Reading: Volz, E. M., Kosakovsky Pond, S. L., Ward, M. J., Leigh Brown, A. J., & Frost, S. D. (2009). Phylodynamics of infectious disease epidemics. Genetics, 183(4), 1421-1430. https://doi.org/10.1534/genetics.109.106021.
Note on grading: Class 2 was graded as: 0 points for not attending; 1 point for attending but not contributing; 2 points for attending and contributing. Overall, the discussion was constructive and participation was broad, so we will follow the same format for next class. If you were not in a position to participate, you should consider preparing a discussion point in advance. The goal is for everyone to participate in every class.
You are expected to spend at least 2hr studying this paper. A key theme is the extent to which Kingman’s coalescent needs modification when the population size is changing rapidly. Inference typically proceeds via the log-likelihood function given in equation (12), so that is worth special attention.