Skyline Plots
https://slides.com/nicolamueller/skyline-plots
Bayesian Analysis requires to put priors on everything
What are tree priors?
- Backwards in time Coalescent processes
- Forward in time Birth-Death processes
Tree priors are tree generating processes
Coalescent processes model the coalescence of lineages from present to past
Coalescent processes model the coalescence of lineages from present to past
Coalescent processes model the coalescence of lineages from present to past
Coalescent processes model the coalescence of lineages from present to past
Changing the number of bubbles through time can be used to model population dynamics
Drummond et al. 2003
Birth-death models model the birth, death and sampling of lineages
Coalescent
- Conditions on sampling, assumes only a small portion of the population is sampled
- Effective population size corresponds to "size of a population"
- 1 parameter to infer
Birth-Death
- models the sampling process
- birth and death rates correspond to how "a population is changing" (growing declining)
- 3 parameters out of which two can be inferred.
How do birth-death and coalescent models differ?
- In the way the times of rate changes are defined.
- In the smoothing priors.
How do birth-death and coalescent models differ
Skyline plots allow to have different rates or effective population sizes at different points in time.
- In the way the times of rate changes are defined.
- In the smoothing priors.
How do different skyline models differ?
https://taming-the-beast.org/tutorials/Skyline-plots/