Measuring Genetic Variation in Natural Populations Historical Method: Examining protein variation...

Measuring Genetic Variation in Natural Populations

Historical Method: Examining protein variation via electrophoresis

Modern Method: DNA sequencing and typing

More than one allele at 30-50% of all loci in a population.Such loci are called polymorphic.

LDH-B cline in Fundulus

Most populations harbor considerable genetic diversity

Heterozygosity0.10 0.20 0.30

Heterozygosity has a couple of interpretations:

1) Average percentage of loci that are heterozygous per individual.

or2) Average percentage of individuals that are heterozygous per loci.

DNA Sequencing : How is it done?

Heat : Single strands separate

PrimerAnneals

Only use one primerDNA polymerase

All possible DNAfragments are synthesized

ATGCTAACGCCATTCGA

TTA

TAC

TACG

TACGA

TACGAT

2 kinds of nucleotides

(1) Regular Nucleotides

(2) Fluorescent (ACGT) terminating nucleotides

Double Stranded DNAATGCTAACGCCATTCGA

TACGATTGCGGTAAGCT

Laser

TACGAT

TACGA

TACG

TAC

TAT

(-) Cathode

(+) Anode

Gel Electrophoresis

SynthesizedDNA

TAC

ComputerInterprets

FluorescentCode

TTCTTCAGGGGAGGGGGTGGAANATAAAAACAAAAACCCTACAATGTATATTCATCGCCCATAATCGGCTACTTAGACA

Electropherogram

DNA Sequence DataFrom Automated Sequencer

Another Way to Isolate Genes : Polymerase Chain Reaction (PCR)

Heat Single Strands SeparateHeat

Double Stranded DNA

Heat Resistant DNAPolymerase makesnew strands

PrimersAnneal

PrimersAnneal

Two DNA fragmentsare produced

PCR

1 2 3

Cycles

4

Copies

2 4 8 16

etc

etc

DNA is Amplified

Anode (+)

Cathode (-)An Agarose Gel

DNA DNA DNA DNA DNA

BasePairs

1000

600

300

(75 x 2) + (24) / (102 x 2) = 85.3

75/102 + 1/2 (24/102) = 85.3

Counting alleles

or

Genotypic frequencies

Sequencing Studies Have Revealed Enormous Genetic Diversity

CFTR Locus

Population Genetics

Evolution depends upon mutation

to create new alleles.

Evolution occurs as a result of population

level changes in allele frequencies.

What evolutionary forces alter

allele frequencies?

How do allele frequencies changein a population from generationto generation?

Hardy-Weinberg Principle

(1) Allele frequencies in a population will not change, generation after generation.

(2) If allele frequencies are given by p and q, the genotype frequencies will be given by p2, 2pq, and q2.

When none of the evolutionary forces (selection, mutation, drift, migration, non-random mating) are operative:

Allele frequencies in the gene pool:

A: 12 / 20 = 0.6a: 8 / 20 = 0.4

Alleles Combine to Yield Genotypic Frequencies

Our mice grow-up and generate gametesfor next generations gene pool

Allele frequency across generations: A General Single Locus, 2 Allele Model

Freq A1 = pFreq A2 = q

One locus, 2 Allele Model

Genotype A1A1 A1A2 A2A2

Frequency of allele A1 = pFrequency of allele A2 = 1 - p = q

In a diploid organism, there are two alleles for each locus.Therefore there are three possible genotypes:

Given:

Then:Genotype A1A1 A1A2 A2A2

Frequency p2 2pq q2

A population that maintains such frequencies is said to be at Hardy-Weinberg Equilibrium

Hardy-Weinberg Principle

(1) Allele frequencies in a population will not change, generation after generation.

(2) If allele frequencies are given by p and q, the genotype frequencies will be given by p2, 2pq, and q2

When none of the evolutionary forces (selection, mutation, drift, migration, non-random mating) are operative:

Hardy-Weinberg Principle Depends Upon the Following Assumptions

1. There is no selection

2. There is no mutation

3. There is no migration

4. There are no chance events

5. Individuals choose their mates at random