Chapter 16: Random genetic drift

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Chapter 16 Random genetic drift
Definition Random genetic drift chance
fluctuations in allele frequencies - especially
in small populations as a result of random
sampling among gametes.
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Result of genetic drift differentiation Genet
ic differentiation vs genetic diversity? Genetic
differentiation The process where different
populations become less similar Genetic
diversity Amount of geversity (alleleic
diversity) within a population
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Large interbreeding populations are essential to
maintain HWE
Degree of fluctuation increases as the population
size decreases Genetic Drift
Genetic drift can lead to fixation of one
allele to the exclusion of another allele
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Example

• Pingelap atoll typhoon 30 people left

• 4-10 of current population - colourblind

• Recessive disorder - achromatopsia

After typhoon - one individual heterozygote
1/60 0.016 Currently 7 affected -
frequency increased to 0.26
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16.2 Levels of population structure Heterozygos
ity or H Observed heterozygosity (ho) (
proportion of individuals that are
heterozygous) Expected heterozygosity (he) ( h
based on allele frequencies)
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• Levels of population structure continued.
• A sub-divided population has 3 distinct levels of
  complexity
• Individual organisms I
• sub-populations S
• Total population T

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• A sub-divided population has 3 distinct levels of
  complexity
• Individual organisms I
• sub-populations S
• Total population T
• Therefore

Inbreeding Coefficient (FIS) measures the
reduction in heterozygosity in an individual due
to non-random mating within its sub-population
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• A sub-divided population has 3 distinct levels of
  complexity
• Individual organisms I
• sub-populations S
• Total population T
• Therefore

• Fixation index (FST) measures the effects of
  population sub-division. This quantifies the
  reduction in heterozygosity of a sub-population
  due to random drift.
• Can also be used to quantify genetic divergence
  between populations

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• A sub-divided population has 3 distinct levels of
  complexity
• Individual organisms I
• sub-populations S
• Total population T
• Therefore

Overall Inbreeding Coefficient (FIT) is based on
the deviation of an individual from
heterozygosity expected in the entire population
system if there were no sub-divisions and mating
occurred at random
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Calculating FST Pop1 Pop2 AA AA AB
AA AB AA AA AB BB AB A 6/10 0.6 A
8/10 0.8 B 4/10 0.4 B 2/10 0.2 ho
2/5 0.4 ho 2/5 0.4
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A 6/10 0.6 A 8/10 0.8 B 4/10 0.4 B
2/10 0.2 ho 2/5 0.4 ho 2/5 0.4
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HT 2(0.7)(0.3) 0.42
0.048
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• 16.5 Genetic divergence among sub-populations
• FST can be used to quantify genetic divergence
  between populations.
• Theoretical minimum 0
• Theoretical maximum 1
• Common ranges
• 0 0.05 little differentiation
• 0.05 0.15 moderate differentiation
• 0.15 0.25 great differentiation
• above 0.25 very great differentiation
• BUT, genetics software can add a P value, which
  is much more descriptive.

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What is the difference between Genetic distance
and FST? Genetic distance Mainly used to
describe allopatric taxa, i.e. taxa whose
distribution do not overlap. FST Assumes that
sub-populations diverged from a common population
( effect of genetic drift).
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Calculating FST (2) showing large
differences Pop1 Pop2 AA AB AB AB
AB BB AA BB BB BB A 6/10 0.6 A
2/10 0.2 B 4/10 0.4 B 8/10 0.8 ho
2/5 0.4 ho 2/5 0.4
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A 6/10 0.6 A 2/10 0.2 B 4/10 0.4 B
8/10 0.8 ho 2/5 0.4 ho 2/5 0.4
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HT 2(0.4)(0.6) 0.48
0.167
(Compared to 0.048 before)
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Practical example of the use of FST
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• Hybridization between blue- and black wildebeest
• (Connochaetes taurinus C. gnou)
• diverged 1-2m years ago
• same chromosome number (2n58)
• many morphological similarities
• fertile hybrids (Fabricius et al., 1988)

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A further application of FST values Gene flow
or Nm
For previous example where FST 0.048 Nm
0.25 (1 0.048) 0.048 5.0
Individuals per generation And for FST 0.167,
Nm 1.247 Individuals per generation
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16.4 Effective population number The effective
number of a population is usually smaller than
the actual population size.
Effective population size (Ne) number of
individuals in a population having an equal
probability of contributing gametes to the next
generation.
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Calculating the effective population size
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Example
Population 100 males and 100 females
4(100 x 100) / (100 100) 200
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Population 180 females and 20 males
4(20 x 180) / (20 180) 72
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Bottlenecks
Population or species is reduced to a few
reproducing individuals whose offspring then
increase in numbers re-establish the population
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Bottlenecks
Population or species is reduced to a few
reproducing individuals whose offspring then
increase in numbers re-establish the population
Number of individuals restored genetic
diversity severely reduced
Bottlenecks can occur naturally migration of
few individuals to start a new population or
artificially through bad management founder
effect (reduced levels of genetic diversity)
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Chapter 17 Inbreeding (Genetic diversity)
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• Effects of inbreeding
• (well known)
• Increased juvenile mortalities
• Reduced growth rate
• Reduced fecundity
• Increased susceptibility to disease parasites
• All of which affect production potential,

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Inbreeding in white clover
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Sperm abnormalities
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Genetic diversity in impala

• 1962 2 m / 2 f
• 1963a 2 m / 2 f
• 1963b 2 m / 1 f
• 1964a 1 m / 1 f
• 1964b 1 m / 2 f
• 1964c 1 f
• 1964d 15

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11000
300
30
150
6,000 150 6
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Genetic diversity in blue wildebeest
505
200
141
150 70 8 11
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Genetic diversity in African buffalo

• Carriers of
• Foot mouth disease
• Corridor disease
• Tuberculosis
• Brucellosis

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15000
95

• carriers
• no translocations allowed

• disease free
• from 2 bulls / 6 cows
• price?

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• 17.2 Inbreeding depression
• A reduction in fitness ( ability to survive and
  reproduce)
• Examples
• reduced sperm viability (cheetah)
• reproductive abnormalities (African lion)
• increase offspring mortality (elephant seals)

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• 17.3 Applications of inbreeding
• ( some positive outcomes associated with
  inbreeding)
• Line crosses between inbred lines result in
  mostly heterozygous individuals which might be
  superior to inbred parents (heterosis).

AA AA AA AA
BB BB BB BB
x
AB AB AB AB
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• 17.3 Applications of inbreeding
• ( some positive outcomes associated with
  inbreeding)
• Line crosses between inbred lines result in
  mostly heterozygous individuals which might be
  superior to inbred parents (heterosis).
• Inbreeding can be used to fix a desirable trait
  and achieve greater uniformity (size
  temperament).
• Inbreeding increases the chance of expression of
  deleterious recessive alleles, that can then be
  culled, reducing the frequency of such alleles.

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17.5 (b) Other ways to determine and quantify
genetic diversity Average heterozygosity
(H) Average number of alleles per locus
(A) Polymorphism (P) NB these coefficients
are calculated from molecular data, therefore
prior knowledge of relationships are not needed.
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Microsatellite regions .ACGT-CG-CG-CG-CG-CG-TCG
AT. (CG x 5)
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Example Imagine 2 lion populations, one
in the KNP and one in the Lion Park
(Midrand). Compare levels of genetic diversity
in these 2 populations.
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Genotype 10 individuals from each
population KNP Lion Park Locus 1 AA AB
AB AA AA AA AA AB AA AA AB BB BB AA
AB AB AA AA AA BB Locus 2 AA AB AB AA
BB AA AA AA AB AA BB AB BC CC AC AB
AA AA BB AA Locus 3 AA AB AB AA AA AA
AA AA AA AA AA AA AB AA AA AA AA AA
AA AA
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Locus 1 KNP Lion Park AA AB AB AA
AA AA AA AB AA AA AB BB BB AA AB AB
AA AA AA BB
Allele frequencies A 12/20 0.6 A 16/20
0.8 B 8/20 0.4 B 4/20 0.2 Single
locus heterozygosity h h 1 (0.62
0.42) h 1 (0.82 0.22) 1
(0.360.16) 1 (0.64 0.04) 1
0.52 1 0.68 0.48 0.32
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Locus 2 KNP Lion Park AA AB AB AA
BB AA AA AA AB AA BB AB BC CC AC AB
AA AA BB AA
Allele frequencies A 8/20 0.4 A 16/20
0.8 B 8/20 0.4 B 4/20 0.2 C 4/20
0.2 Single locus heterozygosity h h 1
(0.42 0.42 0.22) h 1 (0.82 0.22) 1
(0.16 0.16 0.04) 1 (0.64 0.04)
0.64 0.32
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Locus 3 KNP Lion Park AA AB AB AA
AA AA AA AA AA AA AA AA AB AA AA AA
AA AA AA AA
Allele frequencies A 17/20 0.85 A
20/20 1.0 B 3/20 0.15 B 0/20 0
Single locus heterozygosity h h 1
(0.852 0.152) h 1 (1.02 0.02) 1
(0.723 0.023) 1 (1.0 0) 0.254 0
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Single locus heterozygosity values
(h) KNP Lion Park Locus
1 0.48 0.32 Locus 2 0.64 0.32 Locus
3 0.254 0.0 Average heterozygosity (H) H
0.48 0.64 0.254 0.32 0.32 0
3 3 0.458 0.213
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KNP Lion Park Locus 1 AA AB AB AA
AA AA AA AB AA AA AB BB BB AA AB AB
AA AA AA BB Locus 2 AA AB AB AA BB AA
AA AA AB AA BB AB BC CC AC AB AA AA
BB AA Locus 3 AA AB AB AA AA AA AA AA
AA AA AA AA AB AA AA AA AA AA AA AA
Average no. of alleles per locus (A) ( allelic
diversity) A 2 3 2 2 2 1
3 3 2.333 1.667
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KNP Lion Park Locus 1 AA AB AB AA
AA AA AA AB AA AA AB BB BB AA AB AB
AA AA AA BB Locus 2 AA AB AB AA BB AA
AA AA AB AA BB AB BC CC AC AB AA AA
BB AA Locus 3 AA AB AB AA AA AA AA AA
AA AA AA AA AB AA AA AA AA AA AA AA
Polymorphism (P) P 3 / 3 2 / 3
100 66.7
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• 17.7 Inbreeding and behaviour
• The effect of genes on behaviour has been
  demonstrated experimentally in mice.
• Inbreeding lowers IQ children of marriages
  between 1st cousins perform worse than controls.
  The risk of mental retardation 3x greater than
  for unrelated controls.
• Inbreeding does not have a significant effect in
  general human populations, because it is rare,
  except in a few societies and in small
  populations.