Transcript What is Population Genetics?

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
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
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.
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
Armillaria gallica
“Humongous Fungus”
rhizomorphs
What is Population Genetics?
 About microevolution (evolution of species)
 The study of the change of allele frequencies,
genotype frequencies, and phenotype
frequencies
Goals of population genetics
• Natural selection (adaptation)
• Chance (random events)
• Mutations
• Climatic changes (population expansions and contractions)
•…
To provide an explanatory framework to describe the evolution
of species, organisms, and their genome, due to:
Assumes that:
• the same evolutionary forces acting within species
(populations) should enable us to explain the differences we see
between species
• evolution leads to change in gene frequencies within populations
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
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
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
Evolutionary principles: Factors causing
changes in genotype frequency
• 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.
The smaller the sample, the greater
the chance of deviation from an ideal
population.
Genetic drift at small population
sizes often occurs as a result of two
situations: the bottleneck effect or
the founder effect.
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”
Bottleneck Effect
• The bottleneck effect occurs when the numbers of
individuals in a larger population are drastically reduced
• By chance, some alleles may be overrepresented and
others underrepresented among the survivors
• Some alleles may be eliminated altogether
• Genetic drift will continue to impact the gene pool until
the population is large enough
Founder vs Bottleneck
Northern Elephant Seal:
Example of Bottleneck
Hunted down to 20 individuals in 1890’s
Population has recovered to over 30,000
No genetic diversity at 20 loci
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
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) Discrete generations (no overlap)
4) mating occurs at random
5) large population size (infinite)
6) No migration (closed population)
7) Mutations can be ignored
8) No selection on alleles
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
Pop 3
Pop 4
FST = 0.30
Pop 2
Pop 1
FST = 0.02
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
F Stats
Proportions of Variance
• FIS = (HS – HI)/(HS)
• FST = (HT – HS)/(HT)
• FIT = (HT – HI)/(HT)
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
Host islands within the California
Northern Channel
Islands create fine-scale genetic
structure in two sympatric
species of the symbiotic
ectomycorrhizal fungus
Rhizopogon
Rhizopogon occidentalis
Rhizopogon vulgaris
Rhizopogon sampling & study area
• Santa Rosa, Santa Cruz
– R. occidentalis
– R. vulgaris
• Overlapping ranges
– Sympatric
– Independent evolutionary
histories
Sampling
Bioassay – Mycorrhizal pine roots
Local Scale Population Structure
Rhizopogon occidentalis
FST = 0.26
N
5 km
T
B
Populations are similar
Grubisha LC, Bergemann SE, Bruns TD
Molecular Ecology in press.
FST = 0.24
FST
E
W
8-19 km
FST = 0.33
= 0.17
Populations are different
Local Scale Population Structure
Rhizopogon vulgaris
FST = 0.21
N
FST = 0.20
E
W
FST = 0.25
Populations are different
Grubisha LC, Bergemann SE, Bruns TD
Molecular Ecology in press