CHAPTER 13

POPULATION
GENETICS
POPULATION GENETICS
1. studies the genetic makeup of groups of individuals and
how a group’s genetic composition changes with time.
2. focus their attention on a Mendelian population, which
is a group of interbreeding, sexually reproducing
individuals that have a common set of genes, the gene
pool
3. this chapter will present
1.how the gene pool of a population is measured and
2.what factors are responsible for shaping it
3.molecular studies of genetic variation and evolution
GENETIC VARIATION
1. Almost all organisms exhibit the variation in
phenotype and much of this variation is
hereditary
2. Much variation exists at molecular level
owning to the redundancy of the genetic codes
 The amount of genetic variation within natural population and the
force that limit and shape it are of primary interest of population
genetics

3. Tool used in the population genetics is

mathematical model
CALCULATION OF
GENOTYPIC FREQUENCY
The frequency is the proportion or percentage,
expressed as the decimal fraction
In the large population, where it is not practical to
determine the genes of all individuals, the sample
of population is taken and the allelic and
genotypic frequency are calculated for this
sample  gene pool of population
Genotypic frequency
In the population with N individuals, a gene with
2 alleles A and a is spreader in 3 genotypes AA,
Aa and aa. Frequency of each genotype is
CALCULATION THE
ALLELIC FREQUENCY
Genotypes are temporary assemblages of alleles where
alleles can pass from generation to the next
There are usually fewer alleles than genotype so gene pool
may be expressed in fewer terms
Frequency of allele
For a locus with 2 alleles A and a, the allelic frequencies are
calculated as
Where:
nAA, nAa, naa: number of AA, Aa, aa individuals
N: total number of individuals in the population
LOCI WITH MULTIPLE
ALLELES
Locus with 3 alleles: A1, A2, A3

Or
X-LINKED LOCI
Suppose that there are 2 alleles at an X linked
locus XA and Xa. Female is either XAXA, XAXa or
XaXa, male is either XAY or XaY
The frequencies of alleles XA and Xa
THE HARDY-WEINBERG
LAW
Assumption
 Population is large
 Randomly mating
 Not affected by mutation, migration or natural selection

Prediction
 Allelic frequency of the population do not change
 the genotypic frequencies stabilize (will not change) after one
generation in the proportions p2 (the frequency of AA), 2pq
(the frequency of Aa), and q2 (the frequency of aa), where p
equals the frequency of allele A and q equals the frequency of
allele a.
EXAMINATION OF THE
ASSUMPTION OF THE
HARDY-WEINBERG LAW
1. Large population size: need only be large
enough that chance deviations from expected
ratios do not cause significant changes in
allelic frequencies
2. Mate randomly: each genotype mates in
proportion to its frequency
3. No mutation, natural selection: should be low
enough not to affect the prediction of the law
IMPLICATION OF HARDY-
WEINBERG LAW
1. Population can not evolve if it meets the
Hardy-Weinberg assumption
2. When a population is in Hardy-Weinberg
equilibrium, the genotypic frequencies are
determined by the allelic frequencies
 f(AA) = f(a)2 ; f(aa) = f(a)2 ; f(Aa) = 2.f(A).f(a)
 The frequency of the heterozygote is greatest when
the frequency of two alleles is between 0.33-0.66
3. Single generation of random mating produces
the equilibrium frequencies of p2, 2pq, and q2.
EXAMPLES
Allele for black coat is recessive. Find the
frequency of allele for white coat.

Gene for coat color in pig has two alleles, say, W

and w.
Black color is recessive  genotype is ww
f(ww) = 4/16 = 0.25
f(ww) = f(w)2  f(w) = √0.25 = 0.5
f(W) + f(w) = 1  f(W) = 1 – 0.5 = 0.5
EXTENSION OF THE HARDY-
WEINBERG LAW
Hardy-Weinberg expectation for loci with multiple alleles
 For loci with 2 alleles:

 For loci with 3 alleles: A1, A2 and A3  produces 6 genotypes A1A1, A1A2,
A1A3, A2A2, A2A3, A3A3. If the frequencies of alleles A1, A2, A3 are p, q,
respectively, then the equilibrium phenotypic frequencies will be
Hardy-Weinberg expectation for the X-linked
loci
 For the X linked locus with 2 alleles XA and Xa, there are 5
possible phenotypes XAXA, XAXa, XaXa, XAY, XaY
 In the female group, frequency
where p2 = f(XAXA), q2 = f(XaXa), pq = f(XAXa)
 In the male group, frequency p = f(XAY), q = f(XaY)
TESTING WITH HARDY-
WEINBERG PROPORTIONS
Consider the following population: Genotype count: AA 30, Aa 55, aa 15
Allele frequencies: f(A) 0.575; f(a) 0.425. Check the X 2
ESTIMATING THE
ALLELIC FREQUENCY
WITH THE HARDY-
WEINBERG LAW
NONRANDOM MATING
Non random mating affects the way to in which
alleles combine to form genotypes and alter the
genotypic frequency of the population
2 types of non random mating
 Positive assortative mating: tendency for like individuals to mate
 inbreeding: mating among the related individuals
 Negative assorttative mating: tendency for unlike individuals to
mate
Inbreeding is usually measured by the inbreeding coefficient F
(probability 2 alleles are “identical by decent” (all allele copies
originated from single allele)
F ranges from 0 to 1
 0 indicates random mating
 1 indicates that all alleles are identical by descent

The frequencies
In self fertilization, F=1
CHANGES IN ALLELIC
FREQUENCIES
1. Mutation
2. Migration
3. Genetic drift
4. Natural selection
1. Mutation
 Influence the rate at which one genetic variant
increases at the expense of the other
 While one increase, another is decreased
 Suppose that allele G1 mutates to G2, the amount of
G2 will change Δq depending on
 Rate of G1 to G2 mutation (μ)
 Frequency of G1 (p) in the population
 Δq = μp
2. Migration
 Migration or gene flow changes the allelic frequency in the
population
 prevent the genetic divergence between populations
 Increase genetic variation within population
The change in the allelic frequency is equal the new
frequency of allele a (q’II) minus the original frequency
(qII)
∆q = q’II – qII
As presented above, q’II = qI m + qII (1-m)
 ∆q = qI m + qII (1-m) – qII
 ∆q = m(qI – qII)
The change in allelic frequency is dependent on the
migration m and the allelic frequencies of 2 populations
Effect of migration
 Cause the gene pool of population to become more similar
 Add genetic variation to populations
Cause of genetic drift
 Population size decrease after generations
 Founder effect: limit in establishment of the population samples
 Genetic bottleneck: when population undergo the drastic reduction in size

Effect of genetic drift:

 Change the allelic frequency
 Decrease the genetic variation within
population
 Fixation: when the allele reaches the frequency of 1
 Different population diverge genetically
with time
4. Natural selection
 When individuals with adaptive traits produce more
offsprings  appear with more frequency
 Effect of natural selection on a gene pool of
population depends on the fitness value of
genotype
 Fitness (W): relative reproductive success of genotype
compared with other genotype in the population
 To calculate: take the mean number of offsprings
produced by each genotype and divide it by the
number of offsprings produced by the most prolific
genotype
Genotypes: A1A1 A1A2 A2A2
Mean number of
offspring produced: 10 5 2

The fitness 10/10 5/10 2/10

 Selection coefficient (s): relative intensity of selection
against genotype s = 1 - W
 MOLECULAR EVOLUTION
Three area of molecular evolution study
1.Determine the extent and causes of genetic variation in
natural populations.

2.Examine molecular processes that influence evolutionary

events.

3.Apply molecular techniques to constructing phylogenies

(evolutionary trees) of various groups of organisms.
 PROTEIN VARIATION
1. Measure of genetic variation:
 proportion of polymorphic loci is the proportion of
examined loci in which more than one allele is
present in a population
 expected heterozygosity is the proportion of
individuals that are expected to be heterozygous at a
locus under the Hardy-Weinberg conditions (2pq for
locus with 2 alleles)
The percentage of polymorphic loci and the expected
heterozygosity have been determined by protein
electrophoresis for a number of species
2. Explanation for the protein variation
 Hypotheses were proposed (Neutral-mutation hypothesis and
Balance hypothesis) to explain the presence of the genetic
variation in protein
 However, these hypotheses can not explain how much variation
occur in the population, technique electrophoresis also was not
enough to detect changes in DNA even though these changes
produce the same protein product
 DNA SEQUENCE
VARIATION
Techniques were developed for isolating, sequencing, restricting
DNA  powerful tool in DNA research (and DNA variation, in
particular)
RFLP: using REs to cut DNA at the specifically recognized
sequences. The cutting patterns show the difference among
sequence  variation in DNA
Sequencing + bioinformatics: provide the highest resolution
information of DNA. This could help to compare numbers of
DNA sequences with each other.
Evolutionary tree and nucleic sequence comparison showing the relationships of HIV isolates from a
dentist, seven of his patients (A through G), and other HIV-positive persons from the same region (local
controls, LC).
PATTERN OF MOLECULAR
VARIATION
Different genes and different parts of the same gene often evolve at
different rates
Rate of evolutionary change in Nu sequence = rate of Nu
substitution: number of substitution per Nu site per year
Nonsynonymous substitutions: Nucleotide changes in a gene that
alter the amino acid sequence of a protein
Synonymous substitutions: Nucleotide changes, particularly those
at the third position of the codon, that do not alter the amino acid
sequence
Different parts of the gene evolve
differently
The highest rate found in regions that
affects the function of the protein