- You compare two circular genomes from closely related organisms using a Genome Dot Plot. How would you detect an inversion that occurred symmetrically around the origin of replication. Draw a sketch of the gene plot:
- How would the plot change, if for one of the genomes the origin of replication were not coinciding with the origin of the coordinate system? Draw a sketch of the gene plot:
- Molecular phylogenies are usually calculated as unrooted trees. Correct/incorrect
- Proteins are believed to evolve by natural selection (in addition to drift:)). Most approaches to in vitro evolution use molecules that are both the genetic material and the catalyst (or where the genetic material can be created by reverse transcription from the catalyst). Describe at least two approaches by which the desirable trait in the protein (the fitness) can be linked to the encoding nucleic acids.
A) ___________________________________________________________________
B) ___________________________________________________________________
- Which of the following is a good approaches to create diversity on which selection can act?
A) puromycin linked to the 3'end of the mRNA
B) synonymous substitutions
C) recombination between divergent homologs
- What, if any, is the difference between a mutation and a substitution?
- Why do some substitution events not change the encoded protein?
- What is the chance (probability) that a mutation that arose in a single copy and that provides no selective advantage or disadvantage is fixed in population of 500 haploid organisms?
- What is the chance (probability) that a mutation that arose in a single copy and that provides no selective advantage or disadvantage is fixed in population of 500 diploid organisms?
- What is the relationship between the mutation rate and the substitution rate for selectively neutral mutations?
- How would this relationship (between mutation rate and the substitution rate) change if the mutation would lower the fitness of the organism carrying the mutation?
A) same
B) substitution rate decreases relative to mutation rate
C) substitution rate increases relative to mutation rate
- How would this relationship (between mutation rate and the substitution rate with selective advantage being zero) change if the mutation would increase the fitness of the organism carrying the mutation?
A) same
B) substitution rate decreases relative to mutation rate
C) substitution rate increases relative to mutation rate
- You consider mutations that provide no selective advantage or disadvantage. The mutation rate is assumed to be constant. You compare two populations of different size over long periods of time.
A) The substitution rate in the smaller population would be higher, because the mutations that occur are more easily fixed in the smaller population due to genetic drift.
B) The substitution rate is approximately the same in the two population.
C) The larger population generates more mutations and therefore has higher diversity and a higher substitution rate.
- A neutral allele is fixed in a population due to random genetic drift.
The average the time for fixation of a neutral mutation
A) is shorter in smaller populations.
B) is independent of population size.
C) is shorter in larger populations, because the mutation occurs more frequently in the larger population.
- On average it takes 4*Ne generations (Ne is the effective generation time) until a neutral mutation is fixed in a diploid population. An advantages mutation is fixed already after (2/s) ln (2Ne) generations.
How many generations will it take a neutral mutation to become fixed in populations of 1000, 10000, 200 000 individuals. How long would it take (according to the formula) for a mutation with a selective advantage of S=0.05 (or 5%)?
- Assume the the mitochondrial genome of Mitochondrial Eve did not provide a selective advantage over other versions of the mitochondrial genome. If Mitochondrial Eve (i.e. the ancestor of all mitochondrial genomes existing in the human population today) lived about 200 000 years ago, and if the average generation time of humans is 20 years, what estimate would result for the average population size.
- The fixation probability of a single neutral mutation in a population of 10 individuals as compared to a population of
200 000 organisms is
A) the same, B) higher, C) lower
- The time till fixation for a single neutral mutation in a population of 10 individuals as compared to a population of
200 000 organisms is
A) the same, B) shorter, C) longer
- The size of successive populations is 500, 8 billion, 8 billion, 8 billion, 8 billion. What is the "effective population size" for the 5 generations (ignoring spatial heterogeneity, mating etc.) ?
- Kimura's theory of neutral evolution says that
A) Most mutation are selectively neutral
B) Most differences between alleles coexisting in a population are selectively neutral
C) Evolution by natural selection does not occur
- The fact that some parts of proteins are under such a high selection pressure that hardly any amino acid substitutions occur in these regions is proof that Kimura's theory of neutral evolution is wrong. Correct / Incorrect
|