NOTE: The hardcopies of the parts of this assignment are due at the beginning of the class period. This means that if you are even a minute late, you lose 20%. If you are worried about potentially being late, turn in your assignments ahead of time. Do this by submitting them to me during office hours or by sliding them under my office door. Electronic copies are due by 4:00 pm on the due date. Submit them through D2L before the time they are due. Do not send assignments to me through email or leave them in my departmental mail box.
It is known that in evolutionary systems with only selection and no mechanism for introducing variation, populations will shift composition, monotonically losing diversity (as measured by total distinct genomes), until they converge to a fixed point in which all members of the population are identical. This is even true when selection is “neutral,” that is, stochastic with no bias toward any particular genome, in which case this shift is known as “drift.” Convergence is an important feature of selection-only evolutionary systems that should be understood to comprehend more complex evolutionary systems in which variation can take place.
The goal of this assignment is to give you experience with selection-only models of evolutionary computation.
De Jong gives good empirical evidence that the average rate of of genome loss under neutral selection is approximately one genotype every two generations for several population sizes from 200 on down, although there is a wide variance. However, he does not give an estimate for the rate of genome loss on a per generation basis. Your job is to provide that estimate, at least for one population size.
Assume that you begin with a population P(0) of 100 individuals, each with its own unique genotype. Answer the following questions:
You will turn in both a typed hard copy and a machine readable electronic copy of your homework that answers the questions above, including your explanation and justification. If your approach is empirical, you will also need to submit both hard and electronic copies of your code and an electronic copy of all data generated.