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Arrival and Departure
Thursday July 19 - Monday July 30
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 26 2018) 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.
- Morning: Introduction to the coalescent Coalescence2018talk
- Afternoon: extending the basic coalescent Coalescence2018talk2
- 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 bugsinbox.app).
- 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 26 2018. The tutorial is about estimating divergence times, gene flow, and model selection with MIGRATE 4.4. 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
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:
- Lecture on Bayes factor that may help to understand the tasks in the MIGRATE lab.
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: