What you’ll learn to do: Describe classification and organizational tools biologists use, including modern taxonomy

Photo depicts Earth from space.

Figure 1. Our planet

Viewed from space, Earth offers no clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today.

When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions. In this outcome, we will discuss taxonomy, which both demonstrates the vast diversity of life and tries to organize these organisms in a way we can understand.

Learning Outcomes

  • Explain the diversity of life
  • Explain the purpose of phylogenetic trees
  • Explain how relationships are indicated by the binomial naming system

The Diversity of Life

A photo collage of a tiger, a lizard, mushrooms, a fish, an ant, trees, a parrot, pine needles, and a flower.

Figure 2. Life on earth is incredibly diverse.

Biological diversity is the variety of life on earth. This includes all the different plants, animals, and microorganisms; the genes they contain; and the ecosystems they form on land and in water. Biological diversity is constantly changing. It is increased by new genetic variation and reduced by extinction and habitat degradation.

What Is Biodiversity?

Biodiversity refers to the variety of life and its processes, including the variety of living organisms, the genetic differences among them, and the communities and ecosystems in which they occur. Scientists have identified about 1.9 million species alive today. They are divided into the six kingdoms of life shown in Figure 3. Scientists are still discovering new species. Thus, they do not know for sure how many species really exist today. Most estimates range from 5 to 30 million species.

Three pie charts showing the diversity of life. The first shows the known species of organisms. The total equals roughly one million eight hundred thousand species. Animals take up approximately 72 percent of the chart, plants 17, fungi 6, protists 4, and eubacteria 1. The second chart shows the know species of animals. The total equals roughly on millions three hundred fifteen thousand and three hundred seventy eight. Invertebrates total one million two hundred fifty-six thousand and eight hundred eighty (about 95 percent) and vertebrates total fifty-eight thousand and four hundred ninety-eight (about 5 percent). Invertebrates include insects, arachnids, nematode worms, annelid worms, mollusks, flatworms, cnidarians, sponges, echinoderms, and crustaceans. Vertebrates include fish, amphibians, reptiles, birds, and mammals. The third chart shows the known species of plants. The total equals about 287,655 species. Flowering plants dicots equal about 68.5 percent, flowering plants monocots equal 21, mosses 5, ferns 5, and conifers .5.

Figure 3. Known life on earth. Click for a larger image.

Video Review

Watch this discussion about biodiversity:

Literally, the word biodiversity means the many different kinds (diversity) of life (bio-), or the number of species in a particular area.

Diagram of many different deer around a river labeled Genetic Diversity, many different plants, animals, fish, bugs around a forest labeled Species Diversity, many differently ecosystems (ie.e Grassland, Rocky Mountains, Boreal Forest) and everything they contain with mountains and streams labeled Ecosystem Diversity.Biologists, however, are always alert to levels of organization, and have identified three unique measures of life’s variation:

  • The most precise and specific measure of biodiversity is genetic diversity or genetic variation within a species. This measure of diversity looks at differences among individuals within a population, or at difference across different populations of the same species.
  • The level just broader is species diversity, which best fits the literal translation of biodiversity: the number of different species in a particular ecosystem or on Earth. This type of diversity simply looks at an area and reports what can be found there.
  • At the broadest most encompassing level, we have ecosystem diversity. As Leopold clearly understood, the “cogs and wheels” include not only life but also the land, sea, and air that support life. In ecosystem diversity, biologists look at the many types of functional units formed by living communities interacting with their environments.

Although all three levels of diversity are important, the term biodiversity usually refers to species diversity!

Scale of Biodiversity

Diversity may be measured at different scales. These are three indices used by ecologists:

  • Alpha diversity refers to diversity within a particular area, community or ecosystem, and is measured by counting the number of taxa within the ecosystem (usually species).
  • Beta diversity is species diversity between ecosystems; this involves comparing the number of taxa that are unique to each of the ecosystems.
  • Gamma diversity is a measurement of the overall diversity for different ecosystems within a region.

Benefits of Biodiversity

Biodiversity provides us with all of our food. It also provides for many medicines and industrial products, and it has great potential for developing new and improved products for the future. Perhaps most importantly, biological diversity provides and maintains a wide array of ecological “services.” These include provision of clean air and water, soil, food and shelter. The quality—and the continuation— of our life and our economy is dependent on these “services.”

Australia’s Biological Diversity

The echidna is a small brown spiney animal. Its spines all face away from the animal’s head, and it has a narrow beak.

Figure 4. The short-beaked echidna is endemic to Australia. This animal—along with the platypus and three other species of  echidnas—is one of the five surviving species of egg-laying mammals.

The long isolation of Australia over much of the last 50 million years and its northward movement have led to the evolution of a distinct biota. Significant features of Australia’s biological diversity include:

  • A high percentage of endemic species (that is, they occur nowhere else):
    • over 80% of flowering plants
    • over 80% of land mammals
    • 88% of reptiles
    • 45% of birds
    • 92% of frogs
  • Wildlife groups of great richness. Australia has an exceptional diversity of lizards in the arid zone, many ground orchids, and a total invertebrate fauna estimated at 200,000 species with more than 4,000 different species of ants alone. Marsupials and monotremes collectively account for about 56% of native terrestrial mammals in Australia.
  • Wildlife of major evolutionary importance. For example, Australia has 12 of the 19 known families of primitive flowering plants, two of which occur nowhere else. Some species, such as the Queensland lungfish and peripatus, have remained relatively unchanged for hundreds of millions of years.

Phylogenetic Trees

In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of one organism to others—such as which organisms it is thought to have evolved from, which species it is most closely related to, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.

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 5).

A rooted phylogenetic tree 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.

Figure 5. This phylogenetic tree was constructed by microbiologist Carl Woese (See inset below) using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes. (credit: modification of work by Eric Gaba)

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 minuscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species (Figure 6).

An unrooted phylogenetic tree. 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 6. An unrooted phylogenetic tree

Carl Woese and the Phylogenetic Tree

In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic groups of microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure 5). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).

Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure 7). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.

Photo depict: A: bacterial cells. Photo depict: B: a natural hot vent. Photo depict: C: a sunflower. Photo depict: D: a lion.

Figure 7. These organisms represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski)


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.

In the eighteenth century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are: species, genus, family, order, class, phylum, kingdom, domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on (Figure 8).

An eight-level structure illustrating the taxonomic hierarchy of the domestic dog. Each level is followed examples of organisms included within the level—note that with the exception of the species, all organisms listed are examples, and the levels include multiple organisms that are not listed as well. The first level is the species: canis lupus, commonly called the domestic dog. The second level is the genus canis, which includes all domestic and wild dogs, wolves, and jackals. The third level is the family candidate, which includes all dogs and dog-like animals (like foxes). Level four is the order carnivora, which includes all animals that only eat flesh (carnivores, like lions). The fifth level is the class mammal, which includes all animals that produce milk to feed their young; this level includes all animals from previous levels, as well as whales and human beings. The sixth level is the phylum chordata, which includes all animals that have a backbone. This level includes animals from previous levels, as well as snakes. The seventh level is the kingdom animalia, which includes all animals. This level includes animals from previous levels, as well as earthworms. The eighth level is the domain eukarya, which includes all organisms whose cells have a nucleus and organelles. This level includes animals from previous levels, as well as trees, mushrooms, and some single-celled organisms.

Figure 8. This diagram shows the levels of taxonomic hierarchy for a dog, from the broadest category—domain—to the most specific—species. Click for a larger image.

The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in Figure 8. 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. Each species has a unique binomial nomenclature to allow for proper identification.

Therefore, the scientific name of the dog is Canis lupus.

It is important that the correct formatting (capitalization and italics) is used when calling an organism by its specific binomial.

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.

Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.