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 (//cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_01">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.

The phylogenetic tree in part a is rooted and resembles a living tree, with a common ancestor indicated as the base of the trunk. Two branches form from the trunk. The left branch leads to the domain Bacteria. The right branch branches again, giving rise to Archaea and Eukarya. Smaller branches within each domain indicate the groups present in that domain. The phylogenetic tree in part B is unrooted. It does not resemble a living tree; rather, groups of organisms within the Archaea, Eukarya, and Bacteria domains are arranged in a circle. Lines connect the groups within each domain. The groups within Archaea and Eukarya are then connected together. A line from the Archaea/ Eukarya domains, and another from the Bacteria meet in the center of the circle. There is no root, and therefore no indication of which domain arose first.
Figure 20.2Both of these phylogenetic trees shows the relationship of the three domains of life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)

In a rooted tree, the branching indicates evolutionary relationships (//cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_02">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.

Illustration shows a phylogenetic tree that starts at a root, indicating that all organisms on the tree share a common ancestor. Shortly after the root, the tree branches out. One branch gives rise to a single, basal lineage, and the other gives rise to all other organisms on the tree. The next branch forks at one point into four different lineages, an example of polytomy. The final branch gives rise to two lineages, an example of sister taxa.
Figure 20.3The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.

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 //cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_03">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.

The ladder-like phylogenetic tree starts with a trunk at the left. A question next to the trunk asks whether a vertebral column is present. If the answer is no, a branch leads downward to lancelet. If the answer is yes, a branch leads upward to another question: is a hinged jaw present? If the answer is no, a branch leads downward to lamprey. If the answer is yes, a branch leads upward to another question: are legs present? If the answer is no, a branch leads downward to fish. If the answer is yes, a branch leads upward to another question: does the egg have amnion? If the answer is no, the branch leads downward to frog. If the answer is yes, the branch leads upward to another question: is hair present? If the answer is no, the branch leads downward to lizard. If the answer is yes, the branch leads upward to rabbit.
Figure 20.4This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.

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 //cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_03">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 //cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_03">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 //cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_03">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.

What is the main function of the ITOL (Interactive Tree of Life) website?
  1. iTOL is a website that provides the history about the Tree of Life.
  2. iTOL is a website that provides guidelines for researching data to create a phylogenetic tree.
  3. iTOL is an online tool that provides the display and manipulation of pre-computed phylogenetic trees, and you can upload and display your own trees and data.
  4. iTOL is a website that explains 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?

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: phylumclassorderfamilygenus, and species (//cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#CNX_AP_Bio_20_01_02ab">Figure 20.5).

The illustration shows the classification of a dog, which belongs in the domain Eukarya, kingdom Animalia, phylum Chordata, class Mammalia, order Carnivore, family Canidae, genus Canis, species Canis lupus, and the subspecies is Canis lupus familiaris.
Figure 20.5The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo. (credit “dog”: modification of work by Janneke Vreugdenhil)

The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in //cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#CNX_AP_Bio_20_01_02ab">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.

//cnx.org/contents/This email address is being protected from spambots. You need JavaScript enabled to view it.:5eUeNbp-@14/20-1-Organizing-Life-on-Earth#fig-ch20_01_05">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

Illustration shows the taxonomic groups shared by various species. All of the organisms shown are in the domain Eukarya: plants, insects, fish, rabbits, cats, foxes, jackals wolves, and dogs. Of theses, insects, fish, rabbits, cats, foxes, jackals, wolves and dogs are in the kingdom Animalia. Within the kingdom Animalia, fish, rabbits, cats, foxes, jackals, wolves, and dogs are in the phylum Chordata. Rabbits, cats, foxes, jackals, wolves, and dogs are in the class Mammalia. Cats, foxes, jackals, wolves, and dogs are in the order Carnivora. Foxes, jackals, wolves, and dogs are in the family Canidae. Jackals, wolves and dogs are in the genus Canis. Wolves and Dogs and have the species name Canis lupus. Dogs have the subspecies name Canis lupus familiaris.
Figure 20.6At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit “plant”: modification of work by "berduchwal"/Flickr; credit “insect”: modification of work by Jon Sullivan; credit “fish”: modification of work by Christian Mehlführer; credit “rabbit”: modification of work by Aidan Wojtas; credit “cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit “wolf”: modification of work by Robert Dewar; credit “dog”: modification of work by "digital_image_fan"/Flickr)
At what levels are cats and dogs considered to be part of the same group?
  1. Cats and dogs are only found together in the Domain level.
  2. Cats and dogs are in the same group beginning at the Domain level and including the sublevels Kingdom, Phylum, Class, and Order.
  3. Cats and dogs are in the same group beginning at the Family level.
  4. Cats and dogs are part of the same group beginning with the Order: Carnivora level.

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.

Using the taxonomic classification system, which Kingdom category best describes a bear?
  1. Plantae: Multicellular organisms that get their energy through photosynthesis.
  2. Animalia: Multicellular organismsthat get their energy through ingesting other organisms.
  3. Fungi: Single-celled and multi-celled organisms that get their energy mainly by absorbing nutrients from their surroundings and not through photosynthesis.

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.