Population Genetics (Learning Objectives)

• Define the terms population, species, allelic and genotypic frequencies, gene pool, and fixed allele, genetic drift, bottle-neck effect, founder effect.

• Explain the difference between microevolution and macroevolution.• Review how genotypic and allelic frequencies are calculated.

Given the appropriate information about a population you should be able to calculate the genotypic and allelic frequencies of homozygous dominant, recessive, or heterozygous individuals (following the example discussed in class).

• Visit this website to learn the factors that lead to changes in genotypic and allelic frequencies between generations: http://zoology.okstate.edu/zoo_lrc/biol1114/tutorials/Flash/life4e_15-6-OSU.swf

• What is the Hardy-Weinberg Equilibrium and what are its conditions.• What are the factors that lead to microevolution?• What is the source of new alleles within any population?

Definitions• Gene pool = The collection of all alleles in the

members of the population

• Population genetics = The study of the genetics of a population and how the allele frequencies vary with time

• Gene Flow = Movement of alleles between populations when people migrate and mate

Changes allelic frequencies in populations

Populations not individuals are the units of evolution

- If all members of a population are homozygous for the same allele, that allele is said to be fixed

Allele Frequencies

Allele frequency =# of particular allele

Total # of alleles in the population

Count both chromosomes of each individual Allele frequencies affect the frequencies of the three

genotypes

Evolution

Microevolution small changes due to changing allelic frequencies within a population from generation to generation

Macroevolution large changes in allelic frequencies over 100’s and 1000’s of generations leading to the formation of new species

What is the allelic frequency (of R and r) in this population?

Calculating the allelic frequencies from the genotypic frequencies

Genotypic frequencyRR= 320/500 = 0.64Rr = 160/500= 0.32rr = 20/500 = 0.04

What is the allelic frequency in a population of 500 flowers?

How many total alleles are there? 500 X 2 = 1000

Frequency of R allele in populationRR + Rr = 320 X 2 + 160= 640+160= 800

800/1000 = 0.8 =80%Frequency of r allele = 1- 0.8 = 0.2 =20%

or rr +Rr = 20 X 2+ 160= 200200/1000 = 0.2

- Meiosis and random fertilization do not change the allele and genotype frequencies between generations

- The shuffling of alleles that accompanies sexual reproduction does not alter the genetic makeup of the population

The Hardy-Weinberg theorem describes the gene pool of a non-evolving population

Hardy Weinberg animationhttp://zoology.okstate.edu/zoo_lrc/biol1114/t

utorials/Flash/life4e_15-6-OSU.swf

p + q = 1

p = allele frequency of one alleleq = allele frequency of a second allele

p2 + 2pq + q2 = 1

p2 and q2 Frequencies for each homozygote

2pq Frequency for heterozygotes

All of the allele frequencies together equals 1

All of the genotype frequencies together equals 1

Hardy-Weinberg Equation

Populations at Hardy-Weinberg equilibrium must satisfy five conditions.(1) Very large population size. In small populations,

chance fluctuations in the gene pool, genetic drift, can cause genotype frequencies to change over time.

(2) No migrations. Gene flow, the transfer of alleles due to the movement of individuals or gametes into or out of our target population can change the proportions of alleles.

(3) No net mutations. If one allele can mutate into another, the gene pool will be altered.

(4) Random mating. If individuals pick mates with certain genotypes, then the mixing of gametes will not be random and the Hardy-Weinberg equilibrium does not occur.

(5) No natural selection. If there is differential survival or mating success among genotypes, then the frequencies of alleles in the next variation will deviate from the frequencies predicted by the Hardy-Weinberg equation.

Evolution results when any of these five conditions are not met - when a population experiences deviations from the stability predicted by the Hardy-Weinberg theory.

Genetic Driftchanges allelic frequencies in populations

The bottleneck effect

The founder effect

Caused by four factors:1. Non-Random mating2. Genetic drift – due to sampling/ bottleneck &

founder effects, geographic & cultural separation

3. Migration- of fertile individuals4. Mutation- in germline cells transmitted in

gamete5. Natural selection- accumulates and maintains

favorable genotypes in a population

Microevolution

Frequency of a trait varies in different populations. Example: PKU an autosomal recessive trait

Table 14.1

Phenotype Frequencies

Calculation of % PKU carriers from screening

About 1 in 10,000 babies in US are born with PKU- The frequency of homozygous recessive individuals = q2 = 1

in 10,000 or 0.0001.- The frequency of the recessive allele (q) is the square root

of 0.0001 = 0.01.- The frequency of the dominant allele (p) is p = 1 - q or 1 -

0.01 = 0.99.The frequency of carriers (heterozygous individuals) is

2pq = 2 x 0.99 x 0.01 = 0.0198 or about 2%.About 2% of the U.S. population carries the PKU allele.

Figure 14.3

Source of the Hardy-Weinberg Equation

Figure 14.3

Solving a Problem

Figure 14.4

Solving a Problem

Figure 14.4

Figure 14.3

Calculating the Carrier Frequency of an Autosomal Recessive

Figure 14.5

Table 14.3

Calculating the Carrier Frequency of an Autosomal Recessive

Figure 14.3

Calculating the Carrier Frequency of an Autosomal Recessive

What is the probability that two unrelated Caucasians will have an affected child?

Probability that both are carriers =1/23 x 1/23 = 1/529

Probability that their child has CF = 1/4 Therefore, probability = 1/529 x 1/4 =

1/2,116

Calculating the Risk withX-linked Traits

• For females, the standard Hardy-Weinberg equation applies

p2 + 2pq + q2 = 1

• However, in males the allele frequency is the phenotypic frequency

p + q = 1

Allelic frequency determined from the incidence in new born males

Calculating the Risk withX-linked Traits

Figure 14.6 28

Calculating the Risk withX-linked Traits

Hardy-Weinberg Equilibrium

• Rare for protein-encoding genes that affect the phenotype

• Applies to portions of the genome that do not affect phenotype

• Includes repeated DNA segments– Not subject to natural selection

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DNA and Genomic Technological applications

• DNA Technology and its tools (DNA modification Enzymes and plasmids, DNA Gel Electrophoresis, PCR)

– DNA Finger Printing/Profiling, The FBI's Combined DNA Index System (CODIS)

– Production of recombinant proteins and transgenic organisms

• Gene Editing– Gene-specific replacement using homologous recombination– Gene specific cutting- CRISPR-Cas9

• Animal Reproductive cloning by nuclear transplantation and therapeutic production of organs and tissues

DNA technology to produce genetically modified organisms and recombinant proteins

Genetic and Genomic Technologies

• Genetic Variability and DNA Technologies– Single nucleotide polymorphisms (SNPs)– Short Tandem Repeats (STRs)

– Biotechnology tools for DNA Profiling or fingerprinting

• Restriction Fragment length polymorphism– Restriction enzymes– DNA Gel Electrophoresis

• Polymerase Chain Reaction (PCR)

DNA Repeats

• Short repeated segments are distributed all over the genome

• Repeat numbers can be considered alleles and used to classify individuals

• Types– Variable number of tandem repeats

(VNTRs)– Short tandem repeats (STRs)

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DNA Repeats

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DNA Profiling

• Developed in the 1980s by British geneticist Sir Alec Jeffreys

• Also called DNA fingerprinting• Identifies individuals• Used in forensics, agriculture, paternity

testing, and historical investigations• http://highered.mheducation.com/sites/dl/free/007283512

5/126997/animation40.html• http://science.howstuffworks.com/dna-profiling.htm

DNA Profiling Techniques

• RFLPs- Restriction Fragment length polymorphisms (limited utility)

• PCR- Amplification of select genomic regions spanning stretches of STRs

Box Figure 14.1 38

Practical Applications of DNAFingerprinting

• Paternity and Maternity• Personal Identification/

Criminal Identification and Forensics

Practical Applications of DNAFingerprinting

“Forensic Biotechnology Whodunit?” by Jenny Shaw, Vanessa Petty, Theresa Brown, and Sarah Mathiason

Practical Applications of DNAFingerprinting

DNA Profiling• Technique that detects differences in repeat

copy number (current)• Calculates the probability that certain

combinations can occur in two sources of DNA by chance

• DNA evidence is more often valuable in excluding a suspect– Should be considered along with other types

of evidence

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Comparing DNA Repeats

Figure 14.7

Comparing DNA Repeats

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• DNA can be obtained from any cell with a nucleus

• STRs are used when DNA is scarce

• If DNA is extremely damaged, mitochondrial DNA (mtDNA) is often used

• For forensics, the FBI developed the Combined DNA Index System (CODIS)

• Uses 13 STRs

DNA Sources

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Probability that any two individuals have same thirteen markers is 1 in 250 trillionDNA Profiling updated

CODIS

Figure 14.10

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• Power of DNA profiling is greatly expanded by tracking repeats in different chromosomes

• Number of copies of a repeat are assigned probabilities based on their observed frequency in a population

• Product rule is then used to calculate probability of a certain repeat combination

Population Statistics Used to Interpret DNA Profiles

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47Figure 14.12

• Recent examples of large-scale disasters

• World Trade Center attack (2001)

• Indian Ocean Tsunami (2004)

• Hurricane Katrina (2005)

Using DNA Profiling to Identify Victims

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Challenges to DNA Profiling

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• Today’s population genetics presents a powerful way to identify individuals

• Our genomes can vary in more ways than there are people in the world

• DNA profiling introduces privacy issues

• Example: DNA dragnets

Genetic Privacy

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Gene Editing– Gene-specific replacement using homologous

recombination

– Gene specific cutting- CRISPR-Cas9

Gene Disruption by Homologous Recombination/Recombineering

λ Red recombinase*

lacZ gene

*Steps:

1. Design primers with lacZlinkers

2. PCR amplify D.S. DNA of kanR with lacZ linkers from plasmid pKD4

3. Induce expression of λ Red in MG1655/pKD46

4. Electroporate MG1655/pKD46 cells with D.S. DNA lacZ-FRT-kanR-FRT-lacZ

5. Select for successful disruption by growing cells on LB/ Kanamycin IPTG/X-gal plates

lacZlinkers

lacZ geneDistance between primers

Color of colonies (IPTG/X-gal)

Number of recombinant/ electroporation

Uninterrupted 1108 BlueKanR-interrupted 1500 white 6

1108 bp

kanR cassette

1500 bp

Successful λ-Red-Stimulated Recombineering

lacZ gene

• Scarless Cas9-assisted Recombineering (λ-Red-stimulated)

• Choice and design of Cas-9 target sequence (lacZ gene)

• Plasmids used• Circular Polymerase

Extension Cloning (CPEC) of the lacZ target to make pKDsgRNA-lacZplasmid

Cas-9- Directed Gene Replacement Steps

gRNA Scaffold

Cas-9- Directed Gene Replacement Concepts

Successful Cas-9-targeted cutting of lacZ gene with designed guides in living cells

No expression of Cas-9 (-aTC)

Expression of Cas-9 (+aTC)

lacZ F4 lacZ N20

Animal Cloning

• ReproductiveOrganism

• TherapeuticTissues & Organs

Different types of cell in an organism have the same DNA but they transcribe different genes

Nuclei do change as cells differentiate:DNA sequences do not changeChromatin structure does

Cloning of a Mammal

In 1997 by Ian Wilmut

http://learn.genetics.utah.edu/units/cloning/whatiscloning/

Other mammals have been cloned

The possibility of cloning humans raises unprecedented ethical issues.

Stem Cell ResearchStem cells

– unspecialized cells, continually reproduce can differentiate into specialized cell types.

– can differentiate into multiple cell types

Two types of stem cells1. Adult stem cells & Cord Blood stem cells2. Embryonic stem cells

Under the right conditions, cultured stem cells derived from either source can differentiate into specialized cells.

Omnipotent

Adult stem cells• Bone marrow stem cells- different kinds of

blood cells

Embryonic stem cells• immortal

Somatic Cell reprogramming (2007) Induced Pluripotent Stem Cells (iPSC)

Oct 20 2009, 11:21 AM ESTInduced Pluripotent Stem Cell Technology Used to Generate Hepatocytes from Skin CellsGEN News Highlightshttp://learn.genetics.utah.edu/content/tech/stemcells/ips/

Induced Pluripotent Stem Cells (iPSC)