell to read a pair, and compare the hippo’s numbers with everyone else’s.
Number of casein DNA differences between mammals.
Casein DNA differences from the hippo:
The hippo differs from the whales and dolphin by only 3–4, but the cow, pig, deer and camel differ from them by 8–16. So the hippo is the whales’ and dolphins’ closest living relative — even though it looks nothing like one. Molecules reveal a relationship the eye would never guess.
Which tree fits the data?
Two proposed trees. In one, the cetacean sits far from the hippo; in the other, the cetacean and hippo share a recent common ancestor. Tap the tree the casein data supports.
Five Kingdoms → three Domains
Classification has two systems. The older one has five Kingdoms (Animalia, Plantae, Fungi, Protoctista, Prokaryotes), based largely on morphology. The modern one has three Domains and is based on molecular evidence — and it changed where the microbes belong.
Woese found that the “prokaryotes” had too many molecular differences to be a single group — and that some of them were actually more similar to eukaryotes than to other prokaryotes. He split the prokaryotes into two domains: those more similar to eukaryotes became Archaea, the rest became Eubacteria. The four eukaryote kingdoms all fall under Eukaryota.
The four eukaryote kingdoms (Animalia, Plantae, Fungi and Protoctista) all fall inside one domain, Eukaryota. The old “prokaryotes” split into two separate domains — Archaea and Eubacteria — because molecular evidence showed archaea are as different from bacteria as they are from us. Five kingdoms became three domains.
Diagram © Biology Education.
🌋 “Aren’t archaea just the extremophiles?”
Many archaea are extremophiles, living in harsh conditions — high temperature (thermophiles), high methane (methanophiles), high salt (halophiles) or high sulphur (sulphurphiles). But where an organism lives is a lifestyle, not a measure of ancestry. Plenty of archaea live in ordinary places too. Archaea are placed near eukaryotes because of their molecules, not their habitat.
👀 Why morphology got it wrong
Archaea and eubacteria look almost identical — both tiny, both with no nucleus — so the morphology-based five-Kingdom system lumped them together as “prokaryotes”. It took molecular evidence to reveal they are two fundamentally different groups.
Test yourself
Check your understanding with the tabs below. Look back at the sections above if you get stuck.
Frequently asked questions
How do I read a phylogenetic tree?
Look at the branch points, not the order of the tips. Two organisms are more closely related the more recent the common ancestor they share. Trace each one back to the most recent branch point they have in common; an organism that branches off near the base on its own lineage is the outlier.
What are the different ways a tree can be drawn?
The same relationships can be shown as a rectangular tree (right-angled branches), a diagonal tree (slanted branches), or with the branches at any branch point rotated. All mean the same thing because the branch points are identical. Most trees are rooted, with a common ancestor at the base and time running past → present.
What’s the difference between homologous and analogous structures?
Homologous structures share the same basic structure but perform different functions, inherited from a common ancestor (e.g. the pentadactyl limb) — real evidence of relatedness, produced by divergent evolution. Analogous structures perform the same function but have a different structure and evolved separately (e.g. an insect wing vs a bird wing) — produced by convergent evolution, and not evidence of a shared ancestor.
Why is molecular evidence better than comparing body structures?
Morphology can be misled by convergent evolution — analogous structures make unrelated organisms look related. Comparing DNA base sequences, amino-acid sequences or using DNA hybridisation examines the genetic blueprint itself, so fewer differences reliably means a more recent common ancestor.
Why did the five Kingdoms become three Domains?
Carl Woese used biochemical analysis and found the prokaryotes were too different to be one group — some were more similar to eukaryotes than to other prokaryotes. He split them into two domains, Archaea and Eubacteria, with the four eukaryote kingdoms forming Eukaryota: three domains in total.