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Title: P1252109267JwvkG


1
Populational and Evolutional Genetics   Population
al genetics focus on how genetic characters of
populations are maintained over time.
  Evolutionary genetics focus on the factors
that may lead to new species. Evolution -
changes in gene frequencies in a population.
2
Geneticists are interested in the relationship
between different populations of a species. And
what causes one species to evolve into the other
species.  
3
In the case of diseases causing gene, HbS,
analyzing the distribution pattern between
populations may help to understand the origin
and maintenance of the disease.
Surveys of HbS allele frequency revealed 1).
The geographic origin of the disease 2). There
is correlation between sickle cell anemia
and the resistance to malarial infection.
4
Populations and gene pools are the focus of
study in population genetics. The key is to
focus on populations, but not on individual
organisms.
Gene pool A gene pool consists of all the
gametes made by all the breeding members of a
population in one generation.
5
  • If consider a single locus, different individuals
    in a
  • population have different genotypes. Also,
    different
  • gametes in a gene pool may carry different
    alleles.
  • Genotype frequency - The fraction of the
  • population that has a particular genotype.
  • Allele frequency - The fraction of the
  • gametes in the gene pool that carry a
  • particular allele.

6
Populations are dynamic they may expand or
diminish and may change by migration. Over
time, these may lead to structure change in a
population.
  The first step in studying the genetic
structure of a population is to calculate the
frequencies of alleles.  
7
In 1996, two individuals were found to be
immune to AIDS. They are homozygous for a
mutant allele, CC-CKR-5.   The CC-CKR-5 gene,
located on chromosome 3, encodes a cell-surface
protein, CCR5.
To gain entry into the host's cells, HIV-1 virus
bind to two receptors on the host cell surface
CD4 and CCR5. Binding of HIV and CCR5
initiates the fusion of the viral envelope with
the host cell membrane.  
8
The mutant allele of the CCR5 gene contains a
32-bp deletion in its coding sequence. The
protein product is severely shortened and is
nonfunctional. So one of the HIV binding sites
is missing.   The normal allele of the gene is
called CCR5 (or ) and the mutant is called
CCR5-?32 (or just ?32). The two individuals
who are immune to HIV had the genotype, ?32 /
?32.  
9
Homozygous ?32/?32 individuals are immune to
HIV. The heterozygotes (/?32) are susceptible
to HIV- I infection, but their symptoms progress
slowly.   Questions Which human populations
harbor the ?32 allele, and how common is it?  
A survey a population of 100 French individuals
from Brittany, 79 had genotype /, 20 had
genotype /?32, and 1 had genotype ?32/?32.
10
To calculate the allele frequencies, imagine a
gene pool of 100 people. Each contributes two
gametes, ... There are 200 gametes in this
gene pool. Those that carry CCR5 allele 158
(/) 20 (/?32) 178.   The frequency of
the CCR5 allele is thus 178 / 200 0.89 89.
   
11
For ?32 alleles, 20 (/?32) 2 (?32/?322) 22.
The frequency of the ?32 allele is thus 22 /200
0.11 11. Allele frequency is the focus of
populational genetics.
12
The Hardy-Weinberg Law A mathematical model
which shows that under certain assumptions,
allele frequencies of a population do not change
from one generation to the next.  
13
Five assumptions 1. Individuals of all
genotypes have equal rates of survival and equal
reproductive success. That is, there is no
selection.   2. There are no mutations that
create new alleles or convert one allele into
another.  
14
3. There is no migration of individuals into or
out of the population.   4. The population is
infinitely large enough that sampling errors and
other random effects are negligible.   5. The
individuals in the population mate at random.  
15
The Hardy-Weinberg law demonstrates that such a
population has the following properties   1.
The allele frequencies in the population do not
change from generation to generation in other
words, the population does not evolve. 2.
After one generation of random mating, the
genotype frequencies can be predicted from the
allele frequencies.  
16
Demonstration of the Hardy-Weinberg Low   Focus
on a single locus with two alleles, A and a.
  Imagine the frequency of allele A is 0.7 for
both eggs and sperms. The frequency of allele a
is 0.3.   We also assume that individuals mate
randomly. Use the Punnet square to predict
the genotype frequencies.  
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18
Fr (AA) 0.49 49 Fr (Aa)  2 x 0.21 0.42
42 Fr (aa) 0.09 9 Note that 0.49 0.42
0.09 1.0, this confirms that we have accounted
for all of the zygotes.
After one generation of random mating, the
genotype frequencies can be predicted from the
allele frequencies.
19
When these zygotes develop into adults and
reproduce, what will be the allele frequencies
in the new gene pool of next generation?    
AA constitute 49 of the population, Aa
constitute 42 of the population, half gametes
A. aa 9 fr(A) in the new gene pool is 0.49
(1/2) 0.42 0.7 fr(a) in the new gene pool
is 0.09 (1/2) 0.42 0.3
20
A population that has allele frequencies remained
constant from generation to generation and
whose genotype frequencies can be predicted from
the allele frequency is said to be in a state of
Hardy- Weinberg equilibrium. Such a population
does not evolve. The Hardy-Weinberg Law holds
true, as long as the frequencies sum to 1 and
the five assumptions hold.
21
It is interesting to study the assumptions
of Hardy - Weinberg Law.
By specifying the ideal conditions under which
allele frequencies will not change, the
Hardy- Weinberg law can be used to identify the
forces in real world that cause allele
frequencies to change. In other words, the
Hardy-Weinberg law identifies the forces of
evolution.
22
  • Natural selection is a potent force of
  • evolution
  •  
  • The first assumption of H-W law
  • All genotypes have equal rates of survival and
  • reproductive success.
  • If this assumption is violated, allele
    frequencies
  • will change between generations.
  •  

23
Consider a population of 100 individuals. fr(A)
0.5 and fr(a) 0.5. After random mating the
genotype frequency for AA would be 0.25, Aa
0.5 and aa 0.25.   Imagine in an environment,
the survival rate of AA is 100 (25 out of 100).
Whereas, 90 of Aa (or 45 of 100) survive to
reproduce and 80 of aa (or 20 of 100) survive
to reproduce.  
24
If each individual contributes 2 gametes to the
new gene pool 2(25) 2(45) 2(20) 180
gametes.
Among the 180, what are the frequencies of the
two alleles? 50 A from AA individuals, plus
45 A from Aa individuals fr(A) (50
45)/180 0.53 For a allele 45 a (from Aa)
40 (from aa) 85. fr(a) 85 /180 0.47
25
These numbers are different from the frequencies
we started with (0.5 and 0.5), the frequency of
A has increased, while the frequency of a has
declined.
A difference among individuals in the rate of
survival and/or reproduction is called natural
selection. Natural selection is the principal
force that shifts allele frequencies within
large populations and is one of the most
important factors in evolutionary change.  
26
Fitness and Selection   Selection occurs when
some individuals with a particular genotype are
having advantage in survival over other
genotypes.   An individual's genetic
contribution to future generations is called its
fitness. Genotypes with high rates of survival
or reproductive success are said to have high
fitness.  
27
According to Darwin, adaptive evolution or
natural selection favors the fittest genetic
variants in a population.   By convention, w
represents fitness. wAA - the relative fitness
of genotype AA wAa, - relative fitness of
genotype Aa waa - relative fitness of genotype
aa.   For the above case, wAA 1, wAa, 0.9,
and waa 0.8, which means all AA individuals
survive, 90 of Aa survive, and 80 of aa
survive.  
28
If consider selection against deleterious
alleles. Fitness values wAA 1, wAa, 1, and
waa. 0 describe a situation in which allele a
is lethal recessive. As homozygotes, aa, die
without leaving offspring, the frequency of
allele a will decline.  
29
2. Mutation is the source of new alleles, but
a weak force of change in allele frequencies
  Mendelian assortment and recombination do not
produce new alleles. Mutation alone acts to
create new alleles.   It is important to keep
in mind that mutations are random events. They
may be beneficial and may also be harmful to the
organism. By itself, mutation has very little
effect on allele frequency.  
30
For exp.,   In humans, gene mutation that causes
dwarfism showed mutation rate as 1.4 x 10-5 -
0.5 x 10-5   To estimate the
impact of this mutation on allele Frequencies
  d - normal allele, D - allele for dwarfism.  
31
In a population of 500,000 The initial
frequency of d is 1, that of D is 0. Each
individual contributes 2 gametes to the gene
Pool ? 1000,000 gametes all carrying d. Since
the mutation rate of d ? D is 1.4 x 10-5, the
fr (d) would be (1000,000 - 14)/1000,000
0.999986, and fr (D) 14/1000,000 0.000014.
Mutations cause very little change on allele
frequencies.
32
The fate of alleles created by mutation is more
likely to be determined by natural selection and
genetic drift.
33
3. Migration homogenizes allele frequencies
across population.   Migration can be regarded as
the flow of genes between populations. Allele
frequencies for two different alleles of one
locus, FY-NULL, have been measured in
African-American and European- American
populations.   FY-NULL1 and FY-NULL2.  
34
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35
The simplest explanation there has been mixture
of genes between American populations with
African ancestry and American populations with
European ancestry. Based on FY-NULL and
several other loci, it was estimated that
African-American populations derive 11.6 -
22.5 of their ancestry from Europeans, and
European-American populations derive 0.5 -1.2
of their ancestry from Africans.  
36
4. Nonrandom mating changes genotype
frequencies, but not allele frequencies
  Nonrandom mating does not directly alter the
frequencies of alleles. Instead, it alters the
frequencies of genotypes in a population and
thereby indirectly affect the course of
evolution.   The most important form of
nonrandom mating, is inbreeding mating between
relatives. For a given allele, inbreeding
increases the proportion of homozygotes in the
population.  
37
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38
In humans, inbreeding (consanguineous marriage)
is related to population size, mobility, and
social customs.   Genetic effects of
inbreeding   Inbreeding can cause the
production of individuals to be homozygous for
recessive alleles that were previously concealed
in heterozygotes.  
39

Inbreeding can cause increased chance for an
individual to be homozygous for a recessive
deleterious allele. Inbred populations often
have a lowered fitness. Inbreeding depression -
loss of fitness caused by inbreeding.
40
Molecular Evolution   Nucleotide and amino acid
differences are used to establish
phylogenies.   Phylogeny - evolutionary history
of a species. By comparing the DNA sequences
and amino acid sequences between proteins, one
can trace the evolutionary history of a species
or the genetic relationship between species.  
41
The amino acid sequence of Cytochrome c has
changed very slowly during evolution   Amino
acid sequence comparison showed that closely
related species share more similarity than
distantly related species. Human Cytochrome c
has 0 difference in amino acid sequence compared
to chimpanzee, but show 9 amino acid difference
from rabbit, and 24 amino acid difference from
moth.  
42
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43
DNA sequence can also be used to compare the
evolutionary histories of different organisms.
When the nucleotide changes necessary for all
amino acid differences in a protein are totaled,
the minimal mutational distance (MMD) between
any two species can be established.
44
A molecular phylogeny based on MMD data of
cytochrome c from 19 different organisms.
45
  Another commonly used method to estimate
evolutionary distances is UPGMA - unweighted
pair group method using arithmetic averages.
Data is dirived from DNA hybridization study.
 
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