Skills you'll gain in this topic:
- Explain how phylogenetic trees represent evolutionary relationships among species
- Distinguish between phylogenetic trees and cladograms and their specific applications
- Interpret evolutionary diagrams using key concepts like shared derived characters and outgroups
- Analyze how morphological and molecular data contribute to constructing phylogenies
- Evaluate phylogenetic hypotheses and understand how they are continually revised with new evidence
Understanding Evolutionary Relationships
Evolutionary biologists use various tools to visualize and understand the relationships between different species across time. These visual representations help scientists track evolutionary history, identify common ancestors, and understand how species are related to one another. The two primary tools used for this purpose are phylogenetic trees and cladograms, which each provide unique insights into evolutionary relationships.
Phylogenetic Trees
Phylogenetic trees offer a visual representation of evolutionary relationships, showing not just which species are related but also the approximate timeline of their divergence. These diagrams illustrate evolutionary history through both branching patterns and branch lengths, with longer branches indicating more genetic change over time. By examining these trees, scientists can understand both the pattern and timing of evolutionary events.
Phylogenetic trees are particularly valuable because they:
- Show the relative timing of speciation events
- Indicate the amount of genetic or morphological change between lineages
- Represent evolutionary time, often calibrated using fossil evidence or molecular clock data
- Allow scientists to see patterns of evolution across many species simultaneously
The branch lengths in a phylogenetic tree are meaningful - they represent the amount of evolutionary change that has occurred in that lineage. Species that have undergone rapid evolution or adaptation will have longer branches, while those that have remained relatively unchanged will have shorter branches.
Cladograms vs. Phylogenetic Trees
Both cladograms and phylogenetic trees show evolutionary relationships, but they differ in some important ways. A cladogram focuses primarily on showing branching order and grouping organisms based on shared derived characteristics, while a phylogenetic tree adds information about time and the amount of evolutionary change. These differences make each type of diagram useful for different purposes in evolutionary biology.
| Feature | Cladogram | Phylogenetic Tree |
|---|---|---|
| Branch lengths | Equal (not to scale) | Proportional to evolutionary change |
| Time representation | Not explicit | Often calibrated to show time |
| Primary focus | Grouping organisms by shared traits | Showing both relationships and degree of change |
| Calibration | Not typically calibrated | Often calibrated using fossils or molecular clock |
Cladograms are useful when scientists want to focus solely on the pattern of evolutionary branching without making claims about the timing or amount of change. Phylogenetic trees provide more detailed information but require more evidence to construct accurately.
Building Evolutionary Trees
Scientists use multiple types of evidence to construct phylogenetic trees and cladograms. These evidence sources have different strengths and limitations, and are often used in combination to provide the most accurate representation of evolutionary relationships. Both traditional and modern methods contribute valuable information to our understanding of how species are related.
Morphological Evidence
Traditional phylogenetic analysis relied heavily on comparing physical traits between organisms:
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Shared characters - Features present in multiple lineages (like vertebrae in all vertebrates)
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Shared derived characters - Specialized features that evolved in a specific lineage and are passed to all descendants (like hair in mammals)
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Homologous structures - Structures with similar organization but different functions (like bat wings and human arms)
While morphological evidence is readily observable, it can sometimes be misleading due to:
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Convergent evolution - when similar features evolve independently in unrelated groups
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Vestigial structures - reduced features that may be difficult to identify
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Subjective interpretation - different researchers might classify traits differently
Molecular Evidence
Modern phylogenetic analysis increasingly relies on comparing DNA and protein sequences:
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DNA sequences - Direct comparison of genetic code between species
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Protein sequences - Comparison of amino acid sequences in proteins
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Whole genome analysis - Examining gene order, chromosome structure, and other genomic features
Molecular evidence typically provides more accurate and reliable information than morphological traits because:
- It's less influenced by environmental factors
- It can reveal relationships between organisms that look very different
- It provides quantifiable data about the degree of difference between species
- It can detect evolutionary changes that aren't visible in physical appearance
A well-constructed phylogeny usually incorporates both molecular and morphological data to provide the most complete picture of evolutionary relationships.
Key Concepts in Phylogenetic Analysis
Understanding several key concepts is essential for correctly interpreting evolutionary diagrams. These concepts help scientists organize and analyze evolutionary relationships in a systematic way. Mastering these ideas allows for accurate interpretation of phylogenetic information.
Nodes and Branches
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Nodes - Points where lineages diverge, representing the most recent common ancestor of the branching groups
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Branches - Lines connecting nodes, representing lineages evolving through time
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Terminal nodes - Tips of the tree representing existing species or groups
Every node on a phylogenetic tree represents a speciation event - the point at which one ancestral species divided into two or more descendant species. By examining the pattern of nodes, scientists can reconstruct the sequence of evolutionary events.
Clades and Monophyletic Groups
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Clade - A group consisting of an ancestor and all its descendants
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Monophyletic group - Another term for a clade; a complete evolutionary branch
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Paraphyletic group - A group containing an ancestor but not all its descendants
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Polyphyletic group - A group whose members come from different evolutionary lineages
For a grouping to be considered natural in evolutionary terms, it should form a monophyletic group (clade). Traditional classification sometimes creates paraphyletic groups (like "reptiles" that exclude birds) which don't accurately reflect evolutionary history.
Outgroups
The outgroup in a phylogenetic analysis represents the lineage that is least closely related to all the other organisms being studied. Including an outgroup helps to root the tree and establish the direction of evolution. It also provides a reference point for determining which traits are ancestral and which are derived.
Reading and Interpreting Phylogenies
Learning to read phylogenetic trees and cladograms is an essential skill in evolutionary biology. These diagrams can be rotated around any node without changing the relationships they represent. Understanding how to interpret these visualizations allows biologists to extract valuable information about evolutionary history.
To properly interpret a phylogeny:
- Identify the outgroup (usually at the base of the tree)
- Follow branches from the base to the tips to trace evolutionary history
- Note that species connected through fewer nodes are more closely related
- Remember that branch lengths in phylogenetic trees (but not cladograms) represent amount of change
- Look for clades - groups that include an ancestor and all its descendants
Common misconceptions to avoid:
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Species at the top of the tree are not "more evolved" than those lower down
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Proximity of species on paper doesn't indicate relatedness - only the branching pattern matters
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Modern species at the tips of branches aren't ancestors of other modern species
Remember that extant (living) species are all at the tips of branches - none are ancestors of others. The ancestors are found at the nodes, representing species that no longer exist but gave rise to multiple descendant lineages.
Phylogenies as Scientific Hypotheses
It's crucial to understand that phylogenetic trees and cladograms represent hypotheses about evolutionary relationships, not proven facts. These hypotheses are constantly being revised as new evidence emerges. This tentative nature is characteristic of how science progresses through continuous refinement and testing of ideas.
Factors that might lead to revising a phylogeny include:
- Discovery of new fossil evidence
- Advanced DNA sequencing techniques revealing new genetic relationships
- Identification of previously unknown species
- Improved statistical methods for analyzing evolutionary data
The tentative nature of phylogenies doesn't mean they're unreliable - it's simply how science works. Current phylogenies represent our best understanding based on available evidence, and they're incredibly useful tools for organizing biological knowledge and making predictions.
Applications of Phylogenetic Analysis
Phylogenetic analysis has applications far beyond academic evolutionary biology. Scientists use these tools to track diseases, conserve endangered species, and understand human evolution. These practical applications demonstrate the importance of evolutionary thinking in addressing real-world problems in biology and medicine.
Specific applications include:
- Tracking the evolution and spread of diseases like influenza and COVID-19
- Identifying the origins of emerging pathogens
- Predicting which endangered species most need conservation resources
- Understanding the evolution of antibiotic resistance
- Reconstructing the evolutionary history of human populations
- Determining which model organisms might be most useful for specific research questions
By understanding evolutionary relationships, scientists can make more informed predictions and decisions across many fields of biology and medicine.
Phylogenetic trees and cladograms are powerful tools that help scientists visualize and understand the complex relationships among living and extinct organisms. These evolutionary diagrams allow us to trace the history of life on Earth, identify patterns of speciation, and make predictions about shared characteristics between related species. While phylogenies represent scientific hypotheses that are continually revised with new evidence, they provide a fundamental framework for organizing biological knowledge according to evolutionary history. As you study biology, understanding how to interpret these diagrams will help you see the connections between seemingly diverse organisms and appreciate the unity of all life on Earth.
Vocabulary
The following words are mentioned explicitly in the College Board Course and Exam Description for this topic.
| Term | Definition |
|---|---|
| cladogram | A branching diagram that shows hypothetical evolutionary relationships among lineages without indicating time scale or the amount of evolutionary change between groups. |
| DNA sequence similarities | Resemblances in the order of nucleotides in DNA between different organisms, used to infer evolutionary relationships. |
| evolutionary relationship | A connection between organisms based on their shared ancestry and descent from a common ancestor. |
| molecular clock | A method that uses the rate of molecular change (mutations) to estimate the time since organisms diverged from a common ancestor. |
| molecular evidence | Data from DNA nucleotide sequences and protein amino acid sequences that demonstrates evolutionary relationships between organisms. |
| morphological similarities | Structural and physical resemblances between organisms based on body form and anatomy. |
| morphological traits | Physical characteristics or structures of organisms used to determine evolutionary relationships. |
| most recent common ancestor | The most immediate ancestral species or population from which two or more groups diverged during evolution. |
| nodes | Points on a phylogenetic tree or cladogram that represent the most recent common ancestor of two or more groups or lineages. |
| out-group | The lineage in a phylogenetic tree or cladogram that is least closely related to the remainder of the organisms being compared. |
| phylogenetic tree | A diagram that shows hypothetical evolutionary relationships among lineages, including time scale and the amount of evolutionary change over time. |
| protein sequence similarities | Resemblances in the order of amino acids in proteins between different organisms, used to infer evolutionary relationships. |
| shared derived characters | Traits that are present in multiple lineages and were inherited from a common ancestor, indicating common ancestry and used to construct phylogenetic trees and cladograms. |
| speciation | The evolutionary process by which new species arise from existing species through reproductive isolation and genetic divergence. |
Frequently Asked Questions
What is phylogeny and why do we need to learn about it?
Phylogeny is the study of evolutionary relationships—usually shown as phylogenetic trees or cladograms—that hypothesize how lineages are related over time. You learn to read nodes (most recent common ancestors), identify outgroups, and use synapomorphies (shared derived characters), molecular data, fossils (for calibration), and molecular clocks to infer relatedness. Trees are testable hypotheses that get revised as new morphological or DNA/protein evidence appears; molecular data is often more reliable than morphology. Why learn it? AP Bio (Unit 7) asks you to interpret trees/cladograms, connect traits to common ancestry vs. homoplasy (convergent evolution), and use trees to argue evolutionary scenarios on free-response questions (see LO 7.9.A and 7.9.B). Practice reading and building trees—this appears on multiple-choice and FRQs (example: Question 5). For a focused review, see the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk), Unit 7 overview (https://library.fiveable.me/ap-biology/unit-7), and thousands of practice problems (https://library.fiveable.me/practice/ap-biology).
How do you read a phylogenetic tree without getting confused?
Quick checklist so you won’t get confused reading trees: - Start at the nodes: each node is the most recent common ancestor of the branches that come off it (CED EK 7.9.B.1). To ask “who’s most closely related?” find the most recent common node between two taxa—the closer (more recent) the node, the more closely related they are. - Don’t read left-to-right like a timeline unless branch lengths/time scale are shown. Cladograms show relationships, phylogenetic trees may show time or amount of change (EK 7.9.A.2). - Identify the outgroup first—it’s the least related lineage and sets character polarity (EK 7.9.A.3). - Use shared derived characters (synapomorphies) to group monophyletic clades; beware homoplasy (convergent traits). - Remember: trees are hypotheses and get revised with new molecular data (EK 7.9.B.3). For quick practice and AP-style questions on this, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and plenty of practice problems at (https://library.fiveable.me/practice/ap-biology).
What's the difference between a phylogenetic tree and a cladogram?
Short answer: both are hypotheses of relationships, but a phylogenetic tree includes information about amount of change or time (often calibrated with fossils or a molecular clock), while a cladogram only shows branching order (who’s more closely related) without indicating time or evolutionary distance. Why that matters for AP: nodes on both diagrams represent most recent common ancestors (EK 7.9.B.1). Cladograms are built from shared derived characters (synapomorphies) and show branching patterns useful for identifying monophyletic groups; phylogenetic trees add a timeline or “branch length = amount of change” interpretation (EK 7.9.A.2). Outgroups help polarize character changes in both (EK 7.9.A.3). If you want practice reading both for the exam, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and hundreds of practice problems (https://library.fiveable.me/practice/ap-biology).
Why are molecular data better than just looking at how animals look similar?
Morphology can mislead because similar looks can come from convergent evolution (homoplasy) rather than common ancestry. Molecular data (DNA/protein sequences) give thousands of characters (nucleotide sites) you can compare quantitatively, so they: 1) detect true homology vs. convergence, 2) let you use molecular clocks to estimate amount/time of change (EK 7.9.A.2), and 3) support trees with stats (maximum likelihood, Bayesian methods, bootstrapping). That makes phylogenies more testable and revisable—exactly what the CED expects: build trees from molecular data as well as morphology (EK 7.9.B.2) and prefer molecular evidence when available (EK 7.9.A.3.ii). For practice interpreting trees and doing AP-style questions, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and more unit review (https://library.fiveable.me/ap-biology/unit-7) or practice problems (https://library.fiveable.me/practice/ap-biology).
I'm confused about what nodes represent on phylogenetic trees - can someone explain?
A node on a phylogenetic tree marks a branching point—the most recent common ancestor (MRCA) of the two lineages that split there. In other words, each internal node represents a speciation event where one ancestral population diverged into two descendant lineages (EK 7.9.B.1). Terminal tips are living or extinct taxa; internal nodes are ancestral taxa (hypothesized). In phylogenetic trees (not just cladograms) branch lengths can show amount of change or time (EK 7.9.A.2). Nodes and tree topology are hypotheses based on data (morphology, DNA—molecular data is usually more reliable; EK 7.9.A.3) and can be revised with new evidence. Use the outgroup to root the tree and polarize trait changes. For more practice interpreting nodes and clades, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and the Unit 7 overview (https://library.fiveable.me/ap-biology/unit-7). For extra practice, try problems at (https://library.fiveable.me/practice/ap-biology).
How do scientists use fossils to figure out evolutionary relationships?
Fossils help you test and calibrate phylogenies in a few key ways. Morphology from fossils gives characters (shared derived traits/synapomorphies) you can code into a character matrix to build trees or cladograms. Fossils also provide minimum ages for nodes and calibrate phylogenetic trees (not cladograms) using stratigraphy and radiometric dating or a molecular clock (EK 7.9.A.2). Transitional fossils show how traits were gained or lost, help determine character polarity (ancestral vs derived), and distinguish homology from homoplasy (convergent traits). Finally, fossil placement tests tree hypotheses: if a fossil’s traits and age conflict with a tree, you revise the hypothesis (EK 7.9.A.1, EK 7.9.B.3). For practice on building trees and using characters, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk), the Unit 7 overview (https://library.fiveable.me/ap-biology/unit-7), and tons of practice Qs (https://library.fiveable.me/practice/ap-biology).
What is an outgroup and why do we need it when making these trees?
An outgroup is a lineage known to be less closely related to the group you’re studying (the ingroup). You include an outgroup to “root” the tree and establish character polarity—that is, to tell which traits are ancestral (present before the ingroup split) and which are derived (new, shared changes = synapomorphies). Without an outgroup you can make an unrooted cladogram but you can’t reliably say which direction evolution went. That matters on the AP: EK 7.9.A.3 calls out-groups as the least related lineage and LO 7.9.B ties trees to ancestry and nodes (most recent common ancestors). For quick review, check the Topic 7.9 study guide on Fiveable (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and try practice problems (https://library.fiveable.me/practice/ap-biology) to get comfortable identifying synapomorphies and rooting trees.
Why do phylogenetic trees keep changing if they're supposed to show evolution?
Short answer: phylogenetic trees are scientific hypotheses, so they change as we get new evidence or better methods. Why: trees (and cladograms) are built from morphological traits, fossil calibration, and—most reliably—molecular data (EK 7.9.A.1–A.3). New DNA/protein sequences, newly discovered fossils, or better analyses (maximum likelihood, Bayesian inference, bootstrapping for clade support) can change which relationships are most supported. Also, traits can be misleading because of homoplasy (convergent evolution), so reinterpreting character polarity or finding shared derived characters (synapomorphies) can rearrange the tree. Molecular clocks and fossil dates can shift branch timing too (EK 7.9.A.2). Remember: nodes show most recent common ancestors and trees represent tested, revisable hypotheses (EK 7.9.B.1, B.3). For AP prep, be ready to explain how different evidence changes trees and to read trees for relationships and time. If you want a clear refresher, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) or unit overview (https://library.fiveable.me/ap-biology/unit-7) and practice problems (https://library.fiveable.me/practice/ap-biology).
What evidence do scientists actually use to build phylogenetic trees?
Scientists use multiple lines of evidence to build phylogenetic trees—and the AP CED expects you to know the main ones. Key data types: morphological characters (shared derived traits/synapomorphies from living or fossil species), fossil age information (to calibrate time on phylogenies), and molecular data (DNA or protein sequence similarities—usually the most reliable). Scientists also evaluate homology vs homoplasy (convergent traits) and use an outgroup to determine character polarity. Analytical methods include character matrices with maximum parsimony, maximum likelihood, and Bayesian inference, plus bootstrapping for clade support; molecular clocks estimate amount of change over time. Remember: trees and cladograms are hypotheses that get revised as new evidence appears (EK 7.9.A.1–3, EK 7.9.B.2). For a compact review and practice, see the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and more unit resources (https://library.fiveable.me/ap-biology/unit-7) or practice questions (https://library.fiveable.me/practice/ap-biology).
Why would morphological traits sometimes give us wrong information about evolution?
Morphological traits can mislead because similar-looking features don’t always mean shared ancestry. Convergent evolution (a type of homoplasy) produces analogous traits—like wings in bats and birds—that evolved independently under similar selective pressures, so they aren’t synapomorphies (shared derived characters) you can use to group taxa. Also, traits can be lost or highly modified, hiding true relationships (homology may be masked). That’s why molecular data (DNA/protein sequences, molecular clocks) usually give more reliable signals for building phylogenies and testing tree hypotheses (LO 7.9.A; EK 7.9.A.3 and EK 7.9.A.2). On the AP exam you should be able to explain homology vs. homoplasy and why cladograms built from shared derived characters are better than ones relying only on superficial morphology. For a quick refresher, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and practice problems (https://library.fiveable.me/practice/ap-biology).
How does a molecular clock work and what does it tell us?
A molecular clock is a method that uses the rate at which neutral DNA or protein changes accumulate to estimate when two lineages diverged. You compare sequences (molecular phylogenetics) between species, count differences, and—assuming a roughly constant mutation rate—convert that genetic distance into time. Clocks must be calibrated with fossils or known dates (fossil calibration) or by using genes with known mutation rates. On phylogenetic trees a molecular clock lets you put dates or relative timing on nodes (EK 7.9.A.2; LO 7.9.B.2). Limitations: mutation rates can vary by gene, lineages, or selection, and generation time affects rate estimates, so clocks give hypotheses, not absolute certainty. For AP review, see the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk), the Unit 7 page (https://library.fiveable.me/ap-biology/unit-7), and more practice problems (https://library.fiveable.me/practice/ap-biology).
What happens at the nodes of a phylogenetic tree and how do they represent common ancestors?
A node on a phylogenetic tree marks a branching (a speciation)—it’s the point where one lineage split into two. According to the CED, each node represents the most recent common ancestor of the two lineages that branch from it (EK 7.9.B.1). Nodes are usually internal and hypothetical: they’re inferred from shared derived characters (synapomorphies) or molecular data, not necessarily an organism you’ve seen in the fossil record. Tips (terminal branches) are the living or fossil taxa; internal nodes are ancestors that gave rise to those tips. Remember: phylogenetic trees can also show amount of change or time (fossil calibration/molecular clock; EK 7.9.A.2), while cladograms only show branching order. For more practice reading nodes and mapping synapomorphies, check the Topic 7.9 study guide (https://library.fiveable.me/ap-biology/unit-7/phylogeny/study-guide/jpSuwEfOUXMb3aXNAeBk) and try practice questions (https://library.fiveable.me/practice/ap-biology).