Title : Population Genetics- The Hardy-Weinberg Principle, Evolution and Computer Simulations

Objective(s) : 1.To compare phenotypic frequencies of inherited human traits in a class.

2.To determine if the inherited traits conform tp the Hardy-Weinberg equlibrium.
3.To stimulate a simple population of interbredding organisms and determine how
changes in the characteristics of the population and its environment can affect the
direction and rate of evolution.
4.To stimulate a hypothetical population to determine the factors thar may effect
genotypic and allelic frequencies at one locus within the population.
Introduction
The biological sciences now generally define evolution as being the sum total of the
genetically inherited changes in the individuals who are the members of a population's gene pool. It
is clear that the effects of evolution are felt by individuals, but it is the population as a whole that
actually evolves. Evolution is simply a change in frequencies of alleles in the gene pool of a
population. For instance, let us assume that there is a trait that is determined by the inheritance of a
gene with two alleles--B and b. If the parent generation has 92% B and 8% b and their offspring
collectively have 90% B and 10% b, evolution has occurred between the generations. The entire
population's gene pool has evolved in the direction of a higher frequency of the b allele--it was not
just those individuals who inherited the b allele who evolved.

This definition of evolution was developed largely as a result of independent work in the
early 20th century by Godfrey Hardy, an English mathematician, and Wilhelm Weinberg, a German
physician. Through mathematical modeling based on probability, they concluded in 1908 that gene
pool frequencies are inherently stable but that evolution should be expected in all populations
virtually all of the time. They resolved this apparent paradox by analyzing the net effects of
potential evolutionary mechanisms.

Hardy and Weinberg went on to develop a simple equation that can be used to discover the
probable genotype frequencies in a population and to track their changes from one generation to
another. This has become known as the Hardy-Weinberg equilibrium equation. In this equation
(p² + 2pq + q² = 1), p is defined as the frequency of the dominant allele and q as the frequency of
the recessive allele for a trait controlled by a pair of alleles (A and a).
 II. Population Genetics
Stimulation 1
Generation Class Data
AA Aa aa p q
Start-P 16 - 16 0.5 0.5
F1 - 32 - - -
F2 10 14 8 0.531 0.469
F3 10 17 5 0.578 0.422
F4 12 11 9 0.547 0.453
F5 10 12 10 0.5 0.5
F6 12 7 13 0.484 0.516
F7 12 6 14 0.469 0.531
F8 14 2 16 0.469 0.531
F9 12 4 16 0.438 0.563
F10 13 2 17 0.438 0.563

For population of F2 generation

Total = 10 (AA) +14 (Aa) +8 (aa) =32
Genotypic frequencies expected according to the Hardy-Weinberg Equlibrium at p2 +2pq +q2=1.0
AA= p2 = (0.531)2 =0.282
Aa=2pq=2x0.531x0.469=0.498
aa=q2 =(0.469)2 =0.220
Number of AA= 0.282x 32=9
Number of Aa = 0.498x32 =16
Number of aa = 0.22x32 =7

Chi-square test
Genotypes O E O-E (O-E)2 (O-E)2/E
AA 10 9 1 1 0.11
Aa 14 16 -2 4 0.25
 aa 8 7 1 1 0.14
Total 32 32 0 X2= 0.504

H0 = Population at F2 generation conforms to the Hardy-Weinberg equlibrium distribution of

genotypes
H1 = Population at F2 generation does not conforms to the Hardy-Weinberg equlibrium distribution
of genotypes
df = number of classes – number of alleles =3-2=1
Confidence limit=95% Tabulated x2= 3.841
Since calculated x2 < tabulated x2, H0 accepted. This sample is in Hardy-Weinberg equlibrium

For population of F5 generation

Total = 10 (AA) +12 (Aa) +10(aa) =32
Genotypic frequencies expected according to the Hardy-Weinberg Equlibrium at p2 +2pq +q2=1.0
AA= p2 = (0.5)2 =0.25
Aa=2pq=2x0.5x0.0.5=0.5
aa=q2 =(0.5)2 =0.25
Number of AA= 0.25x 32=8
Number of Aa = 0.5x32 =16
Number of aa = 0.25x32 =8

Chi-square test
Genotypes O E O-E (O-E)2 (O-E)2/E
AA 10 8 2 4 0.5
Aa 12 16 -4 16 1
aa 10 8 2 4 0.5
2
Total 32 32 0 X = 2.0

H0 = Population at F2 generation conforms to the Hardy-Weinberg equlibrium distribution of

genotypes
H1 = Population at F2 generation does not conforms to the Hardy-Weinberg equlibrium distribution
of genotypes
df = number of classes – number of alleles =3-2=1
Confidence limit=95% Tabulated x2= 3.841
Since calculated x2 < tabulated x2, H0 accepted. This sample is in Hardy-Weinberg equlibrium
Stimulation 2
Calculation of χ2 analysis at the F2 generation

Classes Observed Expected (E) Deviations (O-E)2 (O-E)2/ E

(genotypes) (O) (O-E)
AA 9 8 1 1 0.125

Aa 7 9 -2 4 0.444
aa 4 3 1 1 0.333
2
Total 20 20 - - χ =0.902

Allelic Frequencies
Total number of alleles = 2 x 20
= 40
Frequency of p = [2(9) + 7] /40
= 0.625
Frequency of q = 1- 0.625
= 0.375
Genotype frequencies
AA = p2 = (0.625)2 = 0.3906
Aa = 2pq = 2 x (0.625) x (0.375)
= 0.4688
aa = q2 = (0.375)2 = 0.1406

Expected Values
AA = 0.3906 x 20
= 7.816
=8
Aa = 0.4688 x 20
= 9.376
=9
aa = 0.1406 x 20
= 2.816
=2

H0 = this sample conforms to the HWE distribution of genotypes

H1 = this sample does not conform to the HWE distribution of genotypes

In this activity, the calculated χ2 = 0.902

Probability level is 0.05 or at 95% confidence limit, therefore the P value = 0.05

Degrees of freedom, df = 3-2 = 1

Hence the critical value = 3.84

Conclusion:
Since, χ2 value of is 0.902 < 3.84, H0 hypothesis is accepted.
Therefore, this sample is in HW equilibrium.

Calculation of χ2 analysis at the F5 generation

Table 6.3b: χ2 calculation for chi-square test for conformity of class data to
Hardy-Weinberg Equilibrium
Classes Observed Expected (E) Deviations (O-E)2 (O-E)2/ E
(genotypes) (O) (O-E)
AA 9 8 1 1 0.125

Aa 4 7 -3 9 1.286
aa 3 1 2 4 4.000
2
Total 16 16 - - χ =5.411

Allelic Frequencies
Total number of alleles = 2 x 16
= 32
Frequency of p = [2(9) + 4] /32
= 0.6875
Frequency of q = 1- 0.6875
= 0.3125
Genotype frequencies
AA = p2 = (0.6875)2 = 0.4727
Aa = 2pq = 2 x (0.6875) x (0.3125)
= 0.4297
aa = q2 = (0.3125)2 = 0.09766

Expected Values
AA = 0.4727x 16
= 7.5632
=8
Aa = 0.4297x 16
= 6.8752
=7
aa = 0.09766 x 16
= 1.4562
=1
H0 = this sample conforms to the HWE distribution of genotypes

H1 = this sample does not conform to the HWE distribution of genotypes

In this activity, the calculated χ2 = 5.411

Probability level is 0.05 or at 95% confidence limit, therefore the P value = 0.05

Degrees of freedom, df = 3-2 = 1

Hence the critical value = 3.84

Conclusion:
Since, χ2 value of is 5.411 > 3.84, H0 hypothesis is rejected.
Therefore, this sample is not in HW equilibrium.

Question 6

What has happened to p and q in each simulation? Are there recessive alleles remaining in the
population at the end of each simulation? Justify your answers.
In simulation 1 (Hardy-Weinberg Equilibrium), it is noticed that the p and q is not the same with
initial value. In parental generation, p = 0.5 and q = 0.5. However in generation F10, p decreases to
0.438 while q = 0.563. The recessive allele’s frequencies are increasing along the generations. In
simulation 2 (Selection against Recessive Alleles), p is always more than q, showing that frequency
of dominant alleles are always higher than recessive alleles. There is still recessive alleles
remaining in the population but they are decreasing while dominant alleles are increasing. This is
due to the reason that homozygous recessive is lethal

PART B
QUESTIONS:

1. Based on the generated plots, briefly describe what happens to the mouse population before

and after owls are introduced. You will need to attach the printouts of the graphs in your

report.

Answer:

Natural selection is the process by which genetically heritable traits become more or less

common in a population over successive generations. It is a key mechanism of evolution.

From Graph A1, fluctuation of mouse population can be observed before owls are

introduced. Owls in this case describe the migration of new species into the population.In

this case with no mutation or migration, with the B allele favored by natural selection as the

bb (white mouse) is prey of owls. The fixation probability of population with selection is

larger than initial frequency with no selection.

The organisms in better adapted to their environment, so giving the spurious impression that

the organisms were designed to fit their environment. B alleles will be favoured. As a result,

black mouse (BB) and grey (Bb) will survive and white mouse (bb) will be lost in the long

run.
2. Explain the effects of small population size on an isolated community of organisms. Attach

the relevant graphs.

Answer:

The small population size of 10 mice shows that the genotypes of the mice are quickly fixed

around the 60th generation and remained fixed. There is random mating, no mutation in coat

colour alleles, no predation by owls and no differential survival among coat colour phenotypes.

In small population, significant random fluctuations in allele frequencies are made possible by

chance deviation. The degrees of fluctuation increases as the population size decreases. In

extreme case (as shown in N=10), genetic drift lead to the chance fixation of one allele to the

exclusion of another allele. Drift erodes genetic variability in populations. Small populations are

more susceptible to drift than large populations.

3. Why do the plots display more wavy lines as population size decreases? What do the wavy

lines represent?

Answer:

In simulation C, the plots display more wavy lines as population size decreases from N =

200 to N = 10. The wavy lines shown in the plots for the extremely small population groups

represent the huge and major deviations from the theoretical and mathematical ratio

expected. In small populations, significant random fluctuations in allele frequencies are

possible by chance deviation; and in extreme cases, genetic drift can lead to the chance

fixation of one allele to the exclusion of another allele. All attempts to generate the graphs of

gene frequencies for effects of both genetic drift with selection simultaneously results in

extremely uncertain plots where some may end up with all fixed and the results are seriously

fluctuating.
Conclusion

As a conclusion when agents of evolution favor the survival and/or reproduction of some
individuals and their alleles over others, the population’s allele frequencies change over time and
the population is said to evolve.When all individuals are equally likely to survive and to produce
offspring that survive, allele frequencies do not change from one generation to the next because
alleles end up in fertilization events, and thus the offspring generation, in proportion to their relative
frequency in the parental generation.