Tutorials

Tutorial 1: Setting up and running PHRAPL (Beginners start here)

Simple example to get familiar with the basics of PHRAPL and analyze a simulated dataset of 3 populations.
Read these papers before starting the tutorial:

• Jackson N, Morales AE, Carstens BC, O’Meara BC (2017) PHRAPL: Phylogeographic Inference using Approximate likelihoods. Systematic Biology. 66:1045-1053.
  
• Carstens BC, Morales AE, Jackson N, O’Meara BC (2017) Objective choice of Phylogeographic Models. Molecular Phylogenetics and Evolution. 116:136-140.
  

Tutorial 2: Fixing migration time and performing sensitivity analyses (Intermediate)

Example to explore models with different intervals of migration and perform sensitivity analyses in subsets of loci. Dataset of 2 populations Plethodon salamanders.
Recommended reads of empirical examples before starting the tutorial:

• Morales AE, Jackson N, Dewey T, O’Meara BC, Carstens BC (2017) Speciation with gene flow in North American Myotis bats. Systematic Biology. 66:440-452.
• Denton RD, Morales AE, Gibbs HL (2018) Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species. Evolution. 72:1689–1700.

Tutorial 3: Testing species delimitation hypotheses (Advanced)

Example to test hypotheses of species limits (3 vs 2 vs 1). Simulated dataset.

Read this paper before starting the tutorial:

• Jackson N, Carstens BC, Morales AE, O’Meara BC (2017) Species delimitation with gene flow. Systematic Biology. 66:799-812.