Phylogeny and Classification

Reading Phylogenetic Trees

Part 1 of 7 — Phylogenetics & Cladistics

Phylogenetic trees are visual hypotheses about evolutionary relationships among organisms. Learning to read them is one of the most testable skills on the AP Biology exam.

What is a phylogenetic tree?

A phylogenetic tree (also called an evolutionary tree) is a branching diagram that depicts the inferred evolutionary relationships among a group of organisms. Each tree is a hypothesis based on available evidence — it can be tested, and it is revised when new evidence appears.

Anatomy of a phylogenetic tree

Important reading rules

• Branch length may or may not represent time, depending on the tree style
• The order of tips does not matter — you can rotate around any node without changing the meaning
• Two taxa are more closely related if they share a more recent common ancestor
• Always trace back to the nearest shared node to determine relatedness

Concept Check — Tree Anatomy 🎯

Clades, Out-groups & Tree Styles

Clades

A clade is an ancestor plus all of its descendants. On a tree, a clade is everything you could cut away with a single snip just below one node.

🦎 Example: On the tree (Frog, (Lizard, (Crocodile, Bird))), the group {Lizard, Crocodile, Bird} is a clade: it contains their common ancestor and every descendant of it. The group {Lizard, Crocodile} is not a clade, because it leaves out the bird, which descends from the same ancestor.

A grouping that leaves out some descendants, or that lumps lineages together because of a look-alike trait (such as "flying vertebrates" for birds plus bats), does not reflect shared ancestry.

The out-group

The out-group is the lineage that is least closely related to the remainder of the organisms on the tree. It branches off first, closest to the root, and serves as the reference for deciding which traits are ancestral. In the tree above, the frog is the out-group.

Cladograms vs. phylogenetic trees

Reading any tree in three steps

1. Find the two taxa you are comparing.
2. Trace each one back toward the root until the two paths meet.
3. The node where they meet is their most recent common ancestor. The farther that node is from the root, the more closely related the two taxa are.

Concept Check — Clades & Out-groups 🎯

Fill in the Blanks — Phylogenetic Tree Vocabulary 🔍

Fill in the Blanks — Interpreting Trees 🔍

Building Cladograms

Part 2 of 7 — Phylogenetics & Cladistics

A cladogram is a branching diagram that groups organisms by shared derived characters. Building one from a table of traits — and reading one that someone else built — is a core AP Biology skill.

Key terminology

• Character — any heritable trait that can be compared across taxa (e.g., vertebral column, feathers, mammary glands, a DNA base at one position)
• Ancestral character — a trait already present in the common ancestor of the whole group, so it is usually shared with the out-group
• Derived character — a trait that changed within the group being studied; it can be a trait that was gained (feathers) or one that was lost (legs in snakes)
• Shared derived character — a derived trait present in two or more lineages, inherited from the common ancestor in which it first appeared. These are the informative characters for building trees and cladograms.

🦴 Example: Having a vertebral column is an ancestral character for mammals (shared with fish, amphibians, reptiles). Having hair/fur is a derived character that unites mammals specifically.

Why ancestral characters don't help

A trait that every taxon in the analysis has — including the out-group — was present before any of the splits you are trying to sort out, so it cannot tell you which ingroup taxa are closest relatives.

Concept Check — Characters 🎯

Out-groups & Building the Cladogram

What is an out-group?

An out-group is a taxon that diverged before the group being studied (the ingroup) diversified. It is the lineage least closely related to the rest of the organisms in the analysis, and it serves as a reference point.

Why do we need an out-group?

The out-group lets us decide which state of each character is ancestral and which is derived:

1. If the out-group shares a trait with some ingroup members → the trait is likely ancestral
2. If only some ingroup members have the trait (and the out-group does not) → the trait is likely derived

🐸 Example: When studying mammals, a frog can serve as an out-group. Because the frog lacks hair, we infer that hair is a derived character that evolved in the ancestor of the mammals.

Steps to build a cladogram

1. Select taxa to include (ingroup) and an appropriate out-group
2. List characters and record each taxon's state (present/absent; 1/0)
3. Use the out-group to sort ancestral states from derived states
4. Group taxa by shared derived characters
5. Draw the cladogram — taxa sharing the most derived characters are grouped most closely
6. Mark character changes on branches with hash marks or labels

Character matrix example

From this matrix: the vertebral column is ancestral (the out-group has it). Hair unites all three mammals. Carnassial teeth unite cat + dog. Retractable claws appear only in the cat, so they do not group the cat with anyone.

The resulting cladogram: (Frog, (Mouse, (Cat, Dog))). Mark "hair" on the branch leading to the three mammals, "carnassial teeth" on the branch leading to cat + dog, and "retractable claws" on the cat's own branch.

Concept Check — Out-groups & Cladogram Construction 🎯

Fill in the Blanks — Cladogram Construction 🔍

Fill in the Blanks — Applying Cladistic Principles 🔍

Molecular Phylogenetics

Part 3 of 7 — Phylogenetics & Cladistics

Modern phylogenetics relies heavily on molecular data — DNA nucleotide sequences and protein amino acid sequences — to reconstruct evolutionary relationships. Molecular data typically provide more accurate and reliable evidence than morphological traits, and they sometimes overturn relationships inferred from anatomy alone.

Why molecules?

How molecular comparison works

1. Choose a gene or protein shared by all taxa being compared (a homologous gene)
2. Align sequences — match corresponding positions across species
3. Count differences — more differences = more time since divergence
4. Build the tree — taxa with fewer differences are placed closer together

🧬 Example: Cytochrome c is an electron transport chain protein found in the mitochondria of nearly all eukaryotes. Comparing the amino acid sequences:

• Human vs. chimpanzee: 0 differences (identical)
• Human vs. rhesus monkey: 1 difference
• Human vs. dog: 11 differences
• Human vs. tuna: 21 differences
• Human vs. yeast: 44 differences

This gradient of differences matches the relationships inferred from anatomy and the fossil record.

Concept Check — Molecular Comparison 🎯

Molecular Clocks

A molecular clock uses the number of sequence differences between species to estimate how long ago their lineages diverged. Phylogenetic trees can show the amount of change over time because they are calibrated by fossils or a molecular clock.

The molecular clock idea

If a gene accumulates differences at a roughly constant rate, then the number of differences between two species is proportional to the time since they diverged.

Calibrating the clock

The rate must first be calibrated using a divergence whose date is known from independent evidence:

• Fossil evidence — the first appearance of a lineage in the fossil record
• Geological events — such as the separation of continents or the formation of islands

$\text{Time since divergence} = \frac{\text{Differences between the two species}}{\text{Differences per million years (from calibration)}}$

🕐 Example: Fossils show that species A and B diverged 20 million years ago, and a gene differs at 40 positions between them. The calibrated rate is 40 ÷ 20 = 2 differences per million years. If species A and C differ at 10 positions in the same gene, they diverged about 10 ÷ 2 = 5 million years ago.

Limitations of molecular clocks

Despite these caveats, molecular clocks remain a powerful tool for estimating divergence times, especially when several genes and calibration points are used.

Concept Check — Molecular Clocks 🎯

Fill in the Blanks — Molecular Phylogenetics 🔍

Homology, Analogy & Convergent Evolution

Part 4 of 7 — Phylogenetics & Cladistics

A tree is only as good as the characters used to build it. To choose good characters, you need to tell apart similarities that were inherited from a common ancestor from similarities that evolved independently.

Divergent evolution

Divergent evolution occurs when related lineages become increasingly different as they adapt to different habitats, producing phenotypic diversification.

🦴 Classic example — vertebrate forelimbs:

• Human arm (grasping)
• Whale flipper (swimming)
• Bat wing (flying)
• Dog leg (running)

All share the same underlying bone structure (humerus → radius/ulna → carpals → digits) inherited from a common ancestor, but have diverged dramatically in form and function.

The structures produced by divergent evolution are called homologous structures — same ancestral origin, often different current function.

Convergent evolution

Convergent evolution occurs when similar selective pressures produce similar phenotypic adaptations in different lineages.

🦈 Classic examples:

• Shark (fish) and dolphin (mammal) — streamlined body shape
• Insect wings vs. bird and bat wings — insect wings are outgrowths of the exoskeleton, while bird and bat wings are modified forelimbs
• Cactus (Americas) and euphorbia (Africa) — succulent, spiny desert plants

The structures produced by convergent evolution are called analogous structures — similar function, different evolutionary origin.

⚠️ Watch the level of comparison: Bird wings and bat wings are homologous as forelimbs (same bones inherited from a four-limbed ancestor) but analogous as wings, because flight evolved separately in each lineage.

Concept Check — Divergent vs. Convergent 🎯

Why Convergence Misleads — and How to Catch It

Homologous vs. analogous structures — summary

How scientists detect convergence

1. Look beneath the surface. Analogous structures often differ in their underlying anatomy or development.
2. Check other characters. A convergent trait usually conflicts with most of the other characters in the analysis.
3. Compare molecules. DNA and protein sequences rarely converge across many positions, so molecular data can expose a misleading look-alike.

🦔 Example: Tenrecs of Madagascar look and live like hedgehogs — spiny coats, insect diets. DNA sequence comparisons place tenrecs closer to elephants than to hedgehogs, showing that their spines are analogous to hedgehog spines.

Vestigial structures

Vestigial structures are reduced remnants of structures that served a function in an ancestor. Like other homologies, they provide evidence of common ancestry.

🐍 Examples:

• Tiny pelvic and leg-bone remnants in whales and in pythons and boas (their ancestors walked on four legs)
• The human tailbone (coccyx), a remnant of the tail of our ancestors
• The small, flightless wings of emus and kiwis

Vestigial structures make sense only in the context of descent with modification.

Concept Check — Choosing Characters 🎯

Fill in the Blanks — Types of Evolution 🔍

Fill in the Blanks — Identifying Evolutionary Patterns 🔍

Evidence for Common Ancestry

Part 5 of 7 — Phylogenetics & Cladistics

Phylogenetic trees and cladograms are hypotheses, and they are built and tested with evidence. Evolution is supported by data from many disciplines — geographical, geological, physical, biochemical, and mathematical — and evidence from both living (extant) and extinct organisms adds to the picture.

Lines of evidence used to build trees

Dating fossils

Fossils can be dated by several methods:

1. The age of the rocks where a fossil is found — deeper layers are generally older, and dated layers above and below a fossil bracket its age
2. The rate of decay of isotopes, including carbon-14 — carbon-14 works for remains up to roughly 50,000 years old; older fossils are dated with longer-lived isotopes in the surrounding rock
3. Geographical data — for example, where a fossil formation sits relative to others of known age

Dated fossils are what calibrate a phylogenetic tree's time scale.

Common ancestry of all eukaryotes

All eukaryotes share structural and functional features that point to a single common ancestor:

• Membrane-bound organelles (nucleus, mitochondria, endoplasmic reticulum, Golgi)
• Linear chromosomes
• Genes that contain introns

Prokaryotes, by contrast, have no membrane-bound organelles, usually carry a single circular chromosome, and rarely have introns in their genes. A shared package of complex features like this is very unlikely to have evolved independently more than once.

Concept Check — Lines of Evidence 🎯

When New Evidence Revises a Tree

Phylogenetic trees and cladograms are constantly being revised as new evidence appears. When morphological and molecular evidence disagree, the molecular evidence is usually given more weight, because it supplies many more characters and is less affected by convergent evolution.

Case 1 — Whales and hippos

• Older view: Based on anatomy, whales were placed in a group of their own, outside the even-toed hoofed mammals (pigs, camels, deer, hippos).
• Molecular evidence: DNA comparisons placed whales within the even-toed hoofed mammals, with hippos as their closest living relatives.
• Test: If the DNA tree is right, early fossil whales should share skeletal features with even-toed hoofed mammals. In 2001, fossil whale ancestors were described with the distinctive double-pulley ankle bone found only in that group — supporting the molecular tree.

Case 2 — Two kinds of prokaryotes

• Older view: All organisms without a nucleus were grouped together.
• Molecular evidence: Comparisons of ribosomal RNA sequences showed that archaea share a more recent common ancestor with eukaryotes than with bacteria, even though archaea and bacteria look alike under the microscope.

Evolution is ongoing

All species have evolved and continue to evolve. Evidence includes genomic changes over time, continuous change in the fossil record, and the evolution of resistance to antibiotics, pesticides, herbicides, and chemotherapy drugs. Trees built today are a snapshot of lineages that are still changing.

Concept Check — Revising Trees 🎯

Fill in the Blanks — Evidence for Evolution 🔍

Fill in the Blanks — Trees as Hypotheses 🔍

Speciation & Adaptive Radiation on Trees

Part 6 of 7 — Phylogenetics & Cladistics

Phylogenetic trees and cladograms illustrate speciation that has occurred: every node marks a point where one lineage split into two. This part connects the shape of a tree to how, where, and how fast speciation happened.

What happens at a node

Speciation occurs when two populations become reproductively isolated from each other.

Using geography to date a node

When a barrier forms at a known time, sister species on either side of it give a calibration point. The Isthmus of Panama closed about 3 million years ago and separated the Pacific from the Caribbean. Many snapping shrimp species come in sister pairs — one on each side — so the node joining each pair is dated by the closing of the isthmus.

A revised hypothesis: ratites

Ratites are large flightless birds such as ostriches (Africa), rheas (South America), emus (Australia), and kiwis (New Zealand).

• Older hypothesis: A flightless ancestor was split apart as the southern supercontinent broke up, so the tree should match the order in which the continents separated.
• Molecular evidence: DNA, including ancient DNA from extinct moas and elephant birds, shows that tinamous — birds that can fly — fall inside the ratite group, and that kiwis are most closely related to the extinct elephant birds of Madagascar rather than to emus.
• Revised interpretation: Flying ancestors dispersed between landmasses, and flightlessness evolved more than once — a case of convergent evolution that the older tree had mistaken for shared ancestry.

Tempo: gradualism vs. punctuated equilibrium

Concept Check — Speciation on Trees 🎯

Adaptive Radiation

Divergent evolution occurs when adaptation to new habitats results in phenotypic diversification. Speciation rates can be especially rapid during adaptive radiation, as new habitats become available — after colonizing an island, after a mass extinction removes competitors, or after a new trait opens a new way of life.

What adaptive radiation looks like on a tree

On a time-scaled tree, an adaptive radiation appears as many nodes clustered within a short span of time, all descending from a single ancestral lineage.

🐦 Darwin's finches (Galápagos):

• A single ancestral finch species colonized the Galápagos from the American mainland
• Within the last few million years, it diversified into about 18 species
• Each species evolved a beak shape suited to a specific food source:
  • Large ground finch → large, crushing beak (hard seeds)
  • Warbler finch → thin, probing beak (insects)
  • Cactus finch → elongated beak (cactus flowers and fruit)
  • Woodpecker finch → straight beak plus tool use (insect larvae)

More radiations

• Hawaiian honeycreepers — more than 50 species (many now extinct) from a single colonizing ancestor, with beaks for nectar, seeds, and insects
• Hawaiian Drosophila — hundreds of fruit fly species on a young island chain
• Caribbean Anolis lizards — on each large island, lizards evolved into similar forms for twigs, trunks, and treetops. Trees show that each lizard's closest relatives live on its own island, so the matching forms evolved separately on each island: convergent evolution layered on top of divergent radiations.

Concept Check — Adaptive Radiation 🎯

Fill in the Blanks — Speciation & Trees 🔍

Fill in the Blanks — Tempo of Evolution 🔍

AP Exam Problems — Phylogenetics & Cladistics

Part 7 of 7 — Phylogenetics & Cladistics

This final part focuses on AP-style problem solving. You will practice interpreting cladograms, choosing the simplest tree, analyzing molecular data, and tackling the kinds of questions that appear on the AP Biology exam.

What the AP exam tests

The AP Biology exam frequently asks you to:

1. Read and interpret phylogenetic trees and cladograms
2. Determine relatedness between taxa from the most recent shared node
3. Identify shared derived characters and the out-group
4. Evaluate molecular data (sequence alignments, percent similarity)
5. Build a tree or cladogram from a table of characters or sequence differences
6. Distinguish homologous from analogous structures
7. Explain how trees are revised when new fossil or molecular evidence appears

Choosing the simplest tree

When the same data could be drawn as several different trees, scientists generally prefer the tree that requires the fewest evolutionary changes (trait gains, trait losses, or sequence changes). This principle is called parsimony — the simplest explanation that fits the data is preferred.

🌳 Example: Four trees are drawn from the same character table. Tree C explains the data with only 7 character changes, fewer than any other, so it is preferred.

Caution with the simplest tree

Evolution does not always take the simplest path. Convergent evolution and traits that are lost and regained can make the simplest tree incorrect. That is why scientists compare many characters — especially molecular data — and treat every tree as a hypothesis.

AP-Style Problem Set — Cladogram Interpretation 🎯

Interpreting Molecular Data on the AP Exam

Sequence alignment problems

The AP exam may present aligned DNA or amino acid sequences and ask you to determine relationships.

Example alignment:

Counting differences:

• A vs. B: 1 difference (position 10)
• A vs. C: 3 differences (positions 3, 5, 10)
• A vs. D: 7 differences (positions 1, 3, 5, 6, 7, 8, 10)
• B vs. C: 2 differences (positions 3, 5)
• B vs. D: 6 differences (positions 1, 3, 5, 6, 7, 8)
• C vs. D: 4 differences (positions 1, 6, 7, 8)

Conclusion: A and B are most closely related (1 difference). C joins the A–B pair next, and D is most distantly related to all the others. The tree would be (((A, B), C), D).

Percent similarity vs. number of differences

Some problems give you a similarity matrix instead:

Higher percent similarity → more closely related. A and B (95% similar) are sister taxa.

Key tips for molecular data questions

1. Count differences carefully — mark or highlight changed positions
2. Build the tree from the most similar pair outward
3. Check all pairwise comparisons — don't just look at the first two
4. For time estimates, set the rate from a calibrated pair first, then divide

AP-Style Problem Set — Molecular Analysis 🎯

Fill in the Blanks — AP Exam Strategies 🔍

Fill in the Blanks — Putting It All Together 🔍