Population Genetics PBG 430 - PowerPoint Presentation

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Population Genetics

PBG 430

What is Population Genetics?

Describes allele and genotype frequencies in populations over space and time

Models evolutionary forces (survival, mutation, migration, etc.)

Models are generally limited to one or a few loci

Foundational concepts for quantitative genetics and genomics tools

Populations, Gene Pools and Gene frequenciesPopulation:

a group of individuals that interbreed freely and randomly and normally are members of the same species

“Gene pool”:

sum of alleles of all genes in the population

Gene frequency:

ratio of a particular genotype or allele to the sum of all genotypes/alleles of that gene in a population

Populations can undergo changes in:

Size

Composition

Behavior

Population genetics – descriptive statisticsExample:

Population



500 individuals

Two alleles



A = orange petals; a = white petals

“A” is completely dominant over “a”SSR marker  Co-dominant marker for colorin 500 individualsResulting Genotypes  AA = 320; Aa = 160; aa = 20Descriptive statistics permits defining the genetic structure of a population based on:Genotype frequencies (i.e. Aa, Aa, aa)Allele frequencies (i.e. A and a)

Plant

California Poppy

(

Eschscholzia californica

)

Formula

2n = 2x = 12

Genome size

502 Mb

Approximate number of genes

Unknown

Genome sequence

Sequenced! See supplementary materials

Pollination biology

Obligate

out-crossing (insects)

Center of origin

Unknown

Calculating genotype and allele frequencies

Genotype frequencies

on 500 individuals

Assuming:

P

AA

: Genotype frequency AA

PAa: Genotype frequency AaPaa: Genotype frequency aaOther statisticsNumber of alleles = 2H0 = observed heterozygosity = 0.32

Genotype

AA

Aa

aa

Total

PhenotypeOrangeOrangeWhite# of Individuals32016020500Code:PAAPAaPaaPAA+PAa+PaaGenotype Frequency0.640.320.041.0

Allele frequencies in the population (1,000 alleles)Assuming:p: Frequency of “A” alleleq: Frequency of “a” allele

Allele

A

a

Total

Derived from:

AA + Aa

aa + Aa

# of alleles in pool

(320*2) + 160

(20*2) + 160

800

200

1000

Allele code:

p

q

p + q

Allele Frequency

0.8

0.2

1.0

Why calculate genotype and allele frequencies?

Stability of gene pool (stable or changing)

Estimate rate of change

Predict trends for future generations

Important in conservation and breeding programs

Is there any rule that defines how genes in a population behave from one generation to next generation?

Yes, the Hardy-Weinberg Theorem!

The Hardy-Weinberg Theorem (HWT)HWT states that:

Allele and genotype frequencies remain constant from one generation to the next

Genotype frequencies in progeny can be predicted from allele frequencies of the parents

Assuming a diploid and sexually reproducing individuals in a population carrying two alleles

p

and

q

, the expected genotype frequencies of the progeny are p2, 2pq, and q2Equilibrium attained after one generation of random matingHardy-Weinberg theory applies under the following population assumptions:No natural selection, mutation, migration Large, random-mating populationNormal segregationEqual gene frequencies in males and femalesNote that assumptions only need to be true for the locus in question

Hardy-Weinberg Equation

Recall probabilities from the poppy example:

p

: Frequency of A = 0.8

q

: Frequency of a = 0.2

What can we say about genotypic frequencies in the next generation?

Rule of multiplication probabilitiesFrom here, we can derive a general formula describing allele and genotype frequencies in a population Hardy-Weinberg equation  p2 + 2pq + q2 = 1Allele frequencies can be calculated if genotype frequencies are knownCan be extended for multiple alleles(p + q + k)2 = 1If allele frequencies do not change over time, population is in a “Hardy-Weinberg equilibrium”

p

2

=0.64

pq

=0.16

q2=0.04pq=0.16 Ap = 0.8PollenEgg aq = 0.2 aq = 0.2

Ap = 0.8Genotype

AA

Aa

aa

Total

Code

p

2

2pq

q

2

Genotype Frequency

0.64

0.32

0.04

1.0

Allele

A

a

Total

Code

p

q

p + q

Allele Frequency

0.8

0.2

1.0

Forces driving changesFactors affecting allele and genotype frequencies:

Mutation

Any change in the DNA

This mutation must be transmitted to the progeny

A mutation will increase in the population if the n

ew

allele is better fit to current conditions, allowing individuals carrying this allele to survive and produce abundant offspring

Natural SelectionIn HWE, all individuals must have equal chances to produce offspringHowever, some variants can produce more progeny than othersThe differences in number of individuals produced in the next generation is called natural selection

Forces driving changes – Cont. Factors affecting allele and genotype frequencies

Genetic drift

By chance

Stronger effects visualized in:

Small populations

Extreme reduction in population size

(bottleneck effect) due to

natural disasters, floods, severe winters, etc.Gene flowExchange of genetic material between isolated populationsThe population may gain or lose allelesSource of gene flowExchange of gametes by wind or insectsNew individuals in the population

More forces driving changesFactors affecting allele and genotype frequencies Mating structure

Chances of mating between individuals are higher between neighbors

Preferential crossing with neighbors



“inbreeding”

Self-pollinated species are the most

severe cases of inbreeding, where

female and male reproductive organs are in the same place Inbreeding leads to decreased genetic variation and increased homozygosity

Inbreeding

Inbreeding:

Mating of individuals that are closely related resulting in increased homozygosity

Causes of inbreeding

Small population size

Mating between relatives

or

self-pollinationMay lead to inbreeding depressionDeleterious recessive allelesOutcrossing species (suffer more)AaA Aa aa

Genotype

Allele

Aa

A

a

Initial Frequency100%50%50%Frequency after selfing 50%50%50%Question: How does self-pollination affect allele and genotype frequencies in a HWE population?Answer: Selfing causes differences in genotype frequencies but not in allele frequencies. Changes are due to a reduction of heterozygous individuals.

By now you should be able to…Calculate genotype and allele frequencies for a given population.

What type of information can you get from collecting these data over time for a specific population?

Describe the Hardy-Weinberg Theorem and its assumptions.

Discuss how these factors drive populations away from the Hardy-Weinberg equilibrium:

Mutations

Natural selection

Genetic drift

Genetic flowMating structureDescribe inbreeding depression. What is the main explanation for this phenomenon? Why is this phenomenon often observed for outcrossing species and assumed not to be a problem in self-pollinating species?