25
Reconstructing and Using Phylogenies
TEST FILE QUESTIONS
Fill in the Blank
1. _______ is the theory and practice of classifying organisms.
Answer: Taxonomy
2. _______ is the scientific study of the diversity of organisms.
Answer: Systematics
3. _______, an eighteenth-century Swedish biologist, developed the classification system
used today.
Answer: Carolus Linnaeus
4. A two-name classification system, referred to as _______, is used today throughout
biology.
Answer: binomial nomenclature
5. A trait such as the modern horse’s single toe, which differs from the trait in an
organism’s ancestors, is called a _______.
Answer: derived trait
6. Any two traits derived from a common ancestral form are called _______.
Answer: homologous traits
7. Traits such as fins in aquatic mammals and fins in fishes exhibit _______; that is, they
evolved in different lineages but are not found in their most recent common ancestor.
Answer: homoplasy
8. Traits that evolved by _______ were formerly very different but now resemble one
Answer: convergent evolution
9. _______ classification shows evolutionary relationships and expresses them in treelike
diagrams.
Answer: Cladistic
10. The entire portion of a phylogeny that is descended from a common ancestor is called
a _______.
Answer: clade
11. The term “Rosaceae” is an example of the taxonomic category of _______.
Answer: family
12. In the Linnaean system, classes are divided into _______, which are then divided into
families.
Answer: orders
13. The operating rule of cladogram design, that it is wiser to postulate a minimal number
of changes in traits, is called _______.
Answer: parsimony
Multiple Choice
1. 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.
Answer: c
2. In the Linnaean system, 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.
Answer: c
3. North America and Great Britain both have birds called robins. These birds all have
brown backs and red breasts, but they are incapable of interbreeding, are different sizes,
and have different diets and habitats. Based on this information, one would expect these
birds to belong to
a. the same species.
b. the same genus, but different species.
c. the same family, but different genera.
d. different species, but more information is needed for further classification.
e. different genera, but more information is needed for further classification.
Answer: d
4. Within a family, the number of species placed into each genus is determined by
a. the evolutionary uniqueness among organisms.
b. an even distribution of the total number of species.
c. an even distribution of the species, based on their sizes.
d. grouping species by their geographic ranges.
e. clustering species based on their habitats.
Answer: a
5. The wing of a bat and the wing of a bird are an example of
a. divergent evolution.
b. vertical evolution.
c. convergent evolution.
d. a derived trait.
e. evolutionary reversal.
Answer: c
6–9. Use the cladogram below to answer the following questions.
6. Assuming the cladogram includes modern species, which of these species is (are) alive
today?
a. A, B, C, D, E
b. B, C, D, E
c. C, D, E
d. D, E
e. E
Answer: b
7. Species D and E share _______ homologous and _______ homoplastic traits.
a. many; many
b. many; few
c. few; many
d. few; few
e. no; no
Answer: b
8. Which species shares the most recent common ancestor with species E?
a. Species A
b. Species B
c. Species C
d. Species D
e. All of the above
Answer: d
9. The position of species B in the cladogram indicates that it
a. became extinct before species C, D, or E.
b. has fewer derived traits than species C, D, or E.
c. has a shorter evolutionary history than species C, D, or E.
d. shares more common ancestors with species C than it does with species D or E.
e. is less fit for its environment than species C, D, or E.
Answer: b
10. When compared to other taxa, a taxon that shares general homologous traits but lacks
special homologous traits is called a(n)
a. clade.
b. genus.
c. homoplasy.
d. outgroup.
e. population.
Answer: d
11. In a comparison of humans and chimps with dogs and cats, a general homologous
trait would be
a. hands specialized for grasping.
b. presence of body hair.
c. standing on two legs.
d. lack of a tail.
e. poor sense of smell.
Answer: b
12. When comparing humans and chimps with dogs and cats, a special homologous trait
would be
a. bony skeleton.
b. presence of body hair.
c. hands specialized for grasping.
d. mouth containing teeth.
e. presence of circulatory system.
Answer: c
13. Which of the statements below is often assumed to be true in the construction of
cladograms?
a. Derived traits appear only once in a lineage.
b. Branching points are determined by the number of homologous traits.
c. Derived traits are never lost.
d. Both a and b
e. Both a and c
Answer: e
14–17. Use the table below to answer the following
Ancestral and Derived Traits Among Five Species
Trait
Species
1
2
3
4
5
A
1
1
0
0
1
B
0
0
1
0
1
C
1
1
0
0
1
D
0
1
0
0
1
The ancestral form of each trait is coded 0, and the derived trait is coded 1.
14. In constructing a cladogram, the oldest divergence would separate
a. A from B, C, and D.
b. B from A, C, and D.
c. C from A, B, and D.
d. D from A, B, and C.
e. A and D from B and C.
Answer: b
15. The two species that diverged most recently from one another are
a. A and B.
b. A and C.
c. A and D.
d. B and C.
e. B and D.
Answer: b
16. Which trait is most recently derived?
a. 1
b. 2
c. 3
d. 4
e. 5
Answer: a
17. Which trait is most ancestral?
a. 1
b. 2
c. 3
d. 4
e. 5
Answer: d
18. Which statement is true about the use of behavioral traits in the reconstruction of
phylogenies?
a. Behavioral traits are never relevant.
b. Behavioral traits are more important than other traits among closely related species.
c. Knowledge of behavioral traits supports knowledge of other traits among closely
related species.
d. Knowledge of behavioral traits supports knowledge of other traits among distantly
related species.
e. Behavioral traits are always relevant.
Answer: c
19. Systematists usually employ parsimony in reconstructing a phylogeny. Parsimony
involves arranging the organisms such that _______ in determining the lineage.
a. the minimal number of changes in traits is postulated
b. the maximum number of traits is used
c. molecular information is given priority over other traits
d. larval traits are included
e. ancestral traits are given priority over derived traits
Answer: a
20. _______ is the study of biological diversity and its evolution.
a. Phylogeny
b. Systematics
c. Taxonomy
d. Classification
e. Nomenclature
Answer: b
21. _______ is the science of biological classification.
a. Phylogeny
b. Systematics
c. Taxonomy
d. Classification
e. Nomenclature
Answer: c
22. Classification systems have many uses. Which of the following is not a goal of
biological classification?
a. To depict convergent evolution
b. To clarify relationships among organisms
c. To help us remember organisms and their traits
d. To clearly identify organisms being studied
e. To provide predictive powers
Answer: a
23. Taxonomic systems used by biologists are hierarchical; that is,
a. taxonomic groups reflect shared characters, not evolutionary relationships.
b. each higher taxonomic group contains all the groups below it.
c. taxonomic groups reflect common habitats.
d. a hierarchy of traits is used to establish
e. phylogenetic relationships do not help us understand evolution.
Answer: b
24. Classification systems serve four important roles. Which of the following is not one
of those roles?
a. To help us remember characteristics of a large number of different things
b. To help us identify shared traits, such as hair, mammary glands, and constant high
body temperature in mammals
c. To reveal the harmony of nature
d. To provide stable, unique, unequivocal names for organisms
e. To help reconstruct evolutionary pathways
Answer: c
25. The biological classification system used today is based on the work of
a. Charles Darwin.
b. Barbara McClintock.
c. Gregor Mendel.
d. Lynn Margulis.
e. Carolus Linnaeus.
Answer: e
26. The biological classification system used today is referred to as
a. dichotomous taxonomy.
b. dichotomous nomenclature.
c. dichotomous keys.
d. binomial taxonomy.
e. binomial nomenclature.
Answer: e
27. Which of the following is the correct hierarchy of categories from most inclusive to
least inclusive in the classification system used today?
a. Division or phylum, kingdom, order, family, class, genus, species
b. Division or phylum, kingdom, order, class, family, genus, species
c. Division or phylum, kingdom, class, order, family, genus, species
d. Kingdom, division or phylum, order, class, family, genus, species
e. Kingdom, division or phylum, class, order, family, genus, species
Answer: e
28. In referring to the species of an organism in writing (e.g., in a newspaper, textbook, or
lab report), which of these rules should be followed?
a. Underline or italicize genus and species
b. The first letter of genus should be uppercase.
c. The first letter of species should be uppercase.
d. Both a and b
e. a, b, and c
Answer: d
29. If you saw the name of a family of organisms and it ended with “-idae” (e.g.,
Formicidae), you would know that it was a family of
a. bacteria.
b. fungi.
c. plants.
d. animals.
e. protists.
Answer: d
30. A consensus tree is produced by
a. merging multiple phylogenetic trees.
b. aligning two phylogenetic trees.
c. subtracting two phylogenetic trees.
d. using only molecular data.
e. using only morphological data.
Answer: a
31. When a research team employs the maximum likelihood method to construct a
phylogeny, what information are they basing it on?
a. Morphological
b. Environmental
c. Molecular
d. Parsimony
e. Fossil
Answer: c
32. In comparing an adult sea squirt to vertebrate animals using morphological data, sea
squirts and vertebrates would seem quite unrelated; what other information could be
useful to verify this conclusion?
a. Fossil
b. Developmental
c. Environmental
d. Asystematic
e. None
Answer: b
33. The molecular structures most often considered in the construction of phylogenies are
those of
a. proteins and nucleic acids.
b. lipids and nucleic acids.
c. carbohydrates and lipids.
d. proteins and lipids.
e. carbohydrates and nucleic acids.
Answer: a
34. In a cladistic classification, each taxon
a. includes several lineages from a single common ancestor.
b. is a single lineage and includes all—and only—the descendants of a single ancestor.
c. shares common morphologies that are homoplasic.
d. shares common morphologies that are derived characters.
e. includes several lineages that share common
Answer: b
35. The excellent fossil record of horses shows that modern horses, which have one toe
on each foot, evolved from ancestors that had multiple toes. A trait that differs from the
ancestral trait in the lineage is called a(n) _______ trait.
a. derived
b. ancestral
c. morphological
d. biochemical
e. fundamental
Answer: a
36. Any two structures derived from a common ancestral trait are said to be
a. analogous.
b. morphological traits.
c. biochemical traits.
d. homologous.
e. homoplasic.
Answer: d
37. Homoplasy can result from convergent evolution, in which
a. structures that formerly were very different come to resemble one another because they
have undergone selection to perform similar functions.
b. the same character evolves in different lineages, often from a common basis.
c. a structure evolves in a lineage that is not found in their common ancestor.
d. a character from a particular ancestral trait evolves in different lineages because of
similar selection pressures.
e. an ancestral trait evolves into different characters in different lineages.
Answer: a
38. Genetic similarities among some vertebrates have been estimated by DNA
sequencing. According to these data, humans are most closely related to
a. gibbons.
b. chimpanzees.
c. baboons.
d. galagos.
e. rhesus monkeys.
Answer: b
39. In groups such as birds, _______ make(s) it difficult to resolve phylogenies using
only morphological data, because the use of different traits produces different
phylogenies.
a. reverse evolution
b. parallel evolution
c. convergent evolution
d. genetic drift
e. founder events
Answer: c
40. A taxon is
a. an archaic concept not used in modern classification systems.
b. any group of organisms treated as a unit.
c. a single species.
d. a group of organisms that are reproductively isolated from the organisms of other such
groups.
e. the smallest grouping in the Linnaean classification system.
Answer: b
41. Which of the following choices is the conventional representation for the name of a
sea star common to the rocky intertidal zone?
a. Pisaster Ochraceous
b. Pisaster Ochraceous
c. Pisaster ochraceous
d. pisaster ochraceous
e. pisaster ochraceous
Answer: c
42. In a scientific paper, which of the following represents, by convention, the correct
binomial name of the English bluebell after the name has already been cited once (i.e.,
earlier in the paper)?
a. Edymion nonscriptus
b. Edymion n.
c. E. nonscriptus
d. E. n.
e. E. nonscriptus
Answer: c
43. In the Linnaean classification system, which one of the following taxa usually ends in
“-idae” when used with animals?
a. Genus
b. Order
c. Division
d. Class
e. Family
Answer: e
44. Which of the following statements about classification is false?
a. Members of a family are less similar than members of an included genus.
b. An order has more members than a genus has.
c. Families have more members than phyla have.
d. The common ancestor shared by members of a family is a more distant ancestor than
the one shared by members of an included genus.
e. The number of species in a taxon depends on the relative similarity of the different
species.
Answer: c
45. All of the following can result in homoplasy except
a. convergent evolution.
b. parallel evolution.
c. reverse evolution.
d. descent from a common ancestor.
e. similar selection pressures.
Answer: d
46. A taxon consisting of members that do not share the same common ancestor is
a. monophyletic.
b. polyphyletic.
c. paraphyletic.
d. unrelated.
e. a clade.
Answer: b
47. A monophyletic group containing all the descendants of a particular ancestor and no
other organisms is also know as a
a. phylogeny.
b. clade.
c. composite.
d. breeding group.
e. species.
Answer: b
48. Which of the following techniques for studying the biochemical traits of organisms
could be used to understand the evolution of cytochrome c (a protein)?
a. Immunological distance determination
b. Amino acid sequencing
c. DNA hybridization
d. Nucleic acid base sequencing
e. cpDNA and mtDNA comparisons
Answer: b
49. Most taxonomists today believe that classification
a. phylogenetic.
b. monophyletic.
c. paraphyletic.
d. polyphyletic.
e. changed.
Answer: b
50. 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 the fossils and analyzed.
e. it is the only type of data useful in reconstructing the past.
Answer: b
51. In reconstructing phylogenies, an outgroup is used to
a. distinguish between ancestral traits and derived traits.
b. exclude a taxon from the phylogenetic group.
c. distinguish homoplasy from convergent traits.
d. gain knowledge of reverse evolution.
e. Both b and c
Answer: a
52. Larval stages can help determine relationships among organisms, but care must be
taken because
a. not all organisms have a larval stage.
b. the larval form is morphologically very different from the adult form.
c. the larval form may closely resemble an organism that the adult stage does not.
d. larval forms all have a notochord and all adult forms do not.
e. Both b and d
Answer: c
53. Reconstructed phylogenies can be useful for all of the following except
a. studying the evolution of human language.
b. studying the migration of human populations.
c. determining if divergent traits occurred from reverse evolution.
d. predicting future trends in evolution.
e. evaluating how a protein has changed in different species.
Answer: d
STUDY GUIDE QUESTIONS
Knowledge and Synthesis Questions
1. Which of the following would not be expected to result in homoplasy?
a. Convergent evolution
b. The independent evolution of similar structures in different lineages
c. Selection for traits that perform similar functions
d. The inheritance of ancestral traits
2. A derived trait is one that
a. differs from its ancestral form.
b. is homologous with another trait found in a related species.
c. is the product of an evolutionary reversal.
d. has the same function, but not the same evolutionary origin, as a trait found in another
species.
3. Which of the following statements about reconstructing phylogenies is false?
a. Traits found in the outgroup as well as in the ingroup are likely to be ancestral traits.
b. Shared traits are generally assumed to be homoplastic until they can be proven to be
homologous.
c. Phylogenies do not include ancestors of modern groups or date the splits between
lineages.
d. Nodes (branching points) in phylogenetic trees have only two branches because during
speciation a lineage normally splits into only two daughter species.
4. The most important attribute of a biological classification scheme is that it
a. avoids the ambiguity created by using common names.
b. reflects the evolutionary relationships among organisms.
c. helps us remember organisms and their traits.
d. improves our ability to make predictions about the morphology and behavior of
organisms.
5. Suppose you are writing a scientific paper about a unicellular green alga called
Chlamydomonas reinhardtii. What would be the proper way to refer to this species after
you had used the full binomial earlier in the same paragraph?
a. Chlamydomonas reinhardtii
b. Chlamydomonas spp.
c. Chlamydomonas sp.
d. C. reinhardtii
6. The organisms that make up a class are __________ diverse and __________
numerous than those in a family within that class. The organisms that make up a phylum
all diverged from a common ancestor __________ recently than did the organisms in an
order within that phylum.
a. more; more; less
b. more; more; more
c. more; less; less
d. less; less; more
7. Which of the following incomplete lists of taxonomic categories ranks them properly
from most inclusive to least inclusive?
a. Phylum, order, family, genus
b. Class, phylum, order, species
c. Order, class, family, genus
d. Family, order, class, kingdom
Answers
Knowledge and Synthesis Answers
1. d. Homoplasy is the appearance of similar structures in different lineages that were not
present in the common ancestor.
2. a. Derived traits are those that have undergone a change during evolution from the
ancestral (original) character state.
3. b. Most shared traits, especially in species with a recent common ancestor, are likely to
be homologous, not homoplastic. Therefore it is more consistent with the parsimony
principle to assume that traits are homologous until proven homoplastic than to assume
the reverse.
4. b. Although all of the statements listed are important attributes of biological
classification schemes, the most important attribute is that biological classification
reflects evolutionary relationships.
5. d. After a scientific name is referenced once in a paragraph, typically the genus is
abbreviated, but the species name is given in full.
6. a. Organisms in a higher taxon are less similar, have diverged from a common ancestor
less recently, and include more species than organisms in a lower, included taxon.
7. a. The complete hierarchy of taxonomic categories, from most to least inclusive, is:
kingdom, phylum, class, order, family, genus, species.
TEXTBOOK SELF QUIZ QUESTIONS
1. Any group of organisms treated as a unit in a classification system is a
a. species.
b. genus.
c. taxon.
d. clade.
e. phylogen.
2. A genus is a
a. group of closely related species.
b. group of genera.
c. group of similar genotypes.
d. taxonomic unit larger than a family.
e. taxonomic unit smaller than a species.
3. A trait that is defined as one that differs from its ancestral form is called
a. an altered trait.
b. a homoplastic trait.
c. a parallel trait.
d. a derived trait.
e. a homologous trait.
4. Identifying ancestral traits is often difficult because
a. traits often become so dissimilar that ancient states are unrecognizable.
b. there may be no fossils of appropriate ancestors.
c. reversals of traits are common during evolution.
d. traits often evolve rapidly.
e. All of the above
5. The parsimony principle is typically used when reconstructing phylogenies because
a. evolution is nearly always parsimonious.
b. it is better to provisionally adopt the simplest hypothesis capable of explaining the
known facts.
c. it is easier to handle parsimonious data with computers.
d. parsimony works well for all kinds of traits, both morphological and molecular.
e. parsimony was used before computers were available and it continues to be used even
though new methods are better.
6. Which of the following is a way of identifying ancestral traits?
a. Determining which traits are found among fossil ancestors
b. Using an outgroup
c. Using a lineage that is closely related to the ingroup
d. Examining the development of the trait
e. All of the above
7. Traits that evolve very slowly are most useful for determining relationships at the level
of
a. phyla.
b. genera.
c. orders.
d. families.
e. species.
8. Homologous traits are
a. similar in function.
b. similar in structure.
c. similar in structure but not in function.
d. derived from a common ancestor.
e. derived from different ancestral structures and have dissimilar structures.
9. The genes that are most extensively used to determine evolutionary relationships
among plants are
a. nuclear genes.
b. chloroplast genes.
c. mitochondrial genes.
d. genes in flowers.
e. genes in roots.
10. Which of the following is not a way in which phylogenies are used?
a. To establish evolutionary relationships
b. To determine how rapidly traits evolve
c. To determine historical patterns of movement of organisms
d. To help identify unknown organisms
e. To infer evolutionary trends
11. Which of the following is not a major role of a classification system?
a. To aid memory
b. To improve predictive powers
c. To help explain relationships among things
d. To provide relatively stable names for things
e. To design identification keys
Answers
1. c
2. a
3. d
4. e
5. b
6. c
7. a
8. d
9. b
10. d
11. e
ONLINE QUIZ QUESTIONS
1.Crocodilians are grouped with turtles, lizards, and snakes in the class Reptilia while
birds are placed in the class Aves because
a.birds have different ancestors than crocodilians.
b.birds have evolved differently.
c.crocodilians are classified differently than birds.
d.crocodilians evolved much more quickly than birds.
e.crocodilians evolved more slowly than birds.
Answer: e
2.The form of classification that always ends in "-idae" for animals and "-aceae" for
plants is the
a.family.
b.genus.
c.taxon.
d.clade.
e.species.
Answer: a
3.A taxon that contains organisms that do not share the same common ancestor is called
a.clade.
b.monophyletic.
c.polyphyletic.
d.paraphyletic.
e.none of the above.
Answer: c
4.A trait that is inherited from a common ancestor is called a/an _______ trait.
a.ancestral
b.homoplastic
c.parallel
d.derived
e.homologous
Answer: a
5.The parsimony principle states that
a.all evolutionary changes occur parsimoniously.
b.the best hypothesis is one that requires a lot of homoplasies.
c.one should prefer the simplest hypothesis that is capable of explaining the observed
data.
d.one should prefer a complex hypothesis that is capable of explaining the observed data.
e.the number of evolutionary changes that need to be assumed over all characters in all
groups in the tree needs to be maximized.
Answer: c
6.Which of the following is not a way of identifying ancestral traits?
a.Determining which traits are found among fossil ancestors
b.Using an outgroup in which the trait is also found
c.Using more than one outgroup that has the trait
d.Determining how many species in the lineage share the trait today
e.Experimentally creating a known lineage
Answer: d
7.The larvae of sea squirts have a notochord that disappears as they develop into adults.
This an example of a/an _______ trait used in reconstructing phylogenies.
a.homoplastic
b.ancestral
c.molecular
d.morphological
e.derived
Answer: d
8.Traits that evolve very slowly are useful for determining relationships at the level of
a.phyla.
b.genera.
c.orders.
d.families.
e.species.
Answer: a
9.Which of the following is not true about homologous traits?
a.An example of a homologous trait in vertebrates is the vertebral column.
b.A homologous trait is shared by two or more species that have been inherited from a
common ancestor.
c.Anatomical features can never be a homologous trait.
d.DNA sequences can be considered a homologous trait.
e.Behavior patterns can be considered a homologous trait.
Answer: c
10.The genes that are most extensively used to determine evolutionary relationships
among animals are
a.nuclear genes.
b.chloroplast genes.
c.mitochondrial genes.
d.genes in DNA from hair samples.
e.genes in saliva.
Answer: c
11.Phylogenies are used to
a.determine modern patterns of movement of organisms
b.increase the speed at which traits evolve
c.determine population size of a species
d.infer evolutionary trends
e.help further identify well-known organisms
Answer: d