Deck 20: Phylogeny

Question 1

Which of the following is true of all horizontally oriented phylogenetic trees, in which time advances to the right?

A) Each branch point represents a point in absolute time.
B) Organisms represented at the base of such trees are descendants of those represented at higher levels.
C) The fewer branch points that occur between two taxa, the more divergent their DNA sequences should be.
D) The common ancestor represented by the rightmost branch point existed more recently in time than the common ancestors represented at branch points located to the left.

Answer 1

D

Question 2

Cladograms (a type of phylogenetic tree) constructed from evidence from molecular systematics are based on similarities in

A) morphology.
B) the pattern of embryological development.
C) biochemical pathways.
D) mutations to homologous genes.

Answer 2

D

Question 3

When using a cladistic approach to systematics, which of the following is considered most important for classification?

A) shared primitive characters
B) analogous primitive characters
C) shared derived characters
D) the number of homoplasies

Answer 3

C

Question 4

Which of the following are the best examples of homologous structures?

A) bones in the bat wing and bones in the human forelimb
B) owl wing and hornet wing
C) bat wing and bird wing
D) eyelessness in the Australian mole and eyelessness in the North American mole

Question 5

What evidence suggests that limbless bodies are the result of convergent evolution of snakes and lizards?

A) Snakes and lizards with limbless bodies evolved from different ancestors of legged lizards.
B) Limbless bodies do not share a most recent common ancestor.
C) Three traits are shared by all snakes.
D) Species adapted to their environments.

Question 6

The various taxonomic levels (genera, classes, etc.) of the hierarchical classification system differ from each other on the basis of

A) how widely the organisms assigned to each are distributed throughout the environment.
B) their inclusiveness.
C) the relative genome sizes of the organisms assigned to each.
D) morphological characters that are applicable to all organisms.

Question 7

Linnaeus was a "fixist" who believed that species remained fixed in the form in which they had been created. Linnaeus would have been uncomfortable with

A) classifying organisms using the morphospecies concept.
B) the scientific discipline known as taxonomy.
C) phylogenies.
D) nested, ever-more inclusive categories of organisms.

Question 8

A potential source of confusion in constructing a phylogeny tree is similarity between organisms that is due to

A) convergent evolution.
B) adaptation.
C) shared ancestry.
D) homology.

Question 9

A polytomy on a phylogenetic tree represents

A) sister taxa.
B) a lineage that diverges from all other lineages in its group.
C) most recent common ancestor.
D) insufficient data to determine lineage relationship.

Question 10

If organisms A, B, and C belong to the same class but to different orders and if organisms D, E, and F belong to the same order but to different families, which of the following pairs of organisms would be expected to show the greatest degree of structural homology?

A) A and B
B) A and C
C) B and D
D) D and F

Question 11

Which of the following are problematic when the goal is to construct phylogenies that accurately reflect evolutionary history?

A) polyphyletic taxa
B) paraphyletic taxa
C) monophyletic taxa
D) polyphyletic and paraphyletic taxa

Question 12

Some molecular data place the giant panda in the bear family (Ursidae) but place the lesser panda in the raccoon family (Procyonidae). Consequently, the morphological similarities of these two species are probably due to

A) inheritance of acquired characteristics.
B) sexual selection.
C) inheritance of shared derived characters.
D) possession of analogous structures.

Question 13

The importance of computers and of computer software to modern cladistics is most closely linked to advances in

A) radiometric dating.
B) fossil discovery techniques.
C) Linnaean classification.
D) molecular genetics.

Question 14

The common ancestors of birds and mammals were very early (stem) reptiles, which almost certainly possessed three-chambered hearts (two atria, one ventricle). Birds and mammals, however, are alike in having four-chambered hearts (two atria, two ventricles). The four-chambered hearts of birds and mammals are best described as

A) structural homologies.
B) vestiges.
C) homoplasies.
D) the result of shared ancestry.

Question 15

There is some evidence that reptiles called cynodonts may have had whisker-like hairs around their mouths. If this is true, then what can be properly said of hair?

A) It is a shared derived character of mammals, even if cynodonts continue to be classified as reptiles.
B) It is a shared derived character of the amniote clade and not of the mammal clade.
C) It is a shared ancestral character of the amniote clade, but only if cynodonts are reclassified as mammals.
D) It is a shared derived character of the mammals, but only if cynodonts are reclassified as mammals.

Question 16

How does phylogeny differ from systematics?

A) in classifying organisms
B) in the classification of organisms by evolutionary history
C) in the naming of organisms
D) in the hierarchy of classification

Question 17

Sister taxa

A) represent the common ancestor of taxa.
B) represent groups of organisms that share an immediate common ancestor.
C) represent a polytomy.
D) diverge from all other lineages early in the history of the group.

Question 18

A shared ancestral character is

A) a character that originated in an ancestor of the taxon.
B) shared by all mammals but not found in their ancestors.
C) an evolutionary novelty unique to a clade.
D) an outgroup character.

Question 19

In addition to naming species, Linnaeus also grouped species into a hierarchy of increasingly inclusive categories. The largest category that would include closely related species is

A) genus.
B) class.
C) order.
D) domain.

Question 20

The term homoplasy is most applicable to which of the following features?

A) the five-digit condition of human hands and bat wings
B) the β hemoglobin genes of mice and humans
C) the fur that covers Australian moles and North American moles
D) the bones of bat forelimbs and the bones of bird forelimbs

Question 21

Figure 20.2
Together, the lesser apes and great apes shared a common ancestor most recently with other members of their

A) order.
B) class.
C) subclass.
D) subfamily.

Question 22

Figure 20.1
Which extinct species should be the best candidate to serve as the outgroup for the clade whose common ancestor occurs at position 2 in Figure 20.1?

A) A
B) B
C) C
D) D
E) E

Question 23

According to the principle of maximum parsimony,

A) phylogenies based in DNA require the most base changes.
B) the preferred tree is the one that minimizes the amount of evolutionary change.
C) in the case of trees based on morphology, a parsimonious tree requires the most changes.
D) a large number of trees should be examined.

Question 24

You discover a fossil with feathers on forelimbs, short hind limbs, and teeth. You conclude that this organism appears early on a phylogenetic tree for which group of organisms?

A) reptiles
B) birds
C) mammals
D) snakes

Question 25

What evidence allowed biologists to conclude that classification of the tree of life required a three-domain system?

A) The validity of three domains is supported by a recent study that sequenced proteins.
B) Most of the currently known prokaryotes belong to three domains.
C) The Archaea domain consists of diverse prokaryotes that inhabit the same habitats.
D) The phylogenetic tree of the three domains of life is based on sequence data for rRNA and other genes.

Question 26

Figure 20.2
From Figure 20.2, which other event occurred closest in time to the divergence of gorillas from the lineage that led to humans and chimpanzees?

A) the divergence of chimpanzees and humans
B) the divergence of Dryopithecus and Ouranopithecus
C) the divergence of gibbons and siamangs
D) could be either the divergence of chimpanzees and humans or that of Dryopithecus and Ouranopithecus
E) could be either the divergence of chimpanzees and humans or that of gibbons and siamangs

Question 27

A phylogenetic tree shows that birds and crocodiles share many features. A hypothesis based on this tree predicts that these features are present in a common ancestor. Which of these predicted traits is supported by fossil evidence?

A) four-chambered heart
B) singing for territory
C) eggs and nests
D) singing to attract mates

Question 28

What kind of evidence has recently made it necessary to assign the prokaryotes to either of two different domains, rather than assigning all prokaryotes to the same kingdom?

A) molecular
B) behavioral
C) nutritional
D) anatomical
E) ecological

Question 29

How does a molecular clock measure time?

A) by observing that some genes and other regions of genomes appear to evolve at different rates
B) by detecting gene irregularities that result from natural selection
C) by counting the number of nucleotide substitutions over fixed period of time
D) by using few gene mutations to calibrate the clock

Question 30

Which kind of DNA should provide the best molecular clock for determining the evolutionary relatedness of several species whose common ancestor became extinct billions of years ago?

A) DNA coding for ribosomal RNA
B) intronic DNA belonging to a gene whose product performs a crucial function
C) paralogous DNA that has lost its function (that is, no longer codes for functional gene product)
D) mitochondrial DNA
E) exonic DNA that codes for a noncrucial part of a polypeptide

Question 31

The kingdom Protista is obsolete because it contains members of how many other kingdoms?

A) two
B) three
C) four
D) five

Question 32

Which of these would, if it (they) had acted upon a gene, prevent this gene from acting as a reliable molecular clock?

A) neutral mutations
B) genetic drift
C) mutations within introns
D) natural selection
E) most substitution mutations involving an exonic codon's third position

Question 33

When it acts upon a gene, which of the following processes consequently makes that gene an accurate molecular clock?

A) transcription
B) directional natural selection
C) mutation
D) proofreading
E) reverse transcription

Question 34

Figure 20.2
Assuming chimpanzees and gorillas are humans' closest relatives, removing humans from the great ape clade and placing them in a different clade has the effect of making the phylogenetic tree of the great apes

A) polyphyletic.
B) paraphyletic.
C) monophyletic.
D) conform with Linnaeus's view of great ape phylogeny.

Question 35

Figure 20.1
If Figure 20.1 is an accurate depiction of relatedness, then which of the following should be correct?
1) The entire tree is based on maximum parsimony.
2) If all species depicted here make up a taxon, this taxon is monophyletic.
3) The last common ancestor of species B and C occurred more recently than the last common ancestor of species D and E.
4) Species A is the direct ancestor of both species B and species C.
5) The species present at position 3 is ancestral to C, D, and E.

A) 1 and 3
B) 3 and 4
C) 2, 3, and 4
D) 1, 2, and 3

Question 36

The most important feature that permits a gene to act as a molecular clock is

A) having a large number of base pairs.
B) having a larger proportion of exonic DNA than of intronic DNA.
C) having a reliable average rate of mutation.
D) its recent origin by a gene duplication event.
E) its being acted upon by natural selection.

Question 37

A phylogenetic tree constructed using sequence differences in mitochondrial DNA would be most valid for discerning the evolutionary relatedness of

A) archaeans and bacteria.
B) fungi and animals.
C) chimpanzees and humans.
D) sharks and dolphins.

Question 38

Which kingdom has been replaced with two domains?

A) Plantae
B) Fungi
C) Animalia
D) Protista
E) Monera

Question 39

Neutral theory proposes that

A) molecular clocks are more reliable when the surrounding pH is close to 7.0.
B) most mutations of highly conserved DNA sequences should have no functional effect.
C) DNA is less susceptible to mutation when it codes for amino acid sequences whose side groups (or R groups) have a neutral pH.
D) DNA is less susceptible to mutation when it codes for amino acid sequences whose side groups (or R groups) have a neutral electrical charge.
E) a significant proportion of mutations are not acted upon by natural selection.

Question 40

Figure 20.2
Figure 20.3
In Figure 20.3, phylogeny branch lengths represent genetic changes. Which organism on the tree has undergone the most genetic changes since divergence from common ancestor?

A) mouse
B) human
C) chicken
D) Drosophila

Question 41

Please use the following information to answer the question(s) below.
Traditionally, zoologists have placed birds in their own class, Aves. More recently, molecular evidence has shown that birds are more closely related to reptiles than their anatomy reveals. Genetically, birds are more closely related to crocodiles than crocodiles are to turtles. Thus, bird anatomy has become highly modified as they have adapted to flight, without their genes having undergone nearly as much change.
Taxonomically, what should be done with the birds?

A) The traditional stance is correct. Such dramatic morphological change as undergone by birds indicates that birds should be placed in their own order, separate from the reptiles.
B) Birds should be reclassified, and their new taxon should be the subclass Aves. Genetic similarity trumps morphological dissimilarity in cases where morphological traits are uninformative.
C) The rest of the reptiles should be reclassified as a subclass within the class Aves.
D) The classification scheme should remain the same because of historical precedence.

Question 42

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
What can be properly inferred from Figure 20.5?

A) In the "without" tree, pigs are more distantly related to hippos than is depicted in the "within" tree.
B) In the "without" tree, pigs are more closely related to hippos than are whales.
C) In the "within" tree, pigs are more closely related to whales than they are to hippos.
D) The "without" tree is more consistent with molecular evidence than is the "within" tree.

Question 43

To apply parsimony to constructing a phylogenetic tree,

A) choose the tree that assumes all evolutionary changes are equally probable.
B) choose the tree in which the branch points are based on as many shared derived characters as possible.
C) choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology.
D) choose the tree with the fewest branch points.

Question 44

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
If it turns out that the whale lineage diverged from the lineage leading to hippos after the divergence of the lineage leading to the pigs and other artiodactyls, and if the whales continue to be classified in the order Cetacea, then what becomes true of the taxon Cetartiodactyla?

A) It should be considered as one monophyletic superorder.
B) It should be considered a superorder that consists of two monophyletic orders.
C) It should be established as a paraphyletic order.
D) It should be thrown out or modified by taxonomists if classification is to reflect evolutionary history.

Question 45

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
If it turns out that the whale lineage diverged from the lineage leading to hippos after the divergence of the lineage leading to the pigs and other artiodactyls, and if the whales continue to be classified in the order Cetacea, then what becomes true of the order Artiodactyla?

A) It becomes monophyletic.
B) It becomes paraphyletic.
C) It becomes polyphyletic.
D) It is incorporated into the order Cetacea.

Question 46

The next question(s) refer to Table 20.1, which compares the % sequence homology of four different parts (two introns and two exons) of a gene that is found in five different eukaryotic species. Each part is numbered to indicate its distance from the promoter (for example, intron I is the one closest to the promoter). The data reported for species A were obtained by comparing DNA from one member of species A to the DNA of another member of species A. Table 20.1
Regarding these sequence homology data, the principle of maximum parsimony would be applicable in

A) distinguishing introns from exons.
B) determining degree of sequence homology.
C) selecting appropriate genes for comparison among species.
D) inferring evolutionary relatedness from the number of sequence differences.

Question 47

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
Placing whales and hippos in the same clade means that

A) these organisms are phenotypically more similar to each other than to any others shown on the trees in Figure 20.5.
B) their morphological similarities are probably homoplasies.
C) they had a common ancestor.
D) all three of the responses are correct.

Question 48

Based on the tree below, which statement is not correct?

A) The salamander lineage is a basal taxon.
B) Salamanders are a sister group to the group containing lizards, goats, and humans.
C) Salamanders are as closely related to goats as to humans.
D) Lizards are more closely related to salamanders than to humans.

Question 49

Please use the following information to answer the question(s) below.
Traditionally, zoologists have placed birds in their own class, Aves. More recently, molecular evidence has shown that birds are more closely related to reptiles than their anatomy reveals. Genetically, birds are more closely related to crocodiles than crocodiles are to turtles. Thus, bird anatomy has become highly modified as they have adapted to flight, without their genes having undergone nearly as much change.
Scientists discovered a fossil in China that belongs to a previously unknown species of an obscure group of small dinosaurs, related to primitive birds such as the famous Archaeopteryx. It had feathers, but they seemed too insubstantial to be useful in flight. Then the scientists said they recognized the unusually long, rodlike bone extending from each of the two wrists: curving structures possibly supporting an aerodynamic membrane. These scientists are grouping the found fossil with birds based on ________ structures.

A) analogous
B) homologous
C) molecular
D) derived

Question 50

The next question(s) refer to Table 20.1, which compares the % sequence homology of four different parts (two introns and two exons) of a gene that is found in five different eukaryotic species. Each part is numbered to indicate its distance from the promoter (for example, intron I is the one closest to the promoter). The data reported for species A were obtained by comparing DNA from one member of species A to the DNA of another member of species A. Table 20.1
Which of these four gene parts should allow the construction of the most accurate phylogenetic tree, assuming that this is the only part of the gene that has acted as a reliable molecular clock?

A) intron I
B) exon I
C) intron VI
D) exon V

Question 51

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
One morphological feature of modern cetaceans is a vestigial pelvic girdle. If it is determined that cetacean lineage diverged from the artiodactyls' lineage after the divergence of pigs and other artiodactyla, then what should be true of the vestigial pelvic girdle of cetaceans?

A) It should be considered a shared ancestral character of the cetartiodactyls.
B) It should be considered a shared derived character of the cetartiodactyls.
C) It should be considered a shared ancestral character of the cetaceans.
D) It should be considered a shared derived character of the cetaceans.

Question 52

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
If cetaceans are determined to have diverged from the lineage leading to the artiodactyls before the divergence of lineages leading to the modern artiodactyls (including hippos), then the cetaceans can be considered
1) a sister order to the order Artiodactyla.
2) an ingroup of the order Artiodactyla.
3) the common ancestor of the order Artiodactyla.

A) 1 only
B) 3 only
C) 1 and 2
D) 1 and 3

Question 53

If you were using cladistics to build a phylogenetic tree of cats, which of the following would be the best outgroup?

A) wolf
B) domestic cat
C) frog
D) leopard

Question 54

The relative lengths of the frog and mouse branches in the phylogenetic tree in the figure given below indicate that Figure 20.7

A) frogs evolved before mice.
B) mice evolved before frogs.
C) the homolog has evolved more rapidly in mice.
D) the homolog has evolved more slowly in mice.

Question 55

Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V. A grouping that consists of species T, X, Y, and Z (but not U or V) makes up

A) a monophyletic taxon.
B) an ingroup, with species U as the outgroup.
C) a polyphyletic group.
D) a paraphyletic group.

Question 56

The next question(s) refer to Table 20.1, which compares the % sequence homology of four different parts (two introns and two exons) of a gene that is found in five different eukaryotic species. Each part is numbered to indicate its distance from the promoter (for example, intron I is the one closest to the promoter). The data reported for species A were obtained by comparing DNA from one member of species A to the DNA of another member of species A. Table 20.1
Based on the tabular data, and assuming that time advances vertically, which cladogram (a type of phylogenetic tree) is the most likely depiction of the evolutionary relationships among these five species?

A)
B)
C)
D)

Question 57

In figure shown below, which similarly inclusive taxon descended from the same common ancestor as Canidae? Figure 20.6

A) Felidae
B) Mustelidae
C) Carnivora
D) Lutra

Question 58

Please use the following information to answer the question(s) below.
Traditionally, whales and hippopotamuses have been classified in different orders, the Cetacea and the Artiodactyla, respectively. Recent molecular evidence, however, indicates that the whales' closest living relatives are the hippos. This has caused some zoologists to lump the two orders together into a single clade, the Cetartiodactyla. There is no consensus on whether the Cetartiodactyla should be accorded order status or superorder status. This is because it remains unclear whether the whale lineage diverged from the lineage leading to the hippos before or after the other members of the order Artiodactyla (pigs, camels, etc.) diverged (see Figure 20.5). Figure 20.5
It was once thought that cetaceans had evolved from an extinct group of mammals called the mesonychids. If, in the future, it is determined that some organisms currently classified as cetaceans did actually evolve from mesonychids, whereas other cetaceans evolved from artiodactyl stock, then what will be true of the order Cetacea?

A) It will be paraphyletic.
B) It will be polyphyletic.
C) It will need to be modified if classification is to reflect evolutionary history.
D) A and C
E) B and C

Question 59

In a comparison of birds and mammals, the condition of having four limbs is

A) a shared ancestral character.
B) a shared derived character.
C) a character useful for distinguishing birds from mammals.
D) an example of analogy rather than homology.

Question 60

Figure 20.2
Figure 20.4
Extrapolating backward in time using the molecular clock indicates that the HIV-1 M strain originated around

A) 1920.
B) 1930.
C) 1950.
D) 1960.