CONCEPTS IN BIOLOGY

PART V. THE ORIGIN AND CLASSIFICATION OF LIFE

20. The Classification and Evolution of Organisms

Taxonomists Needed

Taxonomists are important in medical discoveries

Many scientists are concerned that there is a lack of scientific specialists who identify and classify living things. Although this may seem like a skill with limited value to the general public, it is extremely important to medicine and many other aspects of our modern society. Many of our medicines were originally discovered in other living organisms. Digitalis, which is used to stimulate the heart, comes from the foxglove plant. Chemicals in marijuana are used to treat nausea. Many kinds of antibiotics are derived from fungi. Taxol, which is used to treat ovarian and other forms of cancer, is an extract from the bark of the Pacific yew, Taxus brevifolia (see photo) which has a rather limited distribution along the northwest coast of the United States.

Proper identification of organisms is important because the beneficial chemical may be found in only one species within a group of closely related species that basically all look alike to the general public. Initially taxol was produced by harvesting Pacific yews and extracting taxol from the bark. This was not sustainable and an alternative source of the drug was sought. It was logical to look at closely related but more common species of yews to see if they also produced the drug. Eventually, it was discovered that the common yew, Taxus baccata, which is widely grown throughout the world as an ornamental, produced a compound similar to taxol that could be modified to produce taxol. This discovery greatly increased the source of supply for this valuable drug and protected the Pacific yew from overharvesting. Subsequently, a cell culture method was developed that allows for the production of the drug without harvesting trees.

• Why is precise identification of organisms important?

• What tools do taxonomists use to classify organisms?

• Should governments subsidize the education of taxonomists?

ü  Background Check

Concepts you should already know to get the most out of this chapter:

• The processes of natural selection and evolution (chapter 13)

• Prokaryotic organisms have a simpler cellular structure than eukaryotic organisms (chapter 4)

20.1. The Classification of Organisms

In order to talk about items in our world, we must have names for them. As new items come into being or are discovered, we devise new words to describe them. For example, the words laptop, palm pilot, and text message describe technology that did not exist 30 years ago. Similarly, in the biological world, people have given names to newly discovered organisms so they can communicate to others about the organism.

The Problem with Common Names

The common names people use vary from culture to culture. For example, dog in English is chien in French, perro in Spanish, and cane in Italian. Often different names are used in different regions within a country to identify the same organism. For example, the common garter snake is called a garden snake or gardner snake, depending on where you live (figure 20.1). Actually, there are several species of garter snakes that have been identified as distinct from one another. Thus, common names can be confusing, so scientists sought a more acceptable way to name organisms, one that all scientists would use that would eliminate confusion.

FIGURE 20.1. Names for the Common Garter Snake

Depending on where you live, you may call this organism a garter snake, a garden snake, or a gardner snake. These common names can lead to confusion. However, the scientific name (Thamnophis sirtalis) is recognized worldwide by the scientific community.

The naming of organisms is a technical process, but it is extremely important. When biologists are describing their research, common names, such as robin or maple tree, or garter snake are not good enough. They must be able to identify the organisms involved accurately, so that everyone who reads the report, wherever they live in the world, knows what organism is being discussed. The scientific identification of organisms involves two different but related activities. One, taxonomy, is the naming of organisms; the other, phylogeny, involves showing how organisms are related evolutionarily. In reality, no taxonomic decisions are made without considering the evolutionary history of the organism.

Taxonomy

Taxonomy is the science of naming organisms and grouping them into logical categories. The root of the word taxonomy is the Greek word taxis, which means arrangement.

During the Middle Ages, Latin was widely used as the scientific language. As new species were identified, they were given Latin names, often using as many as 15 words to describe a single organism. Although using Latin meant that most biologists, regardless of their native language, could understand a species name, it did not completely do away with duplicate names. Because many of the organisms were found over wide geographic areas and communication was slow, there could still be two or more Latin names for a species. To make the situation even more confusing, ordinary people used common local names.

The Binomial System of Nomenclature

The modern system of classification began in 1758, when Carolus Linnaeus (1707-1778), a Swedish doctor and botanist, published his tenth edition of Systema Naturae (figure 20.2). (Linnaeus’s original name was Carl von Linne, which he “latinized” to Carolus Linnaeus.) In the previous editions of his book, Linnaeus had used the polynomial Latin system of classification, which required many words to identify a species. However, in the tenth edition, he introduced the binomial system of nomenclature. The binomial system of nomenclature, uses only two Latin names—the genus name and the specific epithet (epithet = descriptive word) for each species of organism. Recall that a species is a population of organisms capable of interbreeding and producing fertile offspring. Individual organisms are members of a species. A genus (plural, genera) is a group of closely related organisms. The specific epithet is a word added to the genus name to identify which one of several species within the genus is being referred to.

FIGURE 20.2. Carolus Linnaeus (1707-1778)

Carolus Linnaeus, a Swedish doctor and botanist, originated the modern system of taxonomy known as binomial nomenclature.

This is similar to the naming system we use with people. When we look in the phone book, we look for a last name (surname), the correct general category. Then, we look for a first name (given name) to identify the specific individual we wish to call. The unique name given to an organism is its species name, or scientific name. In order to clearly distinguish the scientific name from other words, binomial names are either italicized or underlined. The first letter of the genus name is capitalized. The specific epithet is always written in lowercase. For example, Thamnophis sirtalis is the binomial name for the common garter snake.

When biologists adopted Linnaeus’s binomial method, they simplified the names of organisms and eliminated the confusion of using common local names. Since the adoption of Linnaeus’s system, international rules have been established to assure that an orderly system is maintained. The three primary sets of rules are the International Rules for Botanical Nomenclature, the International Rules for Zoological Nomenclature, and the International Bacteriological Code of Nomenclature. Although approximately 1.5 million species have been named, no one knows how many species of organisms live on Earth, but most biologists estimate that several million are yet to be identified.

The Organization of Species into Logical Groups

In addition to assigning a specific name to each species, Linnaeus recognized a need for placing organisms into groups. He originally divided all organisms into two broad groups, which he called the plant and animal kingdoms, and subdivided each kingdom into smaller units. Since Linneaus’s initial attempts to place all organisms into categories, there have been many changes. One of the most fundamental is the recent recognition that there are three major categories of organisms, called domains.

Recall that a domain is the largest category into which organisms are classified, and there are three domains: Bacteria, Archaea, and Eucarya (figure 20.3). Organisms are separated into these three domains based on the specific structural and biochemical features of their cells. The Bacteria and Archaea are prokaryotic and the Eucarya are eukaryotic.

FIGURE 20.3. The Three Domains of Life

The three domains of living things are related to one another evolutionarily. The domain Bacteria is the oldest group. The domains Archaea and Eucarya are derived from the Bacteria.

A kingdom is a subdivision of a domain. There are several kingdoms within the Bacteria and Archaea based primarily on differences in the metabolism and genetic composition of the organisms. Within the domain Eucarya, there are four kingdoms: Plantae, Animalia, Fungi, and Protista (protozoa and algae) (figure 20.4).

FIGURE 20.4. Representatives of the Domain Eucarya

There are four kingdoms in the domain Eucarya, represented by the following organisms: (a) The bracket fungus Trametes versicolor, and the edible mushroom Morchella esculenta of the kingdom Fungi; (b) The protozoan Stentor and the a large alga of the kingdom Protista; (c) The moon jellyfish, and Homo sapiens of the kingdom Animalia; and (d) Ferns and the orchid Cypripedium calceolus of the kingdom Plantae.

A phylum is a subdivision of a kingdom. However, microbiologists and botanists often use the term division rather than phylum. All kingdoms have more than one phylum. For example, the kingdom Plantae contains several phyla that include flowering plants, conifer trees, mosses, ferns and several other less-common groups. Organisms are placed in phyla based on careful investigation of the specific nature of their structure, metabolism, and biochemistry. An attempt is made to identify natural groups, rather than artificial or haphazard arrangements. For example, although nearly all plants are green and carry on photosynthesis, only flowering plants have flowers and produce seeds; conifers lack flowers but have seeds in cones; ferns lack flowers, cones, and seeds; and mosses are so simple in structure that they even lack tissues for transporting water.

A class is a subdivision within a phylum. For example, within the phylum Chordata within the kingdom Animalia, there are seven classes: mammals, birds, reptiles, amphibians, and three classes of fishes.

An order is a category within a class. The order Carnivora is an order of meat-eating animals within the class Mammalia. There are other orders of mammals, including horses and their relatives, cattle and their relatives, rodents, rabbits, bats, seals, whales, humans, and many others.

A family is a subdivision of an order that consists of a group of closely related genera, which in turn are composed of groups of closely related species. Felidae is a family composed of various kinds of cats within the order Carnivora. It includes many species in several genera, including the Canada lynx and bobcat (genus Lynx); the cougar (genus Puma); the leopard, tiger, jaguar, and lion (genus Panthera); the house cat (genus Felis); and several other genera. Thus, in the present-day science of taxonomy, each organism that has been classified has a unique binomial name. In turn, it is assigned to larger groupings that are thought to have a common evolutionary history. Table 20.1 classifies humans to show how the various categories are used.

TABLE 20.1. Classification of Humans

Phylogeny

Phylogeny is the science that explores the evolutionary relationships among organisms, seeking to reconstruct evolutionary history. Taxonomists and phylogenists work together, so that the products of their work are compatible. A taxonomic ranking should reflect the phylogenetic (evolutionary) relationships among the organisms being classified. New organisms and new information about organisms are discovered constantly. Therefore, taxonomic and phylogenetic relationships are constantly being revised. During this revision process, scientists often have differences of opinion about the significance of new information.

The Evidence Used to Establish Phylogenetic Relationships

Phylogenists use several lines of evidence to develop evolutionary histories: fossils, comparative anatomy, life cycle information, and biochemical and molecular evidence.

1. Fossils are physical evidence of previously existing life. There are several forms of fossils. Some fossils are preserved whole and relatively undamaged. For example, mammoths and humans have been found frozen in glaciers, and bacteria and insects have been preserved after becoming embedded in plant resins. Other fossils are only parts of once living organisms. The outlines or shapes of extinct plant leaves are often found in coal deposits, and individual animal bones that have been chemically altered over time are often dug up. Animal tracks have also been discovered in the dried mud of ancient riverbeds (figure 20.5).

FIGURE 20.5. Fossil Evidence

A fossil is any evidence of previously existing life. Fossils can be the intact, preserved remains of organisms, as in (a) the remains of an ancient fly preserved in amber or the preserved parts of an organism, as in (b) the fossilized skeleton and body outline of a bony fish. It is even possible to have evidence of previously existing living things that are not the remains of organisms, as in (c) a dinosaur footprint.

When looking for fossils it is important to understand how various kinds of rocks were formed. Sedimentary rocks are formed by the depositing of eroded particles in layers on the bottom of an ocean, lake, or river. Sedimentary rock is not subject to high temperatures and is usually relatively undisturbed. Thus, sedimentary rock can contain evidence of organisms that were covered by sediments and modified into fossils. Igneous rocks are formed from molten material that cooled and solidified. Metamorphic rocks are formed when a previously existing rock (igneous, metamorphic, or sedimentary) is subjected to high temperature and pressure, causing the form of the rock to change. Thus, fossils are not found in igneous or metamorphic rock.

It is important to understand that some organisms are more easily fossilized than others. Those that have hard parts, such as cell walls, skeletons, and shells, are more likely to be preserved than are tiny, soft-bodied organisms. Aquatic organisms are more likely to be buried in the sediments at the bottom of the oceans or lakes than are their terrestrial counterparts. Later, when sedimentary rock is pushed up by geologic forces, aquatic fossils are found in layers of sediments on dry land.

Evidence obtained from the discovery and study of fossils allows biologists to place organisms in a time sequence. This can be accomplished by comparing the sedimentary layers in which a fossil is found. As geologic time passes and new layers of sediment are laid down, the older organisms should be in deeper layers, assuming that the sequence of layers has not been disturbed (figure 20.6). In addition, it is possible to age-date certain kinds of rocks by comparing the amounts of certain radioactive isotopes they contain. Older rocks have less of these specific radioactive isotopes than do younger rocks. Fossils associated with rocks of a known age are usually of a similar age to the rocks.

FIGURE 20.6. Rock Layers and the Age of Fossils

Because new layers of sedimentary rock are formed on top of older layers of sedimentary rock, it is possible to determine the relative ages of fossils found in various layers. The layers of rock shown here represent millions of years of formation. The fossils of the lower layers are millions of years older than the fossils in the upper layers.

It is also possible to compare subtle changes in particular kinds of fossils over time. For example, in studies of a certain kind of fossil plant, the size of the leaf changed extensively through long geologic periods. If one only looked at the two extremes, they would be classified into different categories. However, because there are fossil links that show intermediate stages between the extremes, scientists conclude that the younger plant is a descendant of the older.

2. Comparative anatomy studies of fossils or currently living organisms can be very useful in developing a phylogeny. Because the structures of an organism are determined by its genes, organisms having similar structures are thought to be related. For example, plants can be divided into several categories: All plants that have flowers are thought to be more closely related to one another than they are to plants that do not have flowers, such as ferns. In the animal kingdom, all organisms that have hair and mammary glands are grouped together, and all animals in the bird category have feathers, wings, and beaks.

3. Life cycle information is another line of evidence useful to phylogenists and taxonomists. Many organisms have complex life cycles, which include many completely different stages. After fertilization, some kinds of organisms grow into free-living developmental stages that do not resemble the adults of their species. These are called larvae (singular, larva). Larval stages often provide clues to the relatedness of organisms. For example, adult barnacles live attached to rocks and other solid marine objects and look like small, hard cones. Their outward appearance does not suggest that they are related to shrimp; however, the larval stages of barnacles and shrimp are very similar. Detailed anatomical studies of mature barnacles confirm that they share many structures with shrimp, such as legs and an external skeleton; their outward appearance tends to be misleading (figure 20.7).

FIGURE 20.7. Developmental Stages and Phylogeny

The adult barnacle (a) and shrimp (b) are very different from each other, but their early larval stages (c and d) look very much alike.

Both birds and reptiles lay eggs with shells. However, reptiles lack feathers and have scales covering their bodies. The fact that these two groups share this fundamental eggshell characteristic implies that they are more closely related to each other than they are to other groups, but they can be divided into two groups based on their anatomical differences.

This kind of evidence also applies to the plant kingdom. Many kinds of plants, such as peas, peanuts, and lima beans, produce large, two-parted seeds in pods. Even though peas grow as vines, lima beans grow as bushes, and peanuts have their seeds underground, all these plants are considered to be related.

4. Biochemical and molecular studies are recent additions to the toolbox of phylogenists. Like all aspects of biology, the science of phylogeny is constantly changing as new techniques develop. Recent advances in DNA analysis are being used to determine genetic similarities among species. In the field of ornithology, the study of birds, there are those who believe that storks and flamingos are closely related; others believe that flamingos are more closely related to geese. An analysis of the DNA points to a closer evolutionary relationship between flamingos and storks than between flamingos and geese.

There are five kinds of chlorophyll found in algae and plants: chlorophyll a, b, c, d, and e. Most photosynthetic organisms contain a combination of two of these chlorophyll molecules. Members of the kingdom Plantae have chlorophyll a and b. The large seaweeds, such as kelp, superficially resemble terrestrial plants, such as trees and shrubs. However, a comparison of their chlorophylls shows that kelp has chlorophyll a and d. Another group of algae, called the green algae, has chlorophyll a and b. Along with other anatomical and developmental evidence, this biochemical information has helped establish an evolutionary link between the green algae and plants. All the kinds of evidence (fossils, comparative anatomy, life cycle information, and biochemical evidence) have been used to develop phylogenetic relationships and taxonomic categories.

A Current Phylogenetic Tree

Given all the sources of evidence, biologists have developed a picture of how they think all organisms are related (figure 20.8). The three domains—Bacteria, Archaea, and Eucarya—diverged early in the history of life. Subsequently, many new kinds of organisms have evolved. It is important to remember that this diagram is a work in progress. As new information is discovered, there will be changes in the way biologists think organisms are related (How Science Works 20.1). Biologists have also developed new techniques that help in determining phylogenies. One such technique is cladistics (How Science Works 20.2).

FIGURE 20.8. A Phylogeny of Life

This diagram shows current thinking about how various kinds of organisms are related to one another phylogenetically. The first living cells probably came into being as a result of chemical evolution. The oldest fossils appear to be similar to the members of the domain Bacteria. Comparisons of DNA and cell structures supports the idea that the Archaea are derived from Bacteria. Some prokaryotic cells probably gave rise to eukaryotic cells through the process of endosymbiosis. The organisms formed from these early eukaryotic cells were probably similar to single-celled members of present-day algae and protozoa. Each of the kingdoms Animalia, Plantae, and Fungi appears to be a valid phylogenetic unit and each appears to have originated separately from single-celled ancestors.

HOW SCIENCE WORKS 20.1

New Information Causes Changes in Taxonomy and Phylogeny

The taxonomy and phylogeny of groups of organisms are constantly changing as new information and new tools become available. In his initial classification of organisms, Linnaeus identified two kingdoms—the plant and animal kingdoms. Plants included all kinds of organisms that were not motile and had cell walls. Animals lacked cell walls and moved. Several major scientific and technical developments over the intervening years allowed for a better understanding of the nature of organisms and how they are related. These developments led to changes in taxonomy:

• Advances in the development of microscopes that could look at the smallest of cells made it clear that some of the smallest organisms previously called bacteria and classified as plants, lacked a nucleus. They were, therefore, reclassified into a separate kingdom, Monera.

• A better understanding of the chemical nature of cell walls led to the discovery that a major group of "plants" had cell walls containing chitin and did not have cellulose. Those with chitin in their cell walls were reclassified into the kingdom Fungi.

• Based on the cellular specialization of organisms, multicellular plants and animals that have specialized groups of cells were separated from protozoa and algae that do not have specialized groups of cells. The protozoa and algae were placed in a separate kingdom, Protista.

• Studies of the structure of DNA and ribosomes led to the development of an entirely new way of looking at living things. A new category—domain—was established above the kingdom level. The prokaryotic organisms, "bacteria," which had formerly been in the kingdom Monera, were divided into two major groups, the domains Bacteria and Archaea, and all the remaining kinds of living things that were eukaryotic were placed in the domain Eucarya.

• Although most people agree that kingdoms Plantae and Animalia are valid collections of organisms with a common ancestry, most people recognize that the kingdom Protista is not a valid phylogenetic unit. In the future, this group of organisms will be divided into distinct categories that will be more phylogenetically meaningful.

• The kingdom Fungi will probably undergo some revision. Some organisms are likely to be moved to other kingdoms or placed in an entirely new kingdom.

• The recognition that endosymbiosis occurs and that many organisms of widely different evolutionary backgrounds have shared genes has further complicated the science of taxonomy.

• Stay tuned.

Changes in Taxonomy with Increase in Knowledge

HOW SCIENCE WORKS 20.2

Cladistics: A Tool for Taxonomy and Phylogeny

Classification, or taxonomy, is one part of the much larger field of phylogenetic systematics. Classification involves placing organisms into logical categories and assigning names to those categories. Phylogeny, or systematics, is an effort to understand the evolutionary relationships of living things in order to interpret the way in which life has diversified and changed over billions of years of biological history. Phylogeny attempts to understand how organisms have changed over time. Cladistics (klados = branch) is a method biologists use to evaluate the degree of relatedness among organisms within a group, based on how similar they are genetically. The basic assumptions behind cladistics are that

1. Groups of organisms are related by descent from a common ancestor.

2. The relationships among groups can be represented by a branching pattern, with new evolutionary groups arising from a common ancestor.

3. Changes in characteristics occur in organisms over time.

Several steps are involved in applying cladistics to a particular group of organisms. First, you must select characteristics that vary and collect information on the characteristics displayed by the group of organisms you are studying. The second step is to determine which expression of a characteristic is ancestral and which is more recently derived. Usually, this involves comparing the group in which you are interested with an outgroup that is related to, but not a part of, the group you are studying. The characteristics of the outgroup are then considered to be ancestral. Finally, you must compare the characteristics displayed by the group you are studying and construct a diagram known as a cladogram. For example, if you were interested in studying how various kinds of terrestrial vertebrates are related, you could look at the following characteristics:

In this example, the shark is the outgroup, and the ancestral conditions are lungs absent, skin not dry, cold-blooded, and hair absent. Using this information, you could construct the following cladogram.

All of the organisms, except sharks, have lungs. Lizards, crows, and bats have dry skin, as well as lungs and so on. Crows and bats share the following characteristics; they have lungs, they have dry skin, and they are warm-blooded. Because they share more characteristics with each other than with the other groups, they are considered to be more closely related.

It is important to recognize that cladistics is a tool and, like any tool, it can be used appropriately or inappropriately. The choice of the outgroup and the characteristics chosen to be evaluated are important to the validity of the process. If a person mistakenly used a whale as the outgroup, they would come to completely different conclusions about how the various kinds of terrestrial vertebrates are related.

It is also important to carefully select the characteristics to be used in making the comparison. Two organisms may share many characteristics but not be members of the same evolutionary group if the characteristics being compared are not from the same genetic background. For example, if you were to compare butterflies, birds, and squirrels using the presence or absence of wings and the presence or absence of bright colors as your characteristics, you would conclude that butterflies and birds are more closely related than birds and squirrels. However, this is not a valid comparison, because the wings of birds and butterflies are not of the same evolutionary origin.

20.1. CONCEPT REVIEW

1. List two ways that scientific names are different from common names for organisms.

2. Who designed the present-day system of classification? How does this system differ from the previous system?

3. What are the goals of taxonomy and phylogeny?

4. Name the categories of the classification system.

5. Describe four kinds of evidence scientists use to place organisms into a logical phylogeny.