1. Overall similarity of phenotypes may not always reflect evolutionary relationships— a. due to convergent evolution b. because of variation in rates of evolutionary change of different kinds of characters c. due to homoplasy d. all of the above The correct answer is d— A. Answer a is incorrect. Although convergence can obscure our interpretation of evolutionary relatedness, it is not the only source of error. The correct answer is d— B. Answer b is incorrect. Although differences in rates of evolution of different characters can make interpretation of evolutionary relationships difficult (for example, chimps and humans are more closely related to one another than either is to gorillas), it is not the only source of error The correct answer is d— C. Answer c is incorrect. Although homoplasy refers to a character that is similar (for example, by the process of convergence) but not homologous, thereby complicating analysis of evolutionary relationships, it is not the only source of error. The correct answer is d—all of the above D. Answer d is correct. All of the source listed contribute to difficulty in inferring evolutionary relationships from overall similarity. 2. Cladistics— a. is based on overall similarity of phenotypes b. requires distinguishing similarity due to inheritance from a common ancestor from other reasons for similarity c. is not affected by homoplasy d. none of the above The correct answer is b— A. Answer a is incorrect. Cladistics is distinguished from some other methods of phylogenetic inference by virtue of it not being based on comparisons of overall similarity. The correct answer is b—requires distinguishing similarity due to inheritance from a common ancestor B. Answer b is correct. Cladistic methods start by using only character states that are shared by species due to inheritance from a common ancestor. The correct answer is b—

C. Answer c is incorrect. Homoplasy complicates cladistic analyses because species may share a derived character state without inheriting it from the same ancestral species. The correct answer is b— D. Answer d is incorrect. One of the answers above is correct, answer b. 3. The principle of parsimony— a. helps evolutionary biologists distinguish among competing phylogenetic hypotheses b. does not require that the polarity of traits be determined c. is a way to avoid having to use outgroups in a phylogenetic analysis d. cannot be applied to molecular traits The correct answer is a—helps evolutionary biologists distinguish among competing phylogenetic hypotheses A. Answer a is correct. Parsimony is an assumption that when there are multiple hypotheses, the one requiring the fewest evolutionary changes is to be favored. The correct answer is a— B. Answer b is incorrect. Establishing which is the most parsimonious hypothesis depends on polarizing character states. The correct answer is a— C. Answer c is incorrect. Outgroups are always used as a point of reference in analyzing the evolution of characters because they allow for establishing the polarity of character states. The correct answer is a— D. Answer d is incorrect. The principle of parsimony does not depend on the kind of traits analyzed; morphological, molecular, and other characters are potentially subject to parsimony. 4. The phylogenetic species concept (PSC)— a. depends on whether individuals from different populations can successfully breed b. is indistinguishable from the biological species concept c. does not apply to allopatric populations d. is based on evolutionary independence among populations The correct answer is d— A. Answer a is incorrect. Successful interbreeding is not a key issue in the PSC; lack of reliance on an interbreeding “test” is an important way in which the PSC differs from the biological species concept (BSC). The correct answer is d—

B. Answer b is incorrect. The BSC relies on a test of interbreeding, whereas the PSC relies on a judgment of evolutionary independence as gauged by phylogenetic analysis of homologous traits. The correct answer is d— C. Answer c is incorrect. One advantage of the PSC relative to the BSC is that it does apply to allopatric populations. The correct answer is d—is based on evolutionary independence among populations D. Answer d is correct. The key aspect of the definition of species in the PSC is whether two groups (populations or species) are on independent evolutionary trajectories, identified by factors such as presence of shared derived characters, etc. 5. Parsimony suggests that parental care in birds, crocodiles, and some dinosaurs— a. evolved independently, multiple times by convergent evolution b. evolved once in an ancestor common to all three groups c. is a homoplastic trait d. is not a homologous trait The correct answer is b— A. Answer a is incorrect. According to parsimony, the independent origins of parental care is less likely, especially since other characters identify a close relationship between crocodilians and birds. The correct answer is b—evolved once in an ancestor common to all three groups B. Answer b is correct. A phylogeny based mostly on morphological characters already established the close relationships among crocodilians, birds, and one group of dinosaurs, leading to the recognition that parental care is in fact an ancestral trait that was inherited among all three groups. The correct answer is b— C. Answer c is incorrect. Parental care seen in all three groups is a homologous trait. The correct answer is b— D. Answer d is incorrect. Parental care seen in all three groups is a homologous trait. 6. The re-evolution of lost traits, especially if they are complex— a. can be identified with phylogenetic analyses b. never happens c. is not an example of a reversal d. does not affect interpretation of evolutionary relationships The correct answer is a—can be identified with phylogenetic analyses A. Answer a is correct. Phylogenetic analyses can reveal when a trait is lost from an ancestor that possessed the trait.

The correct answer is a— B. Answer b is incorrect. It is clear that in some cases reversals of complex traits may have happened, especially given alternative phylogenetic hypotheses that seem even less likely. The correct answer is a— C. Answer c is incorrect. The re-evolution of a lost trait is one way to get a reversal, albeit an extreme one. The correct answer is a— D. Answer d is incorrect. Reversals are one very important source of homoplasy, and homoplasy is a major source of error in phylogenetic analysis. 7. The term molecular clock in the context of evolutionary biology and phylogenetics— a. refers to a group of proteins that induce endogenous circadian rhythms in animals b. is an undisputed assumption that all biological molecules evolve at a constant rate c. may help provide a way to estimate the absolute timing of historical events in evolution d. applies only to organisms that reproduce sexually The correct answer is c— A. Answer a is incorrect. The molecular clock has nothing to do with circadian rhythms. The correct answer is c— B. Answer b is incorrect. Although many think the clock has some value as a timing device, it is widely appreciated that at least under some circumstances, it will provide erroneous estimates. The correct answer is c—may help provide a way to estimate the absolute timing of historical events in evolution C. Answer c is correct. In some cases, the pace of evolution among different characters or different taxa may be similar and constant over time, providing reasonable estimates of the timing of certain events. The correct answer is c— D. Answer d is incorrect. When the clock is useful, it would not be limited to sexually or asexually reproducing animals; it might apply to both. 8. A taxonomic group that contains a common ancestor, but leaves out a descendant group is— a. paraphyletic

b. monophyletic c. polyphyletic d. a good cladistic group The correct answer is a—paraphyletic A. Answer a is correct. The correct answer is a— B. Answer b is incorrect. A monophyletic group contains a most recent common ancestor and all of its descendants. The correct answer is a— C. Answer c is incorrect. A polyphyletic group is one which contains descendants that are derived from more than a single most recent common ancestor. The correct answer is a— D. Answer d is incorrect. By definition, clades are monophyletic. 9. The forelimb of a bird and the forelimb of a rhinoceros— a. are homologous and symplesiomorphic b. are not homologous but are symplesiomorphic c. are homologous and synapomorphic d. are not homologous but are synapomorphic The correct answer is a—are homologous and symplesiomorphic A. Answer a is correct. As forelimbs, the traits were inherited from a common tetrapod ancestor that had forelimbs. They are also ancestral because as forelimbs, they are not derived and shared in form with that ancestor. The correct answer is a— B. Answer b is incorrect. If the traits are not homologous, it makes no sense to talk about them as symplesiomorphies. The correct answer is a— C. Answer c is incorrect. To be recognized as synapomorphies, they would have to be shared and derived traits in birds and rhinos relative to the common ancestor from which the trait evolved. The correct answer is a— D. Answer d is incorrect. Again, if the traits are not homologous, it makes no sense to talk about them as synapomorphic. 10. In order to determine polarity for different states of a character— a. there must be a fossil record of the groups in question b. genetic sequence data must be available c. an appropriate name for the taxonomic group must be selected

d. an outgroup must be identified The correct answer is d— A. Answer a is incorrect. The existence of fossils usually helps make a phylogenetic analysis more complete, but it is not required. In fact, the fossil record preserves so few of the many millions of species that have ever existed that there will be many cases where fossils will never be available. The correct answer is d— B. Answer b is incorrect. Genetic sequence data is just one set of characters that provide information about evolutionary relationships; it is no more or less required than morphological characters. The correct answer is d— C. Answer c is incorrect. A name for the taxonomic group is not required to establish polarity. The correct answer is d—an outgroup must be identified D. Answer d is correct. The method of determining polarity is based on an analysis of the character states in closely related groups that are not in the group under analysis. 11. A paraphyletic group— a. includes an ancestor and all of its descendants b. an ancestor and some of its descendants c. descendants of more than one common ancestor d. all of the above The correct answer is b— Answer a is incorrect. This is the definition for a monophyletic group. The correct answer is b—an ancestor and some of its descendants B. Answer b is correct. When one or more taxa are left out of a monophyletic group, it is paraphyletic. The example discussed in the chapter is birds as a kind of dinosaur. The correct answer is b— C. Answer c is incorrect. This is the definition of a polyphyletic group. The correct answer is b— D. Answer d is incorrect. Some of the answers above are not only incorrect, they are mutually exclusive. 12. Sieve tubes and sieve elements— a. are homoplastic because they have different function b. are homologous because they have similar function

c. are homoplastic because their common ancestor was single-celled d. are structures involved in transport within animals The correct answer is c— A. Answer a is incorrect. Homoplastic traits have similar function (usually due to convergence). The correct answer is c— B. Answer b is incorrect. Similarity of function is not enough. Even though it is true for sieve tubes and elements, the critical feature is independent derivation of the traits. The correct answer is c—are homoplastic because their common ancestor was singlecelled C. Answer c is correct. The most recent common ancestor did not have the trait. The correct answer is c— D. Answer d is incorrect. The trait occurs in plants. 13. The phylogeny of dinosaurs leading to birds— a. demonstrates that the first function of feathers was flight b. demonstrates that feathers and wings evolved simultaneously c. suggests that complex characters evolve rapidly, in one step d. reveals many transitional forms between modern birds and their ancestors The correct answer is d— A. Answer a is incorrect. It is clear that feathers appeared first in an animal that did not have forelimbs modified for flight. The correct answer is d— B. Answer b is incorrect. Feathers and wings arose in different taxa, leading to birds, The correct answer is d— C. Answer c is incorrect. The evidence (many transitional forms) suggests the opposite. The correct answer is d—reveals many transitional forms between modern birds and their ancestors D. Answer d is correct. The evolution of birds, and the characteristics that allow flight, involves many transitional forms, gradually accumulating important characteristics. 14. A phylogenetic analysis of HIV suggests— a. a single origin of HIV from primates b. multiple origins of HIV from several different primate species c. multiple origins of HIV from a single primate species

d. that SIV originated from HIV The correct answer is b— A. Answer a is incorrect. There is clear evidence of multiple origins of HIV. Furthermore, apparently some HIV strains have not spread rapidly at all. The correct answer is b—multiple origins of HIV from several different primate species B. Answer b is correct. There are several independent origins including from chimpanzees and the sooty mangabey. The correct answer is b— C. Answer c is incorrect. There is evidence of transmission from multiple species. The correct answer is b— D. Answer d is incorrect. HIV is always nested within SIV clades. Challenge Questions 1. List the synapomorphy and the taxa defined by that synapomorphy for the groups pictured in Figure 23.2. Name each group defined by a set of synapomorphies in a way that might be construed as informative about what kind of characters define the group. Answer—Naming of groups can be variable; names provided here are just examples. Jaws—shark, salamander, lizard, tiger, gorilla, human (jawed vertebrates); lungs— salamander, lizard, tiger, gorilla, human (terrestrial tetrapods); amniotic membrane— lizard, tiger, gorilla, human (amniote tetrapods); hair—tiger, gorilla, human (mammals); no tail—gorilla, human (humanoid primate); bipedal—human (human). 2. Identifying “outgroups” is a central component of cladistic analysis. As described on page 4, a group is chosen that is closely related to, but not a part of the group under study. If one does not know the relationships of members of the group under study, how can one be certain that an appropriate outgroup is chosen? Can you think of any approaches that would minimize the effect of a poor choice of outgroup? Answer—It would seem to be somewhat of a conundrum, or potentially circular; choosing a closely related species as an outgroup when we do not even know the relationships of the species of interest. One way of guarding against a poor choice for an outgroup is to choose several species as outgroups and examine how the phylogenetic hypothesis for the group of interest changes as a consequence of using different outgroups. If the choice of outgroup makes little difference, then that might increase one’s confidence in the phylogenetic hypotheses for the species of interest. On the other hand, if the choice makes a big difference (different phylogenetic hypotheses result when choosing different outgroups), that might at least lead to the conclusion that one cannot

be confident in inferring a robust phylogenetic hypothesis for the group of interest without collecting more data. 3. As noted in your reading, cladistics is a widely utilized method of systematics, and our classification system (taxonomy) is increasingly becoming reflective of our knowledge of evolutionary relationships. Using birds as an example, discuss the advantages and disadvantages of recognizing them as reptiles (cladistics) versus as a group separate and equal to reptiles (traditional). Answer—Recognizing that birds are reptiles potentially provides insight to the biology of both birds and reptiles. For example, some characteristics of birds are clearly of reptilian origin, such as feathers (modified scales), nasal salt secreting glands, and strategies of osmoregulation/excretion (excreting nitrogenous waste products as uric acid) representing ancestral traits, that continue to serve birds well in their environments. On the other hand, some differences from other reptiles (again, feathers) seem to have such profound significance biologically, that they overwhelm similarities visible in shared ancestral characteristics. For example, no extant nonavian reptiles can fly, or are endothermic and these two traits have created a fundamental distinction in the minds of many biologists. Indeed, many vertebrate biologists prefer to continue to distinguish birds from reptiles rather than emphasize their similarities even though they recognize the power of cladistic analysis in helping to shape classification. Ultimately, it may be nothing much more substantial than habit which drives the preference of some biologists to traditional classification schemes. 4. Across many species of limpets, loss of larval development and reversal from direct development appears to have occurred multiple times. Under the simple principle of parsimony, are changes in either direction merely counted equally in evaluating the most parsimonious hypothesis? If it is much more likely to lose a larval mode than to re-evolve it from direct development, should that be taken into account? How? Answer—In fact, such evolutionary transitions (the loss of the larval mode, and the reevolution of a larval mode from direct development) are treated with equal weight under the simplest form of parsimony. However, if it is known from independent methods (for example, developmental biology) that one kind of change is less likely than another (loss versus a reversal), these should and can be taken into account in various ways. The simplest way might be to assign weights based on likelihoods; two transitions from larval development to direct development is equal to one reversal from direct development back to a larval mode. In fact, there are such methods, and they are similar in spirit to the statistical approaches used to build specific models of evolutionary change rather than rely on simple parsimony (page 6).