Exercise 1:

Rex and Viola are two Great Danes. Like his mother, Rex also has a kink in his tail, but his sister,
Zara, does not. Rex and Viola had a litter of 12 puppies, 6 of them also have a kink in their tails. On
the puppies’ first visit to the vet it was discovered that 3 of them had a condition known as patent
ductus arteriosus (PDA) (a congenital heart defect). Neither Rex nor Viola have this condition, but it is
known that Viola’s maternal grandfather was afflicted.
1. How are these respective traits inherited? Explain your reasoning..

2. With reference to the tail trait, what are the genotypes of Rex and Viola?

3. With reference to PDA what was Viola’s grandfather’s and father’s genotypes?

4. Over the years, Rex and Viola had many puppies, 126 in total including the current litter, with the
following phenotypes:
Healthy, with kinked tail: 50

Healthy, with straight tail: 45

PDA afflicted, with kinked tail: 16

PDA afflicted, with straight tail: 15

Use an appropriate statistical test to support your hypothesis in question 1
5. Benny is a puppy, in the current litter, that is not affected by PDA, how can his genotype be
confirmed? Discuss your reasoning and show diagrams for clarity.

6. Discuss potential ethical concerns relating to this scenario.

Solution:
Rex and Viola are two Great Danes. Like his mother, Rex also has a kink in his tail, but his
sister, Zara, does not. Rex and Viola had a litter of 12 puppies, 6 of them also have a kink in
their tails. On puppies’ first visit to the vet it was discovered that 3 of them had a condition
known as patent ductus arteriosus (PDA) (a congenital heart defect). Neither Rex nor Viola
have this condition, but it is known that Viola’s maternal grandfather was affilicted

Pedigree data Trait information Numbers & Ratios

1. How are these respective traits inherited? Explain your reasoning..

Kinked tail: autosomal dominant
Does not skip a generation and only 1 affected parent is needed to produce affected offspring
PDA: autosomal recessive
Skips a generation and unaffected parents can have affected offspring
2. With reference to the tail trait, what are the genotypes of Rex and Viola?
Rex: Tt Viola: tt

3. With reference to PDA what was Viola’s grandfather’s and father’s genotypes?
Pedigree data OR Ratio data needed
Grandfather: aa Father: A-

4. Over the years, Rex and Viola had many puppies, 126 in total including the current litter, with
the following phenotypes:

Healthy, with kinked tail: 50 More Ratio Data Provided!

Healthy, with straight tail: 45

PDA afflicted, with kinked tail: 16

PDA afflicted, with straight tail: 15

• Use an appropriate statistical test to support your hypothesis in question

Conclusion: Fail to reject hypothesis

5. Benny is a puppy, in the current litter, that is not affected by PDA, how can his genotype be
confirmed? Discuss your reasoning and show diagrams for clarity.

6. Discuss potential ethical concerns relating to this scenario.

Exercise 2a:

In a breed of cattle two alleles are responsible for coat colour; red (CR) and white (CW).
Heterozygous individuals are roan. Shorts legs is a dominant phenotype over normal legs,
however only the heterozygous genotype seems to be observed. Two roan, short legged cattle are
mated. Give the genotypic and phenotypic ratios to be expected amongst the resulting calves.

Solution:

CRCWLSLL CRCWLSLL

• This is co-dominance with coat colour

• In the second punnet square:
o Isn’t any LLLL (normal leg, normal leg) present
o Only heterozygous individuals (LLLS) seem to be observed and homozygous dominant
(LSLS)
o LLLL is lethal

1/ Normal 1/ Red, Normal

3 12
¼ Red
2/ Short 2/ Red, Short
3 12

1/ Normal 2/ Roan, Normal

3 12
½ Roan
2/ Short 2/ Roan, Short
3 12

1/ Normal 1/ White, Normal

3 12
¼ White
2/ Short 2/ White, Short
3 12

VS 9:3:3:1
• Fork line method for each option
• Will give particular ratio which you compare with 9:3:3:1 to identify appropriate extension to
mendelian genetics that’s occurring
Exercise 2b:

In a variety of goldfish, a breeder crosses a pure breeding golden male to a pure breeding
white female. In the F1 all the offspring are golden. When he randomly mates the F1, he finds
the following numbers of offspring amongst the F2:

Golden 323

White 145

Silver 109

a) The breeder thinks that the trait is co-dominantly inherited. (i)Explain why he is incorrect;
(ii) Propose an alternative hypothesis for the mode of inheritance and test it statistically,
using the observed data.

b) He takes an unrelated golden female and mates her to an unrelated white male and only
gets golden and white offspring in a 1:1 ratio. Deduce the genotypes of the parents and
offspring.

Solution:

ai) Co-dominance hypothesis (which is incorrect)

• Golden x white à all golden (F1)

• Mating F1 to get F2
• Expected ratio: 1:2:1

• If we look at the values that we’ve been given

• Ratio: 9:3:4
• Therefore, NOT co-dominance because ratios don’t coincide

ii) Alternative hypothesis: Recessive epistasis

• p>0.05 therefore fail to reject null hypothesis

o Not co-dominance its recessive epistasis
b) Assuming Recessive Epistasis

• Golden (A-B-) x White (A-bb) OR (aabb)

• Offspring in 1:1 ratio

• Can’t be aaB- because it won’t give 1:1 ratio

• Golden (AABB) x White (aabb) à all offspring Golden (AaBb)

• Assuming recessive epistasis

• Golden (AABb) x White (aabb) à Golden (AaBb) + White (Aabb)
• Get desired outcomes
• BUT are the ratios correct?

½ Bb ½ AaBb
1 Aa
½ bb ½ Aabb

Are there any other genotypes that could result in 1:1 ratio?

• Golden (AABb) x White (AAbb) à Golden (AABb) + White (AAbb)

• Get desired outcome
• BUT are the ratios correct?

½ Bb ½ AABb
1 AA
½ bb ½ AAbb

This also works!

Another option

• Golden (AABb) x White (Aabb) à Golden (A-Bb) + White (A-bb)

• Get desired outcomes
• BUT are the ratios correct

½ Bb ¼ AABb
½ AA
½ bb ¼ AAbb

½ Bb ¼ AaBb
½ Aa
½ bb ¼ Aabb

This also works!

• More crosses needed, ideally with individuals with known genotypes to definitively
determine!
• 3 possible answers for this question
Exercise 3: Problem 16, pg 250

The maternal-effect mutation bicoid (bcd) is recessive, and in the absence of the bicoid protein
product, embryogenesis is not completed. Consider a cross with a female heterozygote (bcd+/
bcd-) and a male homozygous for the mutant allele.

a) How is it possible for the male mutant to exist?

b) Predict the outcome of the crosses in the F1 and F2

Solution:

• In the wild-type egg – have a anterior to posterior gradient

o Produces wild-type larvae with head, thorax, abdomen and tail
In the bicoid mutant egg – not gradient
o Larvae have no anterior structures (incomplete embryogenesis)

• Maternal effect:
o Offspring exhibits the phenotype of the maternal genotype, irrespective of offspring
genotype or maternal phenotype.
o Whatever the mom was, the offspring is going to exhibit
o REMEMBER THE SNAILS

• Remember to look at the female (all the offspring is viable because the female is heterozygous
 OR

• Female in this instance is

homozygous recessive and therefore
is embryonically incomplete (not
viable)

• Therefore all the offspring is also not

viable regardless of their genotype
and phenotype

OR

• Even though bcd-/bcd- isn’t supposed to be viable, it is because the mother is viable (not
homozygous recessive)

OR
Exercise 3: Problem 19, pg 250

A family with an interesting distribution of Leigh syndrome symptoms

[loss of motor function, (Ataxia; A) with peripheral neuropathy (PN)].

a) Construct a pedigree
b) Explain the mode of inheritance
c) Why is there so much variation in symptoms?
d) In what way does this condition differ from classical albinism
in terms of expression and transition?

Solutions:

a)

b) Organelle inheritance (via the mitochondria):

• Male and female offspring are affected in every generation
• Mother always have the mutant copy of mtDNA (father does not pass on the mutation)

c) Organelle inheritance (via the mitochondria):

• The is variation in expressivity due the level of heteroplasmy (not all individuals have the
same percentage of the mutant mtDNA
• Number of mutant mitochondria that is contributed by the mother in an egg can be a different
percentage
• The percentage of mutant mitochondria contributes to the expressivity of the phenotype

d)
Exercise 4a:

Two hypothetical autosomal genes S (spotted) and B (banded) give salamanders spotted or banded
patterns. As a test cross, a double recessive salamander is crossed with a double heterozygote.
Predict the phenotypic ratios under the following conditions:

a) S and B are located on separate chromosomes

b) S and B are linked on the same autosome, but are so far apart that crossing over always happens
c) S and B are linked but so close that crossing over never happens
d) S and B are linked on the same autosome about 10cM apart

Solutions:

a) S and B are located on separate chromosomes

With independent assortment, the progeny will be:

• Parentals: SsBb and ssbb
• Recombinants: Ssbb and ssBb
• 50% split which is predicted based on independent assortment

b) S and B are linked on the same autosome, but are so far apart that crossing over always
happens

Similar scenario as a)
• If they are always separated from each other;
phenotypic ratios similar to those with independent
assortment

c) S and B are linked but so close that crossing over never happens

With absolute linkage, there will be no recombinant progeny

• 100% parental
o SsBb – heterozygous parent
o ssbb – testcross parent
• No new combinations – no crossing over occurred

d) S and B are linked on the same autosome about 10cM apart

• The recombination frequency is 10% (10cM à 10%)

• Each of the two classes of recombinant progeny must be 5%
o 5% Sb (Ssbb)
o 5% sB (ssBb)
• The two classes of nonrecombinants are 90% of the progeny
• Each must be 45%
o 45% SB (SsBb)
o 45% sb (ssbb)
Exercise 4b:
In Drosophila melanogaster, black body (b) is recessive to gray body (b+), purple eyes (pr) are
recessive to red eyes (pr+), and vestigial wings (vg) are recessive to normal wings (vg+). The loci
coding for these traits are linked, with the map distances:

The interference among these genes is 0.5.

A fly with black body, purple eyes, and vestigial wings is crossed with a fly homozygous for gray
body, red eyes, and normal wings. The female progeny are then crossed with males that have
black body, purple eyes, and vestigial wings. If 1000 progeny are produced from this testcross,
what will be the phenotypes and proportions of the progeny?

Solution:

• Here it is indicated what the result would be if a double crossover occurred between two
chromosomes of the heterozygous F1 parent

Chiasma Interference
I=1–C
0.5 = 1 -C
C = 0.5

• This value is important as we have a formula to calculate the C value

o Can therefore work backwards to calculate other variables
• C = DCOobs / DCOexp
o Don’t know what observed DCO is
o Can calculate the expected DCO – have the map with distance
 Use the product rule and multiple the probability of the individual single
crossover events
• 0.5 = DCOobs / (0.06 X 0.13)
0.5 = DCOobs / 0.0078
0.0039 = DCOobs

• In total of 1000 progeny : DCOobs = 3.9 ~ 4

o 0.0039 x 1000 progeny
• Need this value when calculating the map distance between genes

Map Distance (b-pr)

• b – pr = 6 cM
o Recombination Frequency (RF) = 6%
• Total number progeny = 6% (1000) = 60
• 60 was value used to calculate this distance

• b – pr distance = (SCO + DCO)

60 = (SCO + 4)
= 56 (SCO 1)
• 56 progeny were observed in SCO class 1
• In this instance, we know this number accounted for the distance between b and pr

• The single crossover phenotypes between b and pr:

o b+ pr vg
o b pr+ vg+
• The total number of individuals in both these classes is 56
o Each class is represented by 28 individuals
o 50% split
o Under test conditions it won’t be exactly 50%: 50% but we assume it to be the
same as we don’t have any other data
o Also working in reverse so just divide by 2

Map Distance (pr-vg)

• pr – vg = 13cM
o Recombination Frequency (RF) = 13%
• Total number progeny = 13% (1000) = 130
o 13% as a number of individuals out of a total of 1000 progeny

• pr – vg distance = (SCO + DCO)

130 = (SCO + 4)
= 126 (SCO 2)
• 126 individuals representing single crossover class 2
o Distance between pr & vg
• If a single crossover occurred between pr & vg
o Expect to see 126 offspring across two classes that would have that would have that
particular combination
• The single crossover phenotypes between pr and vg
o b pr vg+
o b+ pr+ vg
o These are the 2 offspring classes expected
• The total number of individuals in both of these classes is 126
o Each class is represented by 63 individuals (50% of 126)

Parental Classes (NCO)

• NCO
= 1000 – SCO1(b-pr) – SCO2(pr-vg) – DCO
= 1000 – 56 – 126 – 4
= 1000 – 186
= 814

• The nonrecombinant phenotypes

o b+ pr+ vg+ (all 3 dominant alleles in offspring phenotype – F1 heterozygous parent)
o b pr vg (all 3 recessive alleles in offspring phenotype – testcross parent)
• The total number of individuals in both of these classes is 814
o Each class is represented by 407 individuals (50% of 814)

Summary
• b+ pr+ vg+ 407
• b pr vg 407
• b+ pr+ vg 63
• b pr vg+ 63
• b+ pr vg 28
• b pr+ vg+ 28
• b+ pr vg+ 2
• b pr+ vg 2
Exercise 5a:

Solution:

• Only mention the recessive / mutant trait that is expressed

• Assume that individuals are wild type for phenotypes that
aren’t mentioned
• Assign symbols to each phenotype
• For wild type alleles could use + or capital letters

• Only have 6 classes – no DCO

o 2 NCO
o 4 SCO
(2 for SCO 1 and 2 for SCO 2)
• Start by grouping data in reciprocal groups
• Make sure it is correct by checking the numbers
o (must be similar for each group)

• Need to determine order of genes

• Take NCO and write in three potential orders
• Do SCO between gene 1 and 2
• Compare expected results with observed data

• Take NCO and write genes in three potential

orders
• Do SCO between gene 2 and 3
• Compare expected results with observed data
• Middle option is already eliminated so don’t
consider it
• First option is also eliminated
 • Correct order is d c g
• Rewrite data so that the genes are in the correct
order
• Comparisons will be easier

• Take NCO with genes in the correct order and do a

SCO
• SCO 1 offspring was result of crossover between
gene 1 and 2 (d and c)
• Number of offspring in class
o (140+150 / 1840) x 100 = 15.76%
o Represents 15.76% of offspring

• SCO 2 is result of crossover between gene 2 and 3

(c and g)
• Number of offspring
o (70+90 / 1840) x 100 = 8.70%
o Represents 8.70% of offspring
Exercise 5b:
In the model plant Arabidopsis thaliana the following alleles were used in a cross:

T = presence of trichomes
t = absence of trichomes
D = tall plants
d = dwarf plants
W = waxy cuticle
w = nonwaxy cuticle
A = presence of purple anthocyanin
a = absence (white)

The T/t and D/d loci are linked 26cM apart on chromosome 1, whereas the W/w and A/a loci are
linked 8cM apart on chromosome 2.

A purebreeding trichome-less nonwaxy plant is crossed with a purebreeding dwarf White plant.

a) Show the allele arrangements in the parents and the F1

b) If the F1 is testcrossed, what proportion of the progeny will have all four recessive
phenotypes?

Solution:

a)

b)
Recombination
• For the progeny to have all four recessive phenotypes, it must inherit a recombinant t d
chromosome 1 AND a recombinant w a chromosome 2 from its F1 parent.

• Need to use knowledge about distance between genes to give us an idea of how much
crossing over we would expect to see

• RF = 26%
o Recombinant progeny for these genes (t d ; T D)
o t d 13% (recessive will occur in ½ of recombinant offspring)

• RF = 8%
o Recombinant progeny for these genes (w a; W A)
o w a 4%

Independent Assortment vs Linkage

• These 4 genes occur in combinations of 2 each and located on separate chromosomes

• Although have 2 traits on each gene that are linked the chromosomes will assort independently
• Two chromosome independent of each other
• Probability that both events (crossovers) will occur simultaneously is equal to the product of
their individual probabilities

Probabilities

• t d AND w a
o \ 0.13 x 0.04 = 0.52% of the total progeny will have all four recessive phenotypes
(t d w a)
Exercise 6:
In cats, the dominant allele B at an autosomal locus results in a black coat while homozygosity for
the recessive allele b results in a dark brown coat. The dominant O allele at an X-linked locus
results in an orange coat, no matter what alleles are present at the B/b locus, while the recessive
o allele allows the alleles at the B/b locus to be expressed. A calico cat having black and orange
patches had a father with a dark brown coat. She mates with a dark brown male whose parents
were both solid black.

a) What are the genotypes of the animals in this mating, and what phenotypes and frequencies
are expected in the progeny?

b) What phenotypes would be produced if there is paternal sex-chromosome nondisjunction?

Solution:

a) Step 1

Step 2

• Calico female
o Females where we have heterozygosity for a sex-linked locus
 Find that in some instances the 1 X would be inactivated and in other
instances the other X would be inactivated
o See this patching nature is because of the fact that this female is heterozygous for
this sex-linked locus
o Means that if the X for the dominant allele is active, we will have orange fur color
o If the X with the recessive allele is active - that would allow the second locus to be
expressed
o Look at the B locus to see what would be that second color which is expressed
o Know that this female specifically has black patches
 She carries the dominant allele
o But is she homozygous (BB) for heterozygous (Bb)?
 Need to go and look at her father
 Dark Brown coat (recessive – bb)
 Dark Brown is expressed because that allele on the X chromosome is
recessive (XoY)
 Means that whatever is on the 2nd locus will be expressed (bb)
 One of these recessive alleles would have been passed to his daughter
o Therefore, she is heterozygous (Bb)
• Dark Brown Male
o Can conclude he has same genotype as the female’s father .. oYbb)
• Male’s Parents
o Both have black coats
o The B locus must have at least one dominant allele
o Because son has two recessive alleles
 Both must be heterozygous
o The fact that both of them have the recessive allele on the X chromosome means
that the black coat color is expressed

Step 3

b) Step 1
Step 2 Don’t ask for ratios so we don’t have
to include the duplicate genotypes

The simplified table with duplicates removed looks like this:

Exercise 7a:
Species I has 2n = 8 chromosomes and species II has 2n = 14 chromosomes. What would the
expected chromosome numbers be in individual organisms with the following chromosome
mutations? Give all possible answers.

a. Allotriploidy including species I and II d. Monosomy in species II

b. Autotetraploidy in species II e. Tetrasomy in species I
c. Trisomy in species I f. Allotetraploidy in species I and II

Solution:
a.

• Must be a combination of the 2 species

• Don’t know where the 2n and n come from so will have 2 possible answers
o 1. 2n comes from species 1 and n comes from species 2
o 2. 2n comes from species 2 and n comes from species 1
• Won’t be able to pair up because comprise of different species

b.

c.
d.

e.

f.
Exercise 7b:
In maize, the genes for tassel length (alleles T and t) and rust resistance (alleles R and r) are
known to be on separate chromosomes. In the course of making routine crosses, a breeder
noticed that one T/t ; R/r plant gave unusual results in a testcross with the double-recessive pollen
parent t/t ; r/r. The results were:

T/t ; R/r 98
t/ t ; r/r 104
T/t ; r/r 3
t/t ; R/r 5

And in terms of the corncobs: Only about half as many seeds as usual

a. What key features of the data are different from the expected results?
b. State a concise hypothesis that explains the results.
c. Show the genotypes of the parents and progeny.
d. Draw a diagram showing the arrangement of alleles on the chromosomes.
e. Explain the origin of the two classes of progeny with 3 and 5 offspring

Solution:
a.

b.

• It is possible that these genes WERE on separate chromosomes but then translocation
occurred
• This placed the genes close enough for them to become linked
• Originally, rust gene would have been on one chromosome (yellow) and the tassel length
on another chromosome (purple)
• Reciprocal translocation occurred and genes could have come in close proximity and
became linked
c.

• If independent assortment occurred – would expect 1:1:1:1 ratio

• 2 parental types and 2 recombinants

• In the unusual individual where there is translocation

• The two genes have become linked (T/R – translocated chromosome and t/r is
translocated chromosome)
• If did test cross with homozygous recessive individual will get the progeny on the slide
o Contribution from test parent will still be two separate chromosomes
o But have linkage due to translocation
o Will have TR if chromosome separates
o Will have tr if chromosome separates
o If there is crossing over between these chromosomes where genes are located on
same chromosome
 Tr
 tR
 These are recombinant types of offspring

d.
• If have translocation heterozygote, will have cruciform type of pairing configuration
• Happens so that all chromosomes can pair up
• N1 pairs with T2 and T1
• N2 pairs with T1 and T2
• Most viable and feasible way
• This is where the semi-sterility comes into play since only 50% of offspring will be viable

e.

• If take information with regards to T and R traits and include it on the translocation
heterozygote
• Have T1 where T and R allele are on the same chromosome
• What would expect to see if did testcross?
o Parental types if had no crossing over that occurs would be N2 and N1
chromosomes in the same gamete (50% that would be viable)
o If have T1 and T2 in same gamete – would have translocated chromosome
and other chromosome would have none of the two genes

• Also see recombinant types with very low frequency

• If have crossover that occurred between translocation chromosome (T1) and N2
• N2 and N1 will be in the same gamete to give viable offspring
o In this instance will have crossover between recessive r and dominant R allele
o Combination in gamete will be dominant R and recessive t
• In T1 and T2 combination will have dominant T allele and the recessive r allele because of
crossing over
• This would explain results we see
• The low number of progenies are result of crossover between some chromosomes in
translocation heterozygote
• Where we have translocation of the two genes where were unlinked but appear linked
because of translocation
Exercise 7c:
Orangutans are an endangered species in their natural environment (the islands of Borneo and
Sumatra), so a captive-breeding program has been established by using orangutans currently
held in zoos around the world. One component of this program is cytogenetic research. This
research has shown that orangutans from the two islands have different forms of chromosome 2.
Before this cytogenetic difference became known, some matings were carried out between
animals from different islands, and 14 hybrid progeny are now being raised in the breeding
program.

a. What term/s describe the difference/s between these chromosomes?

b. Draw the chromosomes 2 pairing of such a hybrid individual, during the first meiotic prophase.
c. In 40% of meioses, there will be a crossover somewhere in the region between bands p1.1
and q1.2. Draw the chromosomes 2 gametes that would result from a meiosis in which a
single crossover occurred within band q1.1.
d. What fraction of the gametes produced by a hybrid orangutan will give rise to viable progeny,
if only these chromosomes differ between the parents?

Solution:
a.

b.
 c.

d.

• The other 60% would be viable as there would be no crossovers since crossovers only occur
in 40% of meiosis
• Would have normal chromosomes with no deletion and duplication
• 40% where there is crossover – see a 50% viable and 50% non-viable
o 20% viable and 20% non-viable
Exercise 9:

Solution:
• If start off with 2 divergent breeds that represent the phenotypic extremes
o Large broiler (AA)n on one side and the small bantam (aa)n on the other
o They must be homozygous for all of loci associated with the trait of interest
• We cross them and get F1 generation that must be heterozygous (Aa)n for all of the genes
involved
• If ALL F1 individuals are heterozygous – genotypes the same
o Means that the genetic variance amongst F1 is 0 (VG = 0)
• If VG = 0 then we can assume that phenotypic variance should also be zero, right?
o VP = 0?

• Phenotypic variation is due to both variance in genetic composition of individuals

(individuals have different genotypes) and variance in the environment
• Know the F1 is genetically homogenous
o VG = 0
• That variance calculated in a) cannot be due to genetic variance
• So, it must be due to environmental variance
o Non-homogenous environment
• Therefore, VP is NOT equal to 0

• The number of extremes is equal to (1/4)n

• In the question it says that the TOTAL number of extremes for BOTH phenotypes is 4 out
of 400
• We only want the fraction of ONE of those extremes
o Divide 4 by 2
• Why x2?
o We want the number of alleles
o Each individual have 2 alleles per gene
• For every additive allele that an individual has, they will be 0.5kg heavier

• Calculated the mean to be 3kg

• 2 ways of showing validity of 3kg mean
• 1st way:
o Because this is a quantitative trait, the mean value for F1 should be a mid-value of the
two extreme P1 individuals
o 1kg cross with 5kg should result in 3kg chicken
• 2nd way:
o Relates to how additive alleles are being transmitted from one generation to the
next
o If 1kg P1 individual will pass 50% of their genetic component to the offspring
(0.5kg)
o The 5kg chicken again passes 50% of its genetic component to offspring (2.5kg)
o 0.5kg + 2.5kg = 3kg
• BUT we also calculated the number of gene pairs that might be involved in phenotypic
development at this trait (d)
• Also calculated the actual phenotypic value that is contributed by each additive
allele (e)
• If consider F1 individuals to be heterozygous at all 4 genes
o Therefore, will have 4 additive alleles
• If base value is 1
o 1 + 0.5(4) = 3kg
• The 4.5kg entails a base weight (1kg)
• If have no additive alleles you will weigh at least 1kg
• For every additive allele that individual has for the 4 genes adds another 0.5kg to
phenotype
• Need to calculate the number of additive alleles
• Doesn’t matter what the actual genetic combination is as long as individual has 7
additive alleles across the 4 genes
o Will have phenotypic value of 4.5kg
• Need to estimate to get ratio
• If testcross with individual that is homozygous for all the non-additive alleles
• Anything more than the base number observed in offspring must be due to the additive
alleles contributed by the unknown individual
• For that to occur the max # of additive alleles that unknown chicken can donate to the
offspring must be 2

• Have individual that is heterozygous for gene A & B and homozygous for other addive
genes C & D
• Testcrossed to individual that is homozygous for non-additive alleles across all of the
genes
Exercise 10:

Solution:

• What are the non-additive effects?

o Genetic variance due to dominance (VD)
o Epistatic interaction (VI)
• Write down known formulas
• Because have inbred line – any phenotypic variance observed is due to
environmental variance
o Phenotypic variance of inbred line is in fact with reference to the original
colony, the environmental variance
• Substitute number in equation and solve for VG for the colony
• Now can calculate H2
• Using data from the selection experiment, can calculate h2
o h2 = R/S = (M2-M)/(M1-M)
• H – proportion of phenotypic variance that is explained by all genetic factors
2

• h2 – proportion of phenotypic variance that is explained only by additivity

• Deduct h2 from H2
o Left with proportion of phenotypic variance that is explained by non-additive
genetic factors

• Can start off with h2 which can be calculated in 2 ways

o 1. h2 = R/S
o 2. h2 = VA / VP
• Now calculate VA
• Apply VP = VG + VE and solve for VG
• VG is further subdivided
• Solve for VD + VI
• Take value and divide by VP
Exercise 11:

Solution:

• p > 0.05
• Therefore, fail to reject null
hypothesis
• The observed and expected numbers
are pretty much the same
• Population conforms to HWE for this
locus
Exercise 12:

Solution:

• p < 0.05
o Reject null hypothesis
• There is significant difference between observed genotypic numbers and expected
genotypic frequencies/numbers assuming HWE
• For this population, this locus is NOT in HWE
• Our population has specifically been selected for growth
• Also know that growth has a narrow sense heritability of 0.6
o Fairly high value
• Can expect a response to selection
o Change in allele frequencies due to the selective event for any loci that are
associated with the trait being selected for
• In terms of HW – means a deviation from HW will be observed at that locus
• Know that protein zeta is associated with cell cycle regulation
o How cells grow and cycle through
• Can make a fair deduction that because we know that this population has been selected
for growth rate
o If we observe at any locus in this population a deviation from HWE that deviation is
likely because of the selective event
o If that locus contributes to a trait or a phenotype that has been selected for, and if
that trait being selected for has a fairly high narrow sense heritability
(underlying genetic variation that will respond to selection)
• That is exactly what we see
o Protein zeta is associated with a molecular function that could result in a
phenotypic effect of growth
o Know the population is selected for growth
o See that this protein zeta gene deviates from HWE
• The color locus which is not being selected for in this population does not deviation from
HWE
• Have one population with two different loci
o One locus has a functional effect in terms of what the population is being selected
for
§ One of the evolutionary forces (selection) are acting on this locus
§ Therefore, there is deviation from HWE
o The other locus has no effect on how individuals are being selected
§ Color locus is free to conform to HWE

• p > 0.05
o Fail to reject null hypothesis
• Observed and expected numbers are similar
• In the unselected population, the protein zeta locus is in HWE
• Same locus in different populations
o Unselected – in HWE
o Selected – not in HWE
• Now, we have supportive evidence that protein zeta is indeed associated with growth
rate
o In unselected line, protein zeta conforms to HWE
o Selected line, protein zeta it deviates from HWE because of the evolutionary force
(response to selection)
• What we have done here is a classical association type analysis to find a gene that is
associated with a trait of interest
• This is how we can use population genetics to confirm some of the ideas of quantitative
genetics like we’ve done in the previous chapter
Exercise 13:

In the Pygmy population of Central Africa, the frequency of alleles determining the ABO blood
groups were estimated as 0.74 for i, 0.16 for IA and 0.10 for IB. Assuming HWE, what are the
expected frequencies of ABO blood groups, genotypes and phenotypes?

Solution:
Exercise 14:

In a population of Drosophila, an X-linked recessive allele causing yellow

body colour is present in genotypes at frequencies typical of random mating.
The frequency of the recessive allele is 0.20. Among 1000 females and
1000 males, what are the expected numbers of the yellow and wild-type
phenotypes in each sex and what percentage of wild-type females are
carriers for the yellow allele?

Solution:
• Question says “random mating” so can assume that population is in HW equilibrium for that
locus
• Given allele frequency for recessive allele
• Look for expected numbers (not frequencies)!!

• Population is in HW equilibrium
o Expect allele frequencies in males and females to be the same
• However, males are heterogametic sex
o Hemizygous for all X-linked loci
o Observed allele frequencies is the genotypic frequencies
• Know what allele frequency of yellow allele is (q), by implication the wild type allele
frequency can be calculated (p + q = 1)

Females

• 2 copies of X chromosome
• Wild type females will be those that are homozygous and heterozygous for wild type allele
(X+X+ and X+Xy)
o Recessive allele hidden by dominant nature of wild type allele
• Homozygous = p2
• Heterozygous = 2pq
• Substitute allele frequencies
• To get observed numbers – take frequency (0.96) x 1000 (no. of females)
o Therefore, 960 out of the 1000 females should exhibit wild type phenotype
• Want to calculate what % of wild type females are heterozygous to determine how
many females are carriers
• Apply HW equations again
• Frequency of heterozygous / total wild type females x 100
• Therefore, 33% of females that exhibit the wild type of phenotype are actually carriers
of the recessive yellow mutant allele

• Number of yellow females are simple to calculate

• Know allele frequency of yellow allele (q = 0.2)
• Females must be homozygous recessive to be yellow (XyXy)
• Therefore, genotypic frequency is q2
• 40 females out of the 1000 are yellow

Males
 Exercise 15:

Solution:

• i is directional selection – AA has highest relative fitness (one of the extremes phenotypes
selected for)
• ii is stabilizing selection – Aa has highest relative fitness (intermediate phenotype is selected for)

• Allele frequencies are given

• Can calculate the contribution of each genotype to gene pool
o Proportional contribution (%)
• Calculate the total number of gametes in the gene pool for each case
o Case 1 = 152 gametes
o Case 2 = 128.6 gametes
• Can substitute into equations and calculate allele frequencies in next
generation
Exercise 16:

• From data provided, can see that it’s a multiple allele system like dominance series or
blood group system
• Not given phenotypes so mode of inheritance isn’t important
• The fact that we’re given genotypes makes question easier

Solution:

• If positive assortative mating – individuals with similar colouring tend to mate more often
o Should see more homozygotes in population
o Deviation from HWE due to homozygous excess
• If negative assortative mating – individuals with different colouring tend to mate more often
o Expect to see more heterozygotes
o Heterozygous excess and homozygous deficit
o Might cause deviation from HWE expectations
• Must do a Chi-Square Test
• Have 6 genotypes therefore 6 classes
• Given observed numbers
• From those observed numbers can calculate observed frequencies
• Let: A=p; B=q; C=r
• Can calculate genotype frequencies and use them to calculate allele frequencies
• From that calculate expected genotypic frequencies and numbers
o Need to used NUMBER and not frequencies for Chi-Square tests
• Calculate X2 value (don’t be alarmed if very large or small value)

• How to calculate degrees of freedom (df)

o No. of classes – 1 (sampling error) – no. of allele frequencies from observed data
with uncertainty
o df = 6 – 1 – 2 = 3

• P <<<<< 0.05
o Population deviates from HWE
o Cause to thing that there might be some form of assortative mating

• Can quantify that deviation by calculating the fixation index

• Calculate observed frequency of heterozygotes
o AB + AC + BC
• Calculate expected frequency of heterozygotes using formulae
o 2pq + 2qr + 2pr
• F>0
o Significantly more homozygotes in population than
heterozygotes
• This is potential evidence for positive assortative mating