Deck 22: Reconstructing and Using Phylogenies

Question 1

The parsimony principle can be used to infer phylogenetic trees because

A) evolution is nearly always parsimonious.
B) it is logical to adopt the simplest hypothesis capable of explaining the known facts.
C) once a trait changes, it never reverses condition.
D) all species have an equal probability of evolving.
E) closely related species are always very similar to one another.

Answer 1

C

Question 2

Which of the following groups have separate sets of rules for nomenclature?

A) Animals
B) Plants and fungi
C) Bacteria
D) Viruses
E) All of the above

Answer 2

B

Question 3

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

Answer 3

C

Question 4

A shared derived trait, used as the basis for inferring a monophyletic group, is called

A) a synapomorphy.
B) a homoplasy.
C) a parallel trait.
D) a convergent trait.
E) a phylogeny.

Question 5

If two scientific names are proposed for the same species, how do taxonomists decide which name should be used?

A) The name that provides the most accurate description of the organism is used.
B) The name that was proposed most recently is used.
C) The name that was used in the most recent taxonomic revision is used.
D) The first name to be proposed is used, unless that name was previously used for another species.
E) Taxonomists use whichever name they prefer.

Question 6

Which of the following is not true of maximum likelihood or parsimony methods for inferring phylogeny?

A) The maximum likelihood method requires an explicit model of evolutionary character change.
B) The parsimony method is computationally easier than the maximum likelihood method.
C) The maximum likelihood method is easier to treat in a statistical framework.
D) The maximum likelihood method is most often used with molecular data.
E) Parsimony is usually used to infer time on a phylogenetic tree.

Question 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

Question 8

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

Question 9

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

Question 10

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

Question 11

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

Question 12

The study of biodiversity is called

A) homology.
B) homoplasy.
C) systematics.
D) phylogeny.
E) synapomorphy.

Question 13

Phylogenetic trees may be constructed for

A) genes.
B) species.
C) major evolutionary groups.
D) viruses.
E) All of the above

Question 14

The evolutionary relationship among organisms is known as

A) taxonomy.
B) phylogeny.
C) paraphyly.
D) synapomorphy.
E) homoplasy.

Question 15

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.

Question 16

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.

Question 17

A clade is

A) a type of phylogenetic tree.
B) a group of evolutionarily related species that share a common ancestor.
C) a tool for constructing phylogenetic trees.
D) an extinct species.
E) an ancestral species.

Question 18

Which of the following are commonly used to infer phylogenetic relationships among plants but not among animals?

A) Nuclear genes
B) Chloroplast genes
C) Mitochondrial genes
D) Ribosomal RNA genes
E) Protein-coding genes

Question 19

Taxonomists strive to include taxa in biological classifications that are

A) monophyletic.
B) paraphyletic.
C) polyphyletic.
D) homoplastic.
E) monomorphic.

Question 20

Convergent evolution and evolutionary reversal are two sources of

A) homology.
B) parsimony.
C) synapomorphy.
D) monophyly.
E) homoplasy.

Question 21

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.

Question 22

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

Question 23

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

Question 24

Shared derived traits are also known as

A) homoplasies.
B) synapomorphies.
C) sympatries.
D) homologies.
E) paraphylies.

Question 25

Homoplasies can arise via

A) convergent evolution.
B) synapomorphies.
C) evolutionary reversals.
D) Both a and c
E) Both b and c

Question 26

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.

Question 27

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

Question 28

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

Question 29

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

Question 30

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

Question 31

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

Question 32

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

Question 33

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.

Question 34

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

Question 35

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

Question 36

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.

Question 37

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

Question 38

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

Question 39

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

Question 40

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.

Question 41

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.

Question 42

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

Question 43

Which of the following is the smallest taxon?

A) Kingdom
B) Family
C) Phylum
D) Class
E) Order

Question 44

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

Question 45

The system of binomial nomenclature was developed by

A) Motoo Kimura.
B) Emile Zuckerkandl.
C) Carolus Linneaus.
D) Charles Darwin.
E) Alfred Russell Wallace.

Question 46

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

Question 47

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

Question 48

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

Question 49

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

Question 50

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.

Question 51

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

Question 52

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.

Question 53

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

Question 54

Which of the following is the largest taxon?

A) Genus
B) Family
C) Species
D) Order
E) Class

Question 55

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

Question 56

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

Question 57

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

Question 58

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

Question 59

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

Question 60

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

Question 61

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.

Question 62

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

Question 63

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.

Question 64

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.

Question 65

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

Question 66

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

Question 67

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

Question 68

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

Question 69

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.

Question 70

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

Question 71

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

Question 72

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.

Question 73

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

Question 74

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.

Question 75

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.

Question 76

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.

Question 77

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

Question 78

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

Question 79

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

Question 80

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