Zoology Lab Final - Taxonomy and Systematics PDF

# Taxonomy and Systematics Scientists face a monumental challenge in systematically identifying, naming, describing, categorizing, and studying millions of different species of living organisms (likely tens of millions if you include microbes!). More than 1.6 million species of plants and animals a...

# Taxonomy and Systematics Scientists face a monumental challenge in systematically identifying, naming, describing, categorizing, and studying millions of different species of living organisms (likely tens of millions if you include microbes!). More than 1.6 million species of plants and animals already have been described by biologists, and hundreds of new species are discovered every year. Scientists called **taxonomists**, who specialize in identifying and cataloging new species, utilize set principles and rules for naming and classifying organisms, whereas scientists in the field of **systematics** are concerned with the diversity and relatedness of organisms. ## Chapter 5: Taxonomy and Systematics After completing the exercises in this chapter, you should be able to: 1. Understand the modern taxonomic hierarchy and binomial nomenclature. 2. Understand how phylogenies depict relationships between taxa and represent evolutionary histories. 3. Recognize monophyletic, paraphyletic, and polyphyletic groupings. 4. Identify sister taxa and common ancestral traits of taxa. 5. List sources of information that modern systematists use to build phylogenies. 6. Construct phylogenies from morphological data. ### Exercise 5-1: Introduction to Classical Taxonomy #### Naming Earth's Living Things The subdiscipline of biology that deals with naming and classifying living organisms is called **taxonomy**. This system has its roots in the mid-18th century when the Swedish scientist Carl Linnaeus set out on a seemingly daunting mission to name and catalog every known living organism—at the time, only about 12,000 species of plants and animals were known to science. He realized the confusion that can result from having several common names for the same creature. Take, for example, the cougar found throughout the Americas, from Canada to South America (Fig. 5.1). In addition to being called a cougar, it has more than 40 other common names in English, including puma, mountain lion, shadow cat, panther, and catamount, not to mention numerous common names in other languages. But, this species of cat has only one scientific name, *Puma concolor*. When scientists in Mexico, Canada, or the United States (or any other country, for that matter) refer to *Puma concolor*, everyone knows exactly which animal is the subject of discussion. **Latin is used as the conventional standard for scientific names** because Linnaeus established this system at a time when Latin was still widely used among scientists in the Western world. The two-part format for a scientific name is referred to as **binomial nomenclature**. The first word of the name is the **genus** (plural = genera) to which a species belongs. The second word designates a particular species of the genus and is called the **species epithet**. Notice that the first letter of the genus is always capitalized and the entire binomial is always italicized (or underlined if you handwrite the name). The practical importance of combining the genus name and species name in the binomial is that, if we know two organisms are part of the same genus, then we immediately know that they will share many similarities, but not as many as will members of the same species. For example the gray wolf, *Canis lupus*, is a member of the genus *Canis*, along with foxes, coyotes, jackals, and all domestic dogs. So right away we know that all of these organisms share many physical and behavioral characteristics in common due to their inclusion within the same genus. Furthermore, we know to expect at least a few significant differences between the various species within this genus. #### Hierarchical Classification In addition to naming species, Linnaeus also grouped them into a hierarchy of increasingly inclusive categories. There are eight basic categories in use in the modern taxonomic system: **species, genus, family, order, class, phylum, kingdom, and domain**. Each of these categories is more inclusive than the category that precedes it. Figure 5.2 depicts how this taxonomic system is applied to the colorful lazuli bunting. This particular species of songbird common in the western United States belongs to the genus *Passerina* with six other species of buntings. The genus *Passerina* is a small part of the family *Cardinalidae* that contains 10 other genera. This family, in turn, is part of the order *Passeriformes*, the largest order of birds with a total of 87 families of "perching birds". As we continue up the taxonomic hierarchy, each category (or taxon) is more inclusive than the one beneath it, all the way to the highest categories, the kingdom *Animalia*, which includes all animals, and the domain *Eukarya*, which includes all organisms with membrane-enclosed cell organelles (protists, plants, fungi, and animals). Note that in the Linnaean system, taxa above the genus level are not italicized, though they are capitalized. So what is the basis for placing organisms into particular categories such as families and orders? Linnaeus and his contemporaries named and classified thousands of organisms long before evolution became widely accepted as a central concept of biology. Without an understanding of the principles of evolution and modification by descent to guide them, these naturalists described features of organisms and grouped them according to the similarities that seemed most important to them—most often physical or anatomical traits. Today, taxonomists attempt to classify organisms in accordance with how closely they are related, with the goal that our biological classification systems reflect the evolutionary relationships among organisms. Let's return to our example of the gray wolf, *Canis lupus*. It turns out that modern domestic dogs, *Canis familiaris*, are closely related to gray wolves, and are, in fact, descendants of wolves. The differences that exist between them today are the product of a mere 15,000 years or so of selective breeding and domestication by humans. This close evolutionary relationship is likewise reflected in the classification of these animals by their inclusion within the same genus, *Canis*. Domestic dogs are also related to domestic cats, *Felis catus*, if we look far back enough in time. In this case, we must go back a lot further than 15,000 years; we must go back perhaps 60 million years! So there is a big difference in how closely related dogs and wolves are as opposed to dogs and cats. Once again, we see that this more distant evolutionary relationship is reflected in our classification of these animals. Dogs and cats are not only in different genera, but occupy different families: *Canidae* (dogs) and *Felidae* (cats). They both are included within the same order, *Carnivora*, along with a host of other carnivores such as lions, bears, seals, weasels, hyenas, and raccoons. Thus, in an ideal taxonomic system, the further up the taxonomic hierarchy you must go to find a common category shared by two organisms, the longer it has been since they shared a common ancestor, generally speaking. This generalization obviously has limitations and numerous exceptions, but it serves as a guiding principle for naming and categorizing living organisms into a framework that reflects the relationships among those organisms (Fig. 5.3). ### Exercise 5-2: Interpreting and Constructing Phylogenies #### Linking Classification and Systematics Although a well-devised system of taxonomic classification can give general ideas about the evolutionary relationships among groups of organisms, it is the field of **systematics** that tries to ascertain the precise degrees of relatedness that exist between entire lineages of organisms. Systematists attempt to establish the truth about which groups gave rise to other groups, who is more closely related to whom, and which traits are more ancestral and which are more recently derived. They create hypotheses about these evolutionary relationships that are depicted in **phylogenetic trees** (also called **phylogenies** or **cladograms**) that show the order in which lineages split over the course of time. A **phylogenetic tree** is a diagram with a series of dichotomous, or two-way, branch points in which each branch point (or node) represents the divergence of two evolutionary lineages from a common ancestor (Fig. 5.4). A particular tree may portray the evolution of all life, of major evolutionary lineages such as all vertebrates, or of only a small group of organisms, such as a genus of caterpillars. Understanding a phylogeny is a lot like reading a family tree. The base of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the base to the tips, you are moving forward in time. Groups, or taxa, that share an immediate common ancestor (node) are referred to as **sister taxa** and represent each other's closest relatives. Most systematists today believe that taxonomic groups should be **monophyletic**. A **monophyletic group** contains all the descendants of a particular ancestor and no other organisms (Fig. 5.5A). It may help to remember that a monophyletic group (mono means one) can be removed from a phylogenetic tree with a single "cut" to one branch of the tree. A group that contains some, but not all, of the descendants of a particular ancestor is said to be **paraphyletic** (Fig. 5.5B). A group consisting of members that do not share the same common ancestor is referred to as **polyphyletic** (Fig. 5.5C). Polyphyletic groups have at least two separate evolutionary origins, often requiring independent evolutionary acquisition of similar features (such as the wings in bats, birds, and some insects). #### How Phylogenies Are Reconstructed To reconstruct phylogenies, systematists analyze evolutionary changes in the traits (or characters) of related organisms. Characters are heritable features that can be used to study variation within and among species, such as anatomical characteristics, genetic sequences, behaviors, or even ecological factors. The first step is to determine which character state or variant was present in the common ancestor of the entire group; this is known as the **ancestral character state**. A trait that differs from its ancestral form is called a **derived character state**. For example, more than 54,000 species of animals on Earth possess a vertebral column (better known as a backbone). The ancestor to all fishes, amphibians, reptiles, and mammals had such a structure, making the vertebral column an ancestral character for all vertebrates. However, only some vertebrate lineages evolved four limbs (and became known as tetrapods). Thus, the presence of four limbs is a derived character of some vertebrates. Figure 5.6 depicts the results of the continuation of this stepwise process of evermore selective grouping to reveal that only some tetrapods developed mammary glands (mammals), only some mammals became carnivores, and only some carnivores became aquatic. The presumption in reconstructing phylogenies is that shared derived characters are evidence of common ancestry, and the more derived character states two organisms share, the more recently they will have shared a common ancestor compared to other organisms in the phylogeny. Based on the phylogeny depicted in Figure 5.6 which mammal shares the most recent common ancestor with bears (or to put it another way, what is the sister taxon to bears)? A phylogenetic classification system ignores superficial similarities among organisms. Like fish, walruses swim in the water, but walruses share far more derived characteristics with bears than they do with fish-enough to indicate to scientists that walruses have returned to the water in relatively recent times, following a period in which their ancestors lived on land. Notice that we did not say that walruses evolved from bears. We should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it. We can only infer that the lineage leading to bears and the lineage leading to walruses both split off from a common ancestor at some point in the past. To say that certain animals under consideration have derived character states, we must compare them to an outgroup-in this case the lancelet. An outgroup is a species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying. Lancelets suit this purpose in our example because they are believed to be more distantly related to vertebrates than vertebrates are to each other. For all six characters listed in Figure 5.6, "absence" is the ancestral character state because this is the condition found in the outgroup. Thus, the derived traits in this example are those that have been acquired by other members of the lineage since they separated from the ancestral line that leads to lancelets. Reconstructing phylogenies often comes down to counting the number of derived character states present in each taxon. The results are generally depicted in a character table as shown in Table 5-1. The taxon with no derived character states, the lancelet, is the outgroup. The lamprey has only one derived character state, a vertebral column, that happens to be shared with all other taxa-a good indicator that this trait evolved next in the lineage. Thus, we place lampreys next to lancelets on our phylogeny and note that vertebral columns evolved sometime after the split from the common ancestor of lancelets and lampreys. Fish possess two derived character states, a vertebral column and hinged jaws, and thus would be the next descendant in the lineage of organisms. Again, we would place the character state of "hinged jaws" after the split from the common ancestor of lampreys and fish. And so we continue, until we have placed all the taxa and all their derived character states on our phylogeny. Because a phylogenetic tree is a proposition about evolutionary relationships, we must use characters that are reliable indicators of common ancestry. Therefore, we must identify **homologous characters**—shared traits in different groups that are similar because they were inherited from a common ancestor. This is in contrast to **analogous characters**, which are similar structures that have separate evolutionary origins. An example of a homologous character can be found in the forelimb bones of tetrapods. Frogs, crocodiles, birds, bats, and humans all have the same basic bones in their forelimbs-bones that they each inherited from the common ancestor of all tetrapods (Fig. 5.7). We also can see an example of analogous structures in this example. When we examine bird wings and bat wings closely, we see key differences. A bat's wing consists of a flap of skin stretched between the body and the bones of the fingers and arm. A bird's wing, however, consists of feathers extending along the arm. These structural dissimilarities suggest that bird wings and bat wings were not inherited from a common ancestor with wings. Bird and bat wings are therefore analogous-they have separate evolutionary origins, but are superficially similar because they evolved to serve the same function (Fig. 5.8). So we can say that the bones of bird and bat forelimbs are homologous structures because forelimbs were inherited from a common ancestor with forelimbs, but bird and bat wings are analogous structures because they were not inherited from a common ancestor with wings. Would you consider the wings of a moth and the wings of a bird analogous or homologous? Why? What about the heart of a chicken and the heart of a fish? Why? #### Sources of Phylogenetic Information You may be wondering what sources of information systematists use in charting the evolutionary histories of organisms and constructing phylogenies. How do they decide on the groupings of organisms? Rather than being limited only to the observable physical characteristics of species, as were scientists during Linnaeus's time, systematists today have a much wider and more sophisticated range of resources to draw upon to construct phylogenies that more accurately reflect patterns of ancestry. 1. **Radiometric dating**-a technique for determining the age of objects by measuring the decay of radioactive elements within them. 2. **Fossils**-comparing characteristics of different fossils of known ages to determine which species predate others. 3. **Comparative morphology**-comparing the extent to which groups of organisms share similar (homologous) anatomical features to determine their degree of relatedness. 4. **Comparative embryology**-examining the developmental patterns of organisms to make judgments about lines of descent. 5. **Biochemical and molecular analysis** -comparing DNA, RNA, protein sequences, enzymes, and metabolic pathways among organisms to make judgments about lines of descent. An important point to remember is that phylogenies are hypotheses put forth by scientists as the most plausible explanation of the evolutionary relationships among organisms based on the best evidence available at that time. As additional research is conducted and new evidence is uncovered, scientists often propose alternate hypotheses, and our phylogenies shift to reflect these changes in the body of scientific knowledge. Sometimes this means changing just a branch or two; other times it means reconstructing an entire phylogenetic tree. Often it means that disagreements arise among scientists about which phylogeny is more accurate. Sometimes it means that information you read in one book disagrees with that in another book. This apparent lack of finality is actually by design, it's built right into the system of science and illustrates a fundamental ideology-that any conclusion or “fact” in science is subject to modification based solely on the best evidence available. #### Building Simple Phylogenies Now it's time to put this knowledge of systematics to use to construct your own phylogenetic trees. As you build your trees keep the following rules in mind: 1. All taxa are placed on the endpoints of the phylogeny, never at nodes. 2. Each node must have a list of character states common to all taxa above the node (unless the character is later modified). 3. All character states appear on the phylogeny only once (unless the character state was derived separately by more than one group). **Procedure** 1. Use the data in Table 5-2 to complete the phylogeny depicted in Figure 5.9. 2. Place each animal correctly at the ends of the branches and label the branching points (nodes) with the appropriate character states. Hint: A node may have more than one character that defines that branch. 3. The taxa across the top of Table 5-2 are not arranged in order, so you will have to determine the correct order of placement on your phylogeny. Remember to start your phylogeny with the taxon that has the fewest derived character states (the outgroup) and work your way up to the taxon with the most derived character states. 4. You may assume that the absence of a trait represents the ancestral character state. In Table 5-3, we have added another element to the characters listed in the data table. Instead of just determining the presence or absence of a trait, we have included some characters with more complex character states. You may assume that the character states of the outgroup are ancestral character states and any that differ from the outgroup are considered to be derived. As before, remember to start labeling your phylogeny in Figure 5.10 with the taxon that has the fewest derived character states and work your way up to the taxon with the most derived character states. In the final example in Table 5-4, you will have to fill in the data table of character states and draw the entire phylogeny in the space provided at the bottom of this page on your own! If you understand the basic principles of creating phylogenies that we have covered thus far, this shouldn't be too difficult. Think about the familiar animals listed in Table 5-4 and establish which character states are present and which are absent in each taxon. Use a zero (0) to indicate absence of a trait, and a one (1) to indicate the presence of a trait. Next, use the data in Table 5-4 to create a phylogeny for these animals in the space provided. As before, you may assume that the absence of a trait represents the ancestral character state. The taxa across the top of Table 5-4 are again arranged in random order, so you will have to determine the correct order of placement on your phylogeny. Remember to start your phylogeny with the taxon that has the fewest derived character states and work your way up to the taxon (or taxa) with the most derived character states. We have added one more twist to this collection of animals. You will see that multiple taxa in this example have the same number of shared derived character states, meaning that they will have a slightly different branching relationship than in the previous examples. This additional factor will test your ability to construct an accurate phylogeny based on the data presented! When in doubt about a particular grouping, follow the principle of parsimony. In other words, choose the simplest arrangement of branches capable of explaining the data. Even though similar structures may evolve independently in separate lineages through convergent evolution (as we saw earlier with wings), this is assumed to be a rare event. Most major morphological features are assumed to have evolved or to have been lost only rarely. Therefore, unless your evidence suggests otherwise, choose a branching pathway that minimizes the number of times a trait is postulated to have arisen (or been lost). **Check Your Progress** 1. Identify the sister taxa in the phylogeny you created from Table 5-4. 2. Which of the taxon below is most closely related to a mouse? a. shark b. fish c. frog 3. Which taxon should be designated as the outgroup? 4. List all traits present in the direct common ancestor of frogs.