AP Biology

## Learning Outcomes

- Explain how cladograms and phylogenetic trees represent common ancestry.
- Identify roots, nodes, branches, outgroups, clades, and taxa on evolutionary diagrams.
- Distinguish between shared ancestral traits and shared derived characters.
- Use diagram structure to determine which organisms are most closely related.
- Describe how fossil, morphological, DNA, and protein evidence are used to build phylogenies.
- Interpret speciation and extinction events on branching diagrams.
- Avoid common AP Biology mistakes when comparing relatedness on trees.

## AP Biology Syllabus

In AP Biology Unit 7, phylogeny connects natural selection, common ancestry, speciation, and evidence for evolution. You are expected to interpret diagrams rather than memorize specific organism trees. Exam questions often ask you to use a cladogram or phylogenetic tree to support a claim about relatedness, common ancestry, or evolutionary change.

- Phylogeny describes the evolutionary history of a species or group.
- Cladograms and phylogenetic trees are models, or hypotheses, of evolutionary relationships.
- Nodes represent common ancestors or branching points.
- A more recent common ancestor usually indicates closer relatedness.
- Shared derived characters help define clades.
- Outgroups help identify the least closely related taxon in a diagram.
- Molecular evidence, such as DNA or protein sequence similarity, is often used to infer relationships.
- Trees may show speciation and extinction events over evolutionary time.

## Test Your Knowledge

Attempt these questions before reading this article. If you find some difficult or cannot remember the answers, look more closely at that area during your revision.

1. What does a node represent on a phylogenetic tree or cladogram?
2. If two species share a more recent common ancestor than either shares with a third species, what can you infer about their relatedness?
3. Why are DNA and protein sequence comparisons often useful for constructing phylogenies?
4. What is the difference between a shared derived character and a shared ancestral character?
5. Why is it incorrect to say that humans evolved from modern chimpanzees?

## Introduction

Phylogeny is the study of evolutionary relationships. In AP Biology, this usually means reading diagrams that show how groups of organisms are connected by common ancestry. These diagrams are called cladograms or phylogenetic trees. They are not family trees of individual organisms; they are models of how species or larger groups may have descended from earlier ancestral populations.

Cladograms and phylogenetic trees are especially useful because evolution cannot usually be observed across the full timescale of life’s history. Scientists use evidence from fossils, anatomy, embryology, DNA, RNA, and proteins to infer likely relationships. As new evidence is found, these diagrams may be revised. For the AP exam, treat every tree as a hypothesis based on the evidence available.

> **Key Term: phylogeny**
> The evolutionary history of a species or group of organisms, including patterns of common ancestry and descent.

### Reading Branching Diagrams as Evolutionary Hypotheses

A cladogram or phylogenetic tree begins with an ancestral lineage and branches into descendant lineages. Each branch point represents a common ancestor. When one lineage splits into two or more descendant lineages, the diagram is showing a speciation event: the formation of new species from an ancestral population.

> **Key Term: cladogram**
> A branching diagram that shows hypothesized evolutionary relationships based on shared characteristics, without necessarily showing exact time or amount of change.
>
> **Key Term: phylogenetic tree**
> A branching diagram that represents hypothesized evolutionary relationships and may include information about evolutionary time or amount of change if the diagram is scaled.

Although the words are sometimes used together, AP Biology may distinguish them. A cladogram shows the pattern of branching relationships. A phylogenetic tree may also show approximate timing or amount of evolutionary change, especially if branch lengths are scaled. However, if no scale is provided, do not assume that longer drawn branches always mean more time or more change. Many exam diagrams are drawn for clarity rather than precise scale.

The tips of the branches represent the taxa being compared. A taxon may be a species, genus, family, or other group. Internal branch points are nodes.

> **Key Term: node**
> A branch point on a cladogram or phylogenetic tree that represents a common ancestor of the lineages that branch from it.

For example, suppose a simplified tree has birds and reptiles branching from one recent node, while amphibians branch off earlier. You can infer that birds and reptiles are more closely related to each other than birds are to amphibians, because birds and reptiles share a more recent common ancestor. This does not mean birds “came from” modern reptiles. It means that birds and modern reptiles share an ancestral lineage that later split.

A common AP Biology example involves humans and chimpanzees. Humans did not evolve from modern chimpanzees. Instead, humans and chimpanzees share a common ancestor that was neither a modern human nor a modern chimpanzee. After a branching event, one lineage led to modern humans and another led to modern chimpanzees.

> **Exam Warning:**
> Do not describe one living species on a tree as the ancestor of another living species unless the diagram explicitly shows that relationship. Most diagrams show living taxa as related descendants of earlier ancestors.

The bottom or base of a rooted tree is called the root. It represents the common ancestor of all organisms shown in that diagram.

> **Key Term: root**
> The base of a rooted phylogenetic tree, representing the common ancestor of all taxa shown on the tree.

Not all trees are rooted. If a question gives you a rooted tree, you can infer direction of ancestry from the root toward the tips. If a tree is unrooted, it shows relationships but not the direction of evolutionary time unless extra information is given.

### Clades, Outgroups, and Shared Derived Characters

A clade is a group that includes a common ancestor and all of its descendants. Clades are central to modern classification because they reflect evolutionary history.

> **Key Term: clade**
> A group of organisms that includes a common ancestor and all descendants of that ancestor.

For example, if a node gives rise to birds and reptiles, and the diagram identifies a trait shared by both groups but absent from groups outside that node, birds and reptiles may form a clade based on that shared derived character.

> **Key Term: shared derived character**
> A trait found in members of a clade that is not found in more distant groups, suggesting common ancestry within that clade.

Shared derived characters help scientists identify related groups. For example, keratinous scales can be used as a shared derived character linking certain vertebrate groups in a clade, depending on the taxa shown. In a diagram containing lampreys, amphibians, reptiles, birds, and mammals, lampreys may serve as the outgroup because they are least closely related to the other taxa in the tree.

> **Key Term: outgroup**
> A taxon included in a phylogenetic analysis that is less closely related to the other taxa and helps identify ancestral versus derived traits.

The outgroup is used as a reference point. If a trait appears in the outgroup and in many other taxa, it may be an ancestral trait for the set of organisms shown. If a trait is absent from the outgroup but present in a smaller branch of related taxa, it may be derived within that branch.

Consider a simplified example with five hypothetical species:

- Species A: no legs, no wings
- Species B: eight legs, no wings
- Species C: eight legs, no wings
- Species D: eight legs, wings
- Species E: eight legs, wings

If species A is the outgroup, then eight legs may be a shared derived character for species B, C, D, and E. Wings may be a shared derived character for species D and E. On a cladogram, species D and E would likely share a more recent common ancestor with each other than with B or C.

> **Test Tip:**
> To answer relatedness questions, trace backward from each taxon to the nearest shared node. The pair with the most recent shared node is most closely related.

A common mistake is to compare organisms by how close their branch tips appear on the page. This can be misleading. The key feature is the branching pattern, not the physical distance between names. Two taxa placed far apart visually may be closely related if their branches meet at a recent node. Likewise, two taxa printed near each other may not be especially close if their common ancestor is deeper in the tree.

Another common mistake is reading the tree like a ladder, assuming that organisms at the “top” are more advanced than organisms near the “bottom.” Evolution does not aim toward a final goal. All living taxa at the tips have been evolving for the same amount of time since their shared ancestor, although they may have changed in different ways.

> **Exam Warning:**
> Avoid language such as “higher,” “lower,” “more evolved,” or “less evolved” when comparing organisms. Use “more closely related,” “less closely related,” “shares a more recent common ancestor,” or “shares a less recent common ancestor.”

### Evidence Used to Build Phylogenetic Trees

Scientists build phylogenies using evidence. Two major categories are morphological evidence and molecular evidence.

Morphological evidence includes visible structures, body plans, organs, bones, and fossil traits. Fossils can show when traits appeared or disappeared over time. For example, fossils may reveal changes in limb structure, skull shape, or body covering across related lineages. Traits that are gained or lost over evolutionary time can help place organisms on a tree.

> **Key Term: morphological evidence**
> Evidence based on physical structures, body form, fossils, or other observable features of organisms.

However, morphology can sometimes be misleading. Unrelated organisms may evolve similar traits because they face similar environmental pressures. This is often called convergent evolution. For instance, wings in bats and wings in insects both allow flight, but they did not arise from the same winged common ancestor. Their structural origins are different.

Molecular evidence includes DNA sequences, RNA sequences, amino acid sequences in proteins, and other molecular comparisons. In general, species with more similar DNA or protein sequences are inferred to share a more recent common ancestor than species with more differences, assuming the sequences being compared are appropriate for the question.

> **Key Term: molecular evidence**
> Evidence based on DNA, RNA, protein sequences, or other molecules used to infer evolutionary relationships.

Molecular data are often considered especially useful because they provide many comparable characters. A DNA sequence can contain hundreds or thousands of nucleotide positions. These can be compared across species to estimate relatedness. Protein sequences can also be compared; fewer amino acid differences usually suggest closer relationship, although scientists must account for mutation rates and the genes being studied.

Molecular clocks use approximate rates of change in DNA or protein sequences to estimate when lineages may have diverged.

> **Key Term: molecular clock**
> A method that uses the accumulation of changes in DNA or protein sequences over time to estimate when lineages split.

Molecular clocks are estimates, not exact stopwatches. Mutation rates can vary among genes and lineages. Still, molecular data can provide more detail than some anatomical comparisons, especially when fossils are incomplete or when similar traits evolved independently.

> **Test Tip:**
> If an AP Biology question gives a DNA or amino acid sequence comparison, look for the fewest differences when identifying the closest relatives. Then use the tree’s nodes to support your answer.

Evidence from multiple sources is strongest when it agrees. For example, if fossil evidence, body structure, and DNA sequences all support the same branching pattern, scientists have stronger support for that phylogeny. If the evidence conflicts, the tree may be revised as more data are collected.

### Interpreting Speciation, Extinction, and Change Over Time

Phylogenetic trees can show more than relatedness. They can also show speciation and extinction. A branching point represents a speciation event, where one ancestral lineage gives rise to two or more descendant lineages. The descendants may survive to the present or go extinct.

> **Key Term: speciation**
> The formation of one or more new species from an ancestral population.
>
> **Key Term: extinction**
> The death of all members of a species or lineage.

Taxa that survive to the present are called extant. Taxa with no living members are extinct. On some phylogenetic trees, extinct lineages end before reaching the present-day time line. For example, if species B and D end before the top of a time-scaled tree, while species A, C, E, and F extend to the present, B and D are extinct and the others are extant.

> **Key Term: extant**
> Still living; used to describe species or lineages that have surviving members today.

Phylogenetic diagrams also connect to natural selection. Natural selection acts on individuals, but populations evolve over generations. Over time, inherited differences that improve survival and reproduction in a particular environment may become more common. If populations become isolated and accumulate enough genetic differences, speciation may occur.

For example, imagine an ancestral insect population living in a region that later becomes divided by a river. On one side, individuals with darker coloration survive better against dark bark. On the other side, lighter coloration provides better camouflage on pale grasses. If the two populations remain separated and continue to accumulate genetic and reproductive differences, they may eventually become separate species. A phylogenetic tree would show the ancestral population splitting into two lineages at a node.

Extinction can also shape the pattern of life. Some lineages leave no living descendants. This affects how trees are interpreted: the living organisms we see today are only the surviving tips of a much larger evolutionary history. Fossils help fill in parts of this history.

Phylogenies can be updated as new evidence appears. A tree based only on visible traits might group organisms one way, while DNA evidence may suggest a different relationship. AP Biology questions may ask you to evaluate which tree is better supported by a data set. In those questions, use the evidence given rather than outside assumptions.

> **Test Tip:**
> In free-response answers, connect your claim to the evidence. For example: “Species X and Y are most closely related because they share the most recent common ancestor at node 3 and have the fewest DNA sequence differences.”

When writing about phylogenies, use precise language. Instead of saying “species X is close to species Y,” say “species X and species Y share a more recent common ancestor than either shares with species Z.” Instead of saying “trait A caused species X to evolve,” say “trait A may be a shared derived character that supports grouping species X and Y in the same clade.”

AP Biology often rewards reasoning more than vocabulary alone. A strong answer identifies the relevant node, names the evidence, and explains the inference.

## Key Point Checklist

This article has covered the following key knowledge points:

- Phylogeny is the evolutionary history of a species or group.
- Cladograms and phylogenetic trees are hypotheses about evolutionary relationships.
- Nodes represent common ancestors or branching events.
- The root represents the common ancestor of all taxa on a rooted tree.
- A more recent common ancestor usually means closer evolutionary relatedness.
- A clade includes a common ancestor and all of its descendants.
- Shared derived characters help define clades and support common ancestry.
- Outgroups help identify which traits are ancestral and which are derived.
- Molecular evidence includes DNA, RNA, and protein sequence comparisons.
- Fossil and morphological evidence can show traits gained or lost over time.
- Phylogenetic trees may show speciation and extinction events.
- Living species at the tips are not “more evolved” or “less evolved” than one another.

## Key Terms and Concepts

- phylogeny
- cladogram
- phylogenetic tree
- node
- root
- clade
- shared derived character
- outgroup
- morphological evidence
- molecular evidence
- molecular clock
- speciation
- extinction
- extant


Phylogeny - Cladograms and phylogenetic trees