Based on notes by Ida Moltke
The time scale in the trees we have been looking at so far is 2N (assuming we are looking at a diploid organism), where N is the population size. With this in mind answer the following questions:
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How would you expect a tree for five gene copies from a population of size 1000 to differ from a tree for five gene copies from population of size 2000? (if we drew them in real time scale)
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The tree below is simulated assuming a constant population size:
How would the shape of this tree be different if the population size had not been constant, but instead to population size had been 10 times bigger from the time point indicated with ^ to the present? (i.e. the population had increased dramatically in size recently)
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And what if the population size change had not been an increase but instead a decrease?
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And by the same logic, which of the following trees do you think are simulated under decreasing population size, constant population size and increasing population size?
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Which categories would a Site Frequency Spectrum (SFS) for five gene copies have? (e.g. singletons, doubletons,…?)
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Which of these categories would the mutation in this tree (marked by a red star) contribute to:
- Which category of the SFS would this mutation contribute to in an SFS:
- Draw a SFS based on this tree:
Usually the number of mutations that happen on a branch is proportional to the length of the branch. With this and your answers in exercise 1C and 1D in mind answer the following questions:
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How do you think population growth affects the frequency spectrum?
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How do you think population size decrease affects the frequency spectrum?