Chapter 22: Reconstructing and Using Phylogenies

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1. Which of the following properties of HIV makes it difficult to trace the source of the virus from one person to the next?
a. The transmission of the virus involves very few (often just one) viral particles.
b. HIV evolves very slowly within the host.
c. The host can have a genetically diverse population of viruses.
d. Molecular phylogenies of viruses cannot be constructed.
e. None of the above

c. The host can have a genetically diverse population of viruses.

2. What accounts for HIV's rapid rate of evolution?
a. Its poor repair system causes it to have a high mutation rate.
b. It is subject to strong stabilizing selection.
c. Many viral particles are transmitted upon each infection.
d. Both b and c
e. None of the above

a. Its poor repair system causes it to have a high mutation rate.

3. The evolutionary relationship among organisms is known as
a. taxonomy.
b. phylogeny.
c. paraphyly.
d. synapomorphy.
e. homoplasy.

b. phylogeny.

4. The wasp genus Nasonia contains all of the descendants of the common ancestor of its members. This genus therefore would be called
a. a synapomorphy.
b. a polyphyly.
c. a clade.
d. parsimonious.
e. self-compatible.

c. a clade.

5. Drosophila yakuba and D. santomea are each other's closest relatives. Therefore, they are considered _______ species.
a. rooted
b. parapyletic
c. homologous
d. daughter
e. sister

e. sister

6. The study of biodiversity is called
a. homology.
b. homoplasy.
c. systematics.
d. phylogeny.
e. synapomorphy.

c. systematics.

7. The common ancestor of all of the species displayed in a phylogenetic tree lies at the _______ of the tree.
a. node
b. root
c. tip
d. taxon
e. None of the above

b. root

8. Which of the following is formed when two branches diverge from one another in a phylogenetic tree?
a. A population
b. A lineage
c. A node
d. All of the above
e. None of the above

c. A node

9. Which of the following statements is true?
a. Most of the species of animals and plants on Earth have been formally described.
b. New species are continually being discovered.
c. Our knowledge of the "Tree of Life" is nearing completion.
d. There are about one million species living on Earth.
e. None of the above

b. New species are continually being discovered.

10. Which of the following can never be homologous features?
a. DNA sequences
b. Anatomical structures
c. Inherited behavioral patterns
d. Secondary structures of proteins
e. All of the above have the potential to be homologous features.

e. All of the above have the potential to be homologous features.

11. Shared derived traits are also known as
a. homoplasies.
b. synapomorphies.
c. sympatries.
d. homologies.
e. paraphylies.

b. synapomorphies.

12. The antifreeze proteins found in fish that live in very cold waters has evolved independently in the Arctic and in the Antarctic, and not because of shared ancestry. Which of the following can be said about its evolution?
a. The antifreeze proteins in Arctic and Antarctic fish are homologous.
b. The antifreeze proteins in Arctic and Antarctic fish are homoplasies.
c. The Arctic and Antarctic fish form a clade.
d. Both a and c
e. None of the above

b. The antifreeze proteins in Arctic and Antarctic fish are homoplasies.

13. As adaptions for flight, the wings of bats and the wings of birds are an example of
a. synapomorphy.
b. evolutionary reversal.
c. monophyly.
d. paraphyly.
e. convergent evolution.

e. convergent evolution.

14. Which of the following statements is true?
a. All homoplastic traits are due to convergent evolution.
b. All homologous traits are homoplasies.
c. All synapomorphies are derived traits.
d. All derived traits are synapomorphies.
e. None of the above

c. All synapomorphies are derived traits.

15. Homoplasies can arise via
a. convergent evolution.
b. synapomorphies.
c. evolutionary reversals.
d. Both a and c
e. Both b and c

d. Both a and c

16. Snakes, which lack limbs, evolved from vertebrates that had legs. This is an example of
a. convergent evolution.
b. an evolutionary reversal.
c. a synapomorphy.
d. a homology.
e. None of the above

b. an evolutionary reversal.

17. The common ancestor of humans and the other "great apes" walked on all fours, while humans are bipeds. Bipedalism is thus the _______ trait.
a. ancestral
b. homoplasic
c. synapomorphic
d. derived
e. monophyletic

d. derived

18. Humans and African apes (chimpanzees, bonobos, and gorillas) share traits, such as elongated skulls and shortened canine teeth, which other related species do not have. These shared characteristics are called
a. homoplasies.
b. synapomorphies.
c. cladistics.
d. parsimonies.
e. None of the above

b. synapomorphies.

19. Which of the following cannot result in homoplasy?
a. Convergent evolution
b. Evolutionary reversals
c. Descent from a common ancestor
d. Similar selection pressures
e. All of the above can result in homoplasy.

c. Descent from a common ancestor

20. Species A and B have long wings, whereas species C has short wings. Which of the following pieces of evidence would best support the hypothesis that long wings are a synapomorphy?
a. Fossil evidence showing that the common ancestor of species A, B, and C had long wings
b. Fossil evidence showing that the common ancestor of species A, B, and C had short wings
c. DNA evidence showing that species A and C are sister species
d. DNA evidence showing that species B and C are sister species
e. Evidence showing that species A and B live in an environment that favors long wings, whereas species C lives in an environment that favors short wings

b. Fossil evidence showing that the common ancestor of species A, B, and C had short wings

21. Some species in a hypothetical family of beetles are winged, and others are wingless. Which of the following would be most useful in determining whether having wings or being wingless was the ancestral trait?
a. Homoplasies
b. Homologies
c. An outgroup
d. An ingroup
e. Maximum likelihood methods

c. An outgroup

22. According to the principle of parsimony, the best phylogenetic hypothesis is the one that requires the
a. fewest homologies.
b. most homoplasies.
c. fewest homoplasies.
d. most clades.
e. fewest clades.

c. fewest homoplasies.

23. Four different phylogenetic trees of a group of salamanders have been proposed. Trees A and B each require 12 homoplasies, but Tree A requires 14 synapomorphies and Tree B requires 13 synapomorphies. Tree C requires 15 homoplasies and 13 synapomorphies. Finally, Tree D requires 10 homoplasies and 15 synamorphies. According to the principle of parsimony, which tree or trees is the best?
a. Tree A
b. Tree B
c. Tree C
d. Tree D
e. Both Tree A and Tree B

d. Tree D

24. Which of the following is a limitation of the use of morphology in phylogenetic analysis?
a. Some morphological variation has a genetic basis.
b. Few morphological traits can be directly compared across distant taxa.
c. Some taxa exhibit little morphological diversity.
d. Both a and b
e. Both b and c

e. Both b and c

25. Which of the following findings led to the conclusion that sea squirts are more closely related to vertebrates than scientists had previously thought?
a. Data from CT scans
b. The finding that larvae have notochords
c. The discovery of behavioral similarities in sea squirts and vertebrates
d. Newly discovered fossils in China
e. None of the above

b. The finding that larvae have notochords

26. Which of the following kinds of data would be the most useful for distinguishing ancestral traits from derived traits?
a. Developmental data
b. Behavioral data
c. Paleontological data
d. Morphological data
e. Molecular data

c. Paleontological data

27. In systematics and phylogeny, the fossil record is especially important because
a. most groups are well represented.
b. it provides the absolute timing of evolutionary events.
c. random mutations make most biochemical methods unreliable.
d. DNA can be extracted from nearly all ancient fossils and then analyzed.
e. it provides the only data that is useful in reconstructing the past.

b. it provides the absolute timing of evolutionary events.

28. Information about which of the following types of behavior would be least useful in reconstructing phylogenies?
a. Inherited behavior
b. Locomotion behavior
c. Foraging behavior
d. Learned behavior
e. Mating behavior

d. Learned behavior

29. Repetitive DNA sequences usually evolve very quickly. Based on this fact, molecules that have a rapid mutation rate are used to study relationships among
a. very closely related species.
b. all organisms.
c. extinct organisms.
d. duplicated genes.
e. organisms that diverged long ago.

a. very closely related species.

30. Mitochondrial DNA is most useful for phylogenetic analysis
a. in the study of relatively ancient relationships.
b. for groups with few species that have survived to the present.
c. of closely related species.
d. of prokaryotes.
e. Both a and b

c. of closely related species.

31. Histone genes, which evolve very slowly, would most likely be used to study
a. relationships among very similar species.
b. relationships within the same genera.
c. relationships among extinct organisms.
d. organisms that diverged long ago.
e. None of the above

e. None of the above

32. As compared with parsimony, a major advantage of maximum likelihood methods is that they
a. are computationally easier.
b. can be used with molecular data.
c. incorporate more information about evolutionary change.
d. All of the above
e. None of the above

c. incorporate more information about evolutionary change.

33. A major disadvantage of maximum likelihood methods is that they
a. are difficult to fit into a statistical framework.
b. require explicit models of evolutionary change.
c. can be used only on molecular data.
d. can be used only for closely related species.
e. None of the above

b. require explicit models of evolutionary change.

34. Studies testing the creation of phylogenies of phage T7 showed that
a. phylogenetic methods accurately reconstruct the evolutionary history of phage T7.
b. phylogenetic methods perform poorly in reconstructing evolutionary history.
c. the molecular clock is invalid.
d. Both a and c
e. Both b and c

a. phylogenetic methods accurately reconstruct the evolutionary history of phage T7.

35. In the phylogenetic studies, researchers added mutagens over the course of the studies. This method _______ the accuracy of the reconstruction, because the mutagen _______.
a. calls into question; increases the amount of homoplasy
b. calls into question; decreases the amount of homoplasy
c. calls into question; increases the mutation rate
d. confirms; increases the amount of homoplasy
e. confirms; decreases the amount of homoplasy

e. confirms; decreases the amount of homoplasy

36. Species of plants that have evolved mechanisms to prevent self-fertilization are said to be
a. selfing.
b. self-incompatible.
c. synapomorphous.
d. synchronous.
e. None of the above

b. self-incompatible.

37. Which of the following statements about HIV or AIDS is false?
a. AIDS is a zoonotic disease.
b. HIV likely entered into humans from only one animal species.
c. HIV likely entered human populations from hunters who cut themselves as they were skinning animals.
d. HIV likely originated in Africa.
e. All of the above are true; none is false.

b. HIV likely entered into humans from only one animal species.

38. Which of the following statements about HIV is true?
a. HIV in humans forms a clade.
b. All HIV variants in humans were derived from viruses in chimpanzees.
c. HIV likely entered the human population from hunters who cut themselves as they were skinning primates.
d. Both a and b
e. Both a and c

c. HIV likely entered the human population from hunters who cut themselves as they were skinning primates.

39. Studies of female platyfish, whose male counterparts have a variety of tail shapes, show that the females have a preference for male fish with artificial swordlike structures attached to their tails. This observation is most consistent with
a. the notion of a molecular clock.
b. the maximum likelihood principle.
c. the sensory exploitation hypothesis.
d. the principle of homoplasy.
e. the parsimony principle.

c. the sensory exploitation hypothesis.

40. Which of the following scientists proposed the molecular clock hypothesis?
a. Carolus Linnaeus
b. James Watson
c. Linus Pauling
d. Motoo Kimura
e. Charles Darwin

c. Linus Pauling

41. Which of the following statements about the molecular clock is true?
a. It requires monophyletic taxa.
b. It requires calibration with independent data, such as from the fossil record.
c. It requires binomial nomenclature.
d. Both a and b
e. Both b and c

b. It requires calibration with independent data, such as from the fossil record.

42. Which of the following concepts adds a dimension of time to a phylogenetic analysis?
a. Maximum likelihood
b. Parsimony
c. Synapomorphy
d. Occam's razor
e. A molecular clock

e. A molecular clock

43. Humans and chimpanzees diverged about 6 million years ago. If 12 nucleotide substitutions have occurred between human and chimpanzee lineages in a sequence of mitochondrial DNA, and 36 have occurred between humans and gibbons, humans and gibbons, according to the molecular clock, separated _______ million years ago.
a. 2
b. 6
c. 12
d. 18
e. 36

d. 18

44. Suppose that mice and humans differ by 20 substitutions in their globin genes, and rats and mice differ by 5 substitutions. On the basis of other evidence, we know that the ancestor to humans and mice lived 80 million years ago. Assuming the molecular clock is operating, rats and mice split from each other _______ million years ago.
a. 5
b. 10
c. 20
d. 40
e. 80

c. 20

45. Based on the phylogenetic studies and the use of the molecular clock, scientists have determined that humans most likely were first infected with HIV in
a. 1930.
b. 1950.
c. 1965.
d. 1975.
e. 1985.

a. 1930.

46. Studies reconstructing the opsin gene of the common ancestor of birds, dinosaurs, and crocodiles showed that the
a. opsin was red shifted.
b. opsin was blue shifted.
c. common ancestor was likely nocturnal.
d. Both a and c
e. Both b and c

d. Both a and c

47. The system of binomial nomenclature was developed by
a. Motoo Kimura.
b. Emile Zuckerkandl.
c. Carolus Linneaus.
d. Charles Darwin.
e. Alfred Russell Wallace.

c. Carolus Linneaus.

48. Below is a list of several species names. Which of these is not spelled or written correctly?
a. Homo erectus
b. Drosophila Simulans
c. H. sapiens
d. Tribolium castaneum
e. Gavia immer

b. Drosophila Simulans

49. Which of the following is the largest taxon?
a. Genus
b. Family
c. Species
d. Order
e. Class

e. Class

50. Which of the following is the smallest taxon?
a. Kingdom
b. Family
c. Phylum
d. Class
e. Order

b. Family

51. Which of the following represents a correct size ranking of taxonomic categories, from the smallest to the largest?
a. Family, genus, order, species
b. Species, genus, order, family
c. Species, genus, family, order
d. Genus, species, family, order
e. None of the above

c. Species, genus, family, order

52. In modern systematics, each family name is based on
a. the name of the order to which it belongs.
b. a characteristic common to all members.
c. the name of a member genus.
d. the name of the largest member species.
e. the Latin name for the organisms.

c. the name of a member genus.

53. In biological classification, the suffix "-aceae" refers to a(n)
a. genus of plants.
b. genus of animals.
c. family of plants.
d. family of animals.
e. order of plants.

c. family of plants.

54. The suffix "-idae" (e.g., Sciuridae) refers to organisms of which Kingdom?
a. Bacteria
b. Fungi
c. Plant
d. Animal
e. All of the above

d. Animal

55. A taxon that includes a common ancestor, all descendants of that ancestor, and no other organisms is considered to be
a. paraphyletic.
b. polyphyletic.
c. synapomorphous.
d. monogamous.
e. monophyletic.

e. monophyletic.

56. A group that includes the common ancestor and some, but not all, of its descendants is considered to be
a. paraphyletic.
b. polyphyletic.
c. synapomorphous.
d. monogamous.
e. monophyletic.

a. paraphyletic.

57. Which of the following statements about monophyletic groups is true?
a. They are clades.
b. They include all descendants of the common ancestor of the members of the group.
c At least two "cuts" are required to remove a monophyletic group from a phylogenetic tree.
d. Both a and b
e. Both b and c

d. Both a and b

58. Which of the following types of groups can be removed by a single "cut" to a phylogenetic tree, without the removal of any other species outside the group?
a. Paraphyletic
b. Polyphyletic
c. Monophyletic
d. All of the above
e. None of the above

c. Monophyletic

59. Which of the following statements about taxonomy is true?
a. The use of large biological databases makes it less important that each species be given its own unique name.
b. The fields of zoology, botany, and microbiology historically used the same set of taxonomic rules.
c. If the same name is inadvertently given to two different species, a replacement name is given to the one that was named first.
d. All of the above
e. None of the above

e. None of the above

60. According to the practices of biological nomenclature, if the same name is inadvertently given to two different species,
a. the species named first keeps the name and the second species is given a replacement name.
b. the species named last keeps the name and the species named first is given a replacement name.
c. a coin is flipped.
d. the head of the Cladistics Society chooses which species keeps the name.
e. both species are given new names.

a. the species named first keeps the name and the second species is given a replacement name.

61. Which of the following practices tends to hinder taxonomic work?
a. The use of monophyletic groups
b. The historical separation of botany and zoology
c. The use of universal data bases
d. A commonly accepted set of rules
e. All of the above

b. The historical separation of botany and zoology

1. Biologists refer to descriptions of the evolutionary relationships among organisms as _______.

phylogenies

2. Any taxon that consists of all the evolutionary descendants of a common ancestor is called a _______.

clade (also monophyletic group)

3. Tetramorium hispidum and T. spinosum are two species of ants that are related more closely to each other than they are to any other species. Thus, they are known as _______ species.

sister

4. In the last few decades, the number of studies in the study and classification of biodiversity, also called _______, has increased dramatically.

systematics

5. Derived traits that are shared among a group of species are known as _______.

synapomorphies

6. The phenomenon whereby traits may evolve independently in unrelated species because the species are subject to similar selection pressures is known as _______ evolution.

convergent

7. Flies have only a single pair of functional wings, but their ancestors had two pair of wings. Thus, having two pairs of wings is a(n) _______ trait.

ancestral

8. Traits that are similar in different species for reasons other than a shared common ancestor are known as _______.

homoplasies

9. Modern horses have a single toe on each foot, although their ancestors had feet with several digits. The single toe is thus a(n) _______ trait.

derived

10. Gibbons are more distantly related to humans, chimpanzees, and gorillas than the three are related to one another. Thus, gibbons are considered to be a(n) _______ in relation to the other three.

outgroup

11. When constructing phylogenetic trees, biologists often rely on the principle of _______, which states that the preferred phylogeny is the one that requires the fewest homoplasies.

parsimony

12. In addition to the practice described above, biologists reconstructing phylogenies have also employed _______ methods, which make use of a mathematical model of evolutionary change.

maximum likelihood

13. The hypothesis that the rate at which a particular molecule evolved among different species is consistent enough to serve as a guide to evolutionary divergence is known as the _______ hypothesis

molecular clock

14. To make inferences about the vision of the ancestor of birds, dinosaurs, and crocodiles, biologists have used phylogenetic methods to reconstruct a pigment called _______, which was involved in the ancestor's vision.

opsin

15. Our system of classification is derived from one developed by the eighteenth-century Swedish biologist _______.

Carolus Linnaeus

16. Tribolium castaneum is a beetle found in flour and other stored products. Tribolium is the name of the _______ to which this beetle belongs.

genus

17. Phyla are composed of _______, which in turn are composed of _______.

classes; orders

18. In plant classification, the suffix _______ is used to denote names of families.

"-aceae"

19. A taxon that includes the common ancestor and some, but not all, of its descendants, is said to be _______.

paraphyletic

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