Learning Objectives
- What is the difference between homologous and analogous traits? How are these traits used when determining evolutionary relatedness?
- What is cladistics? How does a cladogram differ from a phylogenetic tree?
- What is parsimony?
Connection for AP® Courses
To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections among organisms. Using morphological and molecular data, scientists identify both homologous and analogous characteristics and genes. (In a prior chapter we explored the differences between homologous and analogous traits and how they relate to convergent and divergent evolution.) Similarities among organisms stem either from shared ancestral history (homologies) or from separate evolutionary paths (analogies). Cladograms are constructed by using shared derived traits to distinguish different groups of species from one another. For example, lizards, rabbits and humans all descended from a common ancestor that had an amniotic egg; thus, lizards, rabbits, and humans all belong to the same clade. Vertebrata is a larger clade that also includes fish, lamprey, and lancelets. The closer two species or groups are located to each on a phylogenetic tree or cladogram, they more recently they shared a common ancestor. With the influx of new information, scientists can revise phylogenetic trees; for example, computer programs, such as one called BLAST, which helps determine relatedness using DNA sequencing. Typically, a phylogenetic tree is constructed with the simplest explanation of evolutionary history (maximum parsimony) and the fewest number of evolutionary steps.
Understanding phylogeny extends far beyond understanding the evolutionary history of species on Earth. For botanists, phylogeny acts as a guide to discovering new plants that can be used to make food, medicine, and clothing. For doctors, phylogenies provide information about the origin of diseases and how to treat them, for example, HIV/AIDS.
Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP® Biology Curriculum Framework. The AP® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices.
| Big Idea 1 | The process of evolution drives the diversity and unity of life. |
| Enduring Understanding 1.A | Change in the genetic makeup of a population over time is evolution. |
| Essential Knowledge | 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. |
| Science Practice | 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. |
| Learning Objective | 1.9 The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution. |
| Essential Knowledge | 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. |
| Science Practice | 5.2 The student can refine observations and measurements based on data analysis. |
| Learning Objective | 1.10 The student is able to refine evidence based on data from many scientific disciplines that support biological evolution. |
| Essential Knowledge | 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. |
| Science Practice | 4.2 The student can design a plan for collecting data to answer a particular scientific question. |
| Learning Objective | 1.11 The student is able to design a plan to answer scientific questions regarding how organisms have changed over time using information from morphology, biochemistry, and geology. |
| Essential Knowledge | 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. |
| Science Practice | 7.1 The student can connect phenomena and models across spatial and temporal scales. |
| Learning Objective | 1.12 The student is able to connect scientific evidence from many scientific disciplines to support the modern concept of evolution. |
| Essential Knowledge | 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. |
| Science Practice | 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. |
| Science Practice | 2.1 The student can justify the selection of a mathematical routine to solve problems. |
| Learning Objective | 1.13 The student is able to construct and/or justify mathematical models, diagrams or simulations that represent processes of biological evolution. |
| Big Idea 1 | The process of evolution drives the diversity and unity of life. |
| Enduring Understanding 1.B | Organisms are linked by lines of descent from common ancestry. |
| Essential Knowledge | 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. |
| Science Practice | 3.1 The student can pose scientific questions. |
| Learning Objective | 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth. |
| Essential Knowledge | 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. |
| Science Practice | 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. |
| Learning Objective | 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. |
| Essential Knowledge | 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. |
| Science Practice | 6.1 The student can justify claims with evidence. |
| Learning Objective | 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. |
| Essential Knowledge | 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. |
| Science Practice | 3.1 The student can pose scientific questions. |
| Learning Objective | 1.17 The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram. |
| Essential Knowledge | 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. |
| Science Practice | 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. |
| Learning Objective | 1.18 The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or simple cladogram to determine evolutionary history and speciation. |
| Essential Knowledge | 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. |
| Science Practice | 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. |
| Science Practice | 2.1 The student can justify the selection of a mathematical routine to solve problems. |
| Learning Objective | 1.19 The student is able to create a phylogenetic tree or simple cladogram that correctly represents evolutionary history and speciation from a provided data set. |
The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.15][APLO 1.16][APLO 1.18][APLO 1.17][APLO 1.19][APLO 1.26]
Two Options for Similarities
In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures. This is an example of morphological homology (Figure 20.7).
Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more likely any kind of overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms.
Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very much alike. This usually happens because both organisms share common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures (Figure 20.8).
Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin; analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.
Link to Learning
This website has several examples to show how appearances can be misleading in understanding the phylogenetic relationships of organisms.
Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated.
Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships, and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.
Evolution Connection
Why Does Phylogeny Matter?
Evolutionary biologists could list many reasons why understanding phylogeny is important to everyday life in human society. For botanists, phylogeny acts as a guide to discovering new plants that can be used to benefit people. Think of all the ways humans use plants—food, medicine, and clothing are a few examples. If a plant contains a compound that is effective in treating diseases, scientists might want to examine all of the relatives of that plant for other useful drugs.
A research team in China identified a segment of DNA thought to be common to some medicinal plants in the family Fabaceae (the legume family) (Figure 20.9) and worked to identify which species had this segment. After testing plant species in this family, the team found a DNA marker (a known location on a chromosome that enabled them to identify the species) present. Then, using the DNA to uncover phylogenetic relationships, the team could identify whether a newly discovered plant was in this family and assess its potential medicinal properties.
The image shows a broad phylogenetic tree comparing most organisms.
Make a claim about fungi based on this tree.
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Fungi are closer to bacteria than plants.
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Fungi are closer to animals than plants.
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Fungi are closer to bacteria than animals.
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Fungi are closer to bacteria than plants.
Building Phylogenetic Trees
How do scientists construct phylogenetic trees? After the homologous and analogous traits are sorted, scientists often organize the homologous traits using a system called cladistics. This system sorts organisms into clades: groups of organisms that descended from a single ancestor. For example, in Figure 20.10, all of the organisms in the orange region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include all of the descendants from a branch point.
Visual Connection
Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship. Figure 20.11 shows various examples of clades. Notice how each clade comes from a single point, whereas the non-clade groups show branches that do not share a single point.
Visual Connection
Shared Characteristics
Organisms evolve from common ancestors and then diversify. Scientists use the phrase “descent with modification” because even though related organisms have many of the same characteristics and genetic codes, changes occur. This pattern repeats over and over as one goes through the phylogenetic tree of life:
- A change in the genetic makeup of an organism leads to a new trait which becomes prevalent in the group.
- Many organisms descend from this point and have this trait.
- New variations continue to arise: some are adaptive and persist, leading to new traits.
- With new traits, a new branch point is determined (go back to step 1 and repeat).
If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. The vertebrate in Figure 20.10 is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms in Figure 20.10 have this trait, and to those that do, it is called a shared derived character because this trait derived at some point but does not include all of the ancestors in the tree.
The tricky aspect to shared ancestral and shared derived characters is the fact that these terms are relative. The same trait can be considered one or the other depending on the particular diagram being used. Returning to Figure 20.10, note that the amniotic egg is a shared ancestral character for lizards, rabbits, and humans, while having hair is a shared derived character only for humans and rabbits. For the Amniotes as a group, however, the amniotic egg is a shared derived character that is not seen in fish. These terms help scientists distinguish between clades in the building of phylogenetic trees.
Choosing the Right Relationships
Imagine being the person responsible for organizing all of the items in a department store properly—an overwhelming task. Organizing the evolutionary relationships of all life on Earth proves much more difficult: scientists must span enormous blocks of time and work with information from long-extinct organisms. Trying to decipher the proper connections, especially given the presence of homologies and analogies, makes the task of building an accurate tree of life extraordinarily difficult. Add to that the advancement of DNA technology, which now provides large quantities of genetic sequences to be used and analyzed. Taxonomy is a subjective discipline: many organisms have more than one connection to each other, so each taxonomist will decide the order of connections.
To aid in the tremendous task of describing phylogenies accurately, scientists often use a concept called maximum parsimony, which means that events occurred in the simplest, most obvious way. For example, if a group of people entered a forest preserve to go hiking, based on the principle of maximum parsimony, one could predict that most of the people would hike on established trails rather than forge new ones.
For scientists deciphering evolutionary pathways, the same idea is used: the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand. Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits.
Link to Learning
Head to this website to learn how maximum parsimony is used to create phylogenetic trees.
These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth.
Science Practice Connection for AP® Courses
Activity
Using a data set provided by your teacher or other sources, construct a phylogenetic tree or cladogram to reflect the evolutionary history among a group of organisms based on shared characteristics. Then share the phylogenetic tree or cladogram with peers for review and revision.
AP® Biology Investigative Labs: Inquiry-Based Approach, Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST. Students will learn to use a common tool, BLAST, to compare several genes from different organisms and then use this information to construct a cladogram to determine evolutionary relatedness among species. Then students will use BLAST to track a gene(s) of choice through several species. Bioinformatics has many applications, including understanding genetic disease.
Think About It
Why must scientists distinguish between homologous and analogous characteristics before building phylogenetic trees? Do more closely related organisms share homologous or analogous traits? Which type of trait is used to support convergent or divergent evolution?
Teacher Support
- This activity is an application of AP® Learning Objective 1.19 and Science Practice 1.1, Learning Objective 1.18 and Science Practice 5.3, and Learning Objective 1.7 and Science Practice 1.3 because 1) students are asked to create a phylogenetic tree or cladogram based on evidence provided by a data set; 2) student’s diagram should raise questions about the evolutionary history of the group; and 3) evolutionary history is subject to revision based on interpretation and new evidence.
- This lab investigation is an application of several AP® Learning Objectives and Science Practices described above (Learning Objectives 1.11, 1.16, 1.17, and 1.18) because students will use BLAST to determine evolutionary relatedness among species based on molecular evidence/DNA sequences and then construct a cladogram based on that information.
- The Think About It question is an application of AP® Learning Objective 1.17 and Science Practice 3.1 because students must distinguish between homologous and analogous characteristics when constructing phylogenetic trees.
- Only homologous traits are considered in establishing evolutionary relationships, because they are evidence of evolutionary change. Closely related organisms will share homologous traits, whereas analogous traits are often shared by only distantly related organisms. The study of convergent and divergent evolution also relies on the analysis of analogous and homologous traits.