Learning Objectives
In this section, you will explore the following questions:
- Why do scientists need a comprehensive classification system to study living organisms?
- What are the different levels of the taxonomic classification system?
- How are systematics and taxonomy related to phylogeny?
- What are the components and purpose of a phylogenetic tree?
Connection for AP® Courses
In prior chapters we explored how all organisms on Earth, extant and extinct, evolved from common ancestry. Supporting this claim are core features and processes, such as a common genetic code and metabolic pathways, which evolved billions of years ago and are widely distributed among organisms living today. The evolutionary history and relationship of an organism or a group of organisms is called phylogeny. Scientists often construct phylogenetic trees based on evidence drawn from multiple disciplines to illustrate evolutionary pathways and connections among organisms.
Scientists historically organized Earth’s millions of species into a hierarchical taxonomic classification system from the most inclusive category to the most specific: domain, kingdom, phylum, class, order, family, genus, and species. The traditional five-kingdom system that you might have studied in middle school was expanded (and reorganized) to include three domains: Bacteria, Archaea, and Eukarya, with prokaryotes divided between Bacteria or Archaea depending on their molecular genetic machinery, and protists, fungi, plants, and animals grouped in Eukarya. Today, however, phylogenetic trees provide more specific information about evolutionary history and relationships among organisms. (For the purpose of AP®, you do not have to memorize the taxonomic levels. However, it is important to reiterate that taxonomy is a tool to organize the millions of organisms on Earth, similar to how items in a grocery store or mall shop are organized into different departments. Like new products, organisms are often shifted among their taxonomic groups!)
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.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 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. |
| 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. |
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 1.20][APLO 1.26]
Phylogenetic Trees
Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 20.2).
Unlike a taxonomic classification diagram, a phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains— Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species.
In a rooted tree, the branching indicates evolutionary relationships (Figure 20.3). The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other.
The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the "trunk" of the tree, one can discover that species' ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms.
Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other.
Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.
Limitations of Phylogenetic Trees
It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure 20.4 shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.
Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example, in Figure 20.4, the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again using Figure 20.4, the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and like a real tree, it does not grow in only one direction after a new branch develops. So, for the organisms in Figure 20.4, just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.
Link to Learning
Head to this website to see interactive exercises that allow you to explore the evolutionary relationships among species.
Science Practice Connection for AP® Courses
Think About It
How does a phylogenetic tree relate to the passing of time? What other questions about the evolutionary history of an organism and its relatedness to other organisms can a phylogenetic tree answer?
Teacher Support
- This question is an application of AP® Learning Objective 1.14 and Science Practice 3.1 and Learning Objective 1.17 and Science Practice 3.1 because students must pose questions about evolutionary history before they can answer them.
- Phylogenetic trees approximate the passing of time by the lengths of their branches. Longer branches mean that more time has passed since the organisms shared a common ancestor. Thus, a phylogenetic tree not only shows evolutionary relationships among organisms, but also how long ago the divergence from the common ancestor occurred.
The Levels of Classification
Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system.
The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called a domain: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species (Figure 20.5).
The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in Figure 20.5. Therefore, the full name of an organism technically has eight terms. For the dog, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also called a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors.
Figure 20.6 shows how the levels move toward specificity with other organisms. Notice how the dog shares a domain with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using characteristics, but as DNA technology developed, more precise phylogenies have been determined.
Visual Connection
Link to Learning
Visit this website to classify three organisms—bear, orchid, and sea cucumber—from kingdom to species. To launch the game, under Classifying Life, click the picture of the bear or the Launch Interactive button.
Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative of the whale.