The aim of this course is to provide training in conceptual and practical aspects of biological systematics. Emphasis will be on the use of molecular data for phylogenetic inference. We will present and discuss the main methods of phylogenetic inference (parsimony, maximum likelihood and Bayesian inference), evolutionary models, data combinability, the estimation of divergence times and the use of quantitative approaches to species delimitation. We will also discuss several examples about the use of phylogenetic trees to address fundamental biological questions. In hands on computer sessions, we will introduce the most widely used computer programs for building alignments, selecting evolutionary models, inferring trees under alternative assumptions, estimating divergence times and delimiting species. Finally, students will present and discuss the results obtained during the course using their own data or, alternatively, with example cases provided by the instructors.
The course is aimed at advanced undergrads, PhD students, post-docs and faculty interested in the use of phylogenies for addressing evolutionary and ecological questions but with limited background / experience in systematics and phylogenetic inference.
Basic knowledge of statistics. All participants must bring their own personal laptop.
Monday, June 26th, 2017.
- Introduction to biological and molecular systematics, the basis and principles of phylogenetic inference.
- Gene tree vs. species tree. Homology and alignments.
- Hands on: Data format, Clustal, MAFFT, Gblocks, SeqState.
Tuesday, June 27th, 2017.
- Morphological data: coding, ordering and polarity.
- Gap treatment. Implicit weighting. Support and sensibility.
- Understanding phylogenies.
- Hands on: Mesquite, TNT.
Wednesday, June 28th, 2017.
- Evolutionary models and genetic distances.
- Algorithmic approaches to tree building, Maximum Likelihood and Bayesian Inference. Toplogy test.
- Hand on: PartitionFinder, jModeltest, MEGA; MrBayes; RaxML, CONSEL.
Thursday, June 29th, 2017.
- Morphology and Phylogeny, integrating morphological and molecular data.
- Hands on: BEAST, *BEAST.
Friday, June 30th, 2017.
- DNA and Integrative taxonomy: DNA barcoding, species trees and quantitative species delimitation.
- Hands on: SPLITS (GMYC), BPP.