Module 2.

Genetic variation, adaptation and conservation

L2.1 Introduction to
population genetics

Tongli Wang
Questions for the last lecture
• What are considered as genetic modifications?
• What are the three kinds of GMs?
• What are the three major methods for GM?
• What is the mechanism used in arctic apple to
prevent browning?
• Was the CRISPR/Cas system first discovered in a
prokaryote or eukaryote?
• Is genome editing always safe?
• What are the advantages of genome editing over
traditional GM?
GM in crops – methods
• Gene guns or a biolistic particle
delivery system "shoot" target genes
into plant cells, and some of them
penetrate cell walls and membranes.
• It is the most common method.
• applied successfully for many cultivated
crops, especially monocots like wheat or
maize

www.emaze.com
Module 1 test
• 50 multiple-choice and multiple-answer questions
• Questions are different among students
• No help from each other!
• To be completed in 38 minutes (0.75min x 50)
• To limit the time for finding answers from notes, slides or online
• One question will be available each time, and no multiple
attempts are allowed.
• To prevent from saving time for difficult questions.
• Lockdown Browser is also applied.
• If you miss the test, a makeup test is possible
• 10% of your grade will be deducted
Learning objectives
• To understand the concepts of
• Genetic diversity
• Allele and genotype frequencies in a population
• Describe the Hardy-Weinberg principle
• To understand the effects of the evolutionary forces
on genetic diversity among and within populations
Outline
• Definitions of genetic diversity and population genetics
• Genotype and allele frequencies
• Hardy-Weinberg principle
• Evolutionary forces
What is genetic diversity?
• Genetic diversity is the genetic variation within a
species
• Eye colors: dark, blue, green, …
• Tree crown shape: narrow and wide
• Biodiversity?
• Biodiversity is a general term refers to the variety and
variability of life on Earth. It defines:
• Genetic diversity (within species)
• Species diversity
• Ecological diversity
• Genetic diversity is the basis of
• genetic evolution/adaptation,
• genetic improvement,
• genetic conservation
• Genetic diversity is an important component of
population genetics
What is population genetics?
• Population？
• Population - A population, in genetic Population 1 Population 2

terms, is a randomly breeding group of

individuals that is largely isolated from
others
• Population genetics is the study of
genetic variation within and among
populations and its response to
evolutionary forces over space and
time
• It is a branch of genetics
Why population genetics?

• Individuals exist in communities

(populations).
• Genotypes of individuals are largely
determined by the gene pool of the
population
• Genetic diversity is defined at the
population level,
• Either within or among populations
Outline
• Definitions of genetic diversity and population genetics
• Genotype and allele frequencies
• Hardy-Weinberg principle
• Evolutionary forces
Genotype frequencies
• The proportion of each genotype in a population =

𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝑤𝑖𝑡ℎ 𝑒𝑎𝑐ℎ 𝑔𝑒𝑛𝑜𝑡𝑦𝑝𝑒

𝑡𝑜𝑡𝑎𝑙 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝑠𝑎𝑚𝑝𝑙𝑒𝑑

• Their genotype frequencies:

• f(BB) = 1/4 = 0.25
• f(Bb) = 2/4 = 0.50
• f(bb) = 1/4 = 0.25
• The sum of the genotype frequencies of a population:
• f(BB) + f(Bb) + f(bb) == 1

12
Genotype frequencies
• Example…

Genotype n N F
AA 20 30 = 20 / 30
Aa 5 30 = 5 / 30
aa 5 30 = 5 / 30

N=30

13
Allele frequencies
• The proportion of an allele at a particular locus (of
a gene) in a population for a diploid organism =

𝑐𝑜𝑢𝑛𝑡 𝑜𝑓 𝑎 𝑠𝑝𝑒𝑐𝑖𝑓𝑖𝑐 𝑎𝑙𝑙𝑒𝑙𝑒

2 ∗ 𝑡𝑜𝑡𝑎𝑙 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝑠𝑎𝑚𝑝𝑙𝑒𝑑

• Allele frequencies:
• f(B) = 4/8 = 0.5
• f(b) = 4/8 = 0.5 No. of B = 4
No. of b = 4
• The sum of the allele frequencies of a population:
• f(B) + f(b) == 1

14
Outline
• Definitions of genetic diversity and population genetics
• Genotype and allele frequencies
• Hardy-Weinberg principle
• Evolutionary forces
Hardy-Weinberg principle
Hardy‐Weinberg principle

• Allele and genotype frequencies in a population will remain

constant from generation to generation in the absence of
other evolutionary influences.
• When these conditions are met, the population is said to be in
Hardy-Weinberg equilibrium.
• If the allele frequencies (p and q) are given, genotype frequencies (p2,
2pq and q2) cab be calculated as:
p2 + 2pq + q2=1
• It is called Hardy‐Weinberg proportions or equilibrium
• When the allele frequencies are changed, such a equilibrium
will be reached after one-generation random mating
An example

For the case of one gene with two alleles

Allele Genotype
Type W w WW Ww ww
Freq. p q p2 2pq q2
P=0.5, q=0.5
Freq. value 0.5 + 0.5 = 1 0.25 + 2×0.5×0.5 + 0.25 = 1
Predict allele and genotype frequencies

Allele Genotype

Type K k KK Kk kk

Freq. p + q=1 p2 + 2pq + q2 = 1

q =0.8 P=0.2 P2=0.04 2Pq=0.32 q2=0.64

2Pq=0.32 is the proportion of the heterozygotes - heterozygosity

Exercise 1

• On Princess Royal Island, Kermode bear

population:
• The recessive Kermode white allele (k) is at the
frequency of q=0.3
• The frequency of dark allele K is at p=0.7
• What frequency of white bears would you
expect on Princess Royal Island?
• What is the expected proportion of
heterozygotes (He)?

White bear: 0.09;

He = 0.3*0.7*2=0.42
Exercise 2

• Albinism is caused by to a single recessive allele. It is

in low frequency, but it occurs in many species
including human. In US, for example, the incidence
is 1 in 17,000. Think about how to calculate the
frequency of albinism carrier based on
p2 + 2pq + q2=1

• p2 =
• q2 = 1/17,000, q= sqrt(1/17,000)
• p= 1 – q
• Answer: 2pq + q2 =1/70
Genotype frequencies change along with allele frequencies based on
p2 + 2pq + q2=1

• if p=0,
• q will be 1
• Genotype: aa
• No heterozygotes and no
genetic diversity
• if p=0.5,
• q will be 0.5
• Genotype: AA, Aa, aa
• Highest heterozygotes
• if p=1,
• q will be 0
• Genotype: AA
A
• No heterozygotes a
Measures (indicators) of genetic diversity
• Heterozygosity -- the proportion of
heterozygotes for a particular locus (Aa)
• p = q gives the highest Aa proportion
• Gene diversity -- the proportion of
polymorphic loci across the genome.
• Alleles per locus – number of alleles per locus

p2 + 2pq + q2=1
Assumptions for HW principle
• HW principle is based on an idealized
population with the following assumptions:
• organisms are diploid
• only sexual reproduction occurs Despite many assumptions
• generations are non overlapping are not realistic, the HW
• mating is random principle serves as an
• population size is infinitely large important baseline in
population genetics
• allele frequencies are equal in the sexes
• there is no migration, no mutation and no
selection
• How do you think about these assumptions?
Outline
• Definitions of genetic diversity and population genetics
• Genotype and allele frequencies
• Hardy-Weinberg principle
• Evolutionary forces
Evolutionary forces
• Mutation
• Selection
• Gene flow (migration)
• Genetic drift (random effect)
Mutation
• The source of all genetic variation
• One of the three ingredients for
evolution identified by Darwin
• Variation, heredity and selection
• New alleles arise when changes occur in
the DNA sequence of a gene
• Point mutations - changes in one or a few
nucleotides
• Insertion or deletion of a DNA section (indels)
Mutation
• New alleles arise when changes
occur in the DNA sequence of a
gene
• Point mutations - changes in one or
a few nucleotides
• Insertion or deletion of a DNA
section (indels)
• Chromosome 20 got an insertion
• Chromosome 4 got a deletion
Mutation
• Human mutation rate is 1.0 – 1.5 x 10-8 per bp per
generation: we transmit ~30 new DNA variants with
each gamete
(J. Roach et al., 2010, Science; D. Conrad et al., 2011, Nature Genetics)

• Not every mutation can result in genetic variation

within a species
• More complicated systems become less able to modify
certain parts of their genome.
• It may become difficult to change one for the better
without accidentally “breaking” something elsewhere.
• E.g., nearly all mammals – from giraffes to humans – have
just seven neck bones
Mutation
• Harmful/beneficial/neutral?
• Random
• Most of them are neutral or harmful
• Occasionally beneficial for particular environments
• Ones with small effects have better chance to remain and provide
variation
• Normally not occur in conservative sequences (why?)
• The ones not affecting fitness called selectively neutral mutations
 Mutation - example
Kermode bear – a single SNP at codon 298
replaces amino acid Tyr with Cys

Kermode
mutation!

Melanocortin 1 receptor
The white-phased
“Kermode” black bear

Ritland et al., Current Biology, Sept. 18, 2001

Selection
• Some individuals leave more offspring than others
due to selection
• Natural and artificial
• Climate, predator
• Selective breeding
• Mutation is random while selection is directional
• Natural selection imposes direction on evolution using
unidirectional mutations.
• Effects
• Reduce or eliminate less fit alleles
• Change allele and genotype frequencies
• Reduce genetic variation within populations, but
• Increase among-population variation if only some
populations are under selection
• May decrease among-population variation if all populations
are under selection
The peppered moth (Biston betularia)

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Evolution.html
 Selection - Example

10-15,000
years of
selection

Grey wolf
(Canis lupus)
 Most female elephants had ivories in Africa

Elephants with ivories

were killed for money
during civil war in
Gorongosa

After the strong selection,

female elephant lost ivories
Effects of Breeding

J. Woods photo

Progeny from tallest and shortest family in a Douglas-fir progeny trial

Break: 5 min
Gene flow (migration)
• The movement of genes between populations with
• Gametes (e.g., pollen)
• Individuals (e.g., seed)

• Effects
• Introduces new alleles (both adaptive and neutral)
• Change allele freq.
• Increase within-population genetic variation
• Reduce among population genetic variation
Gene flow – via pollen
From Jack Woods
Gene flow – via seed
Genetic drift
• The change in allele frequency in a
population from generation to generation
due to random sampling
A example of random sampling effect
A simulation of genetic drift

evolgen.wikispaces.com
Effects of genetic drift
• Reduce within population variation
• More alleles get fixed
• More recessive alleles to be expressed
• Increase among population variation
• The effects are more serious in small
populations
Genetic drift – Example
Florida panther
 Like
246K

* Siberian Tiger Population Is Drastically Low, Scientists

Report

The Huffington Post Joanna Zelman Posted: 03/ 7/11 09:01 AM

The effective population of the Amur tiger, also known as the Siberian tiger, is down to just 14 animals, scientists report in the
journal Mammalian Biology.

There are about 500 Amur tigers currently surviving in the wild, but the effective population accounts for genetic diversity. BBC
reports that the tiger has a very low diversity, which means that any disease or rare genetic disorders will probably be passed
on to the next generation. A more diverse genetic population would increase the tiger's chance of survival -- it would be able to
"cancel out" diseases and disorders with healthy genes.

The Amur tiger is the largest cat in the world. It once lived across China, Korea, and Russia, until the early 20th Century, when
human settlements, habitat loss, and poaching drove the cats to near extinction. By the 1940's, less than 30 individual tigers
survived in the wild -- this has now led to a "genetic bottleneck," destroying the Amur tiger gene pool. The results of this are
seen today in the tiger's lack of genetic diversity.

Not just Amur tigers are at risk of extinction. The World Wildlife Fund reports that climate change may be shrinking tigers'
habitat by 96%. Bengal tigers are shrinking in size due to stress over environmental changes. The WWF goes so far as to state
that if no action is taken, tigers may become extinct in the next 12 years.

This past November, a summit was held focused on saving tigers from extinction. The summit's biggest news? It was probably
that Leonardo DiCaprio survived a plane accident and still managed to attend. But also at the summit, countries agreed to
double the tiger population by 2022 and crack down on poaching and illegal trade of tiger parts. It is an uphill battle, but one
Recap of the learning objectives
• To understand the concepts of
• Genetic diversity
• Allele and genotype frequencies in a
population
• Describe the Hardy-Weinberg principle
• To understand the effects of the
evolutionary forces on genetic diversity
among and within populations