Population Genetics I. What is Population Genetics

Population Genetics
I. What is population genetics?
A. Studying Variation
B. Gene frequencies & allele frequencies
II. Hardy-Weinberg equilibrium
III. Factors that change allele frequencies
in populations
I. What is Population Genetics
• Goal: understand the genetic composition of a
population and the forces that determine and
change that composition
• Fundamental measurement =
• Forces that change allele frequency =
Side-blotched lizards (Uta
stansburiana) in central California
experience unusual patterns of
throat color.
Terms for understanding genetic diversity
Genetic Polymorphism – Gene Pool
‣Population, subpopulation, local
population
‣Genetic structure
‣Polymorphic loci
‣Genotype frequency = # individuals with
a particular genotype in a pop / N
‣Allele frequency = # of copies of an
allele in a pop / total # alleles in a pop.
Genetic
Structure
Allele Frequency
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Gene Frequencies & Allele Frequencies
• Gene frequency refers to proportion of particular allelic
form among all copies of gene in population
• Usually estimated by sampling population
– diploid: 2 copies of gene
• homozygotes: 2 copies of allele
• heterozygotes: 1copy of each allele
– haploid: 1 copy of allele
• For two alleles, p + q = 1, where p and q are frequencies
of the two alleles
Calculating Genotype Frequencies
Relative frequencies of genotypes – proportion of organisms
that have the particular genotype
• The proportion of individuals
in a population with a
particular genotype
• fA/A =
• fA/a =
• fa/a =
N
f
A/A
40
0.40
A/a
47
0.47
a/a
13
0.13
Calculating allele frequencies
• If fA/A, and fa/a are the proportions of the
three genotypes at a locus with two
alleles, then the frequency p(A) of the A
allele and the frequency q(a) of the a allele
are obtained by counting alleles:
• p = fA/A + ½ fA/a
• q = fa/a + ½ fA/a
• p + q = fA/A + fa/a + fA/a = 1.00
• q = 1 – p and p = 1 – q
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AA
Aa
aa
total
Mendelian considerations in population genetics…
N
40
47
13
100
# of A
80
47
0
127
# of a
47
26
73
Total
200
Allele Frequency of A = 127/200 = 0.635
p(A) = 0.635
Allele Frequency of a = 73/200 = 0.365
q(a) = 0.365 = 1 - p
II. Hardy Weinberg equilibrium
• Sexual reproduction does not cause a
constant reduction in genetic variation in
each generation; rather the amount of
variation remains constant generation after
generation
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Populations in HW equilibrium have
the following properties:
1) The frequency of alleles does not change
from generation to generation
2) After one generation of random mating,
offspring genotype frequencies can be
predicted from the parent allele
frequencies
3) Why use HW?
80% of all the gametes in the population carry a dominant allele
for black coat (B) and
20% carry the recessive allele for gray coat (b).
Random union of these gametes will produce a generation:
Will the gray phenotype eventually be lost?
Testing for equilibrium
1) Determine the genotype frequencies
– Directly from phenotypes
– Analyzing DNA sequence
2) Calculate allele frequencies
3) Predict the offspring’s genotype
frequencies using HW principle… does
the prediction hold true? Are they similar
to the observed frequencies?
CCR5 genotype example
• N = 238
• 223 – 1/1,
57 – 1/Δ32,
3 - Δ32/Δ32
– f(1/1) = 0.788,
f(1/Δ32) = 0.201,
f(Δ32/Δ32) =
0.011
p = 0.89 q = 0.11
Expected genotype frequency:
p 2 = 0.792
2pq = 0.196
q 2 = 0.012
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• The allele frequency for hemophilia (A) is
1/10,000 or 0.0001.
a) What is the allele frequency for the normal
allele in the human population?
b) Among males, what is the frequency of
affected individuals?
c) Within a population of 100,000 people, what
is the expected number of affected males?
What is the number of expected carrier
females?
III. Factors that change allele frequencies in
populations: Disturbing forces
1) Mutation
2) Non-random mating
3) Gene flow
4) Genetic Drift
5) Natural selection
1) mutation
• Mutation is the Ultimate source of variation,
playing a fundamental role in the process of
evolution
• Mutation rate (μ)= probability that a copy of an
allele changes to some other allelic form in one
generation
– Δq = μp
• p = 0.8, q = 0.2, μ = 10 -5 ,
– Δq = (10 -5 )(0.8) = 0.000008)
• Next generation:
–q n+1 = 0.2 + 0.000008 = 0.20008
–p n+1 = 0.8 – 0.000008 = 0.799992
2) Gene flow
• Gene Flow = migration
Gene flow - Genetic exchange between
populations due to the migration of
individuals between populations
Can offset the effects of genetic drift
Inhibited by isolation
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3) Genetic Drift
• Genetic Drift
Random fluctuations of allele frequencies
between generations
compounded by small population size
alleles can become fixed
The genetic bottleneck effect
4) Inbreeding (non-random mating)
• Inbreeding = Mating between relatives
•IDB– identical by descent, the two alleles
may be copies of the same gene in an
earlier member of the line
5) Natural selection
• Darwinian fitness – relative probability of
survival and rate of reproduction of a
phenotype or genotype
– Differential rates of survival and
reproduction
• Fitness is a consequence of the relation
between the phenotype of the organism
and the environment in which it lives, so
the same genotype will have different
fitnesses in different environments
consequence of relationship between
phenotype and environment
same genotype may have different fitness in
different environments
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Heritability of beak depth
in medium ground
finches.
The red line and circles
are data from 1978, and
the blue line
and circles are from 1976
data. The results from the
two years
are consistent. Both
show a strong
relationship between the
beak depth of parents
and their offspring
In every natural population
studied, more offspring are
produced each generation than
survive to breed. The
reproductive capacity or biotic
potential of organisms is
astonishing
(Table 3.1). It has been shown that
in most populations, some
individuals are more
successful at mating and
producing offspring than others.
Variation in reproductive
success represents an
opportunity for selection, as does
variation in survival.
Combining forces shape genetic
structure
• Natural selection, mutation and genetic
drift all can combine to maintain allele
frequencies
• Populations undergo evolution, not
individuals
• "Evolution is evidenced by changes in the
gene pool which includes all the genes of
any population at any give time."
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