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64 Cards in this Set
- Front
- Back
What is the idea of H-W Eq principle? |
to provide a null model for behavior of genes in populations |
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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 |
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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 |
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What happens if a population is in H-W equillibrium? |
it will never evolve regardless of starting frequencies |
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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) |
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Chi squared formula |
(Observed-Expected)^2 Sum of --------------------------------- Expected |
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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 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 |
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Overdominance, hybrid vigor, heterozygote advantage |
Heterozygotes have higher fitness than eitherhomozygote Overdominance maintains genetic diversity No allele will reach fixation |
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frequency dependent selection |
*think about the left/right mouthed scale eaters maintains genetic diversity |
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underdominance |
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 |
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Cystic fibrosis |
frequency is maintained by heterozygoteadvantage Heterozygotes were partially resistant totyphoid fever infection Cystic fibrosis maintained by mutation andoverdominance |
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equilibrium frequency vs mutation and selection |
^
q = /sqrt(mu/s) ^ q = equilibrium frequency |
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migration equations |
p'r=pr(1-m)+ps+m same as p'i=pi(1-m)+p+m so Delta(p) = m(p-pi) |
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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 |
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what is Fst? |
FST reflects differences in allele frequenciesamong populations of the group Runs from 0 to 1 Larger values representlarger differences in allelefrequencies |
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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 |
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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 |
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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 |
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youtube video for founder effect vs bottleneck vs genetic drift |
https://www.youtube.com/watch?v=Q6JEA2olNts |
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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 |
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What does F_is measure? |
the proportion of the variance in the subpopulationcontained in an individual (Inbreeding coefficient) |
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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) |
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What does F_st measure? |
the level of differentiation among a set ofpopulations "How similar are the allele frequencies among two different populations?" |
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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 |
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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 |
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calculating F_st If the sex ratio is unequal: |
4NmNf Ne = ----------- Nm + Nf Nm=#males Nf=#females |
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calculating F_st If there is sexual selection |
8Na Ne ≈ ------------- Vm + Vf + 4 Vm and Vf are variances in numbers ofoffspring produced by males and females |
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calculating F_st If (when!) there is genetic drift: |
1 Delta F_st = ------ 2Ne Increase in FST due to drift over one generation |
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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 |
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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) |
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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. |
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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. |
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Neutral theory as null hypothesis calculations |
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 |
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Are synonymous mutations exposed toselection? |
Codon bias Codon usage random versus nonrandom Often NONRANDOM Bias is strongest in highly expressed genes |
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Panmixia |
term meaning random mating |
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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 |
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assortative mating vs homozygosity and heterozygosity |
– Individuals mate with others like themselvesso that heterozygous offspring are notproduced as much - Negative assortative mating increasesheterozygosity |
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Most common type of nonrandom mating |
inbreeding – Mating among genetic relatives – Increases homozygosity at all loci – Violates Conclusion 2 but not 1 |
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• Inbreeding |
– Most extreme form is self-fertilizing • Selfing |
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– If all individuals self |
– Frequency of heterozygotes ishalved every generation |
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• 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 |
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– Computing F in real populations |
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 |
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• 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 |
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• Inbreeding Depression – Many plants and animals have evolved mechanisms to avoid it |
• Mate choice • Self-incompatibility • Dispersal • Different phenologies of male and female organs BUT – Small populations cannot avoid it • Endangered species |
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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 |
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epistasis |
Multiple genes often have effectson a single phenotypic character |
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linkage equilibrium |
Loci are in linkage equilibrium if thefrequency of one allele does not affect thefrequency of the other |
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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 |
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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 |
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Calculating linkage equilibrium |
– The quantity D, the coefficient of linkagedisequilibrium, must be equal to zero • D = gABxgab - gAbxgaB g’s are frequencies of chromosomes |
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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 |
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• What creates linkage disequilibrium? |
– Selection on multi-locus genotypes – Genetic drift – Population admixture |
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Haplotypes
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or multi-locus genotypes
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How to eliminate linkagedisequilibrium
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Have sex.
Meiosis, crossing over, outbreeding Meiosis breaks up old genotypecombinations and creates new ones Genetic recombination randomizesgenotypes of loci with respect to eachother
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Study by Clegg
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• 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 |
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Why does linkage disequilibrium matter?
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• 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 |
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What causes linkage disequilibrium |
Inbreeding/selfing |
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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 |
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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 |
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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. |
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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 |
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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 |
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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 |
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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 |