1. science
2. biology
3. zoology
4. endangered species

READING ASSIGNMENTS AND HOMEWORK
in
EVOLUTION
Reading assignments and homework required for Evolution:
Reading Assignment and homeworks (5) will be required from each student. The reading assignment or
homework will be due the date in the syllabus by 12:00 Midnight unless the instructor changes the due
date. Late reading assignments or homeworks of more than a week will not be accepted.
Reading Assignment (Natural Selection) will be a study of the evolution of an adaptation and methods
used to determine the mechanism of evolution (50 pts.).
The reading assignment and homeworks will be posted on the web page.
Web page: http://cees.tamiu.edu/McReynolds/webpage.html
Reading Assignment and some homeworks will require reading a paper(s) from the scientific
literature on the subject and will require critical thinking. The paper can be found on a database in an
online periodical of the TAMIU Library or hard-copy in the TAMIU Library. Science Direct or JSTOR are
some of the databases in the library. Ask the instructor if you need assistance finding the papers.
Answer the questions in the reading assignment. Some questions will be based on information in the
paper and other questions will require applying evolutionary concepts to the case in the paper (answers
will not necessarily be found in the paper).
Reading assignment should be typed and sent by e-mail (send attachments in iWorks, Appleworks,
rtf, pdf, or Word format - the newest version of Word (.docx) can be read. (Check your e-mail. The
instructor will reply and will indicate if the reading assignment has been received.) Note: e-mail all
reading assignments on time to [email protected]. Hard copies will not be accepted for
readings assignment unless discussed with the instructor before due date but hard copies of most
homework will be accepted.
Evolution by Natural Selection
BIOL 3406
Reading Assignment
Due September 10, 2014
The elk population in Wyoming has undergone major changes recently (Middleton et al. 2013). Other
papers in the Forum-Ecological Change and Migratory Ungulates in the issue (Ecology 94(6)) are dealing
with the cause of the decline and an evolutionary question. Is the migration (or lack of migration) by elks
evolving in this elk population?
What is required for the population to stop migrating to evolve by natural selection (be specific)?
1)
2)
3)
4)
Can the change in elk population be due to some other factor besides evolution by natural selection?
Explain.
What evidence is there that the current migration (non-migratory) pattern has evolved by natural
selection?
(You can use other papers in the forum for this issue but cite them properly.)
Literature Cited
Middelton, A. D., M. J. Kauffman, D. E. McWhirter, J. G Cook, R. C. Cook, A. A. Nelson, M. D. Jimenez
and R. W. Klaver. 2013. Animal migration amid shifting patterns of phenology and predation:
lessons from Yellowstone elk herd. Ecology 94:1245-1256.
Homework 1
Evolution - BIOL 3406
Due September 17, 2014
Show your work.
Quantitative Genetics:
1. A population of goldenrod (Solidago sp.) has an average height of 110 cm, but the average height of
individual plants setting seeds is 130 cm. The average height of plants in the next generation is 115 cm.
What is the narrow-sense heritability? What assumption(s) are made to calculate narrow-sense
heritability by this method?
2. Another population of goldenrod (Solidago sp.) has an average height of 85 cm and variance of 25, and
selection gradient of -0.25 for seed set (fitness) vs height of plant.
(a) If the narrow-sense heritability is 0.25, what is the evolutionary response?
(b) If the narrow-sense heritability is 0.35, what is the evolutionary response?
3. Seed production in a daisy species can depend on size of the flower by attracting pollinators. In one
habitat, the average diameter of the flower disc is 33 mm, but the average diameter of flowers setting
seeds is 24 mm.
(a) If the narrow-sense heritability is 0.15 what is the evolutionary response?
(b) If the narrow-sense heritability is 0.4, what is the evolutionary response?
4. In another habitat, the average diameter of the flower disc for the daisy species is 45 mm.
a) In one year, the variance of flowers in the population is 36, selection gradient of seed sets vs flower
diameter is +0.13, and the narrow-sense heritability is 0.3. What is the evolutionary response and the
average diameter of flowers in the next generation (annual plant)?
b) In the second year, the variance of flowers in the population is 22, selection gradient of seed sets vs
flower diameter is -0.22, and the narrow-sense heritability is 0.23. What is the evolutionary response and
the average diameter of flowers in the next generation?
5. Let us imagine a species of ground finch on the imaginary island of Numenor (An island in J.R.R.
Tolkien’s Silmarillion).
In a habitat for Numenor finches, there are two main types of seeds available. One seed type is hard, and
a finch with a beak depth of 11 mm or more is favored (higher fitness). The other seed type is soft, and a
beak depth of 8 mm or less is favored. Gray curves in (b) and (c) are the original curve shown in (a).
Show on graphs (b) and (c) the evolution of beak size after many generations in a heterogeneous
environment with both seed types available with the starting distribution of phenotypes in figure (a)
below: (b) If heritability (h2) = .35? (c) If heritability (h2) = 0? Explain.
After many
generations
6. Medel et al. (2003) determined the selection gradient of corolla size for the Andean monkey flower (see
Fig. 5 in Medel et al. 2003). (a) What mode of selection occurs for corolla size in the monkey flower?
What explains this mode of selection for monkey flowers? What other parameters (values) would need
to be determined or calculated to predict the evolutionary response (R) of monkey flowers?
(b) The current population of monkey flowers has the frequency of CVA2 (see Fig. 5d in Medel et al. 2003)
in the figure below. Gray curve in after many generations is the original curve shown in current
population. Show on graph the frequency of CVA2 after many generations with the evolution of CVA2 if
heritability (h2) = 0.25.
After many
generations
Current
population
-0.5
0.0
0.5
-0.5
CVA2
0.0
0.5
CVA2
(c) The current population of monkey flowers has the frequency of guide size (see Fig. 5b in Medel et al.
2003) in the figure below. Gray curve in after many generations is the original curve shown in current
population. Show on graph the frequency of guide size after many generations with the evolution of
guide size if heritability (h2) = 0.32.
Current
population
(c)
After many
generations
1
0
0
Guide Size
1
Guide Size
Literature Cited
Medel, R., C. Botto-Mahan and M. Kalin-Arroyo. 2003. Pollinator-mediated selection on the nectar guide
phenotype in the Andean monkey flower, Mimulus luteus. Ecology 84:1721-1732.
Homework 2
Evolution - BIOL 3406
Due September 24, 2014
Show your work.
1. The MN blood group has two alleles OM and ON. The genotype OMOM has blood type M, OMON
has MN, and ONON has N. In a human population, the number with M are 289, MN are 125, and N are
86. What is the allelic frequency for OM? ON? What is the expected frequency of M blood type in the
population when in equilibrium? MN? N? Is this population in Hardy-Weinberg equilibrium? Do the
statistics.
What is the inbreeding coefficient(F) for this population?
2.
µ
a
A
pn
ν
qn
What is the equilibrium frequency of A if
a. µ = 5.4 ⨉ 10-7 and ν = 4.2 ⨉ 10-6?
b. µ = 6.2 ⨉ 10-5 and ν = 7.1 ⨉ 10-7?
c. If the mutation rates are µ = 5.9 ⨉ 10-6 and ν ≈ 0, what is the allelic frequency pn with starting p0 = 1.0
after 100 generations?
d. 1000?
e. 10,000?
3. An imaginary genetic disease similar to Phenylketonuria is an autosomal recessive disease. In a
population, 1 in 12,000 infants has this disease. What is the frequency of the allele assuming random
mating? The expected frequency of heterozygous carriers?
4. An endangered species of butterfly has several small populations (demes).
Biologists studying this endangered butterfly ask: Are these populations isolated from each other? One
way to test this is to determine the inbreeding within these populations. The biologists tested a loci in
each population and determined the frequency of an allele (A) in the loci and the frequency of
heterozygotes in each deme for the loci. What demes are more isolated and therefore have a higher
inbreeding coefficient (F)?
Frequency in deme
Frequency of allele of loci (A)
Frequency of hetnerzyogotes (Aa)
Deme 1
0.8
0.26
Deme 2
0.75
0.24
Deme 3
0.85
0.15
Deme 4
0.8
0.11
5. Is this population of wild oat Avena fatu in Hardy-Weinberg equilibrium? Do the statistics. What is the
inbreeding coefficient for the gene in the self-fertilizing wild oat?
Genotype:
Observed:
HH
55
Hh
30
6. (a) What is the inbreeding coefficient for individual I in the figure 1 below?
(b) What is the inbreeding coefficient for individual I in the figure 2 below?
(a)
(b)
hh
15
Homework 3
Evolution - BIOL 3406
Due Oct. 15, 2014
Show your work.
1. What is the equilibrium frequency for a recessive allele when mutation rate is
6.6 ⨉ 10-6 and the selection coefficient is 0.05?
2. The main population has an allelic frequency of 0.75 and “island” population has an allelic frequency of
0.35 and migration rate is 0.045 for mainland to island. Assume migration rate for island to mainland is 0.
(a) What is the allelic frequency after 15 generations?
(b) How many generations are required to change the allelic frequency of the “island” population to 0.8?
(c) How many generations are required to change the allelic frequency of the “island” population to 0.6?
3. If the selection coefficient against the recessive genotype is 0.10 and the equilibrium allelic frequency of
the recessive allele is 0.08, what is the mutation rate to the recessive allele? Is this a realistic mutation
rate?
4. Mutineers of the HMS Bounty lead by Fletcher Christian settled an island in the South Pacific (Pitcairn
Island) in 1789. The population size on the island has remained small every since with no immigration.
What is the FST value for the population after 35 generations assuming N ≈ 28?
5. An endangered species of butterfly has several small populations (demes).
Biologists studying this endangered butterfly ask: If these populations are isolated how important is
genetic drift vs. gene flow within each deme? The biologist have mapped the position of each deme.
Demes 1 and 2 are near each other and near the center of the species distribution. Deme 3 is at the edge
of the distribution and closer to Deme 2. Deme 4 is in the opposite direction and close to Deme 1. The
biologist determined the effective population size and rate of gene flow for each deme. (a) What is the
equilibrium fixation index for each deme? (b) For Deme 3, what is the expected fixation index if gene
flow has no effect (assume m = 0) after 25 generations?
Population Size (N)
Rate of Gene Flow (m)
Deme 1
140
0.16
Deme 2
125
0.12
Deme 3
16
0.01
Deme 4
30
0.1
6. Calculate the equilibrium allelic frequency for the following Darwinian fitnesses. Then calculate the
change in allelic frequency (Δq) for the following Darwinian fitnesses (w) at each of the allelic
frequencies below. Which one has an unstable equilibrium? Why?
Darwinian Fitness (w)
AA
Aa
aa
q^ Δq
a.
q = 0.75
q = 0.5
q = 0.25
1.0
0.68
1.0
__
__
__
__
b.
q = 0.75
q = 0.4
q = 0.25
0.36
1.0
0.45
__
__
__
__
c.
q = 0.75
q = 0.5
q = 0.2
0.32
0.32
1.0
__
__
__
__
d.
q = 0.75
q = 0.4
q = 0.25
1.0
1.0
0.65
__
__
__
__
e.
q = 0.75
q = 0.5
q = 0.1
0.9
1.0
0.65
__
__
__
__
7. In a metapopulation of five demes for another species of insect (same population size in all demes), the
allelic and genotypic frequencies of the demes are:
Frequency in deme
A
AA
Aa
aa
Deme 1
Deme 2
Deme 3
Deme 4
Deme 5
0.2
0.4
0.1
0.8
0.5
0.04
0.16
0.01
0.64
0.25
0.32
0.48
0.18
0.32
0.5
0.64
0.36
0.81
0.04
0.25
Mean
0.4
What is the expected heterozygosity for the whole metapopulation with random mating?
What is the fixation index (FST) for the metapopulation?
8. Random walk: (a) On a graph, show the change in gene frequency over time for a small population
with a starting gene frequency of q = 1.
(b) Large population starting at q = 0.4
(c) Small population starting at q = 0.6.
q
Generation
Homework 4
Evolution - BIOL 3406
Due Nov. 5, 2014
Kin Relationships:
1. (a) In an ant colony with coefficient of relatedness of r = 0.75 between workers and new queens, what
would increase the fitness of the workers more: (1) helping to raise own offspring (sons) or (2) helping to
raise new queens? Why? Explain using Hamilton’s rule.
(b) If the average coefficient of relatedness is r = 0.4 between the female workers and new queens, can the
fitness of the worker still be higher by working at the nest instead of having own offspring? Why?
Explain using Hamilton’s rule.
2. How closely related should the adult donor and young recipient be for altruistic behavior to evolve in
the population, if the increase in fitness for the young by altruistic act is 0.18 and decrease in fitness for
the adult donor is 0.06? Would the inclusive fitness of the adult donor increase, if the young recipient are
nieces and nephews (diploid population)? Full brothers or sisters? First cousins? Non-relatives?
3. In a Hymenoptera with haplodiploidy, what is the coefficient of relatedness between mother (A) and
daughter (B)? Mother (A) and son (Y)? Father (X) and daughter (B)? Father (X) and son (Y)? Sister (B) to
brother (Y)? Sister (B) and sister (C)? Aunt (C) to nephew (Z)? Aunt (C) to niece (D)? Uncle (Y) to niece
(D)? Uncle (Y) to nephew (Z)?
Show the calculations for each case including both r values when the relatedness is asymmetrical.
A
X
B
D
C
Z
Y
4. A species of aphid has an effective alarm signal (release of a pheromone that is detected by the aphids
but not the predator) with limited risk to the signaler [donor]. However, there is a cost in producing,
storing, and releasing the pheromone (We will consider the cost as 0.05 decrease in fitness or individual’s
reproductive success).
Spring: A clutch of winged offspring from one female after sexual reproduction are aggregated on
a young leaf of an oak tree before dispersing to select host plants to lay eggs by parthenogenesis.
The aphids on this leaf are related (average r = 0.33: the female mated with an average of three
males), and the benefit from the alarm signal is high (benefit = 0.2) because escape is possible
from the predator. How would the inclusive fitness of the donor change?
Summer: Wingless aphids on the primary host (roses) are closely related because of
parthenogenesis (r = 1), and the benefit is low (benefit = 0.03) because the aphids do not have an
effective defense against predators. How would the inclusive fitness of the donor change?
Fall: Winged reproductives that aggregate (clump) on a tree to overwinter are not closely related
(r = 0 ) because of dispersal from many host plants, and the benefit from the alarm signal is high
(benefit = 0.8) because winged aphids have an effective escape from the predator. How would
the inclusive fitness of the donor change?
When can the aphid’s use of this alarm signal evolve in this life cycle? Explain. When should
the aphid’s use of this alarm signal not evolve in this life cycle? Explain.
5. Reading Assignment: Search the scientific literature for a paper that tests female preference in mate
choice What experiment(s) were conducted on mating preferences? What are the results and what
hypothesis (hypotheses) are supported or disproven by the results? Cite in the format of American
Naturalist.
Discuss these hypotheses.
a) Direct benefit to female:
b) Good gene hypothesis:
c) Fisher’s runaway sexual selection:
6. What is the coefficient of relatedness between the donor and recipient in the Figures below (both male
and female are diploid)? Would the inclusive fitness of the donor increase, if the increase in fitness for the
recipient is 0.05 and decrease in fitness for the donor is 0.012 for Figure 1? Figure 2?
Figure 1
Donor
Recipient
Figure 2
Donor
Recipient
Homework 5
Evolution - BIOL 3406
Due. Nov. 24, 2014
Phylogeny and Cladistics:
A. Answer the following Questions from Chapter 4 (pp 141-142) (Herron and Freeman 2014): 1, 2, 3, 4, 6,
7, 8, 10, 14, 17.
Answer additional questions based on the question 1, 2, 3, 4, 6, 7, 8. in Herron and Freeman (2014).
1. Can you determine from the cladogram in Figure 4.37, if shrews and moles are more closely related to
rodents or primates? Explain.
2. Can you determine from the cladogram in Figure 4.37, if the last common ancestor of rodents and
primates is earlier than the last common ancestor of bats and whales?
3. In the sketch for question 3 of Figure 4.37, include deer in the cladogram based on Figure 4.31.
4. Aardvark could be used as an outgroup for what monophyletic group in the cladogram of Figure 4.37?
6. Is having a placenta a synapomorphy for one of the clades in Figure 4.37? If yes, what clade?
7. What character(s) (synapomorph) places all four taxa in the same clade?
8. What if blue spots and blue dorsal fin are one synapomorphy? What if they are separate
synapomorphies? Answer question 8 both ways.
B. In Table 1, nucleotide base sequences are shown for six species (including an outgroup). (Insertions or
deletions are shown with blank spaces in the sequence. What are three monophyletic groups in the
cladogram.) Show the most parsimonious cladogram from the data in Table 1. When based on the
parsimonious cladogram, base G in position 15 for species B and D would be a case of what? Explain.
When based on the parsimonious cladogram, the deletion in base 33 for species A and C would be a case
of what? Explain.
Table 1
5
Species A
Species B
Species C
Species D
Species E
Outgroup
GACCA
GACCA
GACCA
GGCCT
GGCCT
GACCT
10
TTAGG
TTGAG
TTAGG
TGGAG
TGGAG
TCGTG
15
TTGGA
TTGGG
TTGGA
TAGGG
TAGGA
TTGGA
20
TTACG
TTACG
TTACA
T_ACG
T_ACG
T_ACG
25
AATTG
AAATG
AATTG
AAGTG
AATTG
AATTG
30
CCCAG
CCCGG
CCCAG
CCCGG
CCCGG
CTCGG
35
GT_AG
GTAAC
GT_AC
GTAAC
GTAAC
GTAAC
40
AACGT
AACGT
AACGT
AAGGT
AAGGA
ATCGT
45
GTACT
GAGCT
GAACT
GTAAT
GAAAT
GACAT
50
CCCTA
CCCTA
CCCTA
CACTG
CACTG
CGCTA