AP Biology

## Learning Outcomes

- Explain how the tree of life represents common ancestry among all organisms.
- Identify the meaning of roots, nodes, branches, clades, and outgroups on phylogenetic trees.
- Describe the last universal common ancestor, or LUCA, and distinguish it from the origin of life.
- Use molecular, fossil, anatomical, cellular, and biogeographical evidence to justify common ancestry.
- Compare phylogenetic trees and cladograms as scientific hypotheses.
- Avoid common AP Biology errors when interpreting relatedness, extinction, and extant taxa.

## AP Biology Syllabus

In AP Biology Unit 7, Natural Selection, common ancestry links evolution, biodiversity, and evidence-based model interpretation. You should be ready to read phylogenetic trees, explain why shared traits suggest common descent, and justify evolutionary relationships using data such as DNA sequences, amino acid sequences, fossils, and cellular features. Unit 7 is often a major exam unit, so questions may appear as multiple-choice tree interpretation, data analysis, or free-response justification.

- Interpret phylogenetic trees and cladograms as models of evolutionary relationships.
- Identify nodes as common ancestors and roots as ancestors of all taxa shown.
- Use the most recent common ancestor to decide which taxa are more closely related.
- Explain how shared derived characteristics identify clades.
- Describe evidence for common ancestry among all organisms, including molecular and cellular similarities.
- Describe evidence for common ancestry among eukaryotes, such as membrane-bound organelles, linear chromosomes, and introns.
- Distinguish homologous traits from analogous traits caused by convergent evolution.
- Recognize LUCA as the last universal common ancestor of all living organisms, not necessarily the first living organism.

## 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. On a phylogenetic tree, what does a node represent?
2. Why are DNA and protein sequence comparisons often stronger evidence for relatedness than body shape alone?
3. What is the difference between LUCA and the origin of life?
4. If two species share a more recent common ancestor than either does with a third species, what can you conclude about their relatedness?
5. Why can similar structures, such as shark and dolphin body shapes, fail to show recent common ancestry?

## Introduction

The tree of life is a model that connects all organisms through lines of descent. AP Biology treats evolution as both a process that changes populations over generations and a historical pattern that explains why organisms share traits. Common ancestry explains why life shows both unity and diversity: organisms differ because lineages have changed over time, but they also share features because they inherited them from common ancestors.

The deepest part of this model is the last universal common ancestor, usually abbreviated LUCA. LUCA is the proposed common ancestor of all living organisms on Earth and is often estimated to have existed about 3.5 billion years ago. From this ancient ancestry, life diversified into the major domains: Bacteria, Archaea, and Eukarya.

> **Key Term: Common ancestry**
> The idea that different organisms are related because they descended from shared ancestral populations.

### Reading the tree of life as a model of descent

A phylogeny is the evolutionary history of a species or group. Scientists represent phylogeny using phylogenetic trees and cladograms. Both are models that show hypothesized relationships among organisms. They are not exact photographs of the past; they are scientific explanations based on available evidence.

> **Key Term: Phylogenetic tree**
> A branching diagram that represents hypothesized evolutionary relationships and may show the approximate timing or amount of evolutionary change.

A phylogenetic tree begins at a root and branches toward the taxa being compared. The taxa at the branch tips may be species, groups of species, or larger categories such as domains. The root represents the common ancestor of all organisms shown on that particular tree. For the full tree of life, the root is associated with the ancestry leading back toward LUCA.

> **Key Term: Node**
> A branch point on a phylogenetic tree that represents a common ancestor where one ancestral lineage gave rise to two or more descendant lineages.

Nodes are one of the most frequently tested parts of phylogenetic trees. If two organisms share a more recent node, they are more closely related than organisms whose shared node is deeper in the tree. For example, humans and chimpanzees share a more recent common ancestor with each other than either shares with dogs. This does not mean humans evolved from chimpanzees. Instead, humans and chimpanzees both descended from an ancestral species that was neither a modern human nor a modern chimpanzee.

> **Exam Warning:**
> Do not write that one living species “came from” another living species when interpreting a tree. More accurate wording is: “These species share a common ancestor.”

A clade is a group containing an ancestor and all of its descendants. Clades are identified by shared derived characteristics: traits that evolved in a common ancestor and were inherited by descendant lineages.

> **Key Term: Clade**
> A group made up of a common ancestor and all of its descendants.
>
> **Key Term: Shared derived characteristic**
> A trait shared by members of a clade that distinguishes that clade from other organisms outside the group.

For example, in a vertebrate tree, keratinous scales may be used as a shared derived characteristic that groups birds and reptiles into a clade, depending on the taxa shown. Because this trait is shared by those lineages and not by the outgroup in that example, it supports the hypothesis that those organisms share a more recent common ancestor.

> **Key Term: Outgroup**
> The taxon on a phylogenetic tree that is least closely related to the other taxa shown and is used as a comparison group.

Outgroups help scientists infer which traits are ancestral and which are derived. If a trait appears in the outgroup and in several members of the main group, it may be an older ancestral trait. If a trait appears only in a smaller branch within the main group, it may be a derived trait for that clade.

Phylogenetic trees and cladograms are related but not identical. A cladogram mainly shows the pattern of branching and shared derived traits. Branches are often drawn with equal spacing, so the diagram does not necessarily show time or amount of change. A phylogenetic tree may use branch lengths to suggest approximate timing or amount of evolutionary change. On the AP Biology exam, always read the labels, axes, and legend before assuming that branch length represents time.

> **Test Tip:**
> To compare relatedness, look for the most recent common ancestor, not physical distance between branch tips. Two tips drawn close together are not necessarily the most closely related unless they share the most recent node.

### Evidence that supports the tree of life

Scientists build and revise phylogenetic trees using several types of evidence. These include molecular evidence, morphology, fossils, vestigial structures, embryological patterns, and biogeography. In AP Biology, you should be able to use evidence to support a claim about common ancestry.

Molecular evidence is especially strong because DNA and protein sequences can be compared directly. Closely related organisms usually have more similar nucleotide or amino acid sequences because less time has passed for mutations to accumulate since their lineages separated.

For example, the GAPDH gene in humans and chimpanzees is more than $$99\%$$ similar in sequence, while the same gene is about $$91\%$$ similar between humans and dogs. This supports the claim that humans and chimpanzees share a more recent common ancestor than humans and dogs do.

> **Key Term: Molecular clock**
> A method for estimating the timing of evolutionary events by comparing accumulated differences in DNA or protein sequences.

Molecular clocks are based on the idea that changes in DNA or protein sequences accumulate over time. They are estimates, not perfect stopwatches. Mutation rates can vary among genes and lineages, so molecular clock evidence is usually combined with fossil evidence and other data. Even so, molecular data are often considered more reliable than outward appearance alone because body shape can be affected by similar environmental pressures.

Morphological evidence is evidence based on body form and structure. Homologous structures are a key example.

> **Key Term: Homologous structure**
> A structure in different organisms that has a shared evolutionary origin, even if it now performs different functions.

Human arms, bat wings, dog forelimbs, and whale fins all contain similar arrangements of bones, even though they are used for grasping, flying, walking, or swimming. This similarity supports common ancestry among these vertebrates.

However, similar function does not always mean recent common ancestry. Sharks and dolphins both have streamlined bodies that help them move through water, but sharks are cartilaginous fish and dolphins are mammals. Their similar body shapes are examples of convergent evolution: unrelated or distantly related lineages independently evolving similar adaptations in similar environments.

> **Exam Warning:**
> Do not assume that similar appearance always means close relatedness. On the exam, ask whether the similarity is homologous, meaning inherited from a common ancestor, or analogous, meaning independently evolved.

Fossils also support common ancestry. Fossils provide evidence of organisms that lived in the past, including extinct species and transitional forms. Transitional fossils show intermediate traits between ancestral and later species. Fossils can be dated using rock layers or radioactive isotopes, helping scientists place evolutionary events in time.

Vestigial structures are another line of evidence. These are anatomical features that may have had a function in ancestral organisms but have reduced or different functions in modern organisms. The human tailbone is a common example; it is interpreted as evidence of ancestry from organisms with tails.

Biogeography, the study of where species live, also supports common ancestry. Species on islands near South America, for example, are often more similar to species on the nearby mainland than to species in distant regions with similar climates. This pattern makes sense if island species descended from colonizing ancestors from nearby areas and then evolved independently.

Embryological evidence can also be used. Vertebrate embryos share early developmental features, which supports shared ancestry among vertebrates. AP Biology questions may ask you to compare developmental, anatomical, or molecular evidence and decide which claim is best supported.

### LUCA and the deepest branches of life

> **Key Term: LUCA**
> The last universal common ancestor; the proposed ancestral population from which all organisms alive today descended.

LUCA is a major idea behind the tree of life. It represents the most recent ancestry shared by all living organisms. This is different from saying LUCA was the first life on Earth. There may have been earlier living forms or early lineages that left no living descendants. LUCA is “last universal” because it is the most recent ancestor common to all modern life.

The estimate often used in AP Biology review is that LUCA existed about 3.5 billion years ago. From lineages related to this deep ancestry, life diversified into the three domains:

- Bacteria
- Archaea
- Eukarya

Bacteria and Archaea are prokaryotic groups. Eukarya includes organisms whose cells have nuclei and membrane-bound organelles, such as animals, plants, fungi, and protists. On a broad tree of life, plants, animals, and fungi are much more closely related to one another than they are to bacteria. This is because they share more recent common ancestry within Eukarya.

Several shared features support the common ancestry of all eukaryotes:

- Membrane-bound organelles
- Linear chromosomes
- Genes containing introns

These features are not typical of prokaryotes, so they support the hypothesis that all eukaryotes share a common eukaryotic ancestor. AP-aligned questions often focus on this cellular and molecular evidence because it connects evolution with cell biology and genetics.

At an even deeper level, all life shares certain basic molecular features. These include DNA or RNA as genetic information, ribosomes for protein synthesis, and a genetic code that is largely shared across organisms. Such similarities are evidence that living organisms are connected through descent.

The origin of life is related to this topic but is not the same as LUCA. Two major ideas often discussed in AP Biology review are:

1. Early Earth chemistry may have produced biological building blocks from inorganic materials. The Miller-Urey experiment supported this possibility by simulating conditions of early Earth’s atmosphere and producing amino acids and other organic molecules.
2. Meteorites may have brought organic molecules to Earth. The Murchison meteorite, found in Australia in 1969, contained sugars and more than 70 amino acids.

These ideas concern how the materials for life may have arisen. LUCA concerns the shared ancestry of organisms that are alive today.

> **Test Tip:**
> If a question asks about LUCA, answer in terms of common ancestry and shared features of living organisms. If it asks about the origin of biological molecules, evidence such as the Miller-Urey experiment or organic molecules in meteorites may be more relevant.

### How phylogenetic trees change with new evidence

Phylogenetic trees are hypotheses. They are based on the best available evidence and can change when new data are found. A tree based mainly on morphology may be revised when DNA sequence data show a different pattern of relatedness.

Molecular data are often useful because they can reveal similarities not obvious from appearance. For example, two species may look similar because they evolved in similar environments, not because they share a recent common ancestor. This can mislead tree construction if scientists rely only on morphology. Molecular comparisons can help separate true homology from analogous similarity.

Still, molecular evidence also requires careful interpretation. Different genes can evolve at different rates. Some DNA changes do not alter amino acid sequences because the genetic code is redundant; multiple codons can code for the same amino acid. For this reason, two organisms could have different nucleotide sequences but the same amino acid sequence for part of a protein. AP Biology may test this idea in questions connecting evolution with translation and codons.

Speciation and extinction are also represented on trees. A node can represent a speciation event, where one ancestral lineage gives rise to two or more descendant lineages. Some descendants survive to the present; others do not.

> **Key Term: Extant**
> Still living today; having surviving members in the present.
>
> **Key Term: Extinct**
> Having no surviving members in the present.

A phylogenetic tree may include both extinct and extant species. Extinct species can still be highly relevant because fossils may show transitional traits or help calibrate the timing of evolutionary events. If a species is extinct, that does not mean it was unsuccessful for its entire history; it only means no members survive today.

When answering free-response questions, use precise cause-and-effect language. If asked to justify a tree, refer to specific evidence: “Species A and B share a derived trait not found in the outgroup,” or “Species A and B have fewer DNA sequence differences, suggesting a more recent common ancestor.” Avoid vague answers such as “they are more evolved” or “they are higher organisms.” Evolution does not have a goal, and modern species are not ranked from primitive to advanced.

## Key Point Checklist

This article has covered the following key knowledge points:

- The tree of life represents evolutionary relationships among all organisms through common ancestry.
- LUCA is the last universal common ancestor of all living organisms, not necessarily the first living thing.
- LUCA is often estimated to have existed about 3.5 billion years ago.
- A phylogenetic tree is a hypothesis based on evidence and may change when new data are found.
- Nodes represent common ancestors; the root represents the common ancestor of all taxa shown.
- Taxa with a more recent common ancestor are more closely related.
- A clade includes a common ancestor and all of its descendants.
- Shared derived characteristics help identify clades and support common ancestry.
- Molecular evidence, such as DNA and amino acid sequence similarity, is strong evidence for relatedness.
- Homologous structures support common ancestry, while analogous structures may result from convergent evolution.
- Shared eukaryotic features include membrane-bound organelles, linear chromosomes, and introns.
- Extant species survive today, while extinct species have no living members.

## Key Terms and Concepts

- Common ancestry
- Phylogenetic tree
- Node
- Clade
- Shared derived characteristic
- Outgroup
- Molecular clock
- Homologous structure
- LUCA
- Extant
- Extinct
- Tree of life
- Cladogram
- Root
- Convergent evolution
- Analogous structure
- Fossil
- Transitional fossil
- Vestigial structure
- Biogeography
- Eukarya
- Bacteria
- Archaea


Common ancestry - Tree of life and last universal common ancestor