Part IX Viruses and simple Organisms Electron micrograph of hepatitis virus. for Hepatitis c virus Responsible Discovering the Vi biotechnology company. What they did was shotgun clone the dna of infected cells. and then screen for hcv The genetic material of HCv, like that of many other You may not be aware that our country is in the midst of vIruses, is RNA. So the first step was to convert HCV RNA an epidemic of this potentially fatal liver disease. Almost to DNA, so that it could be cloned. There was no need to 4 million Americans are infected with the hepatitis C attempt to ach attempt to achieve entire faithful copies, a touchy and diffi- virus, most of them without knowing it. Some 9000 peo cult task, because they did not wish to replicate HCV, only ple will die this year in the United States from liver can identify it. So the researchers took the far easier route of cer and chronic liver failure brought on by the virus, and copying the virus RNa as a series of segments, each carry the number is expected to triple in the next decade. In g some part of the virus genome the first years of the new century, the number of annual Next, they inserted these DNA copies of HCV genes U.S. deaths caused by hepatitis C is predicted to overtake into a bacteriophage, and allowed the bacteriophage to in deaths caused by aIds fect Escherichia coli bacteria. In such a"shotgun"experi ment. millions of bacterial cells are infected with bacterio- epatitis is inflammation of the liver. Researchers in the phages. The researchers grew individual infected cells to 1940s identified two distinct forms. One. called infectious hepatitis or hepatitis A, is transmitted by contact with feces form discrete colonies on plates of solid culture media. The from infected individuals. A second form of hepatitis, called colonies together constituted a"cl serum hepatitis or hepatitis B, is passed only through the blood. Hepatitis B virus was isolated in the mid-1960s, he- essfully received HCV patitis A virus a decade later. This led in the 1970s to the o understand how they did this, focus on the quarry, a development of tests for the two viruses. Disturbingly, a cell infected with an HCV gene. Once inside a bacterial substantial proportion of hepatitis cases did not appear to cell, an HCv gene fragment becomes just so much more Clearly another virus was at work. At first, investigators lular machinery of the bacteria reads it just like bacterial thought it wouldn 't be long before it was isolated. How- genes, manufacturing the virus protein that the inserted ever. it was not until 1990 that researchers succeeded i HCV gene encodes. The secret is to look for cells with isolating the virus responsible for these"non-A, non-B HCV proteins cases, a virus that we now call hepatitis C virus(HCv). How to identify an HCV protein from among a back HCV was difficult to isolate because it cannot be grown ground of thousands of bacterial proteins? Houghton and reliably in a laboratory culture of cells. Making the prob- his colleagues tested each colony for its ability to cause a lem even more difficult, HCV is a strictly primate virus. It visible immune reaction with serum isolated from HCV infects only humans and our close relatives-chimpanzees infected chimpanzees and tamarins. Because it is very expensive to maintain The test is a very simple and powerful one, because its these animals in research laboratories, only small numbers success does not depend on knowing the identity of the of animals can be employed in any one study. Thus, the genes you seek. The serum of HCV-infected animals con- virus could not be isolated by the traditional means of pu- tains antibodies directed against a broad range of HCV rification from extracts of infected cells. What finally suc proteins encountered while combating the animals HCV ceeded, after 15 years of failed attempts at isolation, was infection. The serum can thus be used as a probe for the molecular technology. HCV was the first virus isolated en- presence of HCv proteins in other cells tirely by cloning the infectious nucleic acid Out of a million bacterial clones tested, just one was The successful experiment was carried out by Michael found that reacted with the chimp HCV serum, but not Houghton and fellow researchers at Chiron, a California with serum from the same chimp before infection. 647
647 Discovering the Virus Responsible for Hepatitis C You may not be aware that our country is in the midst of an epidemic of this potentially fatal liver disease. Almost 4 million Americans are infected with the hepatitis C virus, most of them without knowing it. Some 9000 people will die this year in the United States from liver cancer and chronic liver failure brought on by the virus, and the number is expected to triple in the next decade. In the first years of the new century, the number of annual U.S. deaths caused by hepatitis C is predicted to overtake deaths caused by AIDS. Hepatitis is inflammation of the liver. Researchers in the 1940s identified two distinct forms. One, called infectious hepatitis or hepatitis A, is transmitted by contact with feces from infected individuals. A second form of hepatitis, called serum hepatitis or hepatitis B, is passed only through the blood. Hepatitis B virus was isolated in the mid-1960s, hepatitis A virus a decade later. This led in the 1970s to the development of tests for the two viruses. Disturbingly, a substantial proportion of hepatitis cases did not appear to be caused by either of these two viruses. Clearly another virus was at work. At first, investigators thought it wouldn't be long before it was isolated. However, it was not until 1990 that researchers succeeded in isolating the virus responsible for these "non-A, non-B" cases, a virus that we now call hepatitis C virus (HCV). HCV was difficult to isolate because it cannot be grown reliably in a laboratory culture of cells. Making the problem even more difficult, HCV is a strictly primate virus. It infects only humans and our close relatives—chimpanzees and tamarins. Because it is very expensive to maintain these animals in research laboratories, only small numbers of animals can be employed in any one study. Thus, the virus could not be isolated by the traditional means of purification from extracts of infected cells. What finally succeeded, after 15 years of failed attempts at isolation, was molecular technology. HCV was the first virus isolated entirely by cloning the infectious nucleic acid. The successful experiment was carried out by Michael Houghton and fellow researchers at Chiron, a California biotechnology company. What they did was shotgun clone the DNA of infected cells, and then screen for HCV. The genetic material of HCV, like that of many other viruses, is RNA. So the first step was to convert HCV RNA to DNA, so that it could be cloned. There was no need to attempt to achieve entire faithful copies, a touchy and difficult task, because they did not wish to replicate HCV, only identify it. So the researchers took the far easier route of copying the virus RNA as a series of segments, each carrying some part of the virus genome. Next, they inserted these DNA copies of HCV genes into a bacteriophage, and allowed the bacteriophage to infect Escherichia coli bacteria. In such a "shotgun" experiment, millions of bacterial cells are infected with bacteriophages. The researchers grew individual infected cells to form discrete colonies on plates of solid culture media. The colonies together constituted a "clone library." The problem then is to screen the library for colonies that had successfully received HCV. To understand how they did this, focus on the quarry, a cell infected with an HCV gene. Once inside a bacterial cell, an HCV gene fragment becomes just so much more DNA, not particularly different from all the rest. The cellular machinery of the bacteria reads it just like bacterial genes, manufacturing the virus protein that the inserted HCV gene encodes. The secret is to look for cells with HCV proteins. How to identify an HCV protein from among a background of thousands of bacterial proteins? Houghton and his colleagues tested each colony for its ability to cause a visible immune reaction with serum isolated from HCVinfected chimpanzees. The test is a very simple and powerful one, because its success does not depend on knowing the identity of the genes you seek. The serum of HCV-infected animals contains antibodies directed against a broad range of HCV proteins encountered while combating the animal's HCV infection. The serum can thus be used as a probe for the presence of HCV proteins in other cells. Out of a million bacterial clones tested, just one was found that reacted with the chimp HCV serum, but not with serum from the same chimp before infection. Part IX Viruses and Simple Organisms Electron micrograph of hepatitis C virus
How the hepatitis C virus was discovered. Michael Houghton and fellow researchers identified the virus responsible for hepatitis C by making DNA copies of RNA from the cells of infected chimpanzees. They then cloned this DNA, using bacteriophages to carry it into bacterial cells. Colonies of the bacteria were then tested with serum from infected chimps. Any colony that produced an immune reaction would have to contain the virus Using this clone as a toehold the researchers were able Why not move vigorously to produce a vaccine directed to go back and fish out the rest of the virus genome from against hepatitis C? This turns out to be particularly difficult infected cells. From the virus genome, it was a straightfor- for this virus, because antibodies directed against it appear to ward matter to develop a diagnostic antibody test for the be largely ineffective. Those few individuals who do succeed presence of the HCV virus in clearing the virus from their bodies gain no immunity to Using the diagnostic test, researchers found hepatitis C subsequent infection. They produce antibodies directed to be far more common than had been supposed. This is a against the virus, but the antibodies don, t protect them. It ap- problem of major proportions, because hepatitis C virus is pears that hepatitis C virus evades our antibody defenses by unlike hepatitis A or B in a very important respect: it causes high mutation rates, just as the AIDS virus does. By the time chronic disease. Most viruses cause a brief, intense infec- antibodies are being produced against one version of the tion and then are done. Hepatitis A, for example, typically virus, some of the viruses have already mutated to a different lasts a few weeks. Ninety percent of people with hepatitis C form that the antibody does not recognize. Like chasing a ave it for years, many of them for decades burglar who is constantly changing his disguise, the antibod- All during these long years of infection, damage is being ies never learn to recognize the newest version of the virus done to the liver. Cells of the immune system called cyto- To date, attempts to develop a drug to combat hepatitis toxic T cells recognize hepatitis C virus proteins on the C virus focus on the virus itself. This virus carries just one surface of liver cells. and kill the infected cells. Over the gene, a very big one. When it infects liver cells, this gene years, many dead liver cells accumulate, and in response is translated into a single immense"polyprotein. "Enzyme the cells around them begin to secrete collagen and other then cut the polyprotein into 10 functional pieces. Each proteins to cover the mess. This eventually produces pro- piece plays a key role in building new viruses in infected tein fibers interlacing the liver, fibers which disrupt the liver cells. Some of these proteins form parts of the virus flow of materials through the liver's many internal pas- body, others are enzymes needed to replicate the virus sages. Imagine dropping bricks and rubble on a highway- gene. As you might expect, each of these 10 proteins is it gets more and more difficult for traffic to move as the being investigated as a potential target for a drug to fight rubble accumulates the virus, although no success is reported as yet. If this fibrosis progresses far enough, it results in com- Other attempts to fight hepatitis C focus on the part of plete blockage, cirrhosis, a serious condition which may in ur immune system that attacks infected liver cells. Unlike duce fatal liver failure, and which often induces primary the ineffective antibody defense, our bodies' cytotoxic T cells liver cancer. About 20% of patients develop cirrhosis clearly are able to detect and attack cells carrying hepatitis C within 20 years of infection proteins. A vaccine that stimulates these cytotoxic T cells Luckily, hepatitis C is a very difficult virus to transmit. might eliminate all infected cells at the start of an infection Direct blood contact is the only known path of direct trans- stopping the disease in its tracks before it got started. A seri- mission. Sexual transmission does not seem likely, although ous effort is being made to develop such a vaccine the possibility is still being investigated. Married partners It doesnt look like an effective remedy is going to be of infected individuals rarely get the virus, and its incidence available anytime soon. In the meantime, as the death rates among promiscuous gay men is no higher than among the from hepatitis C exceed those for AIDs in the next few la years, we can hope research will further intensify 648 Part IX Viruses and Simple organism
648 Part IX Viruses and Simple Organisms Using this clone as a toehold, the researchers were able to go back and fish out the rest of the virus genome from infected cells. From the virus genome, it was a straightforward matter to develop a diagnostic antibody test for the presence of the HCV virus. Using the diagnostic test, researchers found hepatitis C to be far more common than had been supposed. This is a problem of major proportions, because hepatitis C virus is unlike hepatitis A or B in a very important respect: it causes chronic disease. Most viruses cause a brief, intense infection and then are done. Hepatitis A, for example, typically lasts a few weeks. Ninety percent of people with hepatitis C have it for years, many of them for decades. All during these long years of infection, damage is being done to the liver. Cells of the immune system called cytotoxic T cells recognize hepatitis C virus proteins on the surface of liver cells, and kill the infected cells. Over the years, many dead liver cells accumulate, and in response the cells around them begin to secrete collagen and other proteins to cover the mess. This eventually produces protein fibers interlacing the liver, fibers which disrupt the flow of materials through the liver's many internal passages. Imagine dropping bricks and rubble on a highway— it gets more and more difficult for traffic to move as the rubble accumulates. If this fibrosis progresses far enough, it results in complete blockage, cirrhosis, a serious condition which may induce fatal liver failure, and which often induces primary liver cancer. About 20% of patients develop cirrhosis within 20 years of infection. Luckily, hepatitis C is a very difficult virus to transmit. Direct blood contact is the only known path of direct transmission. Sexual transmission does not seem likely, although the possibility is still being investigated. Married partners of infected individuals rarely get the virus, and its incidence among promiscuous gay men is no higher than among the population at large. Why not move vigorously to produce a vaccine directed against hepatitis C? This turns out to be particularly difficult for this virus, because antibodies directed against it appear to be largely ineffective. Those few individuals who do succeed in clearing the virus from their bodies gain no immunity to subsequent infection. They produce antibodies directed against the virus, but the antibodies don't protect them. It appears that hepatitis C virus evades our antibody defenses by high mutation rates, just as the AIDS virus does. By the time antibodies are being produced against one version of the virus, some of the viruses have already mutated to a different form that the antibody does not recognize. Like chasing a burglar who is constantly changing his disguise, the antibodies never learn to recognize the newest version of the virus. To date, attempts to develop a drug to combat hepatitis C virus focus on the virus itself. This virus carries just one gene, a very big one. When it infects liver cells, this gene is translated into a single immense "polyprotein." Enzymes then cut the polyprotein into 10 functional pieces. Each piece plays a key role in building new viruses in infected liver cells. Some of these proteins form parts of the virus body, others are enzymes needed to replicate the virus gene. As you might expect, each of these 10 proteins is being investigated as a potential target for a drug to fight the virus, although no success is reported as yet. Other attempts to fight hepatitis C focus on the part of our immune system that attacks infected liver cells. Unlike the ineffective antibody defense, our bodies' cytotoxic T cells clearly are able to detect and attack cells carrying hepatitis C proteins. A vaccine that stimulates these cytotoxic T cells might eliminate all infected cells at the start of an infection, stopping the disease in its tracks before it got started. A serious effort is being made to develop such a vaccine. It doesn't look like an effective remedy is going to be available anytime soon. In the meantime, as the death rates from hepatitis C exceed those for AIDS in the next few years, we can hope research will further intensify. How the hepatitis C virus was discovered. Michael Houghton and fellow researchers identified the virus responsible for hepatitis C by making DNA copies of RNA from the cells of infected chimpanzees. They then cloned this DNA, using bacteriophages to carry it into bacterial cells. Colonies of the bacteria were then tested with serum from infected chimps. Any colony that produced an immune reaction would have to contain the virus
32 How We classify Orgo Concept Outline 32.1 Biologists name organisms in a systematic way The Classification of Organisms. Biologists name organisms using a binomial system Species Names. Every kind of organism is assigned a The Taxonomic Hierarchy. The higher groups into which an organism is placed reveal a great deal about the organism. What Is a Species? Species are groups of similar organisms that tend not to interbreed with individuals of other groups. 32.2 Scientists construct phylogenies to understand the evolutionary relationships among organisms Evolutionary Classifications. Traditional and cladistic terpretations of evolution differ in the emphasis they place on particular traits. 32.3 All living organisms are grouped into one of a few FIGURE 32.1 major categories Biological diversity. All living things are assigned to particular The Kingdoms of Life. Living organisms are grouped classifications based on characteristics such as their anatomy into three great groups called domains, and within domains development, mode of nutrition, level of organization, and biochemical n. Coral reefs. like the one seen here are Domain Archaea(Archaebacteria). The oldest domain home to a variety of living things. consists of primitive bacteria that often live in extreme environments Domain Bacteria(Eubacteria). Too small to see with ll organisms share many biological characteristics. the unaided eye, eubacteria are more numerous than any A .They are composed of one or more cells, carry out other organism. metabolism and transfer energy with ATP, and encode Domain Eukarya(Eukaryotes). There are four hereditary information in DNA. All species have evolved kingdoms of eukaryotes, three of them entirely or predominantly multicellular. Two of the most important from simpler forms and continue to evolve. Individuals live haracteristics to have evolved among the eukaryotes are in populations. These populations make up communities multicellularity and sexuality and ecosystems, which provide the overall structure of life Viruses: A Special Case. Viruses are not organisms, and on earth. So far. we have stressed these common themes hus do not belong to any kingdom considering the general principles that apply to all organ isms. Now we will consider the diversity of the biologic world and focus on the differences among groups of organ isms(figure 32. 1). For the rest of the text, we will examine the different kinds of life on earth. from bacteria and amoe- bas to blue whales and
649 32 How We Classify Organisms Concept Outline 32.1 Biologists name organisms in a systematic way. The Classification of Organisms. Biologists name organisms using a binomial system. Species Names. Every kind of organism is assigned a unique name. The Taxonomic Hierarchy. The higher groups into which an organism is placed reveal a great deal about the organism. What Is a Species? Species are groups of similar organisms that tend not to interbreed with individuals of other groups. 32.2 Scientists construct phylogenies to understand the evolutionary relationships among organisms. Evolutionary Classifications. Traditional and cladistic interpretations of evolution differ in the emphasis they place on particular traits. 32.3 All living organisms are grouped into one of a few major categories. The Kingdoms of Life. Living organisms are grouped into three great groups called domains, and within domains into kingdoms. Domain Archaea (Archaebacteria). The oldest domain consists of primitive bacteria that often live in extreme environments. Domain Bacteria (Eubacteria). Too small to see with the unaided eye, eubacteria are more numerous than any other organism. Domain Eukarya (Eukaryotes). There are four kingdoms of eukaryotes, three of them entirely or predominantly multicellular. Two of the most important characteristics to have evolved among the eukaryotes are multicellularity and sexuality. Viruses: A Special Case. Viruses are not organisms, and thus do not belong to any kingdom. All organisms share many biological characteristics. They are composed of one or more cells, carry out metabolism and transfer energy with ATP, and encode hereditary information in DNA. All species have evolved from simpler forms and continue to evolve. Individuals live in populations. These populations make up communities and ecosystems, which provide the overall structure of life on earth. So far, we have stressed these common themes, considering the general principles that apply to all organisms. Now we will consider the diversity of the biological world and focus on the differences among groups of organisms (figure 32.1). For the rest of the text, we will examine the different kinds of life on earth, from bacteria and amoebas to blue whales and sequoia trees. FIGURE 32.1 Biological diversity. All living things are assigned to particular classifications based on characteristics such as their anatomy, development, mode of nutrition, level of organization, and biochemical composition. Coral reefs, like the one seen here, are home to a variety of living things
2.1 Biologists name organisms in a systematic way The Classification of organisms Organisms were first classified more than 2000 years ago by the greek philosopher Aristotle, who categorized living things as either plants or animals. He classified ani mals as either land. water, or air dwellers and he divided plants into three kinds based on stem differences. This simple classifica- tion system was expanded by the greeks and Romans, who grouped anima ants into basic units such as cats, horses. and aks. Eventually, these units began to be Quercus phellos Quercus rubra called genera(singular, genus), the Latin Willow oak word for“ groups.” Starting in the Middle Ages, these names began to be systemati- FIGURE 32.2 cally written down, using Latin, the lan- Two species of oaks. (a) willow oak, Quercus pbellos (6)Red oak, Quercus rubra guage used by scholars at that time. Thus, Although they are both oaks (Quercus), these two species differ sharply in leaf shap cats were assigned to the genus Felis, horses and size and in many other features, including geographical range. to equus, and oaks to Quercus--names that the Romans had applied to these groups For genera that were not known to the Romans, new books, employed the polynomial system. But as a kind of names were invented shorthand. Linnaeus also included in these books a two- The classification system of the Middle Ages, called the part name for each species. For example, the honeybee be- polynomial systemm, was used virtually unchanged for hun- came Apis mellifera. These two-part names, or binomials dreds of years (bi,"two")have become our standard way of designating The Polynomial System a Closer look at linnaeus Until the mid-1700s, biologists usually descriptive terms to the name of the they called a species. These phrases, of organis a series o when they To illustrate Linnaeus's work further, let's consider how he wanted to refer to a particular kind of organism, which treated two species of oaks from North America, which ng with the 1753 had been described by scientists. He grouped all oaks in name of the genus, came to be known as polynomials the genus Quercus, as had been the practice since Roman (poly, "many; nomial,"name"), strings of Latin words and times. Linnaeus named the willow oak of the southeastern phrases consisting of up to 12 or more words. One name United States(figure 32.2a) Quercus foliis lanceolatus inte- for the European honeybee, for example, was Apis pube genTilis glai bris("oak with spear-shaped, smooth leaves with cens, thorace szbgriseo, abdomine fusco, pedibus posticus glabris absolutely no teeth along the margins"). For the common red utrinque margine ciliaris. As you can imagine, these poly- oak of eastern temperate North America(figure 32. 2b), Lin- nomial names were cumbersome. Even more worrisome, naeus devised a new name, Quercus foliis obtuse-sinuatis the names were altered at will by later authors, so that a setaceo-mucronatis ("oak with leaves with deep blunt lobes given organism really did not have a single name that was bearing hairlike bristles"). For each of these species, he also presented a shorthand designation, the binomial names Qn cus pbellos and Quercus rubra. These have remained the official The Binomial System names for these species since 1753, even though Linnaeus did not intend this when he first used them in his book. He con A much simpler system of naming animals, plants, and sidered the polynomials the true names of the species other organisms stems from the work of the Swedish biolo- t Carolus Linnaeus(1707-1778). Linnaeus devoted his life to a challenge that had defeated many biologists before Two-part("binomial")Latin names, first utilized by him--cataloging all the different kinds of organisms. In the Linnaeus, are now universally employed by biologists to 1750s he produced several major works that, like his earlier name particular organisms 650 Part IX Viruses and Simple organism
books, employed the polynomial system. But as a kind of shorthand, Linnaeus also included in these books a twopart name for each species. For example, the honeybee became Apis mellifera. These two-part names, or binomials (bi, “two”) have become our standard way of designating species. A Closer Look at Linnaeus To illustrate Linnaeus’s work further, let’s consider how he treated two species of oaks from North America, which by 1753 had been described by scientists. He grouped all oaks in the genus Quercus, as had been the practice since Roman times. Linnaeus named the willow oak of the southeastern United States (figure 32.2a) Quercus foliis lanceolatis integerrimis glabris (“oak with spear-shaped, smooth leaves with absolutely no teeth along the margins”). For the common red oak of eastern temperate North America (figure 32.2b), Linnaeus devised a new name, Quercus foliis obtuse-sinuatis setaceo-mucronatis (“oak with leaves with deep blunt lobes bearing hairlike bristles”). For each of these species, he also presented a shorthand designation, the binomial names Quercus phellos and Quercus rubra. These have remained the official names for these species since 1753, even though Linnaeus did not intend this when he first used them in his book. He considered the polynomials the true names of the species. Two-part (“binomial”) Latin names, first utilized by Linnaeus, are now universally employed by biologists to name particular organisms. 650 Part IX Viruses and Simple Organisms The Classification of Organisms Organisms were first classified more than 2000 years ago by the Greek philosopher Aristotle, who categorized living things as either plants or animals. He classified animals as either land, water, or air dwellers, and he divided plants into three kinds based on stem differences. This simple classification system was expanded by the Greeks and Romans, who grouped animals and plants into basic units such as cats, horses, and oaks. Eventually, these units began to be called genera (singular, genus), the Latin word for “groups.” Starting in the Middle Ages, these names began to be systematically written down, using Latin, the language used by scholars at that time. Thus, cats were assigned to the genus Felis, horses to Equus, and oaks to Quercus—names that the Romans had applied to these groups. For genera that were not known to the Romans, new names were invented. The classification system of the Middle Ages, called the polynomial system, was used virtually unchanged for hundreds of years. The Polynomial System Until the mid-1700s, biologists usually added a series of descriptive terms to the name of the genus when they wanted to refer to a particular kind of organism, which they called a species. These phrases, starting with the name of the genus, came to be known as polynomials (poly, “many”; nomial, “name”), strings of Latin words and phrases consisting of up to 12 or more words. One name for the European honeybee, for example, was Apis pubescens, thorace subgriseo, abdomine fusco, pedibus posticis glabris utrinque margine ciliatis. As you can imagine, these polynomial names were cumbersome. Even more worrisome, the names were altered at will by later authors, so that a given organism really did not have a single name that was its alone. The Binomial System A much simpler system of naming animals, plants, and other organisms stems from the work of the Swedish biologist Carolus Linnaeus (1707–1778). Linnaeus devoted his life to a challenge that had defeated many biologists before him—cataloging all the different kinds of organisms. In the 1750s he produced several major works that, like his earlier 32.1 Biologists name organisms in a systematic way. Quercus phellos (Willow oak) Quercus rubra (Red oak) FIGURE 32.2 Two species of oaks. (a) Willow oak, Quercus phellos. (b) Red oak, Quercus rubra. Although they are both oaks (Quercus), these two species differ sharply in leaf shape and size and in many other features, including geographical range
Species Names ing living things, and a of or stem is called a taxon ur taxonomists throughout the world, no two organisms can have the same name So that no one country is fa ored, a language spoken by no Latin--is used for the ganism is here in the world, this system provides a standard and precise way of communicating, whether the language of a particular (a) biologist is Chinese, Arabic, Spanish or English. This is a great improve ment over the use of common names which often vary from one place to the next. As you can see in figure 32.3, corn in Europe refers to the plant Americans call wheat; a bear is a large placental omnivore in the United States but a koala(a vegetar- ian marsupial) in Australia; and a robin is a very different bird in Eu- rope and North America lso by agreement the first word of the binomial name is the genus to which the organism belongs. Thi word is always capitalized. The sec ond word refers to the particular (b) species and is not capitalized. The two words together are called the scien tific name and are written in italics or distinctive print: for example, Homo sapiens. Once a genus has been used in the body of a text, it is often abbrevi- ated in later uses. For example, the di nosaur Tyrannosaurus rex becomes T. rex,and the potentially dangerous bacterium escherichia coli is known as E. coli. The system of naming animals, plants, and other organisms estab- lished by Linnaeus has served the sci- ence of biology well for nearly 230 By convention, the first part of a binomial species name identifies the genus to which the species FIGURE 32.3 belongs, and the second part distinguishes that particular Common names make poor labels. The common names corn(a), bear(6), and robin(c) species from other species in the bring clear images to our minds(photos on left), but the images are very different to someone living in Europe or Australia(photos on rigbt). There, the same common names are used to label very different species. Chapter 32 How We Classify Organisms 651
Species Names Taxonomy is the science of classifying living things, and a group of organisms at a particular level in a classification system is called a taxon (plural, taxa). By agreement among taxonomists throughout the world, no two organisms can have the same name. So that no one country is favored, a language spoken by no country—Latin—is used for the names. Because the scientific name of an organism is the same anywhere in the world, this system provides a standard and precise way of communicating, whether the language of a particular biologist is Chinese, Arabic, Spanish, or English. This is a great improvement over the use of common names, which often vary from one place to the next. As you can see in figure 32.3, corn in Europe refers to the plant Americans call wheat; a bear is a large placental omnivore in the United States but a koala (a vegetarian marsupial) in Australia; and a robin is a very different bird in Europe and North America. Also by agreement, the first word of the binomial name is the genus to which the organism belongs. This word is always capitalized. The second word refers to the particular species and is not capitalized. The two words together are called the scientific name and are written in italics or distinctive print: for example, Homo sapiens. Once a genus has been used in the body of a text, it is often abbreviated in later uses. For example, the dinosaur Tyrannosaurus rex becomes T. rex, and the potentially dangerous bacterium Escherichia coli is known as E. coli. The system of naming animals, plants, and other organisms established by Linnaeus has served the science of biology well for nearly 230 years. By convention, the first part of a binomial species name identifies the genus to which the species belongs, and the second part distinguishes that particular species from other species in the genus. Chapter 32 How We Classify Organisms 651 (a) (b) (c) FIGURE 32.3 Common names make poor labels. The common names corn (a), bear (b), and robin (c) bring clear images to our minds (photos on left), but the images are very different to someone living in Europe or Australia (photos on right). There, the same common names are used to label very different species
The Taxonomic hierarch y The categories at the different levels may include many a few, or only one taxon. For example, there is only one liy n the decades following Linnaeus, taxonomists began to ing genus of the family Hominidae, but several living gen- group organisms into larger, more inclusive categories. era of Fagaceae. To someone familiar with classification or Genera with similar properties were grouped into a cluster with access to the appropriate reference books, each taxon called a family, and similar families were placed into the implies both a set of characteristics and a group of organ- ame order(figure 32. 4). Orders with common properties isms belonging to the taxon. For example, a honeybee has were placed into the same class, and classes with similar the species(level 1) name Apis mellifera. Its genus name characteristics into the same phylum(plural, phyla). For (level 2)Apis is a member of the family Apidae(level 3). All historical reasons, phyla may also be called divisions among members of this family are bees, some solitary, others liv plants, fungi, and algae. Finally, the phyla were assigned to ing in hives as 4. mellifera does. Knowledge of its order one of several great groups, the kingdoms. Biologists cur- (level 4), Hymenoptera, tells you that A. mellifera is likel rently recognize six kingdoms: two kinds of bacteria(Ar- able to sting and may live in colonies. Its class (level 5)In chaebacteria and Eubacteria), a largely unicellular group of ecta indicates that A. mellifera has three major body seg- eukaryotes(Protista), and three multicellular groups ments, with wings and three pairs of legs attached to the (Fungi, Plantae, and Animalia). In order to remember the middle segment. Its phylum(level 6), Arthropoda, tells us seven categories of the taxonomic hierarchy in their prop that the honeybee has a hard cuticle of chitin and jointed order, it may prove useful to memorize a phrase such as appendages. Its kingdom (level 7), Animalia, tells us that A kindly pay cash or furnish good security"(kingdom-phy- mellifera is a multicellular heterotroph whose cells lack cell lum-class-order-family-genus-species) wall In addition, an eighth level of classification, called do- mains, is sometimes used. Biologists recognize three do- mains, which will be discussed later in this chapter. The are ped into genera, genera into families, scientific names of the taxonomic units higher than the classes. and classes into Phyla are the basic units within kingdoms; such a genus level are capitalized but not printed distinctively system is hierarchical. talicized. or underlined nN astern gray squirrel FIGURE 32. 4 ciurus carolinensis The hierarchical system Kingdom I in classifying organism. The organism is first recognized as a eukaryote within this domain it is an Claes animal (kingdom: Animalia) ,CA正色的三当当33出 Orde Among the different phyla of ,的 色 (phylum: Chordata, Genus subphylum: Vertebrata). The organism's fur characterizes it ta Sciuridae has four front toes and five back toes. it Mammalia (family: Sciuridae). Within this family, it is a tree squirrel Vernet ala (genus: Sciurus), with gray fur and white-tipped hairs on the Anura carolinensis, the eastern gray 652 Part IX Viruses and Simple organism
The Taxonomic Hierarchy In the decades following Linnaeus, taxonomists began to group organisms into larger, more inclusive categories. Genera with similar properties were grouped into a cluster called a family, and similar families were placed into the same order (figure 32.4). Orders with common properties were placed into the same class, and classes with similar characteristics into the same phylum (plural, phyla). For historical reasons, phyla may also be called divisions among plants, fungi, and algae. Finally, the phyla were assigned to one of several great groups, the kingdoms. Biologists currently recognize six kingdoms: two kinds of bacteria (Archaebacteria and Eubacteria), a largely unicellular group of eukaryotes (Protista), and three multicellular groups (Fungi, Plantae, and Animalia). In order to remember the seven categories of the taxonomic hierarchy in their proper order, it may prove useful to memorize a phrase such as “kindly pay cash or furnish good security” (kingdom–phylum–class–order–family–genus–species). In addition, an eighth level of classification, called domains, is sometimes used. Biologists recognize three domains, which will be discussed later in this chapter. The scientific names of the taxonomic units higher than the genus level are capitalized but not printed distinctively, italicized, or underlined. The categories at the different levels may include many, a few, or only one taxon. For example, there is only one living genus of the family Hominidae, but several living genera of Fagaceae. To someone familiar with classification or with access to the appropriate reference books, each taxon implies both a set of characteristics and a group of organisms belonging to the taxon. For example, a honeybee has the species (level 1) name Apis mellifera. Its genus name (level 2) Apis is a member of the family Apidae (level 3). All members of this family are bees, some solitary, others living in hives as A. mellifera does. Knowledge of its order (level 4), Hymenoptera, tells you that A. mellifera is likely able to sting and may live in colonies. Its class (level 5) Insecta indicates that A. mellifera has three major body segments, with wings and three pairs of legs attached to the middle segment. Its phylum (level 6), Arthropoda, tells us that the honeybee has a hard cuticle of chitin and jointed appendages. Its kingdom (level 7), Animalia, tells us that A. mellifera is a multicellular heterotroph whose cells lack cell walls. Species are grouped into genera, genera into families, families into orders, orders into classes, and classes into phyla. Phyla are the basic units within kingdoms; such a system is hierarchical. 652 Part IX Viruses and Simple Organisms Eastern gray squirrel Sciurus carolinensis FIGURE 32.4 The hierarchical system used in classifying an organism. The organism is first recognized as a eukaryote (domain: Eukarya). Second, within this domain, it is an animal (kingdom: Animalia). Among the different phyla of animals, it is a vertebrate (phylum: Chordata, subphylum: Vertebrata). The organism’s fur characterizes it as a mammal (class: Mammalia). Within this class, it is distinguished by its gnawing teeth (order: Rodentia). Next, because it has four front toes and five back toes, it is a squirrel (family: Sciuridae). Within this family, it is a tree squirrel (genus: Sciurus), with gray fur and white-tipped hairs on the tail (species: Sciurus carolinensis, the eastern gray squirrel)
What Is a Species: In the previous section we discussed how species are named and grouped, but how do biologists decide when one or- ganism is distinct enough from another to be called its own species? In chapter 22, we reviewed the nature of species and saw there are no absolute criteria for the definition of this category. Looking different, for example, is not a use- ful criterion: different individuals that belong to the same (a) ecle dogs)may look very unlike one an- FIGURE 32.5 other, as different as a Chihuahua and a St Bernard. These The biological species very different-appearing individuals are fully capable of hy concept. Horses(a)and one ano donkeys(b) are not the The biological species concept(figure 32.5)essentially same species, be ecause the says that two organisms that cannot interbreed and produce ev produce fertile offspring are different species. This definition of when they interbreed, species can be useful in describing sexually reproducing species that regularly outcross-interbreed with individu als other than themselves. However, in many groups of or- ganisms, including bacteria, fungi, and many plants and an- (c) imals, asexual reproduction--reproduction without sex--predominates. Among them, hybridization cannot be How Many Species Are There? used as a criterion for species recognition Scientists have described and named a total of 1.5 million Defining species species, but doubtless many more actually exist. Some ps of organisms, such as flowering plants, vertebrate Despite such difficulties, biologists generally agree on the animals, and butterflies, are relatively well known with an organisms they classify as species based on the similarity of estimated 90% of the total number of species that actually morphological features and ecology. As a practical defini- exist in these groups having already been described. Many tion, we can say that species are groups of organisms that other groups, however, are very poorly known. It is gener remain relatively constant in their characteristics, can be ally accepted that only about 5% of all species have been distinguished from other species, and do not normally ecos gnized for bacteria, nematodes(roundworms), fungi terbreed with other species in nature and mites(a group of organisms related to spiders) By taking representative samples of organisms from dif- Evolutionary Species Concept ferent environments, such as the upper branches of tropical trees or the deep ocean, scientists have estimated the total This simple definition of species leaves many problems un numbers of species that may actually exist to be about 10 Ived. How, for instance, are we to compare living species million, about 15% of them marine organisms with seemingly similar ones now extinct? Much of the dis agreement among alternative species concepts relates to Most Species Live in the Tropics unique species name, and when do we assign them o solving this problem. When do we assign fossil specimens Most species, perhaps 6 or 7 million, are tropical. Presently species living today? If we trace the lineage of two sister only 400,000 species have been named in tropical Asia, species backwards through time, how far must we go before Africa, and Latin America combined, well the two species converge on their common ancestor? It is species that occur in the tropics. This is an incredible gap often very hard to know where to draw a sharp line be n our knowledge concerning biological diversity in a world tween two closely related species. that depends on biodiversity for its sustainabilit To address this problem, biologists have added an evo- These estimates apply to the number of eukaryotic or- lutionary time dimension to the biological species concept. numk ns only. There is no functional way of estimating the A current definition of an evolutionary species is a single numbers of species of prokaryotic organisms, although it is lineage of populations that maintains its distinctive identity from clear that only a very small fraction of all species have been otber sucb lineages. Unlike the biological species concept, the discovered and characterized so far evolutionary species concept applies to both asexual and sexually reproducing forms. Abrupt changes in diagnostic Species are groups of organisms that differ from one features mark the boundaries of different species in evolu another in recognizable ways and generally do not interbreed with one another in nature tionary time. Chapter 32 How We Classify Organisms 653
What Is a Species? In the previous section we discussed how species are named and grouped, but how do biologists decide when one organism is distinct enough from another to be called its own species? In chapter 22, we reviewed the nature of species and saw there are no absolute criteria for the definition of this category. Looking different, for example, is not a useful criterion: different individuals that belong to the same species (for example, dogs) may look very unlike one another, as different as a Chihuahua and a St. Bernard. These very different-appearing individuals are fully capable of hybridizing with one another. The biological species concept (figure 32.5) essentially says that two organisms that cannot interbreed and produce fertile offspring are different species. This definition of a species can be useful in describing sexually reproducing species that regularly outcross—interbreed with individuals other than themselves. However, in many groups of organisms, including bacteria, fungi, and many plants and animals, asexual reproduction—reproduction without sex—predominates. Among them, hybridization cannot be used as a criterion for species recognition. Defining Species Despite such difficulties, biologists generally agree on the organisms they classify as species based on the similarity of morphological features and ecology. As a practical definition, we can say that species are groups of organisms that remain relatively constant in their characteristics, can be distinguished from other species, and do not normally interbreed with other species in nature. Evolutionary Species Concept This simple definition of species leaves many problems unsolved. How, for instance, are we to compare living species with seemingly similar ones now extinct? Much of the disagreement among alternative species concepts relates to solving this problem. When do we assign fossil specimens a unique species name, and when do we assign them to species living today? If we trace the lineage of two sister species backwards through time, how far must we go before the two species converge on their common ancestor? It is often very hard to know where to draw a sharp line between two closely related species. To address this problem, biologists have added an evolutionary time dimension to the biological species concept. A current definition of an evolutionary species is a single lineage of populations that maintains its distinctive identity from other such lineages. Unlike the biological species concept, the evolutionary species concept applies to both asexual and sexually reproducing forms. Abrupt changes in diagnostic features mark the boundaries of different species in evolutionary time. How Many Species Are There? Scientists have described and named a total of 1.5 million species, but doubtless many more actually exist. Some groups of organisms, such as flowering plants, vertebrate animals, and butterflies, are relatively well known with an estimated 90% of the total number of species that actually exist in these groups having already been described. Many other groups, however, are very poorly known. It is generally accepted that only about 5% of all species have been recognized for bacteria, nematodes (roundworms), fungi, and mites (a group of organisms related to spiders). By taking representative samples of organisms from different environments, such as the upper branches of tropical trees or the deep ocean, scientists have estimated the total numbers of species that may actually exist to be about 10 million, about 15% of them marine organisms. Most Species Live in the Tropics Most species, perhaps 6 or 7 million, are tropical. Presently only 400,000 species have been named in tropical Asia, Africa, and Latin America combined, well under 10% of all species that occur in the tropics. This is an incredible gap in our knowledge concerning biological diversity in a world that depends on biodiversity for its sustainability. These estimates apply to the number of eukaryotic organisms only. There is no functional way of estimating the numbers of species of prokaryotic organisms, although it is clear that only a very small fraction of all species have been discovered and characterized so far. Species are groups of organisms that differ from one another in recognizable ways and generally do not interbreed with one another in nature. Chapter 32 How We Classify Organisms 653 (a) (b) (c) FIGURE 32.5 The biological species concept. Horses (a) and donkeys (b) are not the same species, because the offspring they produce when they interbreed, mules (c), are sterile
32.2 Scientists construct phylogenies to understand the evolutionary relationships among organisms. Evolutionary Classifications Monophyletic group After naming and classifying some 1.5 million organisms what have biologists learned? One very important advan tage of being able to classify particular species of plants, an- imals, and other organisms is that individuals of species that are useful to humans as sources of food and medicine an be identified. For example, if you cannot tell the fungus Penicillium from Aspergillus, you have little chance of pro- ducing the antibiotic penicillin. In a thousand ways, just having names for organisms is of immense importance in our modern world Taxonomy also enables us to glimpse the evolutionary Paraphyletic group istory of life on earth. The more similar two taxa are, the more closely related they are likely to be. By lookin at the differences and similarities between organisms, bi ologists can construct an evolutionary tree, or phy- geny, inferring which organisms evolved from which other ones. in what order. and when. The reconstruction and study of phylogenies is called systematics. Within a phylogeny, a grouping can be either monophyletic, para- phyletic, or polyphyletic. A monophyletic group in-(b) cludes the most recent common ancestor of the group and all of its descendants. A paraphyletic group includes Polyphyletic group le most recent common ancestor of the group but not all of its descendants. And, a polyphyletic group does not include the most recent common ancestor of all the members of the group. Monophyletic groups are com monly assigned names, but systematists will not assign a taxonomic classification to a polyphyletic group. Para- phyletic groups may be considered taxa by some scien lutionary relaton ey do not accurately represent the evo- (figure 32.6) FIGURE 32.6 (a)A monophyletic group consists of the most recent common Cladistics ancestor and all of its descendants. All taxonomists accept monophyletic groups in their classifications and in the above A simple and objective way to construct a phylogenetic example would give the name"Apes"to the orangutans, gorillas, tree is to focus on key characters that a group of organ- chimpanzees, and humans.()A paraphyletic group consists of the isms share because they have inherited them from a com- most recent common ancestor and some of its descendants mon ancestor. A clade is a group of organisms related by Taxonomists differ in their acceptance of paraphyletic groups. For xample, some taxonomists arbitrarily group orangutans, gorillas, descent, and this approach to constructing a phylogeny is and chimpanzees into the paraphyletic family Pongidae, separate called cladistics. Cladistics infers phylogeny (that is, from humans. Other taxonomists do not use the family pongidae builds family trees) according to similarities derived from their classifications because gorillas and chimpanzees are more a common ancestor, so-called derived characters. a de- closely related to humans than to orangutans. () A polyphyletic rived character that is unique to a particular clade is group does not contain the most recent common ancestor of the ometimes called a synapomorphy. The key to the ap- group, and taxonomists do not assign taxa to polyphyletic groups proach is being g able to identify morphological, physio For example, sharks and whales could be classified in the same logical,or behavioral traits that differ among the organ- group because they have similar shapes, anatomical features, and isms being studied and can be attributed to a common habitats. However, their similarities reflect convergent evolution, ancestor. By examining the distribution of these traits not common ancestry among the organisms, it is possible to construct a clado- 654 Part IX Viruses and Simple organism
Evolutionary Classifications After naming and classifying some 1.5 million organisms, what have biologists learned? One very important advantage of being able to classify particular species of plants, animals, and other organisms is that individuals of species that are useful to humans as sources of food and medicine can be identified. For example, if you cannot tell the fungus Penicillium from Aspergillus, you have little chance of producing the antibiotic penicillin. In a thousand ways, just having names for organisms is of immense importance in our modern world. Taxonomy also enables us to glimpse the evolutionary history of life on earth. The more similar two taxa are, the more closely related they are likely to be. By looking at the differences and similarities between organisms, biologists can construct an evolutionary tree, or phylogeny, inferring which organisms evolved from which other ones, in what order, and when. The reconstruction and study of phylogenies is called systematics. Within a phylogeny, a grouping can be either monophyletic, paraphyletic, or polyphyletic. A monophyletic group includes the most recent common ancestor of the group and all of its descendants. A paraphyletic group includes the most recent common ancestor of the group but not all of its descendants. And, a polyphyletic group does not include the most recent common ancestor of all the members of the group. Monophyletic groups are commonly assigned names, but systematists will not assign a taxonomic classification to a polyphyletic group. Paraphyletic groups may be considered taxa by some scientists, although they do not accurately represent the evolutionary relationships among the members of the group (figure 32.6). Cladistics A simple and objective way to construct a phylogenetic tree is to focus on key characters that a group of organisms share because they have inherited them from a common ancestor. A clade is a group of organisms related by descent, and this approach to constructing a phylogeny is called cladistics. Cladistics infers phylogeny (that is, builds family trees) according to similarities derived from a common ancestor, so-called derived characters. A derived character that is unique to a particular clade is sometimes called a synapomorphy. The key to the approach is being able to identify morphological, physiological, or behavioral traits that differ among the organisms being studied and can be attributed to a common ancestor. By examining the distribution of these traits among the organisms, it is possible to construct a clado- 654 Part IX Viruses and Simple Organisms 32.2 Scientists construct phylogenies to understand the evolutionary relationships among organisms. Ray Shark Whale Cow Orangutan Gorilla Chimpanzee Human Monophyletic group Ray Shark Whale Cow Orangutan Gorilla Chimpanzee Human Paraphyletic group Ray Shark Whale Cow Orangutan Gorilla Chimpanzee Human Polyphyletic group (a) (b) (c) FIGURE 32.6 (a) A monophyletic group consists of the most recent common ancestor and all of its descendants. All taxonomists accept monophyletic groups in their classifications and in the above example would give the name “Apes” to the orangutans, gorillas, chimpanzees, and humans. (b) A paraphyletic group consists of the most recent common ancestor and some of its descendants. Taxonomists differ in their acceptance of paraphyletic groups. For example, some taxonomists arbitrarily group orangutans, gorillas, and chimpanzees into the paraphyletic family Pongidae, separate from humans. Other taxonomists do not use the family Pongidae in their classifications because gorillas and chimpanzees are more closely related to humans than to orangutans. (c) A polyphyletic group does not contain the most recent common ancestor of the group, and taxonomists do not assign taxa to polyphyletic groups. For example, sharks and whales could be classified in the same group because they have similar shapes, anatomical features, and habitats. However, their similarities reflect convergent evolution, not common ancestry
Traits. Jaws Lungs Amniotic No tail Bipedal FIGURE 32.7 a cladogram. Morphological data for a group of seven vertebrates is tabulated.A“1” Lamprey 0 indicates the presence of a trait, or derived character,anda“o” indicates the absence of Shark 0 0 0 0 the trait. a tree, or cladogram, diagrams the proposed evolutionary relationships among 0 0 0 based on the derived characters. The derived characters Lizard 0 tween the cladogram branch points are 0 0 shared by all organisms above the branch point and are not present in any below it. The 1 outgroup, in this case the lamprey, does not possess any of the derived characters Human 1 1 Lamprey Shark Salamander Lizard Gorilla Human Amniotic embrane gram(figure 32.7), a branching diagram that represents Cladistics is a relatively new approach in biology and has ogen become popular among students of evolution. This is be- In traditional phylogenies, proposed ancestors will cause it does a very good job of portraying the order in often be indicated at the nodes between branches, and the which a series of evolutionary events have occurred. The lengths of branches correspond to evolutionary time, with great strength of a cladogram is that it can be completely extinct groups having shorter branches. In contrast, clado- objective. In fact, most cladistic analyses involve man grams are not true family trees in that they do not identify characters, and computers are required to make the com- ancestors, and the branch lengths do not reflect evolution ary time(see figure 32. 6). Instead, they convey compara Sometime it is necessary to"weight"characters, or take tive information about relative relationships. Organisms into account the variation in the "strength"of a character that are closer together on a cladogram simply share such as the size or location of a fin or the effectiveness of more recent common ancestor than those that are farther a lung. To reduce a systematist's bias even more, many apart. Because the analysis is comparative, it is necessary to analyses will be run through the computer with the traits have something to anchor the comparison to, some solid weighted differently each time. Under this procedure, ound against which the comparisons can be made. To several different cladograms will be constructed, the goal rather different organism(but not too different)to serve as o ing to choose the one that is the most parsimonious, achieve this, each cladogram must contain an outgroup, amplest and thus most likely. Reflecting the impor a baseline for comparisons among the other organisms tance of evolutionary processes to all fields of biolog ing evaluated, the ingroup. For example, in figure 32.7, most taxonomy today includes at least some element of the lamprey is the outgroup to the clade of animals that cladistic analysis Chapter 32 How We Classify Organisms 655
gram (figure 32.7), a branching diagram that represents the phylogeny. In traditional phylogenies, proposed ancestors will often be indicated at the nodes between branches, and the lengths of branches correspond to evolutionary time, with extinct groups having shorter branches. In contrast, cladograms are not true family trees in that they do not identify ancestors, and the branch lengths do not reflect evolutionary time (see figure 32.6). Instead, they convey comparative information about relative relationships. Organisms that are closer together on a cladogram simply share a more recent common ancestor than those that are farther apart. Because the analysis is comparative, it is necessary to have something to anchor the comparison to, some solid ground against which the comparisons can be made. To achieve this, each cladogram must contain an outgroup, a rather different organism (but not too different) to serve as a baseline for comparisons among the other organisms being evaluated, the ingroup. For example, in figure 32.7, the lamprey is the outgroup to the clade of animals that have jaws. Cladistics is a relatively new approach in biology and has become popular among students of evolution. This is because it does a very good job of portraying the order in which a series of evolutionary events have occurred. The great strength of a cladogram is that it can be completely objective. In fact, most cladistic analyses involve many characters, and computers are required to make the comparisons. Sometime it is necessary to “weight” characters, or take into account the variation in the “strength” of a character, such as the size or location of a fin or the effectiveness of a lung. To reduce a systematist’s bias even more, many analyses will be run through the computer with the traits weighted differently each time. Under this procedure, several different cladograms will be constructed, the goal being to choose the one that is the most parsimonious, or simplest and thus most likely. Reflecting the importance of evolutionary processes to all fields of biology, most taxonomy today includes at least some element of cladistic analysis. Chapter 32 How We Classify Organisms 655 Lamprey Tiger Gorilla Human Jaws Lungs Amniotic membrane Hair No tail Bipedal Shark Salamander Lizard Traits: Organism Jaws Lungs Amniotic membrane Hair No tail Bipedal Lamprey Shark Salamander Lizard Tiger Gorilla Human 00 0 0 0 0 10 0 0 0 0 11 0 0 0 0 11 1 0 0 0 11 1 1 0 0 11 1 1 1 0 11 1 1 1 1 FIGURE 32.7 A cladogram. Morphological data for a group of seven vertebrates is tabulated. A “1” indicates the presence of a trait, or derived character, and a “0” indicates the absence of the trait. A tree, or cladogram, diagrams the proposed evolutionary relationships among the organisms based on the presence of derived characters. The derived characters between the cladogram branch points are shared by all organisms above the branch point and are not present in any below it. The outgroup, in this case the lamprey, does not possess any of the derived characters
Class Reptilia Mammalia Reptilia Class Aves Archosaurs Crocodilians Birds Lizards and Lizards and Mammals Turtles Crocodilians Birds Dinosaur (a) Traditional phylogeny and taxonomic classification FIGURE 32.8 Traditional and cladistic interpretations of vertebrate classification. Traditional and cladistic taxonomic analyses of the same set of traditional analysis, key characteristics such as feathers and hollow bones are weighted more heavily than others, placing the birds in their own group and the reptiles in a paraphyletic group. (b) Cladistic analysis gives equal weight to these and many other characters and places irds in the same grouping with crocodiles, reflecting the close evolutionary relationship between the two. Also, in the traditional phylogeny, the branch leading to the dinosaurs is shorter because the length corresponds to evolutionary time. In cladograms, branch lengths do not correspond to evolutionary time. Traditional Taxonomy cestry but ignores the immense evolutionary impact of a Weighting characters lies at the core of traditional taxon- derived character such as feathers omy. In this approach, taxa are assigned based on a vast Overall, classifications based on traditional taxonomy amount of information about the morphology and biology are information-rich, while classifications based on clado- of the organism gathered over a long period of time. Tradi- grams need not be. Traditional taxonomy is often used tional taxonomists consider both the common descent and when a great deal of information is available to guide char- amount of adaptive evolutionary change when grouping or- little information is available about how the character af- anisms. The large amount of information used by tradi tional taxonomists permits a knowledgeable weighting of fects the life of the organism. DNA sequence comparisons, characters according to their biological significance. In tra for example, lend themselves well to cladistics--you have a ditional taxonomy, the full observational power and judg- great many derived characters(DNA sequence differences) ment of the biologist is brought to bear--and also any bi- but little or no idea of what impact the sequence diffe ses he or she may have. For example, in classifying the ences have on the organ terrestrial vertebrates, traditional taxonomists place birds in their own class(Aves), giving great weight to the characters A phylogeny may be represented as a cladogram based that made powered flight possible, such as feathers. How on the order in which groups evolved. Traditional ever,cladists(figure 32.8) lumps birds in among the rep- taxonomists weight characters according to assumed tiles with crocodiles. This accurately reflects their true an- mportance 656 Part IX Viruses and Simple organism
Traditional Taxonomy Weighting characters lies at the core of traditional taxonomy. In this approach, taxa are assigned based on a vast amount of information about the morphology and biology of the organism gathered over a long period of time. Traditional taxonomists consider both the common descent and amount of adaptive evolutionary change when grouping organisms. The large amount of information used by traditional taxonomists permits a knowledgeable weighting of characters according to their biological significance. In traditional taxonomy, the full observational power and judgment of the biologist is brought to bear—and also any biases he or she may have. For example, in classifying the terrestrial vertebrates, traditional taxonomists place birds in their own class (Aves), giving great weight to the characters that made powered flight possible, such as feathers. However, cladists (figure 32.8) lumps birds in among the reptiles with crocodiles. This accurately reflects their true ancestry but ignores the immense evolutionary impact of a derived character such as feathers. Overall, classifications based on traditional taxonomy are information-rich, while classifications based on cladograms need not be. Traditional taxonomy is often used when a great deal of information is available to guide character weighting, while cladistics is a good approach when little information is available about how the character affects the life of the organism. DNA sequence comparisons, for example, lend themselves well to cladistics—you have a great many derived characters (DNA sequence differences) but little or no idea of what impact the sequence differences have on the organism. A phylogeny may be represented as a cladogram based on the order in which groups evolved. Traditional taxonomists weight characters according to assumed importance. 656 Part IX Viruses and Simple Organisms Mammals Mammals Turtles Turtles Crocodilians Crocodilians Birds Birds Dinosaurs Dinosaurs Lizards and snakes Lizards and snakes Early reptiles Class Mammalia Class Reptilia Class Aves Mammalia Reptilia Archosaurs (a) Traditional phylogeny and taxonomic classification (b) Cladogram and cladistic classification FIGURE 32.8 Traditional and cladistic interpretations of vertebrate classification. Traditional and cladistic taxonomic analyses of the same set of data often produce different results: in these two classifications of vertebrates, notice particularly the placement of the birds. (a) In the traditional analysis, key characteristics such as feathers and hollow bones are weighted more heavily than others, placing the birds in their own group and the reptiles in a paraphyletic group. (b) Cladistic analysis gives equal weight to these and many other characters and places birds in the same grouping with crocodiles, reflecting the close evolutionary relationship between the two. Also, in the traditional phylogeny, the branch leading to the dinosaurs is shorter because the length corresponds to evolutionary time. In cladograms, branch lengths do not correspond to evolutionary time