Reading: Vaughan, T. G., & Stadler, T. (2025). Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data. Molecular Biology and Evolution, 42(6), msaf130. https://doi.org/10.1093/molbev/msaf130.
This is a recent paper bringing us up-to-date with progress from the Stadler group on phylodynamic inference. The model class generalizes the birth-death models of Stadler (2010) in a similar way to the way Volz (2012) generalized Volz et al. (2009).
The methods involve particle filters, building on previous work by Vaughan et al (2019) that proposes a filter methodology similar to the more complete framework developed by King, Lin & Ionides (2022).
As before, you can get your class participation credit by submitting ahead of class, in writing, a few sentences describing (i) something you got out of reading this paper; (ii) something you got stuck on trying to understand. You can email this to ionides@umich.edu and kingaa@umich.edu with subject “700 participation”.
Note that each class is graded with one point for attendance and one for participation.