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64 Cards in this Set

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What is the idea of H-W Eq principle?

to provide a null model for behavior of genes in populations

What are the two fundamental conclusions of

H-W Eq Principle

1. the allele frequencies in a population will not change, generation after generation

2.if the allele frequencies in a population are given by p and q, the genotype frequencies will be given by p2, 2pq, and q2

Assumptions of H-W Eq

1. There is no selection All members contribute equally to gene pool

2. There is no mutation No new alleles are created

3. There is no migration All alleles stay in gene pool

4. There is an infinitely large population size No random events = no genetic drift

5. Panmixia Mates are chosen randomly

What happens if a population is in H-W equillibrium?

it will never evolve regardless of starting frequencies

what do explicit assumptions of H-W eq allow regarding the violations of them?

violations of those assumptions can be used to determine which forces are causing Hardy Weinberg disequilibrium ( = evolution)

Chi squared formula


Sum of ---------------------------------


example of selection violating assumption

1: (There is no selection)

drosophila in presence of alcohol

two alleles for alcohol metabolization in drosophila (one metabolizes it quicker than other).

Two populations of flies exposed to alcohol two controls without.

At each generation, flies sampled


-Control group appeared to be in H-W Eq because allele frequencies remained the same


-Group under selection pressure showed decline in Adh^S allele

Overdominance, hybrid vigor, heterozygote advantage

Heterozygotes have higher fitness than eitherhomozygote

Overdominance maintains genetic diversity

No allele will reach fixation

frequency dependent selection

*think about the left/right mouthed scale eaters

maintains genetic diversity


both homozygous pairs have have a higher fitness than the heterozygous pair.

Also confers genetic diversity because each genotype generally survives better mating with themselves

Cystic fibrosis

frequency is maintained by heterozygoteadvantage

Heterozygotes were partially resistant totyphoid fever infection

Cystic fibrosis maintained by mutation andoverdominance

equilibrium frequency vs mutation and selection


q = /sqrt(mu/s)


q = equilibrium frequency

migration equations


same as


so Delta(p) = m(p-pi)

Migration and potential effects considering one island model

Migration can cause allele frequencies to change

Migration is potent evolutionary force in smallpopulations

Gene flow homogenizes allele frequencies acrosspopulations

what is Fst?

FST reflects differences in allele frequenciesamong populations of the group

Runs from 0 to 1

Larger values representlarger differences in allelefrequencies

Genetic drift (the concept)

Because of the small population, by chance alleleswill not unite in same frequencies

Because Hardy-Weinberg is based onmathematical probabilities, it does not “work” forsmall populations

Can lead to random fixation of alleles

Smaller populations go to fixation faster

Founder effect

Small group of individuals that start a newpopulation

Allelic frequencies are, by chance, different fromsource population

By chance, not all alleles will be represented

Genetic bottleneck

Another phenomenon similar to the founder effect

Random events cause a population to crash to a verylow level

Many alleles are eliminated from the population

The remaining population has different allelic andgenotypic frequencies than the beginning

youtube video for founder effect vs bottleneck vs genetic drift


Sewall Wright and genetic drift

Sewall Wright demonstrated that theprobability of fixation for a particular allele isthe same as its original frequency

If the initial frequency of an allele is 0.8, there is80% it will drift to fixation

What does F_is measure?

the proportion of the variance in the subpopulationcontained in an individual

(Inbreeding coefficient)

how to calculate F_is

F_is=(H_s - H_i)/H_s

H_i=H_o which is the observed heterozygosity in a population

H_s=H_e which is the expected heterozygosity in a population (based on HWE)

What does F_st measure?

the level of differentiation among a set ofpopulations

"How similar are the allele frequencies among two different populations?"

calculating F_st

F_st = (H_t – H_s)/H_t

H_s in F_st is the Average Hs among all populations

ex. [(HS’ + HS”)/2]

H_t = Total expected heterozygosity among all populations you treatall samples from multiple populations as if they come from a singlepopulation

FST depends on population size

Actual population size and effective population sizeare only equal when:

Equal sex ratio

No sexual selection

Subpopulation size remains the same over time

calculating F_st

If the sex ratio is unequal:


Ne = -----------

Nm + Nf



calculating F_st

If there is sexual selection


Ne ≈ -------------

Vm + Vf + 4

Vm and Vf are variances in numbers ofoffspring produced by males and females

calculating F_st

If (when!) there is genetic drift:


Delta F_st = ------


Increase in FST due to drift over one generation

With Genetic Drift removing variation, begs question ofwhy so much variation present in natural populations?

• Two schools of thought

– Neutral theory

• Kimura

• Advantageous mutations are very rare and mostmutations are selectively neutral

• Rate of evolution equals neutral mutation rate

– Selectionist theory

• Advantageous mutations are more common

• Rate of substitution determined by natural selection onadvantageous mutations

Neutral theory of molecular evolution

Contends that:

• A small minority of mutations in DNAsequences are advantageous and arefixed by natural selection and althoughsome are disadvantageous and areeliminated by purifying (negative)selection…

• The great majority of mutations that arefixed are effectively neutral with respect tofitness, and are fixed by genetic drift

• It holds that MOST of the variation we see at the molecularlevel is neutral and has no adaptive role (i.e. no effect onfitness)

Neutral theory of molecular evolution

non synonymous vs synonymous mutations

When sequences evolve by drift andnegative (or purifying) selection,synonymous substitutions outnumbernonsynonymous substitutions.

When sequences evolve by drift and positive(or diversifying) selection, nonsynonymoussubstitutions outnumber synonymoussubstitutions.

Neutral theory as null hypothesis

The neutral theory specifies the rates andpatterns of sequence change that occur inthe absence of natural selection.

If changes occur that are significantlydifferent from the predictions made by theneutral theory, there may be evidence fornatural selection.

Neutral theory as null hypothesis


dN = non-synonymous substitution rate

dS = synonymous substitution rate

dN/dS < 1 when replacements are deleterious

dN/dS = 1 when replacements are neutral

dN/dS > 1 when replacements are advantageous

Are synonymous mutations exposed toselection?

Codon bias

Codon usage random versus nonrandom Often NONRANDOM

Bias is strongest in highly expressed genes


term meaning

random mating

assortative mating

Positive assortative mating

Negative assortative mating

assortive=nonrandom mating

Positive assortative mating

– Individuals choose mates similar to themselves

Negative assortative mating

– Disassortative mating

– Individuals choose mates different from themselves

assortative mating


homozygosity and heterozygosity

– Individuals mate with others like themselvesso that heterozygous offspring are notproduced as much

- Negative assortative mating increasesheterozygosity

Most common type of nonrandom mating


– Mating among genetic relatives

– Increases homozygosity at all loci

– Violates Conclusion 2 but not 1

• Inbreeding

– Most extreme form is self-fertilizing

• Selfing

– If all individuals self

– Frequency of heterozygotes ishalved every generation

• Coefficient of Inbreeding, F

– F ranges from –1 to 1

• F = -1 signifies 100% heterozygotes

• F = 0, the population is panmictic

• F > 0 means some kind of inbreeding

• F = 0.5, the population is selfing

• F = 1, entire population are homozygotes– Locus is fixed for one allele

– Computing F in real populations

H0 – H

– F = -----------


– H = frequency of heterozygotes (observed)

– H0 = expected frequency of heterozygotes = 2pq

– F increases more rapidly over generations withmore closely related mates

– r is coefficient of relatedness

• Inbreeding Depression

– Although inbreeding does not directly causeevolution, it is important because ofinbreeding depression

– Exposure of deleterious alleles ashomozygotes

– Loss of function mutations are usually hiddenas heterozygotes

– Increases frequency at which deleteriousalleles affect phenotypes

• Inbreeding Depression

– Many plants and animals have evolved mechanisms to avoid it

• Mate choice

• Self-incompatibility

• Dispersal

• Different phenologies of male and female organs


– Small populations cannot avoid it

• Endangered species

Conservation genetics

• Accumulation ofdeleterious recessivesleads to reduction inpopulation size

• Effectiveness of geneticdrift is increased

• Speed and proportion ofdeleterious mutationsgoing to fixation increases

• Population size decreasesmore

• Mutational Meltdown


Multiple genes often have effectson a single phenotypic character

linkage equilibrium

Loci are in linkage equilibrium if thefrequency of one allele does not affect thefrequency of the other

Linkage disequilibrium

•Loci can be physically associatedon the same chromosome

allele frequencyat one locus predicts allele frequencies atanother locus

– One locus can influence the evolution ofanother due to genetic linkage

Conditions for Linkage Equilibrium

– The frequency of B on chromosomescarrying A is equal to the frequency of B onchromosomes carrying a

– The frequency of any chromosomehaplotype can be calculated by multiplyingfrequencies of constituent alleles

Calculating linkage equilibrium

– The quantity D, the coefficient of linkagedisequilibrium, must be equal to zero

• D = gABxgab - gAbxgaB

g’s are frequencies of chromosomes

considering linkage equilibrium, when can H-W equations be used?

• If the population is in linkageequilibrium(d=0), Hardy-Weinberg equationscan be used for each locusindependently

• What creates linkage disequilibrium?

– Selection on multi-locus genotypes

– Genetic drift

– Population admixture

or multi-locus genotypes
How to eliminate linkagedisequilibrium
Have sex.

Meiosis, crossing over, outbreeding

Meiosis breaks up old genotypecombinations and creates new ones

Genetic recombination randomizesgenotypes of loci with respect to eachother

Study by Clegg
• Genetic Recombination

– Set up populations with only AB and abchromosomes at frequencies of 0.5

– D = 0.25

– Every generation sampled for the fourgenotypes and calculated rate of linkagedisequilibrium

– Linkage disequilibrium declined to almost zerowith sexual reproduction

Why does linkage disequilibrium matter?
• If two loci are in linkage disequilibrium, selection at onelocus changes allele frequencies at the other

• In practice the change in one locus due to linkagedisequilibrium could erroneously be interpreted as selectionon that locus

What causes linkage disequilibrium


CCR5-Δ32 allele linkage with GAAT and AFMB

Stephens measured linkage disequilibrium inCCR5-Δ32 with two loci nearby on samechromosomeGAAT and AFMB

Neutral alleles

GAAT and AFMB are nearly in linkageequilibriumCCR5-Δ32 in strong linkage disequilibrium withboth

where CCR5-Δ32 allele came from

It has been hypothesized that it protects againstthe bacterium Yersinia pestis, the pathogen thatcaused the Black Death or smallpox

Under second analysis, current frequency can beexplained by genetic drift

sexual vs asexual

all the offspring of aparthenogenetic female are female but theoffspring of a sexual female are a mixture ofdaughters and sons

an asexual female would producetwice as many grandchildren as a sexual female

But many species coexist in both sexual and asexual states

Sex must confer benefits to allow it topersist in spite of the strongreproductive advantage of asexuality.

Empirical test with flour beetles

Sexual strains could evolve in response toselection, asexual clones could not

– Elimination of multi-locus genotypes

– Reduction in linkage disequilibrium

John Maynard Smith’s null model of sexual reproduction

– Two assumptions:

• A female’s reproductive mode does not affect thenumber of offspring she can make

• A female’s reproductive mode does not affect theprobability that her offspring will survive

Muller's ratchet main conclusions

– In a stable environment, asexual females thatare well adapted would have offspring that arewell adapted

– Sexual females that are well adapted may ormay not produce well adapted offspringbecause of genetic recombination

– Could cause sexual extinction before the ratchetcatches up

Red Queen Hypothesis

postulates anevolutionary arms race between parasites andtheir hosts

• An asexual species would have gone extinct andlost the race

• A sexual species doesn’t win the race, but it canrun enough to stay where it is