C18 Population Genetics
22 important questions on C18 Population Genetics
What are the assumptions for the Hardy-Weinberg law?
- Mating is random
- population size is infinitely large
- it never is... But the law is still usefull
- there is no migration, mutation or selection
applies to diploid organisms with sexual reproduction
- Infinite population
- No selection
- Random mating
- No mutation
Explain the rows and columns of this figure
Columns; nucleotide positions in a DNA sequence
In this example all individuals are homozygous for this region
How many SNPs are there in this sequence? For each locus give the most common SNP
2C, 3C, 5T ....
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What is the micro satellite variation?
Are these three individuals diploid or haploid organisms?
A haplotype network shows the relationship among haplotypes
- how many haplotypes are in this figure?
- What is the difference between haplotypes of individuals A and D, and between C and B?
- 6, individuals 5 and 6 have the same haplotype
- A-D: micorsatellite, SNP2, SNP9, SNP17, SNP31 and SNP33; C-B: SNP3 and SNP5
- Explain the last column: Why are these haplotypes subdivided in class I and class II?
- Which SNP(s) can be used to uniquely identify haplotype B?
- Because ABC differ slightly and DEF differ slightly, but have many differences (see A-D) between the classes
- SNP5: B has A all others T
Calculation of allele frequencies
q = f a/a + 1/2 f A/a = frequency of a
p + q = f A/A + f A/a + f a/a = 1 = p^2 + 2pq + q^2
q = 1 - p
Can you conclude that if a population is in HW-equilibrium for one marker, it will also show HW-equilibrium for other markers?
- Explain why isolation by distance violates the Hw-law and may result in population structure.
- Can you expect population structure within short distances as well?
- If there is population structure, it is more likely that individuals with similar genotype marry than expected based on overall allele frequency: "isolation by distance". Therefor, there is no random mating and no HW equilibrium in the whole population
- Yes, if for some other reason mating is non-random, e.g. Because of preferential mating between specific genotypes. This is called (dis)-assortative mating
What is the chance for individual I to be 'identical by descent' for the two red alleles?
How many different functional G6PD alleles and haplotypes are there in the human population?
Why is the number of haplotypes much larger than the number of functional alleles?
Whisch SNPs do not affect the functional allele class?
What is the effect of linkage disequilibrium on the number of haplotypes in the population?
What can cause linkage disequilibrium, and how will it decay?
or Ab and aB are non-viable;
over time recombination will occur and the recombinant types will be formed, and if there are no fitness consequences, there will be linkage equilibrium.
What is the effect of population size on genetic drift?
stochastic outcome at N=10, quite stable at N=500
What is the effect of the initial allele frequency on the chance to lose or to fix an allele?
Why are most mutations present in a population for only a short time?
Why is the initial increase in frequency of a new dominant allele faster than that of a new recessive allele?
Why can a recessive beneficial allele each fixation more easily than a dominant beneficial allele?
What are the forces that can change the frequency of an allele in a population?
The frequency of an allele in a population can be altered by natural selection, mutation,
migration, and genetic drift (sampling errors).
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