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BILD 3 Lecture Notes - Lecture 6: Genotype Frequency, Bild, Selection Coefficient

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School
UCSD
Department
Biology/Lower Division
Course
BILD 3
Professor
Dr. Kimberley Cooper

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BILD 3 Lecture 6
4/13/2018
• You can see if evolution is happening in a real population by asking: is a population in H-
W equilibrium at a particular locus (gene)?
o To figure this out, we will walk through this information:
▪ Note the number of each genotype
▪ Calculate numbers of each allele
▪ Calculate allele frequencies
▪ Calculate expected genotype frequencies using H-W
▪ Compare expected vs observed genotype frequencies
▪ Arbitrary which letter is given p vs q
• How often does a population meet all of the H-W criteria such that it has zero change in
its allelic frequencies over time? Is the H-W equilibrium common in nature?
o Assumptions:
▪ No selection
▪ Mating is random
▪ Populations are always large
▪ No migration between populations
▪ No mutation
▪ Equal number of offspring from each individual
▪ Everyone breeds
o H-W assumptions are rarely ever met
o It’s helpful eause ou a alulated epeted geotpe feueies, ad a
use this null-hpothesis to opae, ad etapolate fo thee hat’s goig o
with a population
• Example of disequilibrium: HLA
o Hypothesis: heterozygotes have fitness advantage
o Test: is a population in H-W equilibrium at these loci?
o Study found that couples with different HLA alleles from each other had more
offspring than that had the same genotype
• Relative fitness
o Is the contribution of an individual to the next generation, relative to the
contribution of other individuals in the population
o It is determined by factors affecting both survival and reproduction
o Selection acts on the phenotype of individuals
o The product of selection is a change in genotype frequencies and thus a
generational change in phenotype frequencies
o Relatie fitess ieases a aial’s elatie ailit to suie
o The elatie fitess affets the aial’s ailit to epodue co
o compared to others in the population
• s= selection coefficient (fitness cost of having that genotype)
o relative fitness when having a good genotype is 1
o 1-s= relative fitness when having bad genotype
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Related Questions

Kermode bears are white bears that are found in the rainforest on Princess Royal and Gribbell islands along the coast of British Columbia. This subspecies of black bears is known as the Spirit Bear. Its white fur is the result of a single nucleotide replacement in the melanocortin-1 (Mc1r) receptor portion of the gene that leads to the production of adenine instead of guanine. The white fur allele (W) is a recessive allele unique to this subspecies. Dr. Kermit Ritland and his colleagues found that approximately out of a total population of 73 bears on Princess Royal and Gribbell Islands 48 were white (WW). Of the black bears (BB and BW), 12 were homozygous and 13 were heterozygous. The percentage of white bears on the mainland drops off drastically with distance from those islands.

Assuming complete dominance, estimate the observed allele frequencies (maintain 3 significant digits for all calculations) (1pt)?
q =
p =
Thus, for a randomly mating population at equilibrium, the Hardy-Weinberg theorem gives us the genotype frequencies expected for Kermode bears (1pt).
The expected frequency of BB genotypes =
The expected frequency of BW genotypes =
The expected frequency of WW genotypes =
If there is a population of 37 bears on Princess Royal Island, how many would you expect to be black (1pt)?
How many would you expect to be white (1pt)?

You can use the Chi-square statistic to test whether the observed numbers of your BB,
BW, and WW genotypes (your categories) differ from your expected proportions morethan you would expect due to chance. The Chi-square statistic is a probability distributionthat we can use to estimate the probability (“p-value”) of finding differences in observedand expected values. If the observed values are very different from the expected values(resulting in a large Chi-square value), we would say there is a low probability (p<0.01)of that difference occurring due to chance alone. This outcome would suggest somemechanism of evolution (drift, natural selection, etc.) is pushing allele frequencies out ofHardy-Weinberg equilibrium. Use the Chi-square calculator to test for differences in your observed numbers of the three genotypes and the expected frequencies on Princess RoyalIsland (using the “fraction expected” option) at:https://graphpad.com/quickcalcs/chisquared1.cfm.

Are the observed numbers and expected frequencies significantly different? What doesthis mean is happening to white bears on Princess Royal Island (2pts)?

Kermode bears are white bears that are found in the rainforest on Princess Royal and Gribbell islands along the coast of British Columbia. This subspecies of black bears is known as the Spirit Bear. Its white fur is the result of a single nucleotide replacement in the melanocortin-1 (Mc1r) receptor portion of the gene that leads to the production of adenine instead of guanine. The white fur allele (W) is a recessive allele unique to this subspecies. Dr. Kermit Ritland and his colleagues found that approximately out of a total population of 73 bears on Princess Royal and Gribbell Islands 48 were white (WW). Of the black bears (BB and BW), 12 were homozygous and 13 were heterozygous. The percentage of white bears on the mainland drops off drastically with distance from those islands.

Assuming complete dominance, estimate the observed allele frequencies (maintain 3 significant digits for all calculations) (1pt)?
q =
p =
Thus, for a randomly mating population at equilibrium, the Hardy-Weinberg theorem gives us the genotype frequencies expected for Kermode bears (1pt).
The expected frequency of BB genotypes =
The expected frequency of BW genotypes =
The expected frequency of WW genotypes =
If there is a population of 37 bears on Princess Royal Island, how many would you expect to be black (1pt)?
How many would you expect to be white (1pt)?

You can use the Chi-square statistic to test whether the observed numbers of your BB,
BW, and WW genotypes (your categories) differ from your expected proportions morethan you would expect due to chance. The Chi-square statistic is a probability distributionthat we can use to estimate the probability (“p-value”) of finding differences in observedand expected values. If the observed values are very different from the expected values(resulting in a large Chi-square value), we would say there is a low probability (p<0.01)of that difference occurring due to chance alone. This outcome would suggest somemechanism of evolution (drift, natural selection, etc.) is pushing allele frequencies out ofHardy-Weinberg equilibrium. Use the Chi-square calculator to test for differences in your observed numbers of the three genotypes and the expected frequencies on Princess RoyalIsland (using the “fraction expected” option) at:https://graphpad.com/quickcalcs/chisquared1.cfm.

Are the observed numbers and expected frequencies significantly different? What doesthis mean is happening to white bears on Princess Royal Island (2pts)?

Need help with evolution questions:

1.) A haplotype is best defined as the ________________.

haploid genotypes of all the gametes produced by a diploid individual
ABO blood type conferred by an individual gamete
genotype of either the paternal or maternal chromosomal complement
multilocus genotype of a chromosome or gamete

2.) Which of the following statements regarding linkage disequilibrium is true?

Exists when D is less than zero, but not when it is greater than zero.
Is reduced by sexual reproduction.
Is increased by crossing-over during meiosis.
Is increased by any random sampling error that happens to create or destroy certain chromosome genotypes but not others.

Is reduced by selection that favors certain combinations of genotypes.

3.) Selection on multilocus genotypes in random-mating populations leads to linkage disequilibrium when _______________.

it reduces mutation rates
it eliminates all haplotypes from the population
it prevents crossing-over during meiosis

some allele combinations confer greater fitness than do others

4.) When two loci are in linkage equilibrium, the allele carried on a chromosome at one locus is independent of the allele carried on the chromosome at another locus. When this is the case, _________________.

allele frequencies will not change over time
the two loci (or, more specifically, their protein products) do not interact
the frequency of each haplotype can be calculated by multiplying the frequency of its two alleles

all possible haplotypes occur at equal frequency

5.) Which of the following accurately characterize(s) Muller's ratchet model for the selective advantage of sexual reproduction?

Drift establishes linkage disequilibrium because multilocus genotypes with few mutations are eliminated by chance events.
In populations without sexual reproduction, deleterious mutations accumulate, eventually imposing such a burden that the population goes extinct.
Sex is favored selectively because it recreates the zero-mutation genotypes lost due to drift.
All of the above correctly characterize Muller's ratchet model for the evolution of sexual reproduction.

6.) The genetic signature of recent positive selection on a locus is _______________.

high frequency and low linkage disequilibrium
low frequency and low linkage disequilibrium
low frequency and high linkage disequilibrium

high frequency and high linkage disequilibrium

7.) Sexual reproduction is advantageous both in changing environments and in constant environments, compared to asexual reproduction.

True

False

8.) Sexual reproduction causes genetic recombination via crossing-over, which combines genotypes from different parents.

True

False

9.) One reason sex may be maintained in natural populations is proposed by the "Red Queen Hypothesis", which states that.....

genotypes created by sex are created by natural selection over and over
recombination creating novel genotypes that can resist infection by parasites
mutation load is reduced by novel adaptive mutations
the ability of sex to fix multiple