Lecture 13 Bio 2b

8/7/2019 Lecture 13 Bio 2b

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GRADE SCORE # % Cum %

A+ 97+ 1 0.00 0.20

A93-96.5 10 0.02 2.22

A- 90-92.5 15 0.03 5.25

B+ 87-89.5 30 0.06 11.31

B83-86.5 36 0.07 18.59

B- 80-82.5 35 0.07 25.66

C+ 77-79.5 43 0.09 34.34

C73-76.5 66 0.13 47.68

C- 70-72.5 43 0.09 56.36

D+ 67-69.5 47 0.09 65.86

D63-66.5 50 0.10 75.96

D- 60-62.5 37 0.07 83.43

F


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The Hardy-Weinberg Theorem:The Hardy-Weinberg Theorem: In diploid organisms, allele frequencies &In diploid organisms, allele frequencies &

genotypic ratios in large biparental populations reach an equilibrium in onegenotypic ratios in large biparental populations reach an equilibrium in one

generation, and remain constant thereafter, unless disturbed bygeneration, and remain constant thereafter, unless disturbed by

Population GeneticsPopulation Genetics

The Hardy-Weinberg EquilibriumThe Hardy-Weinberg Equilibrium

1. M

2. G

3. G

4. N

5. N

Most detectable

Least detectable


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The Hardy-Weinberg Theorem:The Hardy-Weinberg Theorem: In diploid organisms, allele frequencies &In diploid organisms, allele frequencies &

genotypic ratios in large biparental populations reach an equilibrium in onegenotypic ratios in large biparental populations reach an equilibrium in one

generation, and remain constant thereafter, unless disturbed bygeneration, and remain constant thereafter, unless disturbed by

Population GeneticsPopulation Genetics

The Hardy-Weinberg EquilibriumThe Hardy-Weinberg Equilibrium

1. Mutation1. Mutation2. Gene flow2. Gene flow

3. Genetic drift3. Genetic drift

4. Non-random mating4. Non-random mating

5. Natural selection5. Natural selection

Helpful Hank says, memorize this list


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MutationMutation is the source of all novel genetic variation.is the source of all novel genetic variation.

Mutation is any change in DNAMutation is any change in DNA

mutations occurmutations occurrandomlyrandomly

with respect to what might bewith respect to what might beadaptively beneficial in a particular selective regimeadaptively beneficial in a particular selective regime

Most mutations are harmful or neutral, but if conditions change,Most mutations are harmful or neutral, but if conditions change,could become advantageouscould become advantageous

1.1. Point mutationsPoint mutations

SubstitutionsSubstitutions

silent (synonymous)silent (synonymous) missense (nonsynonymous)missense (nonsynonymous) nonsense (nonsynonymous)nonsense (nonsynonymous)

Frameshift mutationsFrameshift mutations basepair insertion/deletionbasepair insertion/deletion

2.2. Chromosomal mutationsChromosomal mutations DuplicationsDuplications

DeletionsDeletions InversionsInversions TranslocationsTranslocations TranspositionsTranspositions

Kinds of mutationsKinds of mutations

Causes of EvolutionCauses of Evolution

A. MutationA. Mutation


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i. SILENTi. SILENT (synonymous)

(synonymous)

SomeSome mutations falling on the 3mutations falling on the 3rdrd

positionpositionin a codon (the 3-nucleaotide code for anin a codon (the 3-nucleaotide code for an

AA) have no effect on the AA sequenceAA) have no effect on the AA sequence

due to redundancy in the DNA codedue to redundancy in the DNA code

ii. MISSENSEii. MISSENSE (nonsynonymous)(no

nsynonymous)A change in the DNA code that causes anA change in the DNA code that causes an

change in the AA sequencechange in the AA sequence

iii. NONSENSEiii. NONSENSE (nonsynonymous(

nonsynonymous))A change in the DNA code that creates anA change in the DNA code that creates an

unexpected STOP codon. Typically lethal!unexpected STOP codon. Typically lethal!

Wild-typeWild-type

MISSENSEMISSENSE

Wild-typeWild-type

SILENTSILENT

Wild-typeWild-type

NONSENSENONSENSE

Point MutationsPoint Mutationsalter a single point in the base sequencealter a single point in the base sequence

a. Substitution:a. Substitution:replacement of a single base nucleotide withreplacement of a single base nucleotide withanother nucleotideanother nucleotide


A. Mutation, 1. Point MutationsA. Mutation, 1. Point Mutations


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Sickle Cell Anemia:Sickle Cell Anemia:

A single nucleotide change of theA single nucleotide change of the

-globin gene which codes for-globin gene which codes for

hemoglobinhemoglobin

TheThe pointpoint mutationmutation is from an A to ais from an A to a

T, causing a codon change fromT, causing a codon change fromGAG to GTG, which results in theGAG to GTG, which results in the

substitution of valine instead ofsubstitution of valine instead of

glutamic acid in Hemoglobinglutamic acid in Hemoglobin

Is aIs a missensemissense mutationmutation

Is a recessive character, so only people who are homozygousIs a recessive character, so only people who are homozygous

recessive express full symptoms (heterozygotes have a few sickle-recessive express full symptoms (heterozygotes have a few sickle-

shaped cells, so this is slightlyshaped cells, so this is slightly codominantcodominant))

Causes periods of pain, and a typically shortened life-spanCauses periods of pain, and a typically shortened life-span

Why does this persist? heterozygotes have increased malarial resistanceWhy does this persist? heterozygotes have increased malarial resistance

EXAMPLEEXAMPLE


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Another kind of point mutation is aAnother kind of point mutation is a Frameshift mutationFrameshift mutation

This occurs when there is a basepair insertionThis occurs when there is a basepair insertion orordeletion, whichdeletion, which

causes thecauses the sequence of codons to be read incorrectly...of codons to be read incorrectly... these canthese can

screw things up really badly! Often lethal.screw things up really badly! Often lethal.

Wild-typeWild-type

FrameshiftFrameshift

mutantmutant


A. Mutation, 1. Point MutationsA. Mutation, 1. Point Mutations


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Gene DuplicationGene Duplication

EE

Original chromosomeOriginal chromosome

DeletionDeletionLocus D is DELETED

InversionInversion


A. Mutation, 2. Chromosomal MutationsA. Mutation, 2. Chromosomal Mutations

Chromosomal MutationsChromosomal Mutations

Large-scale mutations of whole genes or parts of chromosomesLarge-scale mutations of whole genes or parts of chromosomes

Often happens during unequalOften happens during unequal

crossing over; can be beneficialcrossing over; can be beneficial

Also often happens during unequalAlso often happens during unequalcrossing over; usually bad news...crossing over; usually bad news...

Can reduce recombination, allowingCan reduce recombination, allowing

genes to be transmitted as a unitgenes to be transmitted as a unit


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A. Mutation, 3. Mutation RatesA. Mutation, 3. Mutation Rates

Rare events: 1 x 10-6


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EachEach LOCUSLOCUS in a gamete has about a 1 in a million chance of mutating eachin a gamete has about a 1 in a million chance of mutating each

generationgeneration

Because of the large number of genes that can mutate, chromosome rearrangements that canBecause of the large number of genes that can mutate, chromosome rearrangements that can

change many genes simultaneously, and large numbers of individuals in a population, thuschange many genes simultaneously, and large numbers of individuals in a population, thus

mutationmutation can generate substantial variationcan generate substantial variation across the genome and in a populationacross the genome and in a population

However:However:

because PER LOCUS mutation rate is low, mutations alone producebecause PER LOCUS mutation rate is low, mutations alone produce

small deviationssmall deviations from Hardy-Weinberg equilibriumfrom Hardy-Weinberg equilibrium at a locus.at a locus.

If there are large deviations from H-W equilibrium at a particular locus,If there are large deviations from H-W equilibrium at a particular locus,

otherotherevolutionary processes are likely to be dominating.evolutionary processes are likely to be dominating.


A. Mutation, 3. Mutation RatesA. Mutation, 3. Mutation Rates


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Spectacular Exceptions

Camissonia campestris

Mojave suncup

1 of ~105 sp, spp, var in genus

Chromosomes form ringsleading to high rates ofreciprocal translocations andnot independently assortingproperly. Major radiations of

species with different ringforming attributes.


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Tetraploids

2N 2N gametes 4N

Tetraploidy is common in plants (and some animals). A failure of chromosomal

segregation leads to 2N gametes that fuse to form 4N individuals. Often the

extra genes can enhance favorable characteristics, such as flower size.


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GENE FLOWGENE FLOWresults from the migration of individuals and gametes (orresults from the migration of individuals and gametes (or

other propagules like seeds or larvae)other propagules like seeds or larvae) from one population to anotherfrom one population to another,,and the incorporation (by successful breeding) of the genes they carryand the incorporation (by successful breeding) of the genes they carry

into the novel gene poolsinto the novel gene pools

seastar larva


B. Gene FlowB. Gene Flow

Before the brown beetleBefore the brown beetle

arrived, the green allelearrived, the green allelefrequency = 1; after, = 0.87frequency = 1; after, = 0.87

(if all homozygous)(if all homozygous)

Honeybees are important vectorsHoneybees are important vectors

for gene flow moving pollen overfor gene flow moving pollen overlong distanceslong distances

These larvae allow gene flow overThese larvae allow gene flow overthousands of kilometers, eventhousands of kilometers, even

though the adults barely movethough the adults barely move


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New alleles can be added to the gene pool, OR allele frequenciesNew alleles can be added to the gene pool, OR allele frequencies

changed by:changed by:

...the...the immigrationimmigration (arrival) of individuals from another population with(arrival) of individuals from another population with

different gene frequencies into a recipient populationdifferent gene frequencies into a recipient population

...the...the emigrationemigration (departure) of individuals out of a population; this has(departure) of individuals out of a population; this has

an especially large effect if the source population is smallan especially large effect if the source population is small




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1.1. Within a populationWithin a population Gene flow can introduce alleles to a population,Gene flow can introduce alleles to a population,

increasing the genetic variation of that populationincreasing the genetic variation of that population

Gene flow can change allelic frequencies, causingGene flow can change allelic frequencies, causingevolutionevolution

Thus it will keep the population out of H-WThus it will keep the population out of H-W

equilibrium as long as it continuesequilibrium as long as it continues

1.1. Across populationsAcross populations

By moving genes around, gene flow can makeBy moving genes around, gene flow can makedistant populations genetically similar to onedistant populations genetically similar to one

another, reducing the chance of geneticanother, reducing the chance of genetic

divergence & speciation.divergence & speciation. The less gene flow between two populations, theThe less gene flow between two populations, the

more likely that two populations will diverge &more likely that two populations will diverge &

evolve into two species.evolve into two species.

MicroevolutionaryMicroevolutionaryconsequencesconsequences

MacroevolutionaryMacroevolutionary

consequencesconsequences



So,So, gene flowgene flow has important effects on evolutionary change athas important effects on evolutionary change at

TWO levels:TWO levels:


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The random change in allele frequencies and loss of alleles, due toThe random change in allele frequencies and loss of alleles, due tochancechance

Genetic drift occurs because populations are not infinitely large:Genetic drift occurs because populations are not infinitely large:

The larger the population, the LESS the importance of driftThe larger the population, the LESS the importance of drift

The smaller the population, the GREATER the importance of driftThe smaller the population, the GREATER the importance of drift

Drift happens to some extent inDrift happens to some extent in allall real populations (though it can be ignored inreal populations (though it can be ignored invery large ones), but there are 2 demographic processes that can makevery large ones), but there are 2 demographic processes that can makedriftdrift extremely strong and importantextremely strong and important::

1)1) Founder effectsFounder effects

2)2) Population bottlenecksPopulation bottlenecks


C. Genetic DriftC. Genetic Drift

These are becoming more common as weThese are becoming more common as we

make populations very small!make populations very small!


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European starlingsEuropean starlings introduced to N. America in 1890 (n=60) & 1891introduced to N. America in 1890 (n=60) & 1891

(n=40) by Eugene Schieffelin, of the Acclimation Society of N. America(n=40) by Eugene Schieffelin, of the Acclimation Society of N. America

Current population in N. AmericaCurrent population in N. America 200,000,000 birds200,000,000 birds

Source population carriesSource population carries >31 alleles at 11 loci>31 alleles at 11 loci

N. American population now carriesN. American population now carries 18 alleles at the same loci18 alleles at the same loci

42% loss relative to native populations42% loss relative to native populations

1890-91 (100 birds)1890-91 (100 birds) Now (200,000,000 birds)Now (200,000,000 birds)


C. Genetic Drift, 1. Founder EffectsC. Genetic Drift, 1. Founder Effects


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Population bottlenecks are very similar to founder effects, but occur whenPopulation bottlenecks are very similar to founder effects, but occur when

populations arepopulations are greatly reduced in size.greatly reduced in size. This can happen through naturalThis can happen through naturalprocesses (e.g., disease) or by humans.processes (e.g., disease) or by humans.

Bottlenecks occur when species are overharvested by humans, or whenBottlenecks occur when species are overharvested by humans, or when

their habitats are reduced or fragmented extensively.their habitats are reduced or fragmented extensively.


C. Genetic Drift, 2. Population BottlenecksC. Genetic Drift, 2. Population Bottlenecks


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Northern Elephant seal (Mirounga angustirostris) Fur seals (Arctocephalus spp. 8 species)

Famous Genetic BottleneckCases


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California fan palms are now restricted to a few oases inCalifornia fan palms are now restricted to a few oases in

southern California (Sonoran Desert) due to climate changesouthern California (Sonoran Desert) due to climate change

& habitat destruction,& habitat destruction, Populations contain measurablePopulations contain measurable

genetic variation (McClenaghan and Beauchamp 1986.)genetic variation (McClenaghan and Beauchamp 1986.)


C. Genetic Drift, 2. Population BottlenecksC. Genetic Drift, 2. Population Bottlenecks

NatureServe ExplorerPink- exotic

Red- critically imperiled

Brown-not yet ranked.


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Bottleneck Hall of FameBottleneck Hall of Fame

Spekes Gazelle-Formerly common over a

narrow distribution in the

Horn of Africa.

-no protected areas in wild;declining populations.

--Zoos may be the best

hope.


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Propithecus verreauxi; Madagascar

Lawler, RR. 2011.

Genetic Bottlenecks 2011

Calystegia soldanalla; Japan

Noda et al. 2011.

Egyptian Vulture.Neophron percnopterus

Agudo et al. 2011.

Orsinis viper. Vipera ursinii ursinii

Ferchauls et al. 2011. (France)

Hihi, Notiomystis cincta

New Zealand.Brekke et al. 2011

Gastropod snail; Lake

Malawi. Schultheiss et

al. 2011


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Nonrandom matingNonrandom matingoccurs when individuals choose mates withoccurs when individuals choose mates with

particular genotypes or phenotypes; there are 2 types:particular genotypes or phenotypes; there are 2 types:

1.1. INBREEDINGINBREEDING (or, more correctly,(or, more correctly, positive assortative matingpositive assortative mating))

occurs when individuals preferentially mate with the sameoccurs when individuals preferentially mate with the same

genotype as themselves.genotype as themselves.

2.2. OUTBREEDINGOUTBREEDING ((negative assortative matingnegative assortative mating) occurs when) occurs when

individuals avoid mating with similar genotypes (or close relatives).individuals avoid mating with similar genotypes (or close relatives).

3.3. Sexual SelectionSexual Selectionalso causes non-random mating (well talkalso causes non-random mating (well talk

about this as a form of selection later).about this as a form of selection later).4.4. Strong DisparityStrong Disparityin mating opportunity. Social dominance.in mating opportunity. Social dominance.


D. Non-Random MatingD. Non-Random Mating


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InbreedingInbreeding (positive assortative mating) occurs when individuals(positive assortative mating) occurs when individuals

preferentially mate with the same genotype as themselves:preferentially mate with the same genotype as themselves:

a.a. Start with 3 genotypes: AStart with 3 genotypes: A11AA11, A, A11AA22, A, A22AA22

pp (A(A11) = 0.5) = 0.5

qq (A(A22) = 0.5) = 0.5

What are the EXPECTED genotype frequencies at H-W equilibrium?What are the EXPECTED genotype frequencies at H-W equilibrium?

b.b. Mating rule: Each genotypeMating rule: Each genotype onlyonly mates with genotypes like itselfmates with genotypes like itself

(i.e. perfect inbreeding)(i.e. perfect inbreeding)c.c. If AIf A11AA11 homozygotes only mate with Ahomozygotes only mate with A11AA11 homozygotes, & Ahomozygotes, & A22AA22

homozygotes only mate with Ahomozygotes only mate with A22AA22 homozygotes,homozygotes, then neither of thesethen neither of these

kinds of inbred matings will have any effect on allelic and genotypickinds of inbred matings will have any effect on allelic and genotypic

frequencies in the next generationfrequencies in the next generation

d.d. What matters is matings between heterozygotes...What matters is matings between heterozygotes...


D. Non-Random Mating, 1. InbreedingD. Non-Random Mating, 1. Inbreeding

C f E l i


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With perfect inbreeding:With perfect inbreeding:

1.1. allele frequencies remain the same, butallele frequencies remain the same, but

2.2. heterozygosity declinesheterozygosity declines dramatically (up to 50% per gen)dramatically (up to 50% per gen)

11stst generation:generation: AA11AA22 xx AA11AA22

FF11ss :: AA11AA11(25%)(25%) AA11AA22(50%) A(50%) A22AA22(25%)(25%)

22ndnd generationgeneration AA11AA22 xx AA11AA22

FF22ss :: AA11AA11(25%)(25%) AA11AA22(50%) A(50%) A22AA22(25%)(25%)

All hetsAll hets

50% hets50% hets

All hetsAll hets

50% hets50% hets

Imagine heterozygote inbred matings...Imagine heterozygote inbred matings...



The number of heterozygotes keeps declining by 50% per generation,The number of heterozygotes keeps declining by 50% per generation,

until theyre gone (not as extreme when inbreeding isnt perfect)until theyre gone (not as extreme when inbreeding isnt perfect)

C fC f E l ti


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Effects of Inbreeding on Fitness: PKU (phenylketonuria)Effects of Inbreeding on Fitness: PKU (phenylketonuria)

Inbreeding increases the likelihood that deleterious recessive alleles willInbreeding increases the likelihood that deleterious recessive alleles will

be present in the homozygous statebe present in the homozygous state



PKU is caused by a recessive mutation in a gene wellPKU is caused by a recessive mutation in a gene well

call the R-locus (mutant allele = r)call the R-locus (mutant allele = r)

RR and Rr (CARRIER) genotypes can convertRR and Rr (CARRIER) genotypes can convert

phenylalanine to tyrosinephenylalanine to tyrosine

rr genotypes cannot do this, so a byproduct ofrr genotypes cannot do this, so a byproduct of

phenylalanine accumulates in nervous tissue andphenylalanine accumulates in nervous tissue and

causescauses severe brain damagesevere brain damage

The observed frequency of the r allele is about 0.01 inThe observed frequency of the r allele is about 0.01 inhuman populations, so the EXPECTED frequency of rrhuman populations, so the EXPECTED frequency of rr

homozygotes (diseased) ishomozygotes (diseased) is (0.01)(0.01)22 = 1/10,000= 1/10,000

In Ireland, p(r) is also about 0.01, yet until recently, theIn Ireland, p(r) is also about 0.01, yet until recently, the

incidence of PKU was closer toincidence of PKU was closer to 1/45001/4500 births.births.

How can this be?How can this be?

C f E l tiC f E l ti


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D. Non-Random Mating, 2. OutbreedingD. Non-Random Mating, 2. Outbreeding

Fig 22.11 inFig 22.11 in

texttext

The pin type has a stigma at theThe pin type has a stigma at the

top; the thrum type is reversedtop; the thrum type is reversed

Insects get pollen on their bodiesInsects get pollen on their bodies

and transfer it between pin andand transfer it between pin and

thrum flowers, or vice versa, tothrum flowers, or vice versa, to

pollinate thempollinate them

Nectar atNectar at

bottombottom

Consequence: over-representation of heterozygosity.

For


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Lecture 13 Bio 2b

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