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Student ID number: __________________________________

Name: _____________________________________________

MASSEY UNIVERSITY
ALBANY CAMPUS
EXAMINATION FOR
196.217 EVOLUTIONARY BIOLOGY
Semester 2 - 2014

TIME ALLOWED: THREE (3) HOURS

Answer ALL questions from SECTION A.

Answer THREE (3) questions from SECTION B.
Section A consists of 10 short answer questions.
Each question is worth 3 marks, 30 marks in total. Allocate 1 hour for Section A.
Section B consists of six long answer questions.
Each question is worth 20 marks, 60 marks in total. Allocate 2 hours for Section B.

TOTAL marks: 90
All answers are to be written in the blue answer book provided.

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SECTION A (Short answer questions)

[Answer ALL questions from SECTION A]
1.

Patterns of development form part of the evidence for evolution through

common descent with modification. What feature of early embryo
development in mammals provides evidence for common descent with
modification, and why is this evidence for common descent with modification?
[3 marks]

2.

Mutations can be classified according to their functional outcome or by their

physical attributes. What are the subclasses in these two categories?
Describe each one in brief. [3 marks]

3.

The low prevalence of lactose intolerance among Northern Europeans is

evidence in favor of:
A) genetic drift in human populations;
B) loss of genetic diversity among Europeans;
C) limited gene flow between Northern Europeans and Eastern Asian
communities;
D) positive selection of a young haplotype;
E) all of the above.
Explain the reasoning behind your chosen answer. [3 marks]

4.

Name two ecological mechanisms that drive adaptive radiation, and

describe an example of each. [3 marks]

5.

Name the evolutionary process

depicted in the image to the right.
Describe the predicted impact of
this process on genetic variation
within and between subpopulations over time. [3 marks]

6.

On a number of occasions during this paper we have discussed examples of

adaptive imperfection a consequence of the constraints that sometimes
limit the range of novelties that evolution can produce. Name two different
kinds of constraint and describe an example of each. [3 marks]

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7.

Mllerian mimicry is a particular type of mimicry

where, typically, two or more poisonous species, that
may or may not be closely related and share one or
more common predators, have come to mimic each
other's warning signals. A classic example is that of the
Heliconius butterflies (right).
(a)
What type of selection is responsible for
maintaining different races of butterflies in a metapopulation? [1 mark]
(b)
Explain how such a polymorphism is maintained
why does selection not fix one race (allele) and drive
all others to extinction? [2 marks]

8.

What is a meme? Briefly describe how language may be considered analogous

to the genetic code. [3 marks]

9.

Provide a succinct definition of cooperation. Explain why cooperation

challenges Darwinian evolution and describe one theoretical framework that
reconciles observation with understanding. [3 marks]

10.

Define co-evolution and describe two examples where coevolution shapes

patterns of biological diversity. [3 marks]

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SECTION B (Long answer questions)

[Answer THREE (3) questions from SECTION B]
1. (a)

Fossils provide an important source of evidence for evolution through

common descent with modification, as they have revealed the existence of
transitional forms that are predicted by the theory of evolution. Explain why
determining the ages of transition fossils is an important part of using fossils
to support common descent with modification. [3 marks]

(b)

Imagine you extract DNA from a fossil that appears to be a common

ancestor of two known, living species. You obtain the DNA sequence of a
gene from this fossil, and compare it to the sequence from the two extant
species. You first make an alignment of the three sequences, so the
nucleotides are correctly aligned. This allows you to treat each nucleotide
position in the alignment as a ________________ character (enter the
correct term in your answer book). [2 marks]

(c)

Relatively speaking, how many mutations are expected between these three
sequences if the gene is highly conserved versus if it is poorly conserved?
[2 marks]

(d)

Discuss what you would expect to see when comparing the fossil DNA
sequence with the DNA sequences of the two extant species if the fossil
really is a common ancestor of the two extant species (assume some
mutations have occurred since the separation of the two species from the
common ancestor). [10 marks]

(e)

Imagine you have another, closely-related fossil of known age from which
you also obtain the sequence of the same gene. You use this information to
calibrate the age of your first fossil, which is of unknown age. Describe the
logic behind this molecular clock approach? [3 marks]
------------------------

2. (a)

In a diploid organism with a trait determined by two alleles, say A and a, if

the frequency of A is given by x (and conversely, the frequency of a by 1-x)
what are the proportions of alleles in the next generation? [2 marks]

(b)

Derive the next generation via proceeding through the life cycle (i.e.
genotype frequencies, mate-pairing probabilities etc.), stating your
assumptions at appropriate points. [6 marks]

(c)

If based on unrealistic assumptions, why is the Hardy Weinberg

equilibrium of such importance in biological theory? [12 marks]

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3.

The table below summarises values for clutch parameters and reproductive
success in the New Zealand endemic Red-crowned parakeet during two
breeding seasons 2004-2005 and 2005-2006. The egg volume and percentage
of fertile eggs in a clutch do not change between seasons. However, the number
of eggs per clutch, the number of eggs hatching (hatching success), the number
of chicks in a brood, and the number of fledglings are significantly higher in the
second breeding season.

(a)

Based on the information contained in the table and our extensive

discussion of life histories in birds in class, answer True or False to the
following statements about the Red-crowned parakeet:
i.

Because reproducing individuals must trade-off between number and

quality of offspring, one could hypothesize that the offspring of large
clutch seasons is of lesser quality than that of small clutch
seasons. [2 marks]

ii.

Females producing large clutches will not experience reduced

survival the following breeding season because the allocation of
resources to produce a large clutch has no effect on the physiology
of hens. [2 marks]

iii.

If we experimentally manipulate the clutch size of Red-crowned

parakeets, we could expect that young hens from enlarged clutches
will lay large clutches themselves. [2 marks]

iv.

The significant increase in hatching success in the second season of

study, without a significant change in fertility, indicates that females
switched to polyandry to maximise the fertilization of more eggs by
various males. [2 marks]

(b)

In four paragraphs describe how you would design an experiment to

measure and determine: i) the optimum clutch size for the Red-crowned
parakeet; ii) offspring quality from clutches of different sizes. [6 marks]

(c)

In four paragraphs describe how you would design an experiment to

measure aging in Red-crowned parakeet hens in relation to predation.
[6 marks]

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4.

(a)

Why is it so difficult to define a species? [2 marks]

(b)

What is the biological species concept? Describe two problems with the
biological species concept, illustrating each with an example. [5 marks]

(c)

What is the phylogenetic species concept? Describe a situation where the

phylogenetic species concept might be problematic. [3 marks]

(d)

Describe, with examples, three different barriers to gene flow that might
give rise to speciation. [10 marks]
------------------------

In a recent publication, a group of researchers examined the sequence of 11

genes located on either the Y chromosome or autosomes of 9 Drosophila (fruit
fly) species in order to investigate how Y-linkage affects gene evolution.
(a)

The figure below shows the phylogeny of the Drosophila species included
in this study.
(i) Briefly describe the evolutionary relationships depicted in the tree. (for
(ii)
(iii)

efficiency, abbreviate the species names to mel, yak, ere etc.) [2 marks]
Is this tree scaled or unscaled? [1 mark]

Is D. ananassae more closely related to D. melanogaster, to D.

erecta, or is it equally related to these two species? [1 mark]

Figures adapted from Singh et al. (2014)

Mol. Biol. Evol. doi:10.1093/molbev/msu203

5.

This study considered the sequence of 11 genes that are all located on the Y
chromosome of D. melanogaster. However, not all of the orthologues of these
same 11 genes are located on the Y chromosome of the other 8 species; in
some species some of the genes are instead located on the autosomes. Gene
names are listed above the branches on which they moved from an autosome
to the Y chromosome. Genes lost from the Y chromosome are listed below the
branch on which the gene was lost.

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Q5. continued.

(b)

List the species in which gene kl-5 is located on the Y chromosome. [1 mark]

(c)

How do species D. virilis, D. mojavensis, and D. grimshawi differ to each

other with respect to genes PRY and Ppr-Y? [1 mark]

Since the 11 Drosophila genes are Y-linked in some species and Not Y-linked
in others, the researchers were able to investigate how evolution of each
particular gene differed when it was on the Y chromosome compared with when
it was located elsewhere.
First, the researchers compared the codons for each gene in the species where it
was Y-linked with the codons of the same gene in species where it was Not Ylinked. Codon usage bias can tell us something about how selection is
operating.
(d)

Explain what is meant by codon usage bias. [2 marks]

The figure below shows the frequency of optimal codons (FOP) for Y-linked vs
Not Y-linked orthologues across the 9 Drosophila species. For Drosophila,
optimal codons are those with more C and G nucleotides and fewer A and T
nucleotides. The results for 5 different genes are shown (x axis).
Describe the trend shown in the data below. [2 marks]

Figures adapted from Singh et al. (2014)

Mol. Biol. Evol. doi:10.1093/molbev/msu203

(e)

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Q5. continued.

(f)

Several evolutionary processes could have caused the differing patterns of

evolution of Y-linked and Not Y-linked genes shown in (e). Select two
evolutionary processes from the list below that could account for these
findings. [2 marks]
A. Genetic drift has had a stronger effect on evolution of Y-linked
genes than on Not Y-linked genes.
B. Genetic drift has had a stronger effect on evolution of Not Ylinked genes than on Y-linked genes.
C. Purifying selection has removed mutations that reduce codon
optimisation in Not Y-linked genes.
D. Positive directional selection for mutations that decrease
codon optimisation in Y-linked genes
Explain how each of the two processes that you selected could have
resulted in the differing patterns of evolution observed. [2 marks]

(g)

Three things in particular distinguish the Y chromosome from the

autosomes in Drosophila:
1. The Y chromosome has no partner with which it can recombine during
meiosis (the X chromosome is much larger and carries a completely
different set of genes);
2. The Y chromosome effective population size is considerably smaller
than that of the autosomes since it is only carried by males, and as a single
copy;
3. The synonymous substitution rate (dS) is much higher for Y-linked
genes than it is for Not Y-linked genes, whereas the non-synonymous
substitution rate (dN) is roughly equivalent for Y-linked and Not Y-linked
genes.
With reference to these three points, explain how the operation of natural
selection is constrained for Y-linked genes relative to autosomal genes.
[6 marks]

------------------------

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Natural populations of the nematode worm C. elegans are composed of males

and hermaphrodites. Hermaphrodites reproduce through either asexual selffertilization (selfing) or by outcrossing (sex) with males. Despite the potential
for outcrossing with males, most C. elegans hermaphrodites reproduce
predominantly via selfing.
(a)

Sex is an inefficient way to reproduce as it is costly in comparison to an

asexual alternative. One of these inefficiencies is the two-fold cost of
males. Explain what is meant by the two-fold cost of males and how it
makes sexual reproduction less efficient than asexual reproduction. [4 marks]

In a recent study, researchers manipulated the C. elegans mating system by

mutating mating genes to make 3 populations that reproduce in 3 different ways:
obligate selfing (reproduces only by selfing), wild type (reproduces by either selfing
or outcrossing), and obligate outcrossing (reproduces only by outcrossing).
(b)

In Experiment 1 the researchers treated the populations with a chemical

mutagen to increase the mutation rate. Control (solid line) and Mutated
(dashed line) populations were then allowed to evolve for 50 generations.
After 50 generations the researchers measured the fitness of the evolved
populations relative to the nave ancestral populations. The results are
shown below.
(i)

Explain why populations experiencing higher mutation rates showed

reduced fitness relative to control populations experiencing lower
mutation rates [3 marks].

(ii)

Outline a genetic hypothesis that accounts for why mutated

populations were significantly fitter when they were able to reproduce
by outcrossing. [3 marks]

Experiment 1

Figure adapted from Morran et al.

(2009) Nature 462: 350-2

6.

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Q6. continued.

In Experiment 2 the researchers started with wild-type populations (that

reproduced by a mixture of selfing and outcrossing). These were allowed to
evolve in the presence (dashed line) or absence (solid line) of mutagen. The
outcrossing rate was measured every 5 generations for a total of 50
generations. The results are shown below.

(iii)

Do the results of Experiment 2 agree with the hypothesis outlined in

(bii)? Why / why not? [3 marks]

In Experiment 3, the three C. elegans populations (obligate selfing, wildtype, and obligate outcrossing) were exposed to either the bacterial
pathogen Serratia marcescens (dashed line) or heat-killed S. marcescens
control (solid line) for 40 generations. The researchers then measured the
fitness of the evolved populations relative to the nave ancestral
populations. The results are shown below.
Experiment 3

(Control)

Figure adapted from Morran et al.

(2009) Nature 462: 350-2

(c)

Figure adapted from Morran et al.

(2009) Nature 462: 350-2

Experiment 2

(i)

Name the ecological hypothesis that accounts for why populations

that are able to reproduce sexually tend to adapt more rapidly to
pathogens? [2 marks]

(ii)

Explain why the populations evolving in the presence of live Serratia

increased in fitness relative to control populations when they were
able to reproduce by outcrossing. [3 marks]

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Q6. continued.

(iii)

Describe what you would expect to see if Experiment 2 was repeated,

but with live vs heat-killed Serratia as the treatment instead of
mutagen. [2 marks]

END OF PAPER
++++++++

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