Genetics Exam 3

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Population Genetics

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1

Population Genetics

study of evolution performed by determining/modeling ethics/genetics in populations over time

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2

population

group of organism belonging to one species that live in place and share common set of genes

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3

Gene pool

shard set of genes, all alleles of a population

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4

genotype frequency

#of individuals with genotype in a population / total # of individuals in population

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5

Allele Frequency

#of copies of an allele in a population / total # of alleles in population

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6

Evolution

Change in allele frequencies over time

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7

Hardy Weinberg Equilibrium

a null hypothesis model where there is no evolutionary change because allele frequencies are not changing over time

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8

What are the assumptions of HWE?

  1. population is infinite, 2) mating is random, 3) no mutation, 4) no migration or gene flow, 5) no natural selection

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9

What is the equation for HWE?

p^2 + 2pq + q^2 = 1

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10

As heterozygosity increases, what happens to allele frequencies?

the more alleles there are and the more equalized the allele frequencies are

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11

What is the most common genotype if the frequencies of A and a are between 0.33 and 0.66?

The heterozygote genotype

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12

If the allele frequency of A or a is less than 0.33, then what is the lease common genotype?

The homozygote for that allele

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13

When an allele is rare where do most of the copies come from?

the heterozygote

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14

How do you determine if a population is in HWE?

  1. determine allele frequencies, 2) determine expected genotype frequencies, 3) determine expected genotype numbers by multiplying by total, 4) calculate a chi square between observed and expected

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15

What is the ultimate source of variation?

Mutation

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16

What are the three kinds of mutations in order from most to least likely?

  1. neutral, 2) deleterious, 3) selectively advantagous

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17

Even though mutations are the ultimate source of variation, why do mutations not always create change in allele frequencies?

Because the other evolutionary forces determine the fate of mutations that create variation. Things like natural selection act on mutation to create allele frequencies changes

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18

What is the result of a forward mutation A → a?

Frequency of A decreases and frequency of a increases

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19

What is the symbol for rate of forward mutations?

u

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20

What is the symbol for the rate of reverse mutations?

v

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21

How do you calculate the change in p (or Freq(A))?

Change in p = vq - up

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22

With both reverse and forward mutation occurring what is the end result?

It will eventually end in equilibrium

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23

How do you find the frequencies at equilibrium?

p at equilibrium = (v)/(u+v) and q at equilibrium = (u)/(u+v)

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24

Why is mutation equilibrium so rare?

Because other evolutionary processes act on mutation

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25

Genetic Drift

random fluctuation of allele frequency due to sampling error within a population

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26

When does genetic drift occur?

occurs in all real populations all of the time

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27

How does population size affect the influence of genetic drift?

The smaller the population, the larger the effect of genetic drift

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28

Effective population size

the effective number of adults contributing gametes to the next generation (not all males and females contribute to the next generation)

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29

How do you determine the magnitude of effective population size?

Ne = (4 x Nf x Nm) / (Nf + Nm), where Nf is the number of breeding females and Nm is the number of breeding males

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30

What is the effect of genetic drift on populations?

  1. reduces genetic variation within a population, 2) increases genetic divergence between populations

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31

What happens to the probability of fixation as allele frequency increases?

The likelihood of an allele fixating increases as that allele’s frequency increases

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32

Bottlenecks

population is significantly reduced by catastrophe

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33

Founder events

dispersal and colonization by small group (ex: new island population)

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34

Migration or gene flow

changes in allele frequency due to movement of individuals

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35

What are the major effects of gene flow?

  1. introduces new alleles, 2) prevents population diversification, 3) reverse effects of genetic drift

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36

Natural selection

process by which traits evolve and create adaptation to environment by acting on randomly generate mutations in a non random way when genotypes do not have equal fitness

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37

fitness

measure of how well certain genotypes are expected to survive and reproduce

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38

absolute fitness (W)

Mean number of offspring an individual of a particular genotype has

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39

Relative fitness (w)

degree to which a particular genotype reproduces relative to individuals with other genotypes

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40

How do you calculate relative fitness?

Set the highest fitness to 1

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41

Mean fitness

how well on average an individual from population survives and reproduces

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42

How do you calculate mean fitness?

The sum of relative fitness x genotype frequency

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43

How do you calculate the magnitude of the change in allele frequency caused by natural selection?

find initial genotype frequency of HWE zygotes from allele frequency given of gen 1, 2) find relative fitness, 3) find mean fitness, 4) find relative genotype frequency after selection, 5) find change in allele frequencies

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44

How do you calculate the relative genotype frequencies after selection?

F(AA) = (p^2 x relative fitness AA) / mean fitness

F(Aa) = 2pq x relative fitness Aa) / mean fitness

F(aa) = q^2 x relative fitness aa) / mean fitness

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45

Speciation

evolution of reproductive isolation W

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46

What is the pathway to speciation?

ancestral population splits → genetic divergence between population occurs during split → populations reunite and hybridization is prevented

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47

Alopatric

no exchange of migrations usually caused by geographic isolation

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48

What are the mechanism of reproductive isolation?

  1. prezygotic barriers, 2) postzygotic barriers

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49

Prezygotic barriers

prevent zygote from ever forming

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50

What are the 4 kinds of prezygotic barriers?

  1. habitat isolation, 2) behavioral isolation, 3) temporal isolation, 4) mechanical isolation

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51

What is one problem that prezygotic barriers create?

Incomplete isolation where pop still splits an genetically diverge but when they reunite they can still hybridize

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52

Postzygotic barriers

zygote forms but cannot genetically contribute

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53

What are the kind of postzygotic barriers?

  1. hybrid unviability, 2) hybrid sterility

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54

Dobzhansky-Muller Model

2 populations splits and fitxate for different alleles and when they reunite mutant alleles are “unfit” because they have never seen each other (postzygotic barrier)

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55

How are mechanisms of reproductive isolation relate to natural selection?

evolution of prezygotic barriers in selective response to postzygotic barriers

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56

Discontinuous traits

discrete, categorical

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57

Continuous traits

measurable, affected by multiple genes, variable expressivity, penetrance, pleiotropy, epistasis, environmental factors

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58

Variance (s^2)

how much individuals deviate from mean

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59

How do you calculate variance?

(sum of (trait value of indivudal - mean trait value )^2) / (n-1)

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60

Standard deviation

s= sqaure root of variance

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61

Why is variance s^2?

It is sqaured because that way it gives equal weight to positive and negative mean deviants

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62

What percent of the population falls into 1, 2, and 3 standard deviations?

66%, 95%, 99% respectfully

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63

How do you calculate the measurable trait value for a phenotype?

= base value + (# of contributing alleles x contribution per allele)

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64

How do you calculate phenotypic variation?

Vp = Vg + Ve

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65

What kind of variation provides the basis for evolution?

Genetic variation, specifically additive genetic variation

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66

Broad-sense heritability (H2

portion of all variation in a quantitative trait due to genetics

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67

How do you calculate broad-sense heritability?

H2 = Vg / Vp, with range of 0-1

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68

In the Duke university model for quantitative traits, what kind of variation did each generation have?

P1 and F1 had only environmental variation, F2 has genetic variation

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69

narrow-sense heritability (h2)

proportion of variation due to additive genetics, also reflects degree to which offspring resemble their parents

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70

How do you calculate narrow sense heritability?

h2 = Va/ Vp

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71

Mid-parent regression

slope of linear regression between midparent and offspring

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72

Mid-parent

average of parent trait values

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73

What does it mean if the slope of the mid-parent regression line is greater than 0?

Will respond to natural selection

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74

What does it mean if the slope of the mid-parents regression line is 1?

It will respond the most to selection, because there is more genetic variation

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75

What are the limitations of hertiability?

  1. cannot apply to the individual, 2) can be overestimated because often times parents and offspring have similar environment

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76

When will heritability be higher?

When individual is in a low variation environment

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77

What does it look like when all variation is attributable to genetic factors?

Ve = 0, Vp=Vg, slopes of lines of both genotype 1 and 2 are flat and parallel

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78

What does it look like when all variation is attributed to envrionment?

Vg = 0, Vp=Ve, slopes of lines of genotype 1 and 2 overlap but are sloped

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79

What does it look like when variation is attributable to both environment and genetics?

Vg>0, Ve>0, slopes of genotypes 1 and 2 are parallel and sloped

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80

What does it look like when genotype 2 responds differently to environmental gradient than does 1 but both repsond

Vg>0, Ve>0, Vg*E>0, both 1 and 2 have positive slopes but 2 is steeper than 1

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81

Selection differential (s)

difference between mean trait value of individuals that contribute MINUS mean traits values of all individuals in population

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82

What does it mean if the selection differential is 0?

Hertiability does note exist because there is no selection

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83

Selection Response (R)

difference between mean trait value of offspring of population and the mean trait value of original parent response

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84

Breeder’s Equation

R = h2 x S

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85

What does Breeder’s equation look at?

How mean phenotypic value changes over time as a result of natural selection using genetic variation

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86

Semiconservative model

each parent-strand pairs with a newly made strand

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87

Conservative model

parent strand reanneal after replication and 2 new strands pair

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88

Dispersive model

parental strands are chopped up and dispersed among new strands

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89

Meselson-Stahl Experiment

manipulate weight in e coli DNA to determine which model DNA follows

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90

After growing the 1 generation, what was the outcome and conclusion in Meselson and Stahl’s experiment?

All DNA had intermediate weight so you could eliminate conservative model

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91

After growing generation 2, what was the outcome and conclusion in Meselson and Stahl’s experiment?

DNA was both light and intermediate which eliminates the dispersive model and leaves DNA to follow the semiconservative model

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92

What are the requirements for PCR?

  1. magnesium ions, 2) DNA polymerase, 3) DNA template, 4) a fragment of DNA primer (or RNA), 5) all 4 dNTPS

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93

In what direction is the template DNA strand read?

3’ → 5’

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94

In what direction is DNA created?

5‘ → 3’

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95

OriC

single point of origins in prokaryotic replication, made up of repeated AT bonds because they are less stable and easy to unzip

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96

What is the replication process in prokaryotes?

  1. initiator proteins (DNAa) binds to OriC, 2) DNA helicase binds and untwists DNA, 3) DNA primase binds to DNA helicase and builds RNA primer, 4) DNA polymerase III binds and begins to synthesize 5’ → 3’

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97

Supercoiling

As DNA helicase unwinds DNA, the ends get twisted really tight creating supercoils

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98

How are supercoils fixed?

DNA gyrase and topoisomerase relax the DNA by cutting it, untwisting and then reattaching

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99

DNA Template

old strand upon which new strand is being synthesized

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100

Primer

RNA nucleotides bound to template strand that acts as substrate for DNA polymerase to bind

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