Deck 16: Reconstructing and Using Phylogenies

Question 1

Shared derived traits are also known as

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

Answer 1

A

Question 2

The common ancestor of humans and the other "great apes" walked on all fours,whereas humans are bipeds.Bipedalism is thus the _______ trait.

A) ancestral
B) homoplasic
C) synapomorphic
D) derived
E) monophyletic

Answer 2

D

Question 3

Which of the following features can never be homologous?

A) DNA sequences
B) Anatomical structures
C) Inherited behavioral patterns
D) Secondary structures of proteins
E) All of the above can be homologous features.

Answer 3

E

Question 4

The evolutionary relationship among organisms is known as

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

Question 5

Use the following to answer questions :
Refer to the figure below.
About when did the common ancestor of humans,chimpanzees,gorillas,and orangutans last exist?

A) 5 million years ago
B) 7.5 million years ago
C) 10 million years ago
D) 12.5 million years ago
E) 20 million years ago

Question 6

Which statement about systematics 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) All homoplasies are homologous traits.

Question 7

Which statement about red fluorescent pigments is true?

A) They are easier to synthesize than other pigments.
B) They existed in the ancestor of present-day corals.
C) They evolved in a single step from green pigments.
D) They do not penetrate tissues as well as green pigments do.
E) They are found naturally in some corals.

Question 8

The wasp genus Nasonia contains all of the descendants of the members' common ancestor.This genus therefore would be called

A) a synapomorphy.
B) a polyphyly.
C) parsimonious.
D) a clade.
E) rooted.

Question 9

Humans and African apes (chimpanzees,bonobos,and gorillas)share traits such as elongated skulls and shortened canine teeth,which other more distantly related species do not have.These characteristics are called

A) homoplasies.
B) synapomorphies.
C) cladistics.
D) parsimonies.
E) evolutionary reversals.

Question 10

Which statement about phylogenies is true?

A) Taxa cannot be placed within other taxa.
B) Rotating lineages around nodes changes the meaning of the information contained within the phylogenetic tree.
C) The evolutionary distance between clades can be determined by examining the vertical distance between them.
D) Any group of species that we designate with a name is a clade.
E) None of the above

Question 11

Use the following to answer questions :
Refer to the figure below.
How long ago did the lineage leading to humans and chimpanzees diverge from the lineage leading to gorillas?

A) 1 million years ago
B) 3 million years ago
C) 5 million years ago
D) 7 million years ago
E) 12 million years ago

Question 12

The common ancestor of all of the species displayed in a phylogenetic tree lies at the _______ of the tree.

A) node
B) taxon
C) tip
D) root
E) twig

Question 13

Drosophila yakuba and D.santomea are the closest relatives to each other.Therefore,they are considered _______ species.

A) rooted
B) sister
C) homologous
D) daughter
E) parapyletic

Question 14

What is formed when any two branches diverge in a phylogenetic tree?

A) A node
B) A lineage
C) A population
D) A root
E) A module

Question 15

Snakes,which lack limbs,evolved from vertebrates that had legs.The limbs of snakes disappeared by _______ and the backbones of snakes are a _______.

A) convergent evolution;synapomorphy
B) an evolutionary reversal;synapomorphy
C) convergent evolution;homoplastic trait
D) an evolutionary reversal;homoplastic trait
E) an evolutionary reversal;heteroplastic trait

Question 16

The antifreeze proteins found in fish that live in very cold waters of the Arctic and Antarctic have evolved independently,not because of shared ancestry.Based on this information,which statement is true?

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) The antifreeze proteins evolved by evolutionary reversals.
E) Convergent evolution does not occur for antifreeze proteins.

Question 17

Matz's discovery of coral proteins that fluoresce in red light was a valuable extension of the Noble Prize-winning work that produced green fluorescent protein because

A) a red pigment degrades much more slowly than a green pigment does.
B) unlike green light,red light does not penetrate tissues.
C) red light penetrates tissues more readily than green light does.
D) red pigment attracts jellyfish.
E) red pigment repels jellyfish.

Question 18

Use the following to answer questions :
Refer to the figure below.
Not counting the root,how many nodes are present?

A) 0
B) 1
C) 2
D) 3
E) 4

Question 19

As adaptations for flight,the wings of bats and the wings of birds are an example of

A) a synapomorphy.
B) evolutionary reversal.
C) a monophyly.
D) a paraphyly.
E) convergent evolution.

Question 20

The study and classification of biodiversity is called

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

Question 21

What is a major advantage of maximum likelihood methods as compared with parsimony methods?

A) Maximum likelihood methods are computationally easier.
B) Maximum likelihood methods can be used with molecular data.
C) Unlike parsimony methods,maximum likelihood methods can be used for studying relationships among very similar organisms.
D) Unlike parsimony methods,maximum likelihood methods can be used for studying relationships among distantly related organisms.
E) Maximum likelihood methods incorporate more information about evolutionary change.

Question 22

Use the following to answer questions :
Refer to figure below.
Which synapomorphy unites the salamander and the lizard?

A) Feathers
B) A gizzard
C) Keratinous scales
D) Claws or nails
E) None of the above

Question 23

Use the following to answer questions :
Refer to figure below.
The position of which pair of taxa could be reversed without changing the meaning of the tree?

A) Crocodile and pigeon
B) Crocodile and lizard
C) Mouse and pigeon
D) Mouse and crocodile
E) Chimpanzee and pigeon

Question 24

Which trait would be least useful in a phylogenetic analysis?

A) A trait that is altered easily by small changes in temperature
B) A trait that involves genetically inherited behaviors
C) A trait that is detectible early in development
D) A trait that can be studied in museum specimens
E) A trait that is encoded by mitochondrial DNA

Question 25

According to the principle of parsimony,the best phylogenetic hypothesis is the one that requires the

A) fewest homoplasies.
B) most homoplasies.
C) fewest homologies.
D) most clades.
E) fewest clades.

Question 26

Species A and species B have long wings,whereas species C has short wings.Which piece 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 short wings and evidence that species A and B are sister species
B) Fossil evidence showing that the common ancestor of species A,B,and C had long wings and evidence that species A and B are sister species
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 27

Use the following to answer questions :
Refer to figure below.
Which synapomorphy unites the pigeon and the lizard?

A) Feathers
B) A gizzard
C) Fur
D) Keratinous scales
E) Mammary glands

Question 28

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 synapomorphies.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 29

Use the following to answer questions :
Consider five species of toads.Species A and B are sister species.Species C and D are also sister species.The clade containing species A and B is sister to the clade containing species C and D.Species E is sister to the clade containing A,B,C,and D.
How many additional nodes would be found in a phylogenetic tree of species A,B,C,D,and E?

A) 1
B) 2
C) 3
D) 5
E) None

Question 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 of animals.
D) of prokaryotes.
E) when one is tracking the paternal lineage.

Question 31

Histone genes,which evolve very slowly,would most likely be used to study relationships

A) among very similar species.
B) within the same genera.
C) among extinct organisms.
D) among phyla of animals.
E) among species of apes.

Question 32

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 33

Which process 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 34

Which finding 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) The development of maximum likelihood methods

Question 35

Members of genus X,a hypothetical taxon of invertebrates,have antennae with a variable number of segments.Species A and B have 10 segments;species C and D have 9 segments;species E has 8 segments;and species F has 7 segments.In all other genera in this family (including genus Y,the sister genus of genus X),all species have antennae with 10 segments.Which character state most likely is a synapomorphy that would be useful for determining evolutionary relationships within genus X?

A) 10-segment antennae in species A and B
B) 10-segment antennae in genus Y and in two species of genus X
C) Antennae with fewer than 10 segments in species C,D,E,and F
D) 8-segment antennae in species E
E) 7-segment antennae in species F

Question 36

Use the following to answer questions :
Consider five species of toads.Species A and B are sister species.Species C and D are also sister species.The clade containing species A and B is sister to the clade containing species C and D.Species E is sister to the clade containing A,B,C,and D.
Not counting the root as a node,how many nodes would be found in a phylogenetic tree containing just species A,B,C,and D?

A) 1
B) 2
C) 3
D) 4
E) 5

Question 37

Information about _______ behavior would be least useful in reconstructing phylogenies.

A) inherited
B) locomotion
C) foraging
D) learned
E) mating

Question 38

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) organisms that diverged long ago.
B) all organisms.
C) extinct organisms.
D) phyla of animals.
E) very closely related species.

Question 39

Use the following to answer questions :
Consider five species of toads.Species A and B are sister species.Species C and D are also sister species.The clade containing species A and B is sister to the clade containing species C and D.Species E is sister to the clade containing A,B,C,and D.
Which species is most likely to share synapomorphies with species C?

A) Species A
B) Species B
C) Species D
D) Species E
E) All of the above are equally likely to share synapomorphies with species C.

Question 40

Use the following to answer questions :
Consider five species of toads.Species A and B are sister species.Species C and D are also sister species.The clade containing species A and B is sister to the clade containing species C and D.Species E is sister to the clade containing A,B,C,and D.
Which species is most likely to share synapomorphies with species E?

A) Species A
B) Species B
C) Species C
D) Species D
E) All of the above are equally likely to share synapomorphies with species E.

Question 41

Which scientist proposed the molecular clock hypothesis?

A) Carolus Linnaeus
B) Linus Pauling
C) James Watson
D) Roger Tsien
E) Charles Darwin

Question 42

The system of binomial nomenclature was developed by

A) Roger Tsien.
B) Emile Zuckerkandl.
C) Charles Darwin.
D) Carolus Linnaeus.
E) Alfred Russel Wallace.

Question 43

In studies of the sensory exploitation hypothesis,which observation would most challenge the validity of the hypothesis?

A) The genes were evolving in a manner consistent with the molecular clock.
B) The genes were evolving in a manner inconsistent the molecular clock.
C) The female preference for swords had evolved before swords evolved in males.
D) The female preference for swords had evolved after swords evolved in males.
E) Males with swords had a shorter life span than males without swords.

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 hypothesis,separated _______ million years ago.

A) 2
B) 6
C) 12
D) 18
E) 36

Question 45

Biologists have used _______ to experimentally verify the accuracy of phylogenetic methods.

A) bacteriophages
B) bacteria
C) yeast
D) nematodes
E) mustard plants

Question 46

Transitions occur _______ frequently than transversions;thus using transitions,as opposed to transversions,will be more useful for reconstructing phylogenetic relationships between _______ organisms.

A) more;closely related
B) less;extinct
C) more;extinct
D) less;closely related
E) more;distantly related

Question 47

A major challenge 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 with molecular data.
D) can be used only for closely related species.
E) can be used only for distantly related species.

Question 48

How did researchers ensure that experiments testing the phylogeny reconstruction method using bacteriophage T7 matched the levels of homoplasy seen in real data sets?

A) They added mutagens to the phage.
B) They used a molecular clock.
C) They used maximum likelihood methods.
D) They used only monophyletic groups.
E) They subjected the viruses to strong natural selection.

Question 49

The figure below shows a phylogenetic tree of immunodeficiency viruses.Suppose biologists had all of the information shown but did not have samples from sooty mangabeys.Under these conditions,what would you infer as the most likely source of HIV-2?

A) Chimpanzees
B) Sykes' monkeys
C) African green monkeys
D) Sun-tailed monkeys
E) Mandrills

Question 50

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) self-compatible.

Question 51

Which nucleotide change is a transition?

A) A to C
B) C to A
C) C to T
D) T to A
E) T to G

Question 52

Which statement 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) It states that all genes evolve at the same rate.
E) It can only be used to date very ancient events (more than about a million years ago).

Question 53

Studies of female platyfish,whose male counterparts have a variety of tail shapes,show that the females prefer male fish with artificial swordlike structures attached to their tails.This observation is most consistent with the

A) notion of a molecular clock.
B) maximum likelihood principle.
C) sensory exploitation hypothesis.
D) principle of homoplasy.
E) parsimony principle.

Question 54

Which study led biologists to infer that the ancient archosaur was active during the night?

A) Ancestral state reconstruction suggesting that these animals had red fluorescent protein
B) Ancestral state reconstruction suggesting that these animals had green fluorescent protein
C) Ancestral state reconstruction suggesting that these animals had opsins that were shifted toward the red
D) Molecular clock analysis suggesting little evolutionary change from the archosaurs to their nocturnal descendants
E) Molecular clock analysis suggesting a great deal of evolutionary change from the archosaurs to their nocturnal descendants

Question 55

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 56

Phylogenetic studies of self-incompatibility in Leptosiphon

A) revealed that self-incompatibility evolved only once.
B) showed that self-incompatibility was the ancestral trait.
C) supported the sensory exploitation hypothesis.
D) could not be performed due to lack of a molecular clock.
E) demonstrated convergent evolution of self-incompatibility.

Question 57

Which of the following represents a legitimate challenge or limitation of the studies presented in the text that examine the accuracy of phylogenetic reconstruction?

A) The level of homoplasy in the experimental studies was much lower than in most studies that reconstruct phylogenies.
B) The experimental studies were performed only in viruses,not in eukaryotes.
C) Different genes evolve at different rates.
D) The experimental studies did not use an outgroup.
E) The organisms in the experimental studies had a known history.

Question 58

Which is an important assumption in dating evolutionary distances by the molecular clock?

A) Different genes evolve at the same rate in the same lineage.
B) A particular gene evolves at the same rate in all lineages of interest.
C) Different genes evolve at different rates in the same lineage.
D) The events being dated happened more than about a million years ago.
E) The events being dated happened less than about a million years ago.

Question 59

Which statement about HIV or AIDS is false?

A) AIDS is a zoonotic disease.
B) HIV likely originated in Africa.
C) HIV likely entered human populations from hunters who cut themselves as they were skinning animals.
D) HIV likely entered humans from only one animal species.
E) Phylogenetic methods have been used to trace the evolutionary history of HIV.

Question 60

HIV was transferred to humans from

A) chimpanzees only.
B) chimpanzees and gorillas.
C) gorillas and sooty mangabeys.
D) gorillas only.
E) chimpanzees and sooty mangabeys.

Question 61

Which sequence represents a correct size ranking of taxonomic categories,from the smallest to the largest?

A) Species,genus,family,order
B) Species,genus,order,family
C) Family,genus,order,species
D) Genus,species,family,order
E) Genus,species,order,family

Question 62

Which of the following is the smallest taxon?

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

Question 63

The ratites are a group of flightless birds comprising the ostrich,emu,cassowaries,rheas,and kiwis.All share certain morphological similarities (such as a breastbone without a keel)not found in other birds,but they live on different continents.In the past,some ornithologists regarded their similarities as homoplasies,but they are now thought to be synapomorphies.Based on this information,you would conclude that the ratites were once regarded as a _______ group but are now believed to be _______.

A) polyphyletic;paraphyletic
B) paraphyletic;monophyletic
C) polyphyletic;monophyletic
D) monophyletic;polyphyletic
E) monophyletic;paraphyletic

Question 64

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 65

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) Monophyletic only
B) Polyphyletic only
C) Paraphyletic only
D) Paraphyletic and polyphyletic
E) Monophyletic and polyphyletic

Question 66

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 to determine which species keeps the name.
D) the head of the Cladistics Society chooses which species keeps the name.
E) both species are given new names.

Question 67

The suffix "-idae" (e.g. ,Sciuridae)refers to organisms of which kingdom?

A) Bacteria
B) Fungi
C) Plant
D) Animal
E) Protist

Question 68

Phylogenetic analysis of HIV and nonhuman SIV demonstrates that HIV is _______ and SIV is _______.

A) monophyletic;monophyletic
B) monophyletic;paraphyletic
C) paraphyletic;monophyletic
D) polyphyletic;monophyletic
E) polyphyletic;paraphyletic

Question 69

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 Latin name for the organisms.
D) the name of the largest member species.
E) the name of a member genus.

Question 70

Which statement about a monophyletic taxon is false?

A) It is a clade.
B) It includes all descendants of the common ancestor of the members of the group.
C) At least two "cuts" are required to remove it from a phylogenetic tree.
D) It is a historical group of related species.
E) It is a complete branch on the tree of life.

Question 71

Which of the following is the largest taxon?

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

Question 72

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

Question 73

According to Linnaean nomenclature,which species name is not written correctly?

A) Homo erectus
B) Drosophila Simulans
C) H.sapiens
D) Tribolium castaneum
E) Gavia immer

Question 74

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 75

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

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.