Materials are being updated (will be available on Wednesday August 18)
Smithsonian Species Delimitation Workshop
August 16-20, 2021 – PHRAPL workshop held on August 18 from 1:00 pm to 2:30 pm (GMT-4). Zoom link (you may need to pre-register). Join the Slack channel.
Installation
Please, install `PHRAPL` before the tutorial session begins.
– Create conda environment and install PHRAPL
Tutorials
Tutorial 1: The basis of demographic model selection with PHRAPL
Simple example to get familiar with the basics of PHRAPL and analyze a simulated dataset of 3 populations. Has gene flow been an important process in my study organism(s)? Exploring a wide set of models, with and without gene flow, will help you to infer what parameters should be included in your set of models to be tested.
Reference papers:
- 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: Sensitivity analyses and fixing migration time
Part 1: Perform sensitivity analyses in subsets of loci. Do I need more data? Calculating model probabilities (~wAIC) with different number of loci can help you answer that question. Dataset of 2 populations of Plethodon salamanders, includes haploid and diploid loci.
Part 2: Compare models with gene flow that occurred at different time intervals. Gene flow has occurred among divergent groups/populations/species. When did it start or stop?” This analysis will help to address such a question. Dataset of 2 unisexual and sexual species of Ambystoma salamanders.
Recommended reads of empirical examples:
- Bats – 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.
- Salamanders – 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.
- Penguins – Mays H, Oehler D, Morrison K, Morales A, Lycans A, et al., Weakley L (2019) Phylogeography, population structure, gene flow and species delimitation in Rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi). Journal of Heredity. esz051, doi.org/10.1093/jhered/esz051.
- Plants – Ruffley M, Smith ML, Espíndola A, Carstens BC, Sullivan J, Tank DC. Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Mol Ecol. 2018; 27: 1012– 1024.
Tutorial 3: Species delimitation
Is there enough information in my data to infer how many groups are diverging independently? This example will guide you for how to test the existance of 1, 2, or 3 species. Simulated data with the first three models from Tutorial 1.
Reference papers:
- Jackson N, Carstens BC, Morales AE, O’Meara BC (2017) Species delimitation with gene flow. Systematic Biology. 66:799-812.
Workshop Info
– Agenda
– Workshop GitHub - materials for other packages
Contact Rebeca Dikow dikowr@si.edu or Andrea Quattrini QuattriniA@si.edu if you want to access recored materials after the workshop.