Genetics Exam 3

Population Genetics

Population Genetics

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

population

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

Gene pool

shard set of genes, all alleles of a population

genotype frequency

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

Allele Frequency

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

Evolution

Change in allele frequencies over time

Hardy Weinberg Equilibrium

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

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

What is the equation for HWE?

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

As heterozygosity increases, what happens to allele frequencies?

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

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

The heterozygote genotype

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

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

the heterozygote

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

What is the ultimate source of variation?

Mutation

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

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

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

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

Frequency of A decreases and frequency of a increases

What is the symbol for rate of forward mutations?

u

What is the symbol for the rate of reverse mutations?

v

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

Change in p = vq - up

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

It will eventually end in equilibrium

How do you find the frequencies at equilibrium?

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

Why is mutation equilibrium so rare?

Because other evolutionary processes act on mutation

Genetic Drift

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

When does genetic drift occur?

occurs in all real populations all of the time

How does population size affect the influence of genetic drift?

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

Effective population size

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

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

What is the effect of genetic drift on populations?

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

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

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

Bottlenecks

population is significantly reduced by catastrophe

Founder events

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

Migration or gene flow

changes in allele frequency due to movement of individuals

What are the major effects of gene flow?

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

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

fitness

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

absolute fitness (W)

Mean number of offspring an individual of a particular genotype has

Relative fitness (w)

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

How do you calculate relative fitness?

Set the highest fitness to 1

Mean fitness

how well on average an individual from population survives and reproduces

How do you calculate mean fitness?

The sum of relative fitness x genotype frequency

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

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

Speciation

evolution of reproductive isolation W

What is the pathway to speciation?

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

Alopatric

no exchange of migrations usually caused by geographic isolation

What are the mechanism of reproductive isolation?

1. prezygotic barriers, 2) postzygotic barriers

Prezygotic barriers

prevent zygote from ever forming

What are the 4 kinds of prezygotic barriers?

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

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

Postzygotic barriers

zygote forms but cannot genetically contribute

What are the kind of postzygotic barriers?

1. hybrid unviability, 2) hybrid sterility

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)

How are mechanisms of reproductive isolation relate to natural selection?

evolution of prezygotic barriers in selective response to postzygotic barriers

Discontinuous traits

discrete, categorical

Continuous traits

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

Variance (s^2)

how much individuals deviate from mean

How do you calculate variance?

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

Standard deviation

s= sqaure root of variance

Why is variance s^2?

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

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

66%, 95%, 99% respectfully

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

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

How do you calculate phenotypic variation?

Vp = Vg + Ve

What kind of variation provides the basis for evolution?

Genetic variation, specifically additive genetic variation

Broad-sense heritability (H2

portion of all variation in a quantitative trait due to genetics

How do you calculate broad-sense heritability?

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

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

narrow-sense heritability (h2)

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

How do you calculate narrow sense heritability?

h2 = Va/ Vp

Mid-parent regression

slope of linear regression between midparent and offspring

Mid-parent

average of parent trait values

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

Will respond to natural selection

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

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

When will heritability be higher?

When individual is in a low variation environment

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

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

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

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

Selection differential (s)

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

What does it mean if the selection differential is 0?

Hertiability does note exist because there is no selection

Selection Response (R)

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

Breeder’s Equation

R = h2 x S

What does Breeder’s equation look at?

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

Semiconservative model

each parent-strand pairs with a newly made strand

Conservative model

parent strand reanneal after replication and 2 new strands pair

Dispersive model

parental strands are chopped up and dispersed among new strands

Meselson-Stahl Experiment

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

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

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

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

In what direction is the template DNA strand read?

3’ → 5’

In what direction is DNA created?

5‘ → 3’

OriC

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

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’

Supercoiling

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

How are supercoils fixed?

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

DNA Template

old strand upon which new strand is being synthesized

Primer

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