During Linnaeus’s time, the only known differences among living things were the fundamental characteristics that separated animals from plants. Animals were organisms that moved from place to place and used food for energy. Plants were green organisms that generally did not move and got their energy from the sun.

As biologists learned more about the natural world, they realized that Linnaeus’s two kingdoms—Animalia and Plantae—did not reflect the full diversity of life. Classification systems have changed dramatically since Linnaeus’s time, as shown below. And hypotheses about relationships among organisms are still changing today as new data are gathered.

Five Kingdoms

As researchers began to study micro organisms, they discovered that single-celled organisms were significantly different from plants and animals. At first all microorganisms were placed in their own kingdom, named Protista. Then yeasts and molds, along with mushrooms, were placed in their own kingdom, Fungi.

Later still, scientists realized that bacteria lack the nuclei, mitochondria, and chloroplasts found in other forms of life. All prokaryotes (bacteria) were placed in yet another new kingdom, Monera. Single-celled eukaryotic organisms remained in the kingdom Protista. This process produced five kingdoms: Monera, Protista, Fungi, Plantae,
and Animalia.

Six Kingdoms

By the 1990s, researchers had learned a great deal about the genetics and biochemistry of bacteria. That knowledge made clear that the organisms in kingdom Monera were actually two genetically and biochemically different groups. As a result, the monerans were separated into two kingdoms, Eubacteria and Archaebacteria, 
bringing the total number of kingdoms to six.

• The six-kingdom system of classification includes the kingdoms Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Animalia.

Three Domains

Genomic analysis has revealed that the two main prokaryotic groups are even more different from each other, and from eukaryotes, than previously thought. So biologists established a new taxonomic category—the domain.

Domain
A larger, more inclusive category than a kingdom

Under this system, there are three domains—domain Bacteria (corresponding to the kingdom Eubacteria); domain Archaea (which corresponds to the kingdom Archaebacteria); and domain Eukarya (kingdoms Fungi, Plantae, and Animalia, and the “Protista”).

Why do we put quotations around about the old kingdom Protista? Well, scientists now recognize that this is a paraphyletic group. This means that there is no way to put all unicellular eukaryotes into a clade that contains a single common ancestor, all of its descendants, and only those descendants. Since only monophyletic groups are valid under evolutionary classification, we use quotations to show that this is not a true clade. A summary of the three-domain system is shown in the following table:

What are the six kingdoms of life as they are now identified?
 

REVIEW & DO NOW Answer the following questions:
How were plants and animals distinguished in Linnaeus' time? How were all micro organisms originally classified? What organisms were placed in the kingdom Monera? What are the six currently recognized kingdoms of life? Give an example of one organism in each kingdom.	What is a domain? How do prokaryotes compare to eukaryotes?  What are the major differences between them? What are the three domains of life? List the kingdoms in each domain. Are the protista a paraphyletic or monophyletic group? Explain your answer.

The Tree of All Life
What does the tree of life show?

Remember that modern evolutionary classification is a rapidly changing science with a difficult goal—to present all life on a single evolutionary tree. As evolutionary biologists study relationships among taxa, they regularly change not only the way organisms are grouped, but also sometimes the names of groups. Remember that cladograms are visual presentations of hypotheses about relationships, and not hard and fast facts.

• The tree of life shows current hypotheses regarding evolutionary relationships among the taxa within the three domains of life.

Domain Bacteria Members of the domain Bacteria are unicellular, microscopic, and prokaryotic. Their cells have thick, rigid walls that surround a cell membrane. The cell walls contain a substance known as peptidoglycan. These bacteria are ecologically diverse, ranging from free- living soil organisms to deadly parasites. Some photosynthesize, while others do not. Some need oxygen to survive, while others are killed by oxygen. This domain corresponds to the kingdom Eubacteria.

A scanning electron micrograph of Salmonella typhimurium invading human epithelial cells.

Domain Archaea Also unicellular, microscopic, and prokaryotic, members of the domain Archaea live in some of the most extreme environments you can imagine—in volcanic hot springs, brine pools, and black organic mud totally devoid of oxygen. Indeed, many of these bacteria can survive only in the absence of oxygen. Their cell walls lack peptidoglycan, and their cell membranes contain unusual lipids that are not found in any other organism. The domain Archaea corresponds to the kingdom Archaebacteria.

Sulfolobus. This member of the domain Archaea is found in hot springs and thrives in in acidic and sulfur-rich environments.

Domain Eukarya

The domain Eukarya consists of all organisms that have a nucleus. It comprises the four remaining major groups of the six-kingdom system: “Protista,” Fungi, Plantae, and Animalia.

The “Protists”: Unicellular Eukaryotes

Recall that we are using quotations with this group to indicate that it is a paraphyletic group. Although some people still use the name “protists” to refer to these organisms, scientists who work with them have known for years that they do not form a valid clade. The Tree of Life, shown below, reflects current cladistic analysis, which divides these organisms into at least five clades. The positions of these groups on the cladogram reflect its paraphyletic nature.

Protists, like the Giardia (seen above and at left), can live just about anywhere.  The Giardia is a parasitic freshwater ciliate that can infect the human intestine. Each group of “the eukaryotes formerly known as protists” is separate, and each shares closest common ancestors with other groups, rather than with each other. Most are unicellular, but one group, the brown algae, is multicellular. Some are photosynthetic, while others are heterotrophic. Some display characters that most closely resemble those of plants, fungi, or animals.

Fungi

Members of the kingdom Fungi are heterotrophs with cell walls containing chitin. Most feed on dead or decaying organic matter. Unlike other heterotrophs, fungi secrete digestive enzymes into their food source. After the digestive enzymes have broken down the food into smaller molecules, fungi absorb their food into their bodies.  Mushrooms and other recognizable fungi are multicellular. Some fungi—yeasts, for example—are unicellular.

Apricot Jelly Fungus

Plantae
Members of the kingdom Plantae are autotrophs with cell walls that contain cellulose. Autotrophic plants are able to carry on photosynthesis using chlorophyll. Plants are nonmotile—they cannot move from place to place. In this book, we follow the lead of the most current cladistic analysis, making the entire plant kingdom a sister group to the red algae, which are “protists.” The plant kingdom, therefore, includes the green algae, along with mosses, ferns, cone-bearing plants, and flowering plants.
 

Plants and Animals Depend Upon One Another. Plants, which are autotrophs, provide food for animals, which are all heterotrophs, like this brown squirrel, who will then spread the seeds of the plants it eats.  This is a symbiotic relationship that has developed over millions of years, and upon which both depend.

Animalia
Members of the kingdom Animalia are multicellular and heterotrophic. Animal cells do not have cell walls. Most animals can move about, at least for some part of their life cycle. As you will see in later chapters, there is incredible diversity within the animal kingdom, and many species of animals exist in nearly every part of the planet.

What does the tree of life show?
 

REVIEW & DO NOW Answer the following questions:
Name the two prokaryotic domains and give three characteristics they both have in common. How do their cell walls differ? What makes each domain unique?	What are the three eukaryotic kingdoms? List three characteristics of each that are unique to that kingdom. Name one specific organism from each kingdom.