CHAPTER 2
1. According to the Theory of Special Creation, species __________.
a. are immutable; they do not change over time
b. were created independently, no species ever gave rise to a new species.
c. are recent
d. all of these.
Answer: d
2. What are the key components of a scientific theory? Was the Theory of Special
Creation a valid scientific theory in Darwin's time? Is it a scientific theory today?
A scientific theory provides a coherent explanation for a body of phenomena; it makes
testable predictions; it; it is in agreement with the known evidence; and it is falsifiable
(that is, it is in principle possible to prove a scientific theory wrong, if its key predictions
fail the tests of experiment and observation.) The Theory of Special Creation, in its
original form, did make testable predictions related to its three key tenets (young Earth,
immutable species, and no common descent). One of the theory's key tenets (young earth)
had already been proven wrong before Darwin's time, and a second was in doubt
(immutable species, cast in doubt by the discovery of extinct fossil species), seriously
crippling its validity as a scientific theory even before Darwin. There is now
overwhelming evidence that all three key tenets are false. Today, proponents of special
creation typically do not state testable predictions and consider the theory to be, in
principle, unfalsifiable; thus it is not a scientific theory.
3. The data presented in these graphs illustrate that _________.
a. Soapberry bugs from Key Largo (southern Florida) have longer beaks, on average, than
do soapberry bugs from Lake Wales (central Florida).
b. Soapberry bugs feeding on flat-podded golden rain tree fruit have shorter beaks, on
average, than do soapberry bugs feeding on balloon vine fruit
c. Soapberry bug beak lengths have decreased over time
Answer: d and c are both correct
4. Look again at textbook Figure 2.3b, which shows beak lengths of soapberry bugs over
time. What happened to variation in beak length when the golden rain trees appeared?
Did soapberry bugs with new beak lengths (not seen before in the population) appear
after the introduction of golden rain trees? Comment on what this pattern shows about the
initial stages of evolution.
Short-beaked and long-beaked soapberry bugs both existed before the change in host
plants. After the new host plant was established, long-beaked bugs vanished. That is,
variation in beak length decreased, but new beak lengths did not (immediately) appear.
This is an example of a widespread feature of natural selection, which is that natural
selection selects among preexisting variation in the population, and does not
instantaneously create new variation. (For evolution to continue, new variation must be
introduced, by mutation or other processes, as will be discussed in later chapters.)
5. What surprising thing do bird embryos' feet and wings do during development? What
is the significance for evolutionary theory?
Bird embryos develop a fourth finger in the hand, and a fifth toe in the feet, which later
vanish during development. This is a vestigial developmental structure, and is evidence
for common descent; it indicates that birds are descended from ancestors that had more
fingers and toes than today's birds.
6. Which of the following best describes vestigial structures?
a. Vestigial structures are similar structurally and functionally to comparable structures in
other organisms.
b. Vestigial structures are small structures that are not present in close relatives.
c. Vestigial structures have not yet been identified in humans.
d. Vestigial structures are well-developed structures that have a different function in close
relatives.
e. Vestigial structures are functionless or rudimentary homologs of characters that are
functional in close relatives.
Answer: Vestigial structures are functionless or rudimentary homologs of characters that
are functional in close relatives.
7. What did Cuvier discover about the Irish elk? What was its significance for
evolutionary theory?
Cuvier proved that the "Irish elk" was not an elk; nor was it a moose, reindeer, or any
other living species of deer. It was a unique species of huge deer that had gone extinct.
Cuvier had previously published a list of 23 other fossil species that were also extinct.
The fact that species could go extinct demonstrated that life on Earth had changed over
time, in contradiction of the Theory of Special Creation.
8. The theory of descent with modification predicts that a regions extant plants and
animals will be most similar to fossils __________.
a. from the same region
b. from regions with the same environment
c. from transitional forms
Answer: c , from transitional forms
9. According to the theory of descent with modification, organisms from the African
tropics should be most similar to organisms from ___________.
a. the South American tropics.
b. other regions of Africa.
c. the Asian tropics.
.Answer: b, other regions of Africa
10. What do Ambulocetus natans and Sinosauropteryx prima have in common?
Both are transitional fossils (fossils that have combinations of traits of ancestral and
descendent species), and both were predicted by evolutionary theory long before they
were discovered. Ambulocetus natans is an early whale that had fully functional hind
legs; Sinosauropteryx prima is a small theropod dinosaur covered with what appear to be
feathers.
11. Creationists commonly state that Archeopteryx should not be regarded as a
transitional fossil, because it has fully developed feathers and therefore is clearly a bird,
and/or because Archeopteryx is not the direct ancestor of modern birds. Do you think
these criticisms are valid? Explain.
Transitional fossils are simply fossils that combine traits that are diagnostic of ancestral
and descendent groups, showing that the two groups are very likely related. Archeopteryx
combined the "bird trait" of fully formed feathers, with abundant reptilian skeletal
features such as teeth, functional fingers with claws, and a long tail. We now know that
feathers were widespread in Mesozoic theropods. Transitional fossils need not be on the
direct line of descent from ancestor to descendent; that is, they may be "uncles" or
"cousins" rather than direct ancestors. (In fact, the vagaries of fossil discovery make it
nearly certain that most transitional fossils will not be directly ancestral to modern
animals. For example, of all the (many) theropod species present on Earth at the time of
the feathered dinosaurs, only one was ancestral to modern birds. Since only a few species
will be discovered as fossils, it is mathematically unlikely that the discovered fossils will
include the actual direct ancestor of modern birds. But we are fairly likely to find a
relative of the ancestor.
12. According to the phylogeny presented in Figure 2.16, the closest relative of leopards
is ____________. FIGURE NOT SHOWN ON QUIZ, IT’S ONLY ON THE BOOK.
a. Lions
b. Jaguars and lions are equally closely related to leopards and are leopards' closest
relatives
c. snow leopards
d. jaguars
13. Homologous characters _________.
a. are superficially similar.
b. are similar in function.
c. show underlying structural similarity even when their superficial structure is different.
15. Look again at bones of the horse foreleg shown in Figure 2.18. One of the horse
bones is shaded two different colors. Why? What does this illustrate about the difficulties
of knowing whether anatomical characters are homologous?
This bone in horses is believed to be a fusion of two ancestral bones, the radius and the
ulna. Developmental biology indicates that this is probably accurate; two separate bones
form early in development, which later fuse. This example indicates that anatomical
homologies can be difficult to establish accurately, due to fusion or loss of structures.
(Look also at Figure 2.6, which shows digits that vanish during bird development. This
Figure is from a study concerned with whether the remnant three fingers of bird wings
are truly homologous with the three fingers of dinosaur hands. The authors concluded
that bird and dinosaur fingers are not homologous, but most biologists dispute their
interpretation.)
17. Uniformitarianism means that _______________.
geological processes (like the deposition of sediments at beaches) have
operated at the same rate throughout the Earth's history
the Earth is very young
extinctions cannot happen
geological processes operating now operated the same way in the past
Your geological processes (like the deposition of sediments at
Answer: beaches) have operated at the same rate throughout the
Earth's history
Correct geological processes operating now operated the same
Answer: way in the past
18. This diagram represents two sedimentary rock layers with one intrusion/dike and a set
of boulders. According to the principles used by 19th-century geologists to establish the
relative ages of the major rock formations of Europe, what is the correct sequence of the
illustrated structures (oldest to youngest)?
a. C, D, A, B
b. A, C, B, D
c. A, B, C, D
d. A, C, D, B
19. Modern geologists believe that dramatic geological catastrophes have occurred
occasionally in the past - for example, occasional cataclysmic floods that occur when ice
dams break below glacial lakes (e.g. the Bonneville Flood of Utah), gigantic lava flows
(e.g. the Deccan traps of India), and meteor impacts (e.g. at the end of the Cretaceous).
Are modern geologists uniformitarians, or catastrophists, or both?
Modern geology includes some features of catastrophism, but is essentially
uniformitarian. That is, modern geologists believe that most features on earth were
produced not by catastrophes, but by gradual processes that are still operating today.
Prehistoric catastrophes are known to have occured several times, but are thought to have
been quite rare. When they did occur, they occurred in accordance with normal physical
laws.
20. Describe two ways in which the discovery of radioactivity has contributed to our
understanding of the history of life on Earth.
The discovery of radioactivity clarified that the heat in the Earth's core is not remnant
heat left over from formation of the Earth, and hence that the Earth could potentially be
very old. Later, radiometric dating was developed, allowing absolute ages to be assigned
to rocks. This confirmed that the Earth is extremely old, and also resulted in development
of a precise and detailed timescale of most known fossils.
CHAPTER 3
1.Successful biology research often depends on choosing a good "model" - a particular
species, population, or locality that is particularly amenable to study, and/or is a
particularly clear case of the research question. Why were the finches of Daphne Major a
good choice for an evolution study?
Many answers are possible. The fact that Daphne Major is an island made it unlikely that
migration would have a great effect. The size of the island made it possible to catch and
measure the entire population of medium ground finches, while still having a large
enough population for genetic drift to not have a major effect. (See Chapter 7 for more
about migration and drift.) With migration and drift minimized and the entire population
measured, it was easier to detect any occurrence of selection. The simplicity of the
ecosystem and the low diversity of the bird's diet made this a particularly clear case of
evolution: a single environmental feature (rain) had a single pronounced effect on diet
(disappearance of small seeds), which in turn was linked to a single, obvious, and easy-
to-measure anatomical trait (beak depth). The choice to study a small bird was probably
not an accident. Small birds tend to have a large population size per unit area, a short
generation time, and they are small enough to catch and handle easily, while also being
large enough to be easy to measure and to collect blood samples from. Birds also keep
their young conveniently grouped in one location (the nest) for two weeks, making it
feasible for researchers to find and measure all offspring, which is a key requirement for
any evolution study. Finally, birds are active in the daytime (unlike most mammals) and
are relatively easy to observe, and they can be identified permanently with colored leg
bands.
2. Successful artificial selection, such as that practiced by plant and animal breeders to
modify their crops and livestock, depends on which of the following:
a. All of these are necessary for artificial selection to take place.
b. When individuals with the most desirable traits are bred, their traits must be passed
from parents to offspring.
c. Some individuals must have more desirable traits than others.
c. Breeders must be able to selectively breed the individuals with the most desirable
traits.
3. Which is the best definition of Darwinian fitness?
a. The ability of a population to survive in any environment, compared to other
populations.
b. The ability of an individual to survive and reproduce in any potential environment,
compared to other individuals.
c. The ability of a species to survive in a certain environment.
d. The ability of a species to survive over time, compared to other species.
4. Name the two scientists who independently discovered the principle of natural
selection. Which one is more famous, and why?
6. Based on their observation of the color preferences of the bumblebees visiting their
snapdragons, Jones and Reithel predicted (and found) that the proportion of white-
flowered plants _________ from the first to the second generation.
a. stayed the same
b. increased.
c. decreased.
7. Through their studies of medium ground finches, the Grants were able to demonstrate
that, as a result of drought ___________.
a. evolution occurred
b. natural selection occurred
c. all of these occurred
d. adaptation occurred
8. By studying medium ground finch populations over the course of several decades, the
Grants and their colleagues have demonstrated that, during drought years, natural
selection favors birds with _______ beaks; during wet years, natural selection favors
birds with ________ beaks.
a. shallow/deep
b. shallow/shallow
c. deep/deep
d. deep/shallow
9.Successful biology research often depends on choosing a good "model" - a particular
species, population, or locality that is particularly amenable to study, and/or is a
particularly clear case of the research question. Why were the finches of Daphne Major a
good choice for an evolution study?
Many answers are possible. The fact that Daphne Major is an island made it unlikely that
migration would have a great effect. The size of the island made it possible to catch and
measure the entire population of medium ground finches, while still having a large
enough population for genetic drift to not have a major effect. (See Chapter 7 for more
about migration and drift.) With migration and drift minimized and the entire population
measured, it was easier to detect any occurrence of selection. The simplicity of the
ecosystem and the low diversity of the bird's diet made this a particularly clear case of
evolution: a single environmental feature (rain) had a single pronounced effect on diet
(disappearance of small seeds), which in turn was linked to a single, obvious, and easy-
to-measure anatomical trait (beak depth). The choice to study a small bird was probably
not an accident. Small birds tend to have a large population size per unit area, a short
generation time, and they are small enough to catch and handle easily, while also being
large enough to be easy to measure and to collect blood samples from. Birds also keep
their young conveniently grouped in one location (the nest) for two weeks, making it
feasible for researchers to find and measure all offspring, which is a key requirement for
any evolution study. Finally, birds are active in the daytime (unlike most mammals) and
are relatively easy to observe, and they can be identified permanently with colored leg
bands.
11. The panda's "thumb" is actually a wrist bone modified by natural selection to perform
a new function. This is an example of a(n) _____________.
The panda thumb arose from a preadaptation - a pre-existing trait that was put to novel
use. The process works in three stages: first, the trait evolves due to some other purpose.
Second, the trait begins to be used for a novel purpose. Third, natural selection acts on
variations to enhance the trait’s adaptation for the new purpose.
13. Although the scientific community rapidly accepted that all organisms are related by
descent, Darwin's mechanism for change over time - natural selection - wasn't fully
accepted until nearly 100 years after the publication of "The Origin." Explain why.
Darwin did not know about the principles of genetics - how variation is created and how
it is inherited. Kelvin's (inaccurate) estimate of the age of the Earth also presented a
problem for evolutionary theory.
14. What is blending inheritance, and why did it pose a problem for Darwin's theory?
Why is it not considered a problem today?
Blending inheritance was the theory that offspring inherit traits by "blending" two
components inherited from each parent, such that each original component is irrevocably
altered. In the analogy of human skin color, if a black parent and a white parent had a
brown-skinned child, the child was thought to have inherited a blended "brown" particle
of inheritance. (The child was not thought to carry unaltered "black" and "white" particles
of inheritance.) The problem for evolution is that, if this theory were true, populations
would eventually arrive at a completely "blended" state, with no further variation for
selection to work on. Blending inheritance was the leading theory of inheritance in
Darwin's day, but we now know that it is false. Inheritance does not work this way.
Instead, offspring inherit two intact genes from each parent, each of which is unaltered,
and which can be passed on intact to succeeding generations.
15. What was the "Modern Synthesis" and why did it lead to widespread acceptance of
the theory of evolution by natural selection?
The missing piece in Darwin's theory was a mechanism of variation and inheritance. The
Modern Synthesis added this piece, by uniting the new discoveries of genetics with
natural selection. This occurred in a series of landmark books published in the 1930s-
1950s, showing that populations have abundant genetic variation, natural selection should
act on this genetic variation to cause microevolution, and that these small changes could,
in theory, accumulate over time to cause macroevolution. The Modern Synthesis showed
that natural selection had a plausible genetic mechanism, and was in full agreement with
the new information on how inheritance actually works. The clarity, logic, and elegance
of this new synthetic theory immediately led to widespread acceptance of natural
selection among the vast majority of scientists.
16. Why did Dawkins refer to evolution as a "blind watchmaker"? What famous
objection to evolution was he arguing against? Do you think his analogy is a good one?
Another analogy that has been proposed is evolution as a "short-order cook." Which do
you think is a better analogy?
Evolutionary biologist Richard Dawkins was referring to cleric William Paley's classic
argument that if one finds a watch lying on the ground, the logical conclusion is that the
watch was created by an intelligent being, not that it arose by natural causes. Dawkins'
analogy is meant to illustrate that natural selection, even though it is "blind" (not goal-
directed, not purposeful, and not directed by an intelligent being) can produce highly
complex structures. The "short-order cook" analogy emphasizes that natural selection is
not goal-directed and does not have a long-term plan for the future - it simply responds to
immediate environmental conditions. The choice of which analogy is better is a matter of
personal preference; they emphasize different features of natural selection.
17. The creationist "argument from design" is based on the idea that complex structures
and organisms can't arise by chance. The argument fails because, although _________ is
random, ___________ is not; it is directed in the sense of increasing adaptation.
a. selection/mutation
b. evolution/selection
b. mutation/selection
d. adaptation/mutation
18. What is unusual about eel sperm, and why is it relevant for a recent United States
district court case?
Eel spermatozoa have flagella that lack several features usually found in flagella and cilia
- the central pair of microtubules, the inner row of dynein, and the radial spokes. The fact
that eel sperm can swim perfectly well, despite lacking many standard flagella
components, demonstrates that the standard flagellum design is not irreducibly complex.
The flagellum was originally one of Behe's key examples of irreducible complexity, and
was discussed in court at the 2005 Dover School District trial on intelligent design.
21. Ivory poachers (illegal hunters) in Africa kill elephants primarily for the ivory in their
tusks, and big tusks are worth more money. Based just on this fact, make a prediction
about how hunting pressure could cause (or might have already caused) evolution in
elephants. Do you think elephant populations meet Darwin's four criteria for selection to
occur? How could you test your ideas?
Poachers are likely to preferentially target elephants with large tusks (and, in fact, they
clearly do). As for Darwin's four postulates: Any glance at an elephant herd shows that
elephants have variation in tusk size. It is quite likely that this variation is heritable
(though testing this would require data on parent and offspring tusk size). Not all
elephants survive. Survival is nonrandom, since poachers prefer elephants with large
tusks. Thus this population satisfies Darwin's four postulates, and selection should be
occurring. As a matter of fact, it appears that evolution is already well underway. Large-
tusked elephants are now extremely rare. An interesting recent development is the
appearance of families of completely tuskless elephants. Tusklessness was formerly rare
in African elephants, though not unheard of, but in some populations the majority of
elephants are now tuskless. Thus, selection by human hunters may be causing the
evolutionary loss of one of the most dramatic anatomical features of African elephants.
22. Most large-scale fishing is done with nets of a certain mesh size, which catch larger
fish while allowing small, undesirable fish to pass through. In the seas of southeast Asia,
fisherpeople have recently had to switch to smaller and smaller mesh sizes. Why? What
is happening to the fish population? Can you think of two possible explanations?
The fishes of southeast Asia have become very small. This is because fisherpeople have
been unintentionally exerting intense selection for small body size. There are at least two
possible explanations for absence of large fishes. First, the small fishes may just all be
young - i.e. young fish may all be caught before they have a chance to grow larger. (This
is a well-known phenomenon called "growth overfishing.") Second, fishes may be
evolving smaller body size and slower growth rate. The fish populations almost definitely
satisfy Darwin's four postulates, and the selection pressure of overfishing in southeast
Asia appears to be intense, so it is likely that evolution for small body size is occurring.
Recent studies have demonstrated evolution of slow growth and small body size in other
over-fished species (Atlantic cod, pink salmon). Interestingly, though evolution of
smaller body size should be a very obvious consequence of overfishing, fisheries
biologists have, until recently, not been aware of it because they are usually not trained to
think like evolutionary biologists; they have instead concentrated on growth overfishing.
The fisheries industry is only now becoming aware of the probably evolutionary
consequences of overfishing.
23. Now consider another ocean example, but with a twist. Lobstermen in Maine measure
every lobster they catch. They throw back all the small individuals, to allow young
lobsters time to grow. This is a fairly common practice in fisheries. However, they also
do two unusual things: they throw back the largest lobsters, keeping only the medium-
sized ones; and they also throw back any female who has ever been found to be carrying
eggs, even if she is not carrying eggs at the moment. ("Eggers," or egg-carrying females,
are permanently marked by cutting a V-shaped notch in their tails.) Why do Maine
lobstermen throw large lobsters and notched females back into the sea?
The Maine lobstermen are trying to avoid the mistakes of other fisheries (like southeast
Asia) by deliberately selecting for large body size and reproduction. Large lobsters are
thrown back to select for the alleles associated with large body size. Notched females are
thrown back, even if they are not carrying eggs at the time, to select for the alleles
associated with successful reproduction. (Males that have bred successfully cannot be
identified as easily.) In this way, the Maine lobstermen hope to breed" a lobster
population that produces large numbers of good-sized lobsters. So far, the strategy may
be working; record numbers of (medium-sized) lobsters have been landed in recent years,
and the lobster fishery is currently the most productive fishery of the Atlantic coast of the
United States. (For an entertaining and informative look at this story, see Trevor Corson's
book The Secret Life of Lobsters, 2004, Harper.
CHAPTER 4
3. Is the genetic code a homologous trait for the clade of mammals? Is the genetic code a
synapomorphy for the clade of mammals? Explain. Generally, what kind of homologies
are not synapomorphies?
The genetic code is homologous among mammals, but is not a synapomorphy, because it
was not changed from the ancestral state (it was not derived) in the last common ancestor
of mammals. Instead, this trait was inherited unchanged from the last common ancestor
of all living organisms, and is shared with all other taxa of living organisms. Generally,
homologies that are not synapomorphies are those that were inherited without
modification from a much older ancestor - i.e., an ancestor that also gave rise to other
groups that also share the trait.
4. Which of the following attributes does not relate to homoplasy?
a. "Noise" in data sets used to construct phylogeny.
b. Especially common in DNA sequence data sets.
c. Often due to reversal or convergent evolution.
d. Especially common in SINE and LINE data sets.
6. A growing body of literature suggests that mutations are surprisingly frequent on a per
genome/per generation basis; most are ___________ or ___________.
a. slightly beneficial/highly beneficial
b. slightly deletrious/extremely deleterious
c. neutral/slightly deleterious
d. neutral/slightly beneficial
8. Half (four) of the statements below describe morphological data, and the other four
describe DNA sequence data. The four that describe morphological data are _________.
a. Only four character states exist for each data point.
b. Particularly subject to homoplasy.
c. Must be used for fossils.
d. Possible to generate large amounts of data at low cost.
e. Possible to minimize the probability of reversals, by careful selection of traits.
f. Homoplasies can often be recognized.
g. Typically requires slow work by an expert in that particular trait and clade.
h. Homoplasies are difficult to recognize
2.Match the description in Column 1 with term in Column 2.
Option Description your answer
homoplasy A group that contains an
ancestor and all of its
descendants
derived A group that contains an
ancestor and some, but not all,
of its descendants
synapomorphy The occurrence of shared traits
that were inherited from a
common ancestor
monophlyetic group, or The occurrence of shared traits
clade that were not inherited from a
common ancestor
paraphyletic group Modified from an ancestral
state to a new state
homology A shared trait that was modified
(changed from an older
ancestral state) in the most
recent common ancestor
outgroup A close relative of the groups
under study, but one that is
known to have branched off
earlier than all the other groups
reversal A change of a modified trait
back to its ancestral state
Reptilia would have to include the birds. (Both these changes have been widely
accepted.) Figures 4.3 and 4.13 do not show enough information about the Agnatha.
Agnatha could be monophyletic or paraphyletic, depending whether lampreys and
hagfishmore closelyinthat lampreys may be more closely related to other vertebrates than
they are to hagfishes. 14. Molecular clocks can be powerful tools for determining the
timing of evolutevents.
CHAPTER 5
3. What are two types of proteins that can cause point mutations?
Point mutations can occur whenever DNA has to be replicated (for cell division) or
repaired. Therefore most common sources of point mutations are errors made by DNA
polymerase during replication prior to cell division, and errors by DNA repair enzymes in
detecting or repairing DNA damage. DNA damage, in turn, may be caused by radiation
or certain toxins.
4. What was the traditional method of estimating mutation rate? Did it result in an
accurate estimation of mutation rate? Why or why not?
The traditional method of estimating mutation rate looked at phenotypes. Observable
changes in phenotypes were assumed to be due to mutation. However, this method
obviously misses all mutations that don't cause changes in the particular trait under study.
It generally misses all silent-site substitutions and some replacement substitutions.
5. Which of the following is not a reason why analyses of loss-of-function mutations
underestimate actual mutation rates?
a. Large-scale phenotypic changes can't be caused by point mutations.
b. Silent site mutations produce no change in amino acid sequences, and so are uncounted
by these analyses.
c. Many replacement mutations have effects too subtle for researchers to detect.
6. Which of the following statements is true?
a. Mutation rate is identical for all species, on a per-cell, per-generation basis.
b. High mutation rates are advantageous in novel environments.
c. Faster DNA polymerases are associated with lower mutation rate.
d. Mutation rate is usually higher for nuclear DNA than for mitochondrial DNA.
e. Lower mutation rates are better than higher mutation rates.
8. A growing body of literature suggests that mutations are surprisingly frequent on a per
genome/per generation basis; most are ___________ or ___________.
a. neutral/slightly deleterious
b. neutral/slightly beneficial
c. slightly deletrious/extremely deleterious
d. slightly beneficial/highly beneficial
9. The most important source of new genes is probably ___________ the underlying
mechanism for this is ___________.
a. polyploidy/duplication of the genome
b. gene duplication/unequal crossing over
c. genetic linkage/chromosome inversions
d. point mutations/errors during DNA replication
10. What are two major processes than can cause gene duplication, and how can we
determine which process is responsible for a certain duplicated gene?
Two major processes can duplicate genes: retrotransposition and unequal cross-over.
Retrotransposition occurs when a messenger RNA molecule is accidentally reverse-
transcribed (often by the viral enzyme reverse transcriptase) to form double-stranded
molecule of DNA, typically lacking introns and with a poly-A tail. This DNA molecule
can sometimes be inserted into a random place in the genome. Genes duplicated this way
lack introns, often have a poly-A tail, and are located far from the original gene. Unequal
cross-over occurs when homologous chromosomes do not align properly during meiosis,
resulting in one chromosome that has a deletion and another that has a
gene duplication. Genes duplicated this way have their introns intact, and are close to the
original gene.
12. Why are the globin genes thought to have arisen by gene duplication? In your
opinion, was the duplication process likely to be retrotransposition or unequal cross-over?
Why?
The globin genes are thought to have arisen by gene duplication because of their highly
similar sequences, and because they share the same introns in exactly the same places.
They are also physically clustered together in two major groups, along with pseudogenes
that appear to have lost function. These patterns, particularly the physical clustering and
presence of identical introns, indicates that these genes were duplicated by unequal cross-
over, and not retrotransposition.
13. What are paralogous genes and orthologous genes? Give an example of each.
Paralogous genes are homologous genes in the same species that arose from one ancestral
gene by gene duplication, such as the delta-globin and beta-globin genes of humans.
Orthologous genes are homologous genes in different species, descended from one
ancestral gene in the last common ancestor of the two species, such as the human beta-
globin gene and the mouse beta-globin gene.
14. The most important evolutionary consequence of chromosomal inversions is:
a. they prevent selection from acting on the alleles within the inverted region, thereby
increasing genetic diversity.
b. they prevent specific groups of alleles from being separated by crossing-over, allowing
them to be inherited together as single "supergenes."
c. they prevent specific groups of alleles from being separated by crossing-over, allowing
them to be inherited together as single "supergenes."
d. polyploidy.
e. that they reduce the rate of point mutations in the alleles within the inversion.
15. What is a chromosome inversion and what usually causes it to happen? What is the
major evolutionary consequence of chromosome inversion? In what organism are they
known to be especially common?
A chromosome inversion is the reversal of a large stretch of a chromosome into the
opposite orientiation. It usually occurs when radiation causes double-stranded breaks at
two different places in a chromosome. The inner section can then flip around and re-
attach in the opposite orientation. The main evolutionary consequence is an increased
effect of linkage that "locks together" all alleles on the inverted section, causing them to
be inherited as a single block. Inversions are common in the fruit fly genus Drosophila.
16. Which of the following statements regarding polyploidy, or genome duplication, is
false?
a. It has not been a major feature of vertebrate evolution.
b. It tends to produce species with even numbers of chromosomes.
c. It can lead to immediate speciation.
d. It is more likely in organisms that can self-fertilize.
e. It is more common in plants than animals.
17. Polyploidy may result in a new species being formed in a single generation. For that
to occur, which of the following conditions must exist?
a. All of the above conditions are required for polyploidy to result in a new species being
formed.
b. The tetraploid offspring must produce triploid offspring when it mates with members
of its parental population.
c. The tetraploid offspring must be able to self-fertilize or to mate with its parent (which
produced the diploid gametes) or a tetraploid sibling.
d. When errors at meiosis produce diploid gametes, the individual with the diploid
gametes must be able to self-fertilize and produce tetrapolid offspring.
19. How common are gene families caused by gene duplication? Do most species have
them? What is the largest gene family discovered to date?
Gene families are quite common - most species have hundreds of gene families of at least
two or more genes, and usually have several dozen gene families that have ten or more
genes. The largest gene family discovered so far is in the mouse, and contains 1292 genes
involved in olfactory reception. Most other mammals also have enormous gene families
associated with olfaction. Humans have this gene family too, but most of the human
olfaction-receptor genes have been rendered functionless by mutation.
20. A hypothetical population has two alleles for a gene, A and a. In a random sample of
50 individuals, 10 are homozygous for a, 15 are homozygous for A, and 25 are
heterozygous. What is the frequency of A?
a. 55%
b. 40%
c. 15%
d. 45%
e. 1.1%
22. Describe two statistical measures of the amount of allelic diversity in a population.
The two classic measures are mean heterozygosity and percentage of polymorphic
locMean heterozygosity can be defined in two equivalent ways: the average frequency of
heterozygotes across loci, or the average number of heterozygote loci per individual. The
percentage of polymorphic loci is simply the percentage of loci that have more than one
allele in the population.
23. Generally speaking, do most populations have a lot of genetic variation, or a little?
How do we know? Why is genetic variation maintained in populations?
There is generally quite a lot of genetic variation in populations. Gel electrophoresis
studies show that average heterozygosity is about 10% across all populations. Detailed
sequence analysis of certain genes, such as the CFTR gene in humans, have shown that
one gene can have hundreds of different alleles in a large population. The two major
hypotheses for what maintains this genetic diversity are, first, natural selection (i.e.
selection for different alleles in different environments or at different times, or selection
for heterozygotes), and, second, many alleles may be selectively neutral.
24. A gene associated with the ability to taste bitter compounds such as PTC
(phenylthiocarbamide) is present in at least two forms in both chimpanzees and humans.
The taster allele, T, is dominant to the nontaster allele, t. In 2006, Stephen Wooding et al.
sequenced these gene in 58 chimpanzees and compared it to sequences from 330 humans.
(Tasting ability in the chimpanzees was assessed by offering them apple slices coated
with PTC.) Several different forms of each allele were found for each species. Shown
below are the nucleotide sites that were found to be variable, compared to an outgroup
(gorilla). (These sites were not contiguous; the invariant stretches of DNA in between
them are not shown). Dots indicate the same nucleotide as the gorilla sequence.
It has been hypothesized that the common ancestor of humans and chimpanzees already
had both taster and nontaster alleles. Under this hypothesis, all human and chimpanzee
taster alleles were derived from the common ancestor's taster allele, and all human and
chimpanzee nontaster alleles were derived from the common ancestor's nontaster allele.
Is this hypothesis supported by the sequence information? Why or why not?
The hypothesis is not supported. Chimp taster alleles are more similar to chimp nontaster
alleles than to any human alleles. Likewise, human taster alleles are more similar to
human nontaster alleles than to any chimp alleles. This indicates each species evolved
one of its class of alles from the other, and did not inherit both types of alleles directly
from the common chimp-human ancestor. (More detailed phylogenetic analysis indicated
that in each species, the T allele is older than the t allele.) Reference for this data:
Wooding, S., B. Bufe, C. Grassi, M.T. Howard, A.C. Stone, M. Vazquez, D.M. Dunn, W.
Meyerhof, R.B. Weiss, and M.J. Bamshad. 2006. Independent evolution of bitter-taste
sensitivity in humans and chimpanzees. Nature 440:930-934.
25. Deciphering the structure of DNA and determining the relationship between DNA
and proteins inspired an explicitly molecular view of genes and their products. Correctly
match each term with its most precise definition.
Option Your
Answer
A. a change in a Gene
single base
sequence of a gene
B. stretch of DNA Alleles
that codes for a
distinctive type of
RNA or protein
product
C. versions of the Mutation
same gene that
differ in their base
sequences
D. any change in Point
the base sequence mutation
of DNA
26. In order for mutation rates to be subject to natural selection, they must meet Darwin's
postulates. Correctly match each finding below with its corresponding postulate.
Option Your Correct Comments
Answer Answer
A. Survival and Researchers have C. Can you infer
reproduction are identified varying Individuals this from the
non-random mutation rates in vary within information
bacteriophages, E. populations provided?
coli, and other
organisms
B. Variations Specific mutations B. Can you infer
among individuals have been identified Variations this from the
are passed from that change the among information
parent to offspring efficiency of DNA individuals provided?
synthesis and repair are passed
enzymes from parent
to offspring
C. Individuals vary E. coli cells with A. Survival Correct!
within populations high mutation rates and
had higher fitness reproduction
than normal cells are non-
when grown in random
novel environments