Population GeneticsPopulation Genetics

What is Population What is Population Genetics?Genetics?

The genetic study of the process The genetic study of the process of natural selection. of natural selection.

(The study of the change of allele (The study of the change of allele frequencies, genotype frequencies, genotype frequencies, and phenotype frequencies, and phenotype frequencies) frequencies) 

Natural selection causes changes in a Natural selection causes changes in a population if population if

(1) There is variation in fitness (1) There is variation in fitness (selection)(selection)

(2) That variation can be passed from (2) That variation can be passed from one one generation to the next (inheritance)generation to the next (inheritance)

Hence the “survival of the fittest” which Hence the “survival of the fittest” which leads to changes within populations.leads to changes within populations.

This is the central insight of Darwin.This is the central insight of Darwin.

What is Natural Selection?

Populations evolve genetically to Populations evolve genetically to survive. We know this happens. survive. We know this happens. Look at the following clip. Look at the following clip.

Newt video clipNewt video clip

http://www.pbs.org/wgbh/evolution/libhttp://www.pbs.org/wgbh/evolution/library/01/3/quicktime/l_013_07.htmlrary/01/3/quicktime/l_013_07.html

Hardy and Weinberg constructed a model of a population that does NOT change.

Who is Hardy and Weinberg?

No mutations – no new alleles enter No mutations – no new alleles enter population. population.

No gene flow (i.e. no migration of No gene flow (i.e. no migration of individuals into, or out of, the population). individuals into, or out of, the population).

Random mating (i.e. individuals must pair Random mating (i.e. individuals must pair by chance) by chance)

Population must be large so that no genetic Population must be large so that no genetic drift (random chance) can cause the allele drift (random chance) can cause the allele frequencies to change. frequencies to change.

No selection so certain alleles are not No selection so certain alleles are not selected for, or against. selected for, or against.

Five factors necessary to remain in equilibrium

Why Hardy Weinberg?Why Hardy Weinberg?

Due to the fact that this balance cannot Due to the fact that this balance cannot work, scientists can use it to detect work, scientists can use it to detect changes from generation to changes from generation to generation. generation.

Thus allowing a simplified method of Thus allowing a simplified method of determining that evolution is determining that evolution is occurring.occurring.

How? How?

If we mate two individuals that are If we mate two individuals that are heterozygous heterozygous

Girl Bb Boy Bb Girl Bb Boy Bb

25% 25% BBBB 50% 50% BbBb 25% 25% bbbb (not like their parents, express (not like their parents, express

the recessive phenotype). the recessive phenotype).

This is what Mendel found when he This is what Mendel found when he crossed monohybrids crossed monohybrids

But the frequency of two alleles in an But the frequency of two alleles in an entire populationentire population of organisms is of organisms is unlikely to be exactly the same. unlikely to be exactly the same.

The Hardy-Weinberg equation The Hardy-Weinberg equation allowed geneticists to do the same allowed geneticists to do the same thing Mendel did for individual thing Mendel did for individual families for entire populations. families for entire populations.

Allele FrequencyAllele Frequency

Let’s talk about p and qLet’s talk about p and q pp = the frequency of the dominant allele = the frequency of the dominant allele

qq = the frequency of the recessive allele = the frequency of the recessive allele

For a population in genetic equilibrium:For a population in genetic equilibrium:pp + + qq = 1.0 (The sum of the frequencies = 1.0 (The sum of the frequencies of both alleles is 100%.)of both alleles is 100%.)

For example: For example: Imagine a Imagine a

'swimming' 'swimming' pool of genes pool of genes as shown in as shown in Figure 1.Figure 1.

Count the Count the number of A and number of A and a inside the pool a inside the pool (not the ones on (not the ones on the outside of the outside of the pool). the pool).

A= 12 A= 12 a = 18 a = 18

Then take (A + a) or Then take (A + a) or

This shows the total population in This shows the total population in the pool is what? the pool is what?

12 +18 = 3012 +18 = 30

To determine the frequencies of To determine the frequencies of A A andand a.a.

Dominant Gene (A)/total population Dominant Gene (A)/total population to equal (p)to equal (p)

Step 1: Frequency of A or f(Step 1: Frequency of A or f(AA) = 12/30 ) = 12/30 = = 0.4 so 0.4 so

p= 0.4 p= 0.4 Recessive gene (a)/total population Recessive gene (a)/total population

to equal (q)to equal (q)

Step 2: Frequency of a or f(Step 2: Frequency of a or f(aa) = 18/30 ) = 18/30 = = 0.6 0.6

q = 0.6 q = 0.6

Then, take what you found for Then, take what you found for p + p + q= 1 q= 1

p= 0.4p= 0.4

q = 0.6 q = 0.6

Step 3: Example: Step 3: Example: 0.4(fA) + 0.6(fa) 0.4(fA) + 0.6(fa) = 1 = 1

Let’s try another one.Let’s try another one.

For example:For example:

The population of squirrels near The population of squirrels near Harvard University has a mix of brown Harvard University has a mix of brown and black squirrels. The students and black squirrels. The students surveyed the number of Brown and surveyed the number of Brown and black squirrels. There are 200 Brown black squirrels. There are 200 Brown squirrels and 400 black squirrels. squirrels and 400 black squirrels. Black is dominant over grey squirrels. Black is dominant over grey squirrels. Brown is recessive. Brown is recessive.

What is the number of black squirrels? What is the number of black squirrels?

A: 400A: 400

What is the number of Brown squirrels? What is the number of Brown squirrels?

A: 200A: 200

What is the total population?What is the total population?p + q = 1p + q = 1

A: 400 + 200 = 600A: 400 + 200 = 600

To determine the To determine the frequencies of frequencies of p p andand q. q.

Dominant Gene A/total population to equal Dominant Gene A/total population to equal (p)(p)

Step 1: Frequency of A or Step 1: Frequency of A or

f(f(AA) = 400/600 ) = 400/600

p=0.7 p=0.7

Recessive gene (a)/total population to equal Recessive gene (a)/total population to equal (q)(q)

Step 2: Frequency of a or Step 2: Frequency of a or

f(f(aa) = 200/600 = 0.6 ) = 200/600 = 0.6

q = 0.3 q = 0.3

Then, take what you found for Then, take what you found for p + p + q= 1 q= 1

Step 3: Step 3: 0.7(fA) + 0.3(fa) = 1 0.7(fA) + 0.3(fa) = 1

Work on problems #1 and 2 in Work on problems #1 and 2 in homework if done.homework if done.

Let’s take both examples one step Let’s take both examples one step further. further.

Genotype FrequencyGenotype Frequency The proportion of individuals in a The proportion of individuals in a

group with a particular genotype. group with a particular genotype. (Genotype can refer to one locus, (Genotype can refer to one locus, two loci, or the whole genome, two loci, or the whole genome, depending on the contextdepending on the context

Starting with the pool Starting with the pool exampleexample

If the Frequency of p= 0.4 If the Frequency of p= 0.4 And the Frequency of q = 0.6 And the Frequency of q = 0.6

Then determine the genotypic frequenciesThen determine the genotypic frequencies of AA, Aa and of AA, Aa and aa.aa. How?How?

Using the following equations: Using the following equations: pp2 + 22 + 2pq + qpq + q2 2 (Same as (Same as AA + Aa + aaAA + Aa + aa))

Step 1: Example: Step 1: Example: pp2 = (0.4 x 0.4) = .162 = (0.4 x 0.4) = .1622pq = 2(0.4 x 0.6) = .48pq = 2(0.4 x 0.6) = .48qq2 = (0.6 x 0.6) = .362 = (0.6 x 0.6) = .36

Which equals: Which equals: .16 + .48 + .36 = 1.16 + .48 + .36 = 1

16% of the population are AA 16% of the population are AA

48% are Aa48% are Aa

36% are aa36% are aa

Let’s try with our Let’s try with our squirrels. squirrels.

If the frequency of p=0.7 If the frequency of p=0.7 The frequency of q = 0.3 The frequency of q = 0.3

Then determine the genotypic frequenciesThen determine the genotypic frequencies of BB, of BB, Bb and bbBb and bb..

How?How?

Using the following equations: Using the following equations: pp2 + 22 + 2pq + qpq + q2 2 (Same as (Same as BB + Bb + BB + Bb +

bbbb))Step 1: Example: Step 1: Example: pp2 = (0.7 x 0.7) 2 = (0.7 x 0.7)

22pq = 2(0.7 x 0.3) pq = 2(0.7 x 0.3) qq2 = (0.3 x 0.3) 2 = (0.3 x 0.3)

Which equals: Which equals: .49 + .42 + .09 = 1.49 + .42 + .09 = 1

49% of the population are BB 49% of the population are BB

42% are Bb 42% are Bb

9% are bb9% are bb

SimplifySimplify

p p = frequency of the dominant = frequency of the dominant genegene

q q = frequency of the recessive = frequency of the recessive genegene

p2 p2 = frequency of the = frequency of the homozygous dominant traithomozygous dominant trait

q2 q2 = frequency of the recessive = frequency of the recessive traittrait

Now, suppose more 'swimmers' dive Now, suppose more 'swimmers' dive in as shown in Figure 2. What will the in as shown in Figure 2. What will the gene and genotypic frequencies be?gene and genotypic frequencies be?

Apply the same thing we did for the first example to the additional members of the population to the swimming pool. Counting the a’s that were outside the pool now entering the pool. What is the frequency of A or p?What is the frequency of a or q?What is the genotypic frequencies?

Solution: f(A) = 12/34 = .35 = 35 % f(a) = 21/34 = .65 = 65%

Genotypic frequencies:f(AA) = .12, f(Aa) = .46 and f (aa) = .41

Which equals: .12 + .46 + .41 = 1

Results:Results:AA: 12%AA: 12%Aa: 46%Aa: 46%Aa: 41%Aa: 41%

The results show that Hardy-Weinberg The results show that Hardy-Weinberg Equilibrium was not maintained. The Equilibrium was not maintained. The migration of swimmers (genes) into the migration of swimmers (genes) into the pool (population) resulted in a change pool (population) resulted in a change in the population's gene frequenciesin the population's gene frequencies

Try problems #1-3 in your Try problems #1-3 in your Homework packet.Homework packet.

Part IIPart II

Now that you know that Hardy-Now that you know that Hardy-Weinberg Equilibrium is not Weinberg Equilibrium is not naturally maintained. naturally maintained.

We can lead into the idea of natural We can lead into the idea of natural selection and a result in the selection and a result in the change in the population's gene change in the population's gene frequencies.frequencies.

Natural Selection is Natural Selection is due to Mutationsdue to Mutations

How do Mutations happen?U.V. RaysRadiationchemicalsMistakes made during DNA replication (approximately 6 every time cells undergo mitosis)

What affects do What affects do mutations have on mutations have on organisms?organisms? Lethal – deadlyLethal – deadly Major: HOX genes cause rather unusual Major: HOX genes cause rather unusual

changes such as an extra limb, antennae, changes such as an extra limb, antennae, etc. etc.

Small Small None – same amino acid or in DNA not used None – same amino acid or in DNA not used Beneficial – leads to a positive change that Beneficial – leads to a positive change that

allows an organisms a better chance of allows an organisms a better chance of survival. survival.

Examples of Natural Examples of Natural SelectionSelection

A. Sickle Cell AnemiaA. Sickle Cell AnemiaProtects those individuals who are Protects those individuals who are

afflicted with this genetic afflicted with this genetic disease from Malaria. disease from Malaria.

B. Antibiotic Resistant B. Antibiotic Resistant BacteriaBacteria

Bacteria reproduce fast so they can produce several generations in a very few hours and therefore evolve in a relatively short time.

Most mutations lead to death but some surviveVideo on antibiotic resistance Part Ihttp://www.youtube.com/watch?v=2L82V6VPJkQ&feature=related

Part IIhttp://www.youtube.com/watch?v=D0_FTJnhzXA&feature=related

C. Peppered MothC. Peppered MothPrior to industrial revolution (1850),

most common phenotype was light colored

After industrial revolution, dark phenotype became more common

D. VirusesD. Viruses

Viruses also Viruses also mutate quickly mutate quickly just as Bacteria just as Bacteria do.do.

They cannot They cannot reproduce reproduce without a hostwithout a host

How do they Trick How do they Trick immune system?immune system?

Viruses mutate to survive the immune Viruses mutate to survive the immune system by changing or evolving to system by changing or evolving to strike againstrike again

Example: Avian fluExample: Avian flu

Let’s look at the life cycle of a virus….Let’s look at the life cycle of a virus….

1. Attachment 2. Penetration3. Un-Coating 4. Assembly5. Release

PBS clipPBS clip

Immunity to HIV?Immunity to HIV?

http://www.pbs.org/wgbh/evolution/http://www.pbs.org/wgbh/evolution/library/10/4/l_104_05.htmllibrary/10/4/l_104_05.html

Immune SystemImmune System

I. Lymph vesselsI. Lymph vessels Immune system pathwayImmune system pathway return water to bloodreturn water to blood Nodes = sites of immune system Nodes = sites of immune system

action, invaders destroyedaction, invaders destroyed

ImmunityImmunity The system that gives the body The system that gives the body

the ability to resist disease.the ability to resist disease.

I. Active - I. Active - the body produces its own the body produces its own antibodies to defend against a certain antibodies to defend against a certain antigen.   antigen.  

II. Passive - II. Passive - is only for a short period of about is only for a short period of about one month because a person is given the one month because a person is given the antibodies required to defend against the antibodies required to defend against the antigen.antigen.

First Line of DefenseFirst Line of Defense

SkinSkin MucusMucus HairHair Ear WaxEar Wax Tear DropsTear Drops Sweat Sweat Stomach AcidStomach Acid

Second Line of Second Line of DefenseDefense

Inflammatory Response – Inflammatory Response – response to response to tissue damage which increase tissue damage which increase white blood cell production and white blood cell production and feverfever

Third Line of DefenseThird Line of Defense

Specific ImmunitySpecific Immunity – – immunity to immunity to specific pathogens by recognizing, specific pathogens by recognizing, attacking, destroying, and then attacking, destroying, and then remembers each foreign substance remembers each foreign substance and pathogen that enters the body. and pathogen that enters the body.  It does this by making specialized  It does this by making specialized cells and antibodies that makes the cells and antibodies that makes the pathogens useless.pathogens useless.

How?How?

Attacks using WBC’s. Two types: Attacks using WBC’s. Two types: B Cells – produce antibodiesB Cells – produce antibodies T Cells – killer cellsT Cells – killer cells

Then produces Antibodies Then produces Antibodies Hold the pathogen so unable Hold the pathogen so unable

to infect other cells until T-to infect other cells until T-cell destroyscell destroys

VaccinationVaccination Give a piece of dead or Give a piece of dead or

weakened virus so body fights weakened virus so body fights off and forms antibodiesoff and forms antibodies