28) Given that phylogenies are based on shared derived characteristics, which of the following
traits is useful in generating a phylogeny of species W, X, Y, and Z?
Species W
Species X
Species Y
Species Z
Trait 1
A
A
A
A
Trait 2
A
A
B
B
Trait 3
A
B
C
D
A) Trait 1
B) Trait 2
C) Trait 3
D) Traits 1, 2, and 3
29) Which of the following is (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 taxa and paraphyletic taxa
30) Phylogenetic trees 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
31) There is some evidence that reptiles called cynodonts may have had whisker-like hairs
around their mouths. If true, then hair is a shared _____.
A) derived character of mammals, even if cynodonts continue to be classified as reptiles
B) derived character of the amniote clade and not of the mammal clade
C) ancestral character of the amniote clade, but only if cynodonts are reclassified as mammals
D) derived character of mammals, but only if cynodonts are reclassified as mammals
Use the figure below to answer the following question(s).
32) Which extinct species should be the best candidate to serve as the outgroup for the clade
whose common ancestor occurs at position 2 in the figure above?
A) A
B) B
C) C
D) E
33) If the figure above 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
Use the following figure and description to answer the question(s) below.
Humans, chimpanzees, gorillas, and orangutans are members of a clade called the great apes,
which shared a common ancestor about fifteen million years ago. Gibbons and siamangs
comprise a clade called the lesser apes. Tree-branch lengths indicate elapsed time.
34) Assuming chimps 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) into a new order
The questions below refer to the following table, 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 another member of species A.
% Sequence Homology
Exon I
Exon V
100%
100%
99%
96%
99%
96%
99%
97%
99%
94%
35) Based on the tabular data, and assuming that time advances vertically, which phylogenetic
tree is the most likely depiction of the evolutionary relationships among these five species?
A)
B)
C)
D)
36) 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
37) In a comparison of birds and mammals, 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
38) 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, either in DNA sequences or
morphology
D) choose the tree with the fewest branch points
39) If you were using cladistics to build a phylogenetic tree of cats, which of the following
would be the best outgroup?
A) lion
B) domestic cat
C) wolf
D) leopard
40) Based upon the figure above, the phylogenetic tree _____.
1. depicts uncertainty about whether the bryophytes or the vascular plants evolved first
2. depicts an evolutionary hypothesis
3. includes polytomies
4. shows that members of the phylum Pterophyta are the closest living relatives to the seed
plants
5. indicates that seeds are a shared ancestral character of all vascular plants
A) 1 and 2
B) 2 and 3
C) 1, 2, and 3
D) 1, 2, and 4
41) Which value(s) would be required to calculate how long ago the most recent ancestor of
ungulates lived?
I) the number of base pairs that differ among species in a certain genetic sequence
II) the total number of base pairs in the genetic sequence examined
III) the age of a fossil ancestor for calibration
A) I
B) II
C) III
D) I, II, and III
42) Concerning growth in genome size over evolutionary time, which of these is LEAST
associated with the others?
A) orthologous genes
B) gene duplications
C) paralogous genes
D) gene families
43) Eukaryotes that are not closely related and that do not share many anatomical similarities can
still be placed together on the same phylogenetic tree by comparing their _____.
A) plasmids
B) mitochondrial genomes
C) homologous genes that are poorly conserved
D) homologous genes that are highly conserved
44) 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
45) The lakes of northern Minnesota are home to many similar species of damselflies of the
genus Enallagma. These species have apparently undergone speciation from ancestral stock
since the last glacial retreat about ten thousand years ago. Sequencing which of the following
would probably be most useful in sorting out evolutionary relationships among these closely
related species?
A) conserved regions of nuclear DNA
B) mitochondrial DNA
C) amino acids in proteins
D) ribosomal RNA
46) Which statement represents the best explanation for the observation that the nuclear DNA of
wolves and domestic dogs has a very high degree of sequence homology? Dogs and wolves
_____.
A) have very similar morphologies
B) belong to the same order
C) are both members of the order Carnivora
D) share a very recent common ancestor
47) The reason that paralogous genes can diverge from each other within the same gene pool,
whereas orthologous genes diverge only after gene pools are isolated from each other, is that
_____.
A) having multiple copies of genes is essential for the occurrence of sympatric speciation in the
wild
B) paralogous genes can occur only in diploid species; thus, they are absent from most
prokaryotes
C) polyploidy is a necessary precondition for the occurrence of sympatric speciation in the wild
D) having an extra copy of a gene permits modifications to the copy without loss of the original
gene product
48) Which of the following items is LEAST likely to form a simple linear relationship with the
number of gene-duplication events, when placed as the label on the vertical axis of the following
graph?
A) number of genes
B) number of DNA base pairs
C) genome size
D) phenotypic complexity
49) The most important feature that permits a gene to act as a molecular clock is _____.
A) a large number of base pairs
B) being acted upon by natural selection
C) a reliable average rate of mutation
D) a recent origin by a gene-duplication event
50) 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) a significant proportion of mutations are not acted upon by natural selection
51) Which of the following would, if it 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
The questions below refer to the following table, 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 another member of species A.
% Sequence Homology
Exon I
Exon V
100%
100%
99%
96%
99%
96%
99%
97%
99%
94%
52) 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
53) Based on cladistics, which eukaryotic kingdom is polyphyletic and, therefore, unacceptable?
A) Plantae
B) Fungi
C) Animalia
D) Protista
54) Which eukaryotic kingdom includes members that are the result of endosymbioses that
included an ancient aerobic bacterium and an ancient cyanobacterium?
A) Plantae
B) Fungi
C) Animalia
D) Protista
55) A large proportion of archaeans are extremophiles, so called because they inhabit extreme
environments with high acidity, salinity, and/or temperature. Such environments are thought to
have been much more common on the primitive Earth. Thus, modern extremophiles survive only
in places that their ancestors became adapted to long ago. Which of the following is,
consequently, a valid statement about modern extremophiles, assuming that their habitats have
remained relatively unchanged?
A) Among themselves, they should share relatively few ancestral traits, especially those that
enabled ancestral forms to adapt to extreme conditions.
B) On a phylogenetic tree whose branch lengths are proportional to the amount of genetic
change, the branches of the extremophiles should be shorter than the non-extremophilic
archaeans.
C) They should contain genes that originated in eukaryotes that are the hosts for numerous
species of bacteria.
D) They should currently be undergoing a high level of horizontal gene transfer with non-
extremophilic archaeans.
Use the following information to answer the question(s) below.
Paulinella chromatophora is one of the few cercozoans that is autotrophic, carrying out aerobic
photosynthesis with its two elongated “chromatophores.” The chromatophores are contained
within vesicles of the host cell, and each is derived from a cyanobacterium, though not the same
type of cyanobacterium that gave rise to the chloroplasts of algae and plants.
56) A crucial photosynthetic gene of the cyanobacterium that gave rise to the chromatophore is
called psaE. This gene is present in the nuclear genome of the cercozoan, but is not in the
genome of the chromatophore. This is evidence of _____.
A) reciprocal mutations in the chromatophore and nuclear genomes
B) horizontal gene transfer from bacterium to eukaryotes
C) genetic recombination involving a protist and an archaean
D) transduction by a phage that infects both prokaryotes and eukaryotes
57) 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) mtDNA
B) rRNA genes
C) morphological
D) ecological
The following questions refer to this phylogenetic tree, depicting the origins of life and of the
three domains. Horizontal lines indicate instances of gene or genome transfer.
A possible phylogenetic tree for the three domains of life.
58) If the early history of life on Earth is accurately depicted by the figure above, then which
statement is most in agreement with the hypothesis proposed by this tree?
A) The last universal common ancestor of all extant species is one individual species.
B) The origin of the three domains appears as a polytomy.
C) Archaean genomes should not contain genes that originated in bacteria, and vice versa.
D) Eukaryotes are more closely related to archaeans than to bacteria.
59) Which of these processes can be included among those responsible for the horizontal
components of the figure above?
A) endosymbiosis
B) mitosis
C) binary fission
D) point mutations
60) Which portion of the figure above may ultimately be better depicted as a “ring”?
A) the bacterial lineage
B) the archaean lineage
C) the eukaryotic lineage
D) the trunk of the tree