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T2 - Biological Classification

I can explain the history of classification of living organisms and use modern classification groupings

Early Classification Systems

One of the first known systems for classifying organisms was developed by Aristotle. Aristotle was a Greek philosopher who lived more than 2,000 years ago. He created a classification system called the “Great Chain of Being” (See Figure below). Aristotle arranged organisms in levels based on how complex, or “advanced,” he believed them to be. There were a total of eleven different levels in his system. At the lower levels, he placed organisms that he believed were less complex, such as plants. At higher levels, he placed organisms that he believed were more complex. Aristotle considered humans to be the most complex organisms in the natural world. Therefore, he placed them near the top of his great chain, just below angels and other supernatural beings.


The Great Chain of Being was Aristotle


Aristotle also introduced two very important concepts that are still used in taxonomy today: genus and species. Aristotle used these two concepts in ways that are similar to, but not as precise as, their current meanings. He used the term species to refer to a particular type of organism. He thought each species was unique and unchanging. He used the term genus (plural, genera) to refer to a more general grouping of organisms that share certain traits. For example, he grouped together in the same genera animal species with similar reproductive structures.

As early naturalists learned more about the diversity of organisms, they developed different systems for classifying them. All these early classification systems, like Aristotle’s, were based on obvious physical traits of form or function. For example, in one classification system, animals were grouped together on the basis of similarities in movement. In this system, bats and birds were grouped together as flying animals, and fishes and whales were grouped together as swimming animals.

Linnaean System of Classification

The most influential early classification system was developed by Carolus Linnaeus. In fact, all modern classification systems have their roots in Linnaeus’ system. Linnaeus was a Swedish botanist who lived during the 1700s. He is known as the "father of taxonomy." Linnaeus tried to describe and classify the entire known natural world. In 1735, he published his classification system in a work called Systema Naturae ("System of Nature").

 A film about Carl Linnaeus can be seen at http://www.youtube.com/watch?v=Gb_IO-SzLgk&feature=related (3:58). 

Linnaean taxonomy divides all of nature into three kingdoms: animal, vegetable (or plant), and mineral. (The mineral kingdom does not include living organisms, so it is not discussed further here.) Both plant and animal kingdoms are subdivided into smaller and smaller categories of organisms. An updated version of Linnaean taxonomy is shown in Figure below.

Linnaean Classification System (Revised)


This is an updated version of Linnaeus


The classification in Figure above includes a few more taxa than Linnaeus identified. However, it follows the same general plan as Linnaeus’ original taxonomy. The taxa are below:

  • Domain--All life can be divided into 3 domains based on basic differences at the cellular level. 
  • Kingdom—This taxon represents the major divisions of organisms. Kingdoms of organisms include the plant and animal kingdoms.
  • Phylum (plural, phyla)—This taxon is a division of a kingdom. Phyla in the animal kingdom include chordates (animals with an internal skeleton) and arthropods (animals with an external skeleton).
  • Class—This taxon is a division of a phylum. Classes in the chordate phylum include mammals and birds.
  • Order—This taxon is a division of a class. Orders in the mammal class include rodents and primates.
  • Family—This taxon is a division of an order. Families in the primate order include hominids (apes and humans) and hylobatids (gibbons).
  • Genus—This taxon is a division of a family. Genera in the hominid family include Homo(humans) and Pan (chimpanzees).
  • Species—This taxon is below the genus and the lowest taxon in Linnaeus’ system. Species in the Pan genus include Pan troglodytes (common chimpanzees) and Pan paniscus (pygmy chimpanzees).

To remember the order of the taxa in Linnaean taxonomy, it may help to learn a mneumonic, a sentence to help remember a list, in which the words begin with the same letters as the taxa: d, k, p, c, o, f, g, and s. One sentence you could use is: Did King Philip Come over from Geneva Swizerland Can you think of others?

Table below shows the classification of the human species. The table also lists some of the physical traits that are the basis of the classification. For example, humans are members of the animal kingdom. Animals are organisms capable of independent movement. Within the animal kingdom, humans belong to the mammal class. Mammals are animals that have fur or hair and milk glands. At each lower taxon, additional physical traits further narrow the group to which humans belong. The final grouping, the species Homo sapiens (as in Homo sapiens), includes only organisms that have all of the traits listed in the table.

Classification of the Human Species
Organisms with complex cells that contain a nucleus and organelles.
Organisms capable of moving on their own.
PhylumChordateAnimals with a notochord (flexible rod that supports the body).
ClassMammalChordates with fur or hair and milk glands.
OrderPrimateMammals with collar bones, grasping hands with fingers.
FamilyHominidPrimates with three-dimensional vision, relatively flat face.
GenusHomoHominids with upright posture, large brain.
SpeciesHomo sapiensMembers of the genus Homo with a high forehead, thin skull bones.

1 Only one or two traits per taxon are listed in the table as examples. Additional traits may be needed to properly classify species. (Source : http://en.wikipedia.org/wiki/Linnaean_taxonomy)

Although Linnaeus grouped organisms according to their physical similarities, he made no claims about relationships between similar species. Linnaeus lived a century before Charles Darwin, so the theory of evolution had not yet been developed. Darwin explained how evolution, or changes in species over time, can explain the diversity of organisms (see the Evolutionary Theory chapter). In contrast, Linnaeus (like Aristotle before him) thought of each species as an unchanging "ideal type." Individual organisms that differed from the species’ ideal type were considered deviant and imperfect.

Binomial Nomenclature

The single greatest contribution that Linnaeus made to science is his method of naming species. This method, called binomial nomenclature, gives each species a unique, two-word name (also called a scientific or Latin name). Just like we have a first and last name, organisms have a distinguishable two word name as well. The two words in the name are the genus name and the species name. For example, the human species is uniquely identified by its genus and species names as Homo sapiens. No other species has this name.

Both words in a scientific name are Latin words or words that have been given Latin endings. The genus name is always written first and starts with an upper-case letter. The species name is always written second and starts with a lower-case letter. Both names are written in italics.


As another example, consider the group of organisms called Panthera. This is a genus in the cat family. It consists of all large cats that are able to roar. Within the genus Panthera, there are four different species that differ from one another in several ways. One obvious way they differ is in the markings on their fur as shown in Figure belowPanthera leo (lion species) has solid-colored fur,Panthera tigris (tiger species) has striped fur, and the other two Panthera species have fur with different types of spots. As this example shows, the genus name Panthera narrows a given cat’s classification to big cats that roar. Adding the species name limits it to a single species of cat within this genus.


. All four species in the Panthera genus are similar, but each is a unique type of organism, clearly identified by its combined genus and species name.


Why is Linnaeus’ method of naming organisms so important? Before Linnaeus introduced his method, naming practices were not standardized. Some names were used to refer to more than one species. Conversely, the same species often had more than one name. In addition, a name could be very long, consisting of a string of descriptive words. For example, at one time, common wild roses were named Rosa sylvestris alba cum rubore folio glabro. Names such as this were obviously cumbersome to use and hard to remember.

For all these reasons, there was seldom a simple, fixed name by which a species could always be identified. This led to a great deal of confusion and misunderstanding, especially as more and more species were discovered. Linnaeus changed all that by giving each species a unique and unchanging two-word name. Linnaeus’s method of naming organisms was soon widely accepted and is still used today.

Changes in the Linnaean System

Linnaean taxonomy has been revised considerably since it was introduced in 1735. One reason revisions have been needed is that many new organisms have been discovered since Linnaeus’ time. Another reason is that scientists started classifying organisms on the basis of evolutionary relationships rather than solely on the basis of similarities in physical traits.

Scientists have had to add several new taxa to the original Linnaean taxonomy in order to accommodate new knowledge of organisms and their evolutionary relationships. Examples of added taxa include the subphylumsuperfamily, and domain.

  • A subphylum is a division of a phylum that is higher than the class. An example of a subphylum is Vertebrates (animals with a backbone). It is a subphylum of the Chordate phylum (animals with a notochord).
  • A superfamily is a taxon that groups together related families but is lower than the order. An example of a superfamily is Hominoids (apes). This superfamily consists of the Hominid family (gorillas, chimps, and humans) and the Hylobatid family (gibbons). Figure belowshows species from both of these families of the Hominoid superfamily.
  • A domain is a taxon higher than the kingdom. An example of a domain is Eukarya, which includes both plant and animal kingdoms. You can read more about domains in Lesson 14.3.


The Hominoid superfamily includes the Hominid and Hylobatid families. Members of the Hominid family are chimpanzees (


Modern Classification Systems

Linnaeus established two kingdoms of organisms in his classification system: Plantae (the plant kingdom) and Animalia (the animal kingdom). Since then, scientists have repeatedly revised the Linnaean system. They have added several new kingdoms and other taxa. These changes were necessary as scientists learned more about life on Earth.

 An overview of the kingdoms can be seen at http://www.youtube.com/watch?v=5uJ8QeFRvJA&feature=related (5:58). 

New Kingdoms

Between 1866 and 1977, a total of four new kingdoms were added to the original plant and animal kingdoms identified by Linnaeus. The new kingdoms include Protista (protists), Fungi, Monera (eubacteria), and Archaea (archaebacteria). Table below identifies the scientists who introduced the kingdoms and the dates the kingdoms were introduced. The table starts with the two-kingdom system introduced by Linnaeus in 1735.

Kingdoms in the Classification of Organisms
Number of KingdomsTwoThreeFourFiveSix
Names of Kingdoms

(Source: http://en.wikipedia.org/wiki/Kingdom_%28biology%29, License: GNU Free Documentation)

The Protist Kingdom

When Linnaeus created his taxonomy, microorganisms were almost unknown. As scientists began studying single-celled organisms under the microscope, they generally classified them as either plants and or animals. For example, bacteria are single-celled organisms, some of which make their own food. They were classified as plants, which also make their own food. Protozoa are single-celled organisms that can move on their own. They were classified as animals, which are organisms that have independent movement.

As more single-celled organisms were identified, many didn’t seem to fit in either the plant or the animal kingdom. As a result, scientists could not agree on how to classify them. To address this problem, in 1866, biologist Ernst Haeckel created a third kingdom for all single-celled organisms. He called this kingdom Protista. Figure below shows drawings that Haeckel made of several different types of protists as they looked under a microscope. The drawings show some of the diversity of microorganisms.


Biologist Ernst Haeckel made these drawings of various types of single-celled organisms as viewed under a microscope. Based on his extensive knowledge of the diversity of microorganisms, Haeckel introduced a new kingdom just for single-celled life forms, called the protist kingdom. This was the first major change in the original Linnaean taxonomy.


The Bacteria Kingdom

Haeckel’s protist kingdom represented all known single-celled organisms, including both bacteria and protozoa. In the early 1900s, scientists discovered that bacterial cells are very different not only from plant and animal cells but also from the cells of protists, such as protozoa. Figurebelow shows a bacterial cell, a protozoan cell, and an animal cell. When you compare the three cells, what differences do you see? The major difference is that, unlike the protozoan and animal cells, the bacterial cell does not contain a nucleus surrounded by a nuclear membrane. Instead, its DNA is found in the cytoplasm of the cell. Organelles in the bacterial cell also lack surrounding membranes.


Prokaryote and eukaryote cells differ significantly in their structure. Unlike prokaryote cells (upper figure), eukaryote cells (middle figure, protist cell; lower figure, animal cell) have a nucleus, which is separated by membranes from the cytoplasm of the cell. Their organelles also have membranes. Herbert Copeland thought that these and other differences were significant enough to place prokaryote and eukaryote organisms in different superkingdoms.


In the 1920s, microbiologist Edouard Chatton gave bacteria the name prokaryotes. He definedprokaryote as an organism whose cells lack nuclei. He gave the name eukaryotes to all other organisms. He defined eukaryote as an organism whose cells have nuclei (see the Cell Structure and Function chapter). Chatton proposed placing prokaryotes and eukaryotes in a new taxon above the kingdom, called the superkingdom. However, this idea did not catch on, and most biologists continued to place bacteria in the protist kingdom.

Over the next several decades, scientists learned more about the tremendous number and diversity of bacteria. They started to see a need for a separate bacteria kingdom. By 1956, biologist Herbert Copeland proposed placing bacteria in a new kingdom called Monera. With the addition of the Monera kingdom, Linnaean taxonomy became a four-kingdom system (See Tablebelow).

Bacteria are the most numerous organisms on Earth. In a single gram of soil, there are typically 40 million bacterial cells. The human body also contains 10 times as many bacterial cells as human cells. Most of these bacteria are on the skin or in the digestive tract.

 Bacteria (10d) are described in the following videohttp://www.youtube.com/user/khanacademy#p/c/7A9646BC5110CF64/16/TDoGrbpJJ14 (18:26). 

The Fungi Kingdom

In the late 1960s, ecologist Robert Whittaker proposed adding a fifth kingdom to Linnaean taxonomy to represent fungi. Fungi are eukaryote organisms such as mushrooms and molds. Up until then, fungi had been classified in the plant kingdom. Whittaker separated fungi from plants on the basis of differences in metabolism. Plants make their own food in the process of photosynthesis, whereas fungi obtain nutrients by breaking down dead organisms (see the Fungichapter). Separating fungi from plants resulted in five kingdoms, which are illustrated in Figurebelow. The five-kingdom system soon became widely accepted.


This five-kingdom system of classification was proposed by ecologist Robert Whittaker in the late 1960s. Whittaker added the Fungi kingdom to the earlier four-kingdom classification system.


Two Bacterial Kingdoms

By the 1970s, scientists had started to classify organisms in ways that reflected evolutionary relationships. They had also started using nucleic acid base sequences to identify these relationships (see Lesson 14.2). Nucleic acid sequence data are especially useful for studying bacteria. These organisms are so small that they have few physical traits.

Studies have bacterial nucleic acid sequences have yielded some surprising results. For example, in their research on ribosomal RNA base sequences, microbiologist Carl Woese and his colleagues discovered that bacteria actually include two very different groups of organisms. They called the two groups Eubacteria and Archaebacteria. Examples of organisms from each group are shown in Figure below. Although the two types of organisms are similar in appearance, their ribosomal RNA sequences are very different. In 1977, Woese and his colleagues suggested that the original bacteria kingdom should be divided into two new kingdoms, called Eubacteria and Archaebacteria. This resulted in a six-kingdom taxonomy that has been widely accepted for many years.


Left, Eubacteria (now called Bacteria), Right, Archaebacteria (now called Archaea). Appearances can be deceiving! These two microorganisms are very different from one another, despite their outward similarities. Both organisms used to be classified in the bacteria kingdom. Woese suggested placing them in different kingdoms, called the eubacteria and archaebacteria kingdoms.



Woese wasn’t completely happy with the six-kingdom system. It didn’t show that all four eukaryote kingdoms are more closely related to each other than to the two bacteria kingdoms. It also didn’t show that the two bacteria kingdoms are as different from each other as they are from the eukaryote kingdoms. To show these similarities and differences, Woese introduced a new taxon called the domain. He defined domain as a taxon higher than the kingdom.

The Three-Domain System

In 1990, Woese and his colleagues proposed a new classification system containing three domains: Bacteria, Archaea, and Eukarya. As shown in Figure below, the Bacteria domain was formerly the Eubacteria kingdom, and the Archaea domain was formerly the Archaebacteria kingdom. The Eukarya domain includes all four eukaryote kingdoms: plants, animals, protists, and fungi. The three-domain system emphasizes the similarities among eukaryotes and the differences among eukaryotes, bacteria, and archaea. By using domains, Woese was able to show these relationships without replacing the popular six-kingdom system.


This diagram shows how the three-domain system of classification is related to the six-kingdom system. Both Eubacteria and Archaebacteria kingdoms are raised to the level of domains (Bacteria and Archaea domains, respectively) in the three-domain system. The other four kingdoms make up the third domain (Eukarya domain).


Archaea were first found in extreme environments. For example, they were found in the hot water geysers in Yellowstone National park. Archaea have since been found in all of Earth’s habitats. They are now known to be present everywhere in high numbers. They may contribute as much as 20 percent to Earth’s total biomass.

Woese’s three-domain system was quickly adopted by many other biologists. There were some critics, however, who argued that the system put too much emphasis on the uniqueness of Archaea. Later studies confirmed how different Archaea are from other organisms. For example, organisms belogning to Archaea were found to differ from both Eukarya and Bacteria in the composition of their cell membranes and the system they use for DNA replication. These differences convinced most critics that the three-domain system was justified. After its introduction in 1990, the three-domain system became increasingly popular. Within a decade of its introduction, it had largely replaced earlier classifications.

How Are the Three Domains Related?

Comparing ribosomal RNA base sequences, Woese and his colleagues also showed that organisms belonging to Eukarya are more similar to Archaea than they are to Bacteria. Figurebelow is a phylogenetic tree based on their analysis. This tree places Archaea and Eukarya in the same clade (see Lesson 2). It represents the hypothesis that Archaea and Eukarya shared a more recent common ancestor with each other than with Bacteria.


This phylogenetic tree is based on comparisons of ribosomal RNA base sequences among living organisms. The tree divides all organisms into three domains: Bacteria, Archaea, and Eukarya. Humans and other animals belong to the Eukarya domain. From this tree, organisms that make up the domain Eukarya appear to have shared a more recent common ancestor with Archaea than Bacteria.


The results of a study published in 2007 seem to conflict with this hypothesis. Comparing DNA base sequences, the 2007 study suggested that the domain Archaea may be older than either Bacteria or Eukarya. That would make Archaea the most ancient group of organisms on Earth. It is not yet known, which, if either, hypothesis is correct. Scientists need to learn more about Archaea and their relationships with other organisms to resolve these questions.

The Future of Classification

The three-domain system is unlikely to be the final word on classification. The system is based on the current state of knowledge. As knowledge increases, the three-domain system may need revision. For example, the number of domains may change as scientists learn more about those life forms we currently know least about.

A recent discovery illustrates this point. In 2003, scientists identified a new virus called mimivirus. It resembles bacteria in size and number of genes. However, the virus cannot respond to stimuli or grow by cell division, both of which are traits of bacteria and other living organisms. Mimivirus’ unique combination of traits seems to place it at the boundary between living and nonliving things. Some scientists think mimivirus might represent a new domain of life.

Lesson Summary

  • Linnaean taxonomy groups organisms in a hierarchy of taxa, based on similarities in physical traits. Linnaeus’ binomial nomenclature gives each species a unique two-word name.
  • By 1977, four new kingdoms had been added to the plant and animal kingdoms of the original Linnaean taxonomy: Protista, Fungi, Eubacteria, and Archaebacteria.
  • In 1990, the three-domain system was introduced and is now the most widely used classification system. The three domains are Bacteria, Archaea, and Eukarya.
  • As knowledge of organisms increases in the future, the three-domain system may need revision. For example, new domains may need to be added

Review Questions

  1. What contributions did Carolus Linnaeus make to taxonomy?
  2. List the order of taxa in Linnaean taxonomy, from most to least inclusive.
  3. What is binomial nomenclature?
  4. Assume that a new organism has been discovered. It has a notochord, fur, forward-facing eyes, and grasping hands with fingers. In which taxa should the new organism be placed? Justify your answer.
  5. Why was Linnaeus’ naming system such an important contribution to biology?
  6. Name four new kingdoms that were added to the original Linnaean taxonomy.
  7. How do prokaryotes and eukaryotes differ?
  8. Why were fungi placed in a separate kingdom from plants?
  9. What is a domain?
  10. Describe the relationship between the original bacteria kingdom called monera and the domain called bacteria.
  11. Explain in which domain you would classify an organism that consists of a single cell with a nucleus.
  12. Compare and contrast bacteria, Archaea, and Eukarya.
  13. What problem with the six-kingdom classification system was addressed by the three-domain classification system? How did it address the problem?