Evo Bio Test 2 Review

Front 1

What is the idea of H-W Eq principle?

Back 1

to provide a null model for behavior of genes in populations

Front 2

What are the two fundamental conclusions of

H-W Eq Principle

Back 2

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

Front 3

Assumptions of H-W Eq

Back 3

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

Front 4

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

Back 4

it will never evolve regardless of starting frequencies

Front 5

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

Back 5

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

Front 6

Chi squared formula

Back 6

(Observed-Expected)^2

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

Expected

Front 7

example of selection violating assumption

1: (There is no selection)

drosophila in presence of alcohol

Back 7

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

Conclusion:

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

BUT

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

Front 8

Overdominance, hybrid vigor, heterozygote advantage

Back 8

Heterozygotes have higher fitness than eitherhomozygote

Overdominance maintains genetic diversity

No allele will reach fixation

Front 9

frequency dependent selection

Back 9

*think about the left/right mouthed scale eaters

maintains genetic diversity

Front 10

underdominance

Back 10

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

Front 11

Cystic fibrosis

Back 11

frequency is maintained by heterozygoteadvantage

Heterozygotes were partially resistant totyphoid fever infection

Cystic fibrosis maintained by mutation andoverdominance

Front 12

equilibrium frequency vs mutation and selection

Back 12

^

q = /sqrt(mu/s)

^

q = equilibrium frequency

Front 13

migration equations

Back 13

p'r=pr(1-m)+ps+m

same as

p'i=pi(1-m)+p+m

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

Front 14

Migration and potential effects considering one island model

Back 14

Migration can cause allele frequencies to change

Migration is potent evolutionary force in smallpopulations

Gene flow homogenizes allele frequencies acrosspopulations

Front 15

what is Fst?

Back 15

FST reflects differences in allele frequenciesamong populations of the group

Runs from 0 to 1

Larger values representlarger differences in allelefrequencies

Front 16

Genetic drift (the concept)

Back 16

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

Front 17

Founder effect

Back 17

Small group of individuals that start a newpopulation

Allelic frequencies are, by chance, different fromsource population

By chance, not all alleles will be represented

Front 18

Genetic bottleneck

Back 18

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

Front 19

youtube video for founder effect vs bottleneck vs genetic drift

Back 19

https://www.youtube.com/watch?v=Q6JEA2olNts

Front 20

Sewall Wright and genetic drift

Back 20

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

Front 21

What does F_is measure?

Back 21

the proportion of the variance in the subpopulationcontained in an individual

(Inbreeding coefficient)

Front 22

how to calculate F_is

Back 22

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)

Front 23

What does F_st measure?

Back 23

the level of differentiation among a set ofpopulations

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

Front 24

calculating F_st

Back 24

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

Front 25

FST depends on population size

Actual population size and effective population sizeare only equal when:

Back 25

Equal sex ratio

No sexual selection

Subpopulation size remains the same over time

Front 26

calculating F_st

If the sex ratio is unequal:

Back 26

4NmNf

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

Nm + Nf

Nm=#males

Nf=#females

Front 27

calculating F_st

If there is sexual selection

Back 27

8Na

Ne ≈ -------------

Vm + Vf + 4

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

Front 28

calculating F_st

If (when!) there is genetic drift:

Back 28

1

Delta F_st = ------

2Ne

Increase in FST due to drift over one generation

Front 29

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

Back 29

• 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

Front 30

Neutral theory of molecular evolution

Back 30

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)

Front 31

Neutral theory of molecular evolution

non synonymous vs synonymous mutations

Back 31

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.

Front 32

Neutral theory as null hypothesis

Back 32

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.

Front 33

Neutral theory as null hypothesis

calculations

Back 33

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

Front 34

Are synonymous mutations exposed toselection?

Back 34

Codon bias

Codon usage random versus nonrandom Often NONRANDOM

Bias is strongest in highly expressed genes

Front 35

Panmixia

Back 35

term meaning

random mating

Front 36

assortative mating

Positive assortative mating

Negative assortative mating

Back 36

assortive=nonrandom mating

Positive assortative mating

– Individuals choose mates similar to themselves

Negative assortative mating

– Disassortative mating

– Individuals choose mates different from themselves

Front 37

assortative mating

vs

homozygosity and heterozygosity

Back 37

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

- Negative assortative mating increasesheterozygosity

Front 38

Most common type of nonrandom mating

Back 38

inbreeding

– Mating among genetic relatives

– Increases homozygosity at all loci

– Violates Conclusion 2 but not 1

Front 39

• Inbreeding

Back 39

– Most extreme form is self-fertilizing

• Selfing

Front 40

– If all individuals self

Back 40

– Frequency of heterozygotes ishalved every generation

Front 41

• Coefficient of Inbreeding, F

Back 41

– 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

Front 42

– Computing F in real populations

Back 42

H0 – H

– F = -----------

H0

– 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

Front 43

• Inbreeding Depression

Back 43

– 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

Front 44

• Inbreeding Depression

– Many plants and animals have evolved mechanisms to avoid it

Back 44

• Mate choice

• Self-incompatibility

• Dispersal

• Different phenologies of male and female organs

BUT

– Small populations cannot avoid it

• Endangered species

Front 45

Conservation genetics

Back 45

• 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

Front 46

epistasis

Back 46

Multiple genes often have effectson a single phenotypic character

Front 47

linkage equilibrium

Back 47

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

Front 48

Linkage disequilibrium

Back 48

•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

Front 49

Conditions for Linkage Equilibrium

Back 49

– 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

Front 50

Calculating linkage equilibrium

Back 50

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

• D = gABxgab - gAbxgaB

g’s are frequencies of chromosomes

Front 51

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

Back 51

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

Front 52

• What creates linkage disequilibrium?

Back 52

– Selection on multi-locus genotypes

– Genetic drift

– Population admixture

Front 53

Haplotypes

Back 53

or multi-locus genotypes

Front 54

How to eliminate linkagedisequilibrium

Back 54

Have sex.

Meiosis, crossing over, outbreeding

Meiosis breaks up old genotypecombinations and creates new ones

Genetic recombination randomizesgenotypes of loci with respect to eachother

Front 55

Study by Clegg

Back 55

• 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

Front 56

Why does linkage disequilibrium matter?

Back 56

• 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

Front 57

What causes linkage disequilibrium

Back 57

Inbreeding/selfing

Front 58

CCR5-Δ32 allele linkage with GAAT and AFMB

Back 58

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

Front 59

where CCR5-Δ32 allele came from

Back 59

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

Front 60

sexual vs asexual

Back 60

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.

Front 61

Empirical test with flour beetles

Back 61

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

– Elimination of multi-locus genotypes

– Reduction in linkage disequilibrium

Front 62

John Maynard Smith’s null model of sexual reproduction

Back 62

– 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

Front 63

Muller's ratchet main conclusions

Back 63

– 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

Front 64

Red Queen Hypothesis

Back 64

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