Peter Beerli

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Arrival and Departure

Thursday July 20 - Monday July 31

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 (Thursday July 27 2017) I will introduce the coalescent and its use for population genetics inference, the first section of the lecture will discuss basics, in the afternoon I will talk about extensions of the basic coalescent, more focused on population processes than speciestrees/genetrees that are discussed by Laura Kubatko and also will talk about the assumptions and problems in more detail.

Teaching Tools

  • Bugs_in_box is a 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
  • PopVizard is a python program that allows to plot pictures of population genealogies like the ones on this page.

Demo and Tutorials

  • MIGRATE tutorial on Thursday July 27 2017. The tutorial is about estimating divergence times, gene flow, and model selection with MIGRATE 4.3. An older gene flow tutorial for 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

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:

MIGRATE can run on many different operating systems and hardware, most efficiently it can run on computers that have more than one core (almost all these days) using parallelization:

Even more talks on the coalescent

Software demonstrated in the course


Other things I like

Waterfrogs, Mountains, Cooking [for example this Swiss recipe], and Art