Peter Beerli
Peter Beerli

Institutional home page

http://people.sc.fsu.edu/~beerli

Arrival and Departure

May 24 - June 4, 2024

Lecture Materials

Note: The presentations may change up until the moment the lecture or lab begins. I will try to post the modified the PDF before the lecture but will post the actual talk-PDF after each talk.

Coalescence lecture (Tuesday, May 28/29 2024): I will introduce the coalescent and its use for population genetics inference. The first section of the lecture will discuss basics; in the second part I will discuss extensions of the basic coalescent. I will focus on neutral population processes, such as population structure, population size changes through time, population divergence, and problems and complications with inferences using the coalescence.

Teaching Tools

Wright-Fisher Model
Wright-Fisher Model
  • Bugs_in_box is a python3 program that visualizes coalescence of bugs (well they are ladybugs and beetles) in a box. They crawl like crazy until they hit another bug, devour it and move on. There is a help menu (press H) that displays all options. This application has a few shortcomings: (1) it does not adjust well for different screen size (for example presentation beamers make the bugs huge); (2) No way to save or print directly out of the app, but Dave Swofford contributed a fun spin when there are two bugs left (see help menu in python bugsinbox.py).
  • PopVizard is a python program that allows to plot pictures of population genealogies like the ones on this page.

Demo and Tutorials

Canning Model
Canning Model
  • Population-model selection using MIGRATE on May 29 2024. The tutorial guides you on estimating the most likely path of the Zika virus and discusses estimation of divergence times, gene flow, and model selection with MIGRATE 5.0.6. An older gene flow tutorial using the older version of migrate 3.x: PDF).
  • If students are interested I am also happy to talk about LAMARC and give a Lamarc tutorial: Recombination estimation with LAMARC

Bayes factors and effect of parallel runs of MIGRATE

Moran Model
Moran Model

This year I will have less time to introduce Bayes factor analysis in MIGRATE (but you will hear about them in Paul Lewis lecture). I gave in 2011 this lecture:

Even more talks on the coalescent

Software demonstrated in the course

Migrate software

Other things I like

Frogs and Toads
Frogs and Toads
Mountains
Mountains
Cooking
Cooking
Art
Art