What is Population Genetics?
 About microevolution (evolution within species)
 The study of the change of allele frequencies,
genotype frequencies, and phenotype
frequencies
Factors causing genotype frequency
changes or evolutionary principles
• Selection = variation in fitness; heritable
• Mutation = change in DNA of genes
• Migration = movement of genes across populations
– Vectors = Pollen, Spores
• Recombination = exchange of gene segments
• Non-random Mating = mating between neighbors
rather than by chance
• Random Genetic Drift = if populations are small
enough, by chance, sampling will result in a different
allele frequency from one generation to the next.
Pathogen Population Genetics
• must constantly adapt to changing environmental
conditions to survive
– High genetic diversity = easily adapted
– Low genetic diversity = difficult to adapt to changing
environmental conditions
– important for determining evolutionary potential of a
pathogen
• If we are to control a disease, must target a population
rather than individual
• Exhibit a diverse array of reproductive strategies that
impact population biology
Molecular Markers
• DNA & PROTEINS
– mtDNA = often used in systematics; in general, no recombination =
uniparental inheritance
– cpDNA = often used in systematics; in general, no recombination =
uniparental inheritance
– Microsatellites = tandem repeats; genotyping & population structure
– Allozymes = variations of proteins; population structure
– RAPDs = short segments of arbitrary sequences; genotyping
– RFLPs = variants in DNA exposed by cutting with restriction enzymes;
genotyping, population structure
– AFLPs = after digest with restriction enzymes, a subset of DNA fragments
are selected for PCR amplification; genotyping
Analytical Techniques
– Hardy-Weinberg Equilibrium
• p2 + 2pq + q2 = 1
• Departures from non-random mating
– F-Statistics
• measures of genetic differentiation in populations
– Genetic Distances – degree of similarity between OTUs
•
•
•
•
Nei’s
Reynolds
Jaccards
Cavalli-Sforza
– Tree Algorithms – visualization of similarity
• UPGMA
• Neighbor Joining
Levels of Analyses

Individual
•

identifying parents & offspring– very important in
zoological circles – identify patterns of mating between
individuals (polyandry, etc.)
In fungi, it is important to identify the "individual" -determining clonal individuals from unique individuals
that resulted from a single mating event.
Armillaria gallica
“Humongous Fungus”
rhizomorphs
Levels of Analyses cont…
• Families – looking at relatedness within colonies (ants,
bees, etc.)
• Population – level of variation within a population.
– Dispersal = indirectly estimate by calculating
migration
– Conservation & Management = looking for founder
effects (little allelic variation), bottlenecks (reduction
in population size leads to little allelic variation)
• Species – variation among species = what are the
relationship between species.
• Family, Order, ETC. = higher level phylogenies
Founder Effects
• Establishment of a population by a few
individuals can profoundly affect genetic
variation
– Consequences of Founder effects
• Fewer alleles
• Fixed alleles
• Modified allele frequencies compared to source pop
– Perhaps due to “new environment”
Potato Blight
• Phytophthora infestans
• great Irish famine of 1845-1849
– 1,000,000 died
• Origin of P. infestans
– Mexico = highest genetic diversity; likely origin
– Ireland = decreased genetic diversity due to founder
effect
– Decreased genetic differentiation in other regions
• Europe, North America
Hardy Weinberg Equilibrium
and F-Stats
• In general, requires co-dominant marker
system
• Codominant = expression of heterozygote
phenotypes that differ from either
homozygote phenotype.
• AA, Aa, aa
Codominant Molecular Tools
– Allozymes = different versions of
proteins.
– Microsatellites = repetitive sequences
in the DNA (e.g. AC)12
• One of the major first tools for
analyzing population structure
• Very popular for analyzing population
structure
• Forensic applications
Advantages:
Inexpensive
Easily Obtained
Advantages:
Hypervariable
Genotyping
Population Structure
Disadvantages:
Disadvantages:
Coding regions = violate assumptions of
analytical techniques
Invariable in many fungi = inadequate for
looking at variation
High cost of Development
Dominant Marker
Allele Frequencies
• Allele frequencies (gene frequencies) =
proportion of all alleles in an all individuals in the
group in question which are a particular type
• Allele frequencies:
p + q = 1
• Expected genotype frequencies:
p2 + 2pq + q2
Hardy-Weinberg Equilibrium
• Null Model = population is in HW Equilibrium
– Useful
– Often predicts genotype frequencies well
Hardy-Weinberg Theorem
if only random mating occurs, then allele frequencies
remain unchanged over time.
After one generation of random-mating, genotype frequencies
are given by
AA
Aa
aa
p2
2pq
q2
p = freq (A)
q = freq (a)
Expected Genotype Frequencies
• The possible range for an allele frequency or genotype
frequency therefore lies between ( 0 – 1)
• with 0 meaning complete absence of that allele or genotype
from the population (no individual in the population carries that
allele or genotype)
• 1 means complete fixation of the allele or genotype (fixation
means that every individual in the population is homozygous for
the allele -- i.e., has the same genotype at that locus).
ASSUMPTIONS
1) diploid organism
2) sexual reproduction
3) generations are non-overlapping
4) mating occurs at random
5) large population size
6) migration = 0
7) mutation = 0
8) no selection on genes
Locus
Sample
1
2
3
1
3,4
2,2
1,1
2
4,4
2,2
1,2
3
4,4
1,2
1,2
4
4,4
2,2
1,1
5
4,4
1,2
1,1
6
1,4
1,2
1,1
7
2,4
2,2
1,1
8
4,4
2,2
1,1
9
2,4
1,2
1,1
10
1,4
2,3
2,2
11
2,4
2,2
2,2
12
2,3
2,2
2,2
13
4,4
1,2
1,1
14
1,4
2,3
1,2
15
4,4
1,2
1,2
16
1,4
1,1
1,1
Locus 1
Allele 1 = 4/32 = 0.125
Allele 2 = 4/32 = 0.125
Allele 3 = 2/32 = 0.0625
Allele 4 = 22/32 = 0.6875
Allele frequencies = 0.125 + 0.125 + 0.00625 + 0.6875 = 1
Locus 2
Allele 1 = 8/32 = 0.2500
Allele 2 = 22/32 = 0.6875
Allele 3 = 2/32 = 0.0625
Locus 3
Allele 1 = 10/32 = 0.3125
Allele 2 = 22/32 = 0.6875
EXP
LOCUS 1
OBS
(OBS-EXP)2/EXP
1,1
(0.1250)2
0.0156
0.0000
0.0156
1,2
(0.125*0.125)*2
0.0313
0.0000
0.0313
1,3
(0.125*0.0625)*2
0.0157
0.0000
0.0157
1,4
(0.125*0.6875)*2
0.1718
0.2500
0.0356
2,2
(0.125)2
0.0156
0.0000
0.0156
2,3
(0.125*0.0625)*2
0.0156
0.0625
0.1410
2,4
(0.125*0.6875)*2
0.1719
0.1875
0.0014
3,3
(0.0625)2
0.0039
0.0000
0.0039
3,4
(0.0625*0.6875)*2
0.0859
0.0625
0.0064
4,4
(0.6875)2
0.4727
0.4375
0.0026
EXP
LOCUS 2
LOCUS 3
OBS
(OBS-EXP)2/EXP
1,1
(0.2500)2
0.0625
0.0625
0.0000
1,2
(0.2500*0.6875)*2
0.3438
0.3750
0.0028
1,3
(0.2500*0.0625)*2
0.0313
0.0000
0.0313
2,2
(0.6875)2
0.4727
0.4375
0.0026
2,3
(0.6875*0.0625)*2
0.0859
0.1250
0.0178
3,3
(0.0625)2
0.0038
0.0000
0.0038
1,1
(0.3125)2
0.0977
0.5625
2.2112
1,2
(0.3125*0.6875)*2
0.4297
0.2500
0.0752
2,2
(0.6875)2
0.4726
0.1875
0.1720
CHI-SQUARED TEST = 2.7858
P
0.999984
IMPORTANCE OF HW THEOREM
If the only force acting on the population is random
mating, allele frequencies remain unchanged and
genotypic frequencies are constant.
Mendelian genetics implies that genetic variability can
persist indefinitely, unless other evolutionary forces act to
remove it
Departures from HW Equilibrium
• Check Gene Diversity = Heterozygosity
– If high gene diversity = different genetic sources due
to high levels of migration
• Inbreeding - mating system “leaky” or breaks
down allowing mating between siblings
• Asexual reproduction = check for clones
– Risk of over emphasizing particular individuals
• Restricted dispersal = local differentiation leads
to non-random mating
F Stats
• FIS = (HS – HI)/(HE)
• FST = (HT – HS)/(HT)
• FIT = (HT – HI)/(HT)
Pop1
Pop2
Pop3
Sample
size
AA
20
20
20
10
5
0
Aa
4
10
8
aa
6
5
12
Pop1
Pop2
Pop3
Freq
p
(20 + 1/2*8)/40 = (10+1/2*20)/40 = (0+1/2*16)/40 =
0.60
.50
0.20
q
(12 + 1/2*8)/40 = (10+1/2*20)/40 = (24+1/2*16)/40 =
0.40
.50
0.80
Local Inbreeding Coefficient
• Calculate HOBS
– Pop1: 4/20 = 0.20
– Pop2: 10/20 = 0.50
– Pop3: 8/20 = 0.40
• Calculate HEXP (2pq)
– Pop1: 2*0.60*0.40 = 0.48
– Pop2: 2*0.50*0.50 = 0.50
– Pop3: 2*0.20*0.80 = 0.32
• Calculate F = (HEXP – HOBS)/ HEXP
• Pop1 = (0.48 – 0.20)/(0.48) = 0.583
• Pop2 = (0.50 – 0.50)/(0.50) = 0.000
• Pop3 = (0.32 – 0.40)/(0.32) = -0.250
Pop
Hs
HI
p
q
1
0.48
0.20
0.60
0.40
2
0.50
0.50
0.50
0.50
3
0.32
0.40
0.20
0.80
Mean 0.43
0.37
0.43
0.57
HT
FIS
FST
0.49
-0.14 0.12
FIT
0.24
Number of Migrants
• FST = (1/(4 Nem + 1))
– Ne = effective number of migrants
– Nem < Nm
Forest Diseases
• Chestnut blight =
Cryphonectria parasitica
– Native to Japan & China
• Blight on chestnut (Castanea
spp.)
– Castanea dentata extremely
susceptible
• Introduced in NA in early
1900’s (not deliberate) from
Japan
• Second introduction =
deliberate introduction of the
fungus from China – is this
the same sp.?
Cryphonectria parasitica
• Using genetic similarities
– Identified probable source population for US introduction as
Japan rather than China
– China & Japan are not closely related
• Longer history of independent evolution
– Two clonal populations = no sexual reproduction
• Likely founded by clones
– Deviations from HW equilibrium
• Unrelated genotypes in populations suggests restricted migration
• Genetic drift main force in evolution