Filogeografía: genética evolutiva espacial
Laboratory excercises in evolutionary genetics
Here are some newer and some older labs from the various incarnations of my Filogeografía course. Most of these lab assignments were designed to be adaptable to any DNA sequence dataset relevant to phylogeography. Click on "Laboratory X" below to download PDF version. For more information, you can email me at andrew-∀-dna.ac (replace "-∀-" with "@", obviously).
Laboratory A: Finding a dataset to re-analyze.
Laboratory B: Alignment and visualization of your data.
Laboratory C: 2009 version: Coalescent simulations using SIMCOAL.
Laboratory D: Summary statistics & population genetic tests using dnaSP.
Laboratory E: Estimating population divergence time and migration rates with IM.
Laboratory F: Calculating F-ST and creating a haplotype network.
Laboratory G: Nested Clade Phylogeographic Analysis (not recommended).
Laboratory H1: 2009 version: Model selection with jModeltest v. 0.1.1 (PAUP* optional).
Laboratory H2: 2009 version: Liklihood ratio test of the molecular clock hypothesis using PAUP*.
Laboratory I: Bayesian phylogenetic inference using MrBayes.
Laboratory Ja: Phylogenetic hypothesis testing with the SH test in PAUP*.
Laboratory Jb: Simple tools for estimating divergence times from phylogenetic data using MEGA, PAUP*, and TreeEdit.