Population genetics basic concepts

Population Genetics
Basic concepts

WHAT IS POPULATION GENETICS?
▪ About microevolution (evolution within species)
▪ The study of the change of allele frequencies,
genotype frequencies, and phenotype
frequencies

An important turning point for evolutionary theory
was the birth of population genetics, which
emphasizes the extensive genetic variation within
populations and recognizes the importance of
quantitative characters.
Advances in population genetics in the 1930s
allowed the perspectives of Mendelism and
Darwinism to be reconciled.
 This provided a genetic basis for variation and natural
selection.

WHAT IS POPULATION GENETICS?
 Analyzes the amount and distribution of genetic variation in populations and the
forces that control this variation.
 mathematically based principles for changes in genotypes through time—
individuals, populations, etc.
 examine mutation, migration, breeding system, among-population interactions,
stochastic forces and selection on allele frequencies
 developed to bridge gap between “genes” and “species evolution”-
microevolution
 “alleles” may be any kind of heritable mutation
Population genetics is a field of biology that studies the genetic composition of
biological populations, and the changes in genetic composition that result from the
operation of various factors, including natural selection.

How does genetic variation increase or decrease?
And what effect do fluctuations in genetic variation have on
populations over time?
When a population interbreeds, nonrandom mating can
sometimes occur because one organism chooses to mate
with another based on certain traits.
In this case, individuals in the population make specific
behavioral choices, and these choices shape the genetic
combinations that appear in successive generations.

Nonrandom mating can occur in two forms, with different
consequences. One form of nonrandom mating is inbreeding,
which occurs when individuals with similar genotypes are more
likely to mate with each other rather than with individuals with
different genotypes.
The second form of nonrandom mating is called outbreeding,
wherein there is an increased probability that individuals with a
particular genotype will mate with individuals of another
particular genotype. Whereas inbreeding can lead to a
reduction in genetic variation, outbreeding can lead to an
increase.

POPULATION GENETICS
 Species-a group of organisms of the same kind that have the ability
to interbreed to produce fertile offspring
 Population-a group of organisms of the same species located in the
same place and time
 A population can be defined by its gene pool (i.e., every allele of
every gene of every organism in the population)
 Alleles occur at certain frequencies (e.g., for a gene with 2 alleles, p
and q, p + q = 1.0)
 Variation exists in populations (e.g., height, weight, eye color, etc.,
and this variation is governed by particular alleles-genetic variation)

Terms to be foundered in mind to understand
population genetics
• Individual:
• Species:
• Sub species:
• Population:
• Subpopulation:
• Genetics
• Population genetics
• Law’s of Mandel and deviation
• Darwinism
• Natural selection
• Adaptation
• DNA and Mutation
• Random mating
• Selection
• Speciation

MICROEVOLUTION-CHANGES IN ALLELE
FREQUENCY OVER TIME; CAUSED BY:
Populations can be small and experience genetic drift
(chance events)/founder effect/population bottleneck
Non-random mating
Gene flow (individuals do leave or enter populations)
Natural selection-nature selects individuals in a
population that have “favorable” alleles which allow for
survival in a given environment (e.g., Peppered moth)
Mutations do occur

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.

 When Mendel’s research was rediscovered in the early
twentieth century, many geneticists believed that the laws
of inheritance conflicted with Darwin’s theory of natural
selection.
 Darwin emphasized quantitative characters, those that
vary along a continuum.
 These characters are influenced by multiple loci.
 Mendel and later geneticists investigated discrete
“either-or” traits.
THE MODERN EVOLUTIONARY SYNTHESIS INTEGRATED
DARWINIAN SELECTION AND MENDELIAN INHERITANCE
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Members of a population are far more likely to breed with
members of the same population than with members of
other populations.
 Individuals near the
populations center
are, on average,
more closely related
to one another than
to members of
other populations.
Fig. 23.2

 The modern synthesis emphasizes:
(1) the importance of populations as the units of evolution,
(2) the central role of natural selection as the most
important mechanism of evolution, and
(3) the idea of gradualism to explain how large changes
can evolve as an accumulation of small changes over long
periods of time.
 While many evolutionary biologists are now challenging
some of the assumptions of the modern synthesis, it shaped
most of our ideas about how populations evolve.

 A population is a localized group of individuals that belong to
the same species.
 One definition of a species (among others) is a group of
populations whose individuals have the potential to interbreed and
produce fertile offspring in a nature.
 Populations of a species may be isolated from each other, such
that they exchange genetic material rarely, or they may
intergrade with low densities in an intermediate region.
A POPULATION’S GENE POOL IS DEFINED
BY ITS ALLELE FREQUENCIES

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

In population genetics, the founder effect is the loss of genetic variation that
occurs when a new population is established by a very small number of individuals
from a larger population. It was first fully outlined by Ernst Mayr in 1942, using
existing theoretical work by those such as Sewall Wright. As a result of the loss of
genetic variation, the new population may be distinctively different,
both genotypically and phenotypically, from the parent population from which it is
derived. In extreme cases, the founder effect is thought to lead to
the speciation and subsequent evolution of new species.
In genetics, a founder mutation is a mutation that appears in the DNA of one or
more individuals which are founders of a distinct population. Founder mutations
initiate with changes that occur in the DNA and can be passed down to other
generations.

DETECTING GENETIC VARIATION
Single nucleotide polymorphisms
(SNPs)
Microsatellites (repeating sequences)
Haplotypes (and the Human Hap
Map)
Other detection methods possible

LEVELS OF ANALYSES
• Individual level
• 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

Population level
Variation
Within any population,
individuals differ from
one another in many
ways.

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
(operational taxonomic units)
 Nei’s
 Reynolds
 Jaccards
 Cavalli-Sforza
 Tree Algorithms – visualization of similarity
 UPGMA
 Neighbor Joining

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

Armillaria gallica
“Humongous Fungus”
rhizomorphs
https://phys.org/news/2018-11-humongous-fungus-years-armillaria-
gallica.html#:~:text=A%20giant%20individual%20of%20the,years%20ago%20by%20James%20B.&text=In%2019
92%2C%20Anderson%20and%20his,kilograms%20and%20covered%2015%20hectares.
In 1992, Anderson and his colleagues estimated that the honey mushroom, which is growing
in a forest on Michigan's Upper Peninsula, was 1,500 years old, weighed 100,000 kilograms
and covered 15 hectares. Using current research and analytic techniques, Anderson took
additional samples in between 2015 and 2017 and can say with confidence that the
mushroom is at least 2,500 years old, weighs 400,000 kilograms and covers about 70
hectares.

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”

The founder effect is the reduction in genetic variation that results when a small subset of a
large population is used to establish a new colony. The new population may be very different
from the original population, both in terms of its genotypes and phenotypes. In some cases, the
founder effect plays a role in the emergence of new species.

https://www.nature.com/scitable/knowledge/library/the-hardy-weinberg-principle-13235724/
Mendel’s Law of Segregation, in modern terms, states that a diploid individual carries
two individual copies of each autosomal gene (i.e., one copy on each member of a
pair of homologous chromosomes). Each gamete produced by a diploid individual
receives only one copy of each gene, which is chosen at random from the two copies
found in that individual. Under Mendel’s Law of Segregation, each of the two copies in
an individual has an equal chance of being included in a gamete, such that we
expect 50% of an individual’s gametes to contain one copy, and 50% to contain the
other copy

Even after many geneticists had accepted Mendel’s laws, confusion
lingered regarding the maintenance of genetic variation in natural
populations. Some opponents of the Mendelian view contended that
dominant traits should increase and recessive traits should decrease in
frequency, which is not what is observed in real populations. Hardy
(1908; Figure 2) refuted such arguments in a paper that, along with an
independently published paper by Weinberg (1908; Figure 3) laid the
foundation for the field of population genetics (Crow 1999; Edwards
2008).

The Hardy-Weinberg Theorem deals with Mendelian genetics in the context of
populations of diploid, sexually reproducing individuals. Given a set of
assumptions , this theorem states that:
1. allele frequencies in a population will not change from generation to
generation.
2. if the allele frequencies in a population with two alleles at a locus are p and q,
then the expected genotype frequencies are p2, 2pq, and q2. This frequency
distribution will not change from generation to generation once a population is
in Hardy-Weinberg equilibrium.

For example, if the frequency of allele A in the population is p and the frequency
of allele a in the population is q, then the frequency of genotype AA = p2, the
frequency of genotype Aa = 2pq, and the frequency of genotype aa = q2.
If there are only two alleles at a locus, then p + q , by mathematical necessity,
equals one. The Hardy-Weinberg genotype frequencies, p2 + 2pq + q2, represent
the binomial expansion of (p + q)2, and also sum to one (as must the frequencies
of all genotypes in any population, whether it is in Hardy-Weinberg equilibrium).

THE GENE POOL CONCEPT AND THE HARDY-
WEINBERG LAW
 Gene pool- the sum total of all alleles in the population
 Genotype frequencies and allele frequencies
 The Hardy-Weinberg Law provides an equation to
relate the genotype frequencies and allele
frequencies in a randomly mating population:
 p2 + 2pq + q2 = 1 for 2 alleles such as A and a
 If no forces act on a population in Hardy-Weinberg
equilibrium, proportion of genotypes will stay the same

39
HARDY–WEINBERG PRINCIPLE
 When gametes containing either of two alleles, A or a,
unite at random to form the next generation, the
genotype frequencies among the zygotes are given by
the ratio
p2 : 2pq : q2
this constitutes the Hardy–Weinberg (HW) Principle
p = frequency of a dominant allele A
q = frequency of a recessive allele a
p + q =1

HARDY-WEINBERG EQUILIBRIUM
p2 + 2pq + q2 = 1
where p, q are
probabilities of
allele frequencies

41
HARDY–WEINBERG PRINCIPLE IMPLICATIONS
 One important implication of the HW Principle is that allelic
frequencies will remain constant over time if the following
conditions are met:
 The population is sufficiently large
 Mating is random
 Allelic frequencies are the same in males and females
 Selection does not occur = all genotypes have equal in
viability and fertility
 Mutation and migration are absent

• 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).
Expected Genotype Frequencies

HARDY-WEINBERG PRINCIPLES
 populations, lacking external forces acting on them,
will achieve H-W equilibrium if:
 truly random mating
 infinitely large population size
 many wild species probably do NOT meet either
criterion, despite theoreticians’ claims

MATING IS OFTEN NOT RANDOM;
THREE COMMON MATING SYSTEMS
Assortive mating (positive and negative)
Isolation by distance (leads to subpopulations
and perhaps new species)
Inbreeding (increases homozygousity and can
result in a reduction in vigor and reproductive
success, i.e., inbreeding depression)

SOURCES OF GENETIC
VARIATION IN POPULATIONS
Mutations
Migration (gene flow)
Recombination (linkage disequilibrium)
Genetic drift (chance)-founder effect
& bottleneck

Two Forces Control the Fate of
Genetic Variation in Populations
• Genetic drift (chance)
• Natural Selection

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

50
EVOLUTION
1. Mutation = the origin of new genetic capabilities
in populations = the ultimate source of genetic
variation
2. Natural selection = the process of evolutionary
adaptation = genotypes best suited to survive
and reproduce in a particular environment give
rise to a disproportionate share of the offspring
3. Migration = the movement of organisms among
subpopulations
4. Random genetic drift = the random, undirected
changes in allele frequencies, especially in small
populations
Changing Allele Frequencies

What was the condition when a population start to grow ?

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.
 One of the major first tools for analyzing
population structure
Advantages:
Inexpensive
Easily Obtained
Disadvantages:
Coding regions = violate assumptions of
analytical techniques
Invariable in many fungi = inadequate for
looking at variation
 Microsatellites = repetitive sequences
in the DNA (e.g. AC)12
 Very popular for analyzing population
structure
 Forensic applications
Advantages:
Hypervariable
Genotyping
Population Structure
Disadvantages:
High cost of Development

HARDY - WEINBERG
 A population that is not changing genetically is said to be at
Hardy–Weinberg equilibrium
 The assumptions that underlie the Hardy–Weinberg equilibrium
are
 population is large
 mating is random
 There is no migration (no immigration or emigration)
 There is no mutation of the alleles
 natural selection is not acting on the population. (all genotypes have an
equal chance of surviving and reproducing)
 Sets up a reference point at equilibrium

HARDY-WEINBERG & EVOLUTION
 Biologists can determine whether an agent of evolution
is acting on a population by comparing the population’s
genotype frequencies with Hardy–Weinberg equilibrium
frequencies.
 If there is no change in frequencies, there is no evolution
 Conversely, if there have been changes in the
frequencies, then evolution has occurred.
 Evolution is change of allelic frequencies

HARDY - WEINBERG
 In a population at Hardy–Weinberg equilibrium, allele frequencies remain
the same from generation to generation, and genotype frequencies
remain in the proportions p2 + 2pq + q2 = 1.
 Two equations
 p + q = 1
 A + a = 1, where A and a equal gene percentages
 All dominant alleles plus all recessive alleles add up to all of the alleles for a particular
gene in a population
 Allele frequencies
 p2 + 2pq + q2 = 1
 AA + 2Aa + aa = 1
 For a particular gene, all homozygous dominant individuals plus all heterozygous
individuals plus all homozygous recess individuals add up to all of the individuals in the
population
 Genotype frequencies

EXAMPLES OF HARDY WEINBERG
A A A a a a
0.49 AA 0.42 Aa 0.09 aa
0.49 + 0.21 0.21 + 0.09
0.7A 0.3a
AA(p2) Aa(pq)
Aa(pq) aa(q2)
A
p a
q
A
p
a
q

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

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)
Hardy-Weinberg Theorem

• 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).
Expected Genotype Frequencies

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
ASSUMPTIONS for Hardy- Weinberg Principle to be
worked

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 OBS (OBS-EXP)2/EXP
LOCUS 1 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 OBS (OBS-EXP)2/EXP
LOCUS 2 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
LOCUS 3 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
AA Aa aa
p2 2pq q2
p = freq (A)
q = freq (a)

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
IMPORTANCE OF HW THEOREM

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

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.?

Population genetics basic concepts

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