(9) (20 pts, graduate/Extra credit): You wish to learn about the long-term human population size. First you sequence 1 Mb of Y chromosome DNA in a sample of 2 chromosomes. You detect 200 differencesbetween this pair of chromosomes. Assume a per base pair per generation mutation rate of 2 x 10-8 for all parts of this question.
(a) Estimate the effective number of males (Nm) from these data.
You also sequence a 1Mb stretch of the autosomes in a sample of 2 chromosomes. You detect 1000
differences between this pair of chromosomes. Assume that this autosomal sequence does not undergo any recombination.
(b) Estimate the effective population size (Ne) of humans from these data.
(c) Assuming there is an equal number of breeding males and females in the population (), what do you expect the ratio of genetic diversity on the Y chromosome relative to the autosomes to be? In other words, πY/πAuto=?
(d) How does your observed ratio compare to this prediction?
(e) Can you conclude that Nm<<Nf based on these results? Hint: Remember what you have sequenced. Hint 2: Recall the variance of coalescent times.
(f) Assume that you were able to conclude that Nm<<Nf. What does this result mean biologically?