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/

Tutorial on the Bayesian skyline plot and the birth death skyline model

2019-02-18: TtB Skyline Plots

By Nicola Mueller

2019-02-18: TtB Skyline Plots

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