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Exam 1 Review
September 21, 2015
Logistics
u 3306 LSB at 6:30 on Wednesday,
September 23
u Closed book, notes, internet
u Computers and software will be available
u Mix of multiple choice, short answer,
and calculations
u 120 points
u Covers everything up to Friday lecture
(except Genetic Drift)
Foundations of Population Genetics
u Familiarize yourself with Mendel,
Lamarck, and Darwin
u Know Mendel’s laws and basics of
Mendelian segregation
u Know major types of molecular markers
and their strengths and weaknesses
u Dominant versus codominant markers
u Probability calculations
Hardy-Weinberg
u Genotype and allele frequency
calculations
u Standard errors
u Hardy-Weinberg assumptions
u Calculations for detecting departure
from HW, including biological
interpretations!
u Calculating allele frequencies for
dominant loci
Important Points about Inbreeding
u Inbreeding affects ALL LOCI in genome
u Inbreeding results in a REDUCTION OF
HETEROZYGOSITY in the population
u Inbreeding BY ITSELF changes only genotype
frequencies, NOT ALLELE FREQUENCIES and
therefore has NO EFFECT on overall genetic
diversity within populations
u Inbreeding equilibrium occurs when there is a
balance between the creation (through
outcrossing) and loss of heterozygotes in each
generation
Fixation Index
u The difference between observed and expected
heterozygosity is a convenient measure of
departures from Hardy-Weinberg Equilibrium
H E  HO
HO
F
 1
HE
HE
Where HO is observed heterozygosity and
HE is expected heterozygosity (2pq under Hardy-Weinberg
Equilibrium)
Estimating Inbreeding from Pedigrees
u Most accurate estimate of f derived from direct
assessment of relationships among ancestors
Half First-Cousins
CA
CA
CA
CA
BB
CC
DD
EE
PP
CA: Common Ancestor
BB
CC
DD
EE
PP
Chain Counting
Count links to Common Ancestor
starting with one parent of
inbred individual and continuing
down to other parent
CA
A1A2
P(A1) = ½
P(A1) = ½
P(A1) = ½
P(A1) = ½
D
E
P(A1) = ½
P(A1) = ½
P
A1A1
 N=5 links
N
C
B
 D-B-CA-C-E
5
1
1
1
f     
2
 2  32
For multiple common ancestors, m:
Ni
1
f    .
i 1  2 
m
If common ancestors are inbred as well:
Ni
1
f     (1  f CAi )
i 1  2 
m
Where fCAi is inbreeding coefficient of common ancestor i
Inbreeding and allele frequency
Inbreeding alone does not alter allele
frequencies
Yet in real populations, frequencies DO
change when inbreeding occurs
What causes allele frequency change?
Why do so many adaptations exist to
avoid inbreeding?
Mechanisms of Inbreeding Depression
Two major hypotheses: Partial Dominance and
Overdominance
Partial Dominance (really a misnomer)
 Inbreeding depression is due to exposure of
recessive deleterious alleles
Overdominance
 Inherent advantage of heterozygosity
 Enhanced fitness of heterozygote due to pleiotropy
(one gene affects multiple traits): differentiation
of allele functions
 Bypass homeostasis/regulation
Heterozygous Effect
A1A1
Relative Fitness (ω)
Relative Fitness (hs)
ω11
1
h = 0, A1 dominant, A2 recessive
h = 1, A2 dominant, A1 recessive
0 < h < 1, incomplete dominance
h = 0.5, additivity
h < 0, overdominance
h > 1, underdominance
A1A2
A2A2
ω12
ω22
1-hs
1-s
Putting it all together
A1A1
Relative Fitness (ω)
ω11
Relative Fitness (hs)
1
Δq =pq[q(ω22 – ω12) - p(ω11- ω12)]
ω
Reduces to:
Δq =-pqs[ph + q(1-h)]
1-2pqhs-q2s
A1A2
A2A2
ω12
ω22
1-hs
1-s
Modes of Selection on Single Loci
Directional – One homozygous genotype
has the highest fitness
 Purifying selection AND
Darwinian/positive/adaptive selection
1
0.8
ω
0.6
0.4
0.2
0
 Depends on your perspective!
AAA
1A1
AAa1A2 A2aaA2
AAA
1A1
aa
AAa
1A2 A2A2
AAA
1A1
AAa1A2 Aaa
2A2
 0 ≤ h ≤ 1
1
Overdominance – Heterozygous
genotype has the highest fitness
(balancing selection)
0.8
ω
Underdominance – The heterozygous
h>1, (1-hs) < (1 – s) < 1 for s > 0
0.4
0.2
0
h<0, 1-hs > 1
genotypes has the lowest fitness
(diversifying selection)
0.6
1
0.8
ω
0.6
0.4
0.2
0
Equilibrium under Overdominance
Allele frequency always
approaches same value of
q when perturbed away
from equilibrium value
Stable equilibrium
Allele frequency change
moves population toward
maximum average fitness
s1
qeq 
s1  s2
Equilibrium under Underdominance
Allele frequency moves
away from equilibrium
point and to extremes
when perturbed
Unstable equilibrium
Equilibrium point is at
local minimum for average
fitness
Population approaches
trivial equilibria: fixation
of one allele
Important Points about Selection
Directional selection usually affects individual
loci
Directional selection removes diversity and
reduces genetic variance
Overdominance and underdominance can help
maintain diversity in a population under certain
conditions
Even in a finite population, diversity can be
maintained by antagonistic pleiotropy, spatial
and temporal variation in selection, frequencydependent selection, and coevolution