Monday – Classes from 09:00 to 17:00 - “DNA and phylogenies”

 

 

Session 1: Introduction (morning)

 

In this session I will kick off with an introduction lecture about the rationale of including DNA sequences and molecular phylogenies in ecological studies. I will use this introduction to motivate the four days of the course. Next, I will explain some theory on molecular phylogenies and which kind of data is needed to obtain phylogenetic reconstructions. Through the morning we will start obtaining our first phylogenies to be used in the following days.

 

 

 

Session 2: Molecular phylogenies (afternoon)

 

 

During the afternoon, we are going through some of the available and easy methods to obtain phylogenies with distance-based (e.g. Neighbour Joining), maximum likelihood, and Bayesian methods. The aim is to understand the use, potentials, and limitations of molecular phylogenies, and to be comfortable with them.

 

 

 

 

Tuesday– Classes from 09:00 to 17:00-  “DNA taxonomy”

 

 

Session 3: Molecular phylogenies continues (morning)

 

We will finish some of the analyses that we started the previous day.

 

 

Session 4: DNA taxonomy (afternoon)

 

This module will introduce the rationale of using DNA sequence data and molecular phylogenies to delimit species. We will cover in detail DNA barcoding and the use of BOLD and BIN, Automatic Barcode Gap Discovery, K/theta, Poisson Tree Process, Generalised Mixed Yule-Coalescent model, haplowebs, and then move to a brief overview of more sophisticated multi-locus methods. Some notion of metabarcoding will be introduced as well. The module on DNA taxonomy will be a mix of theory and hands-on practical exercises for each approach.

 

 

 

 

Wednesday –Classes from 09:00 to 17:00 - “Phylogenetic comparative methods”

 

 

Session 5: Phylogenetic structure in comparative data (morning)

 

We are going to show how statistical analyses comparing traits between species can provide spurious results if the confounding factor of phylogenetic non-independence of the data is not included in the analyses. After going through the methods that are currently used to look for a phylogenetic signal in the data, we will move to statistical approaches that include such phylogenetic structure in the statistical analyses (e.g. Phylogenetic Independent Contrasts and Phylogenetic Generalised Least Squares).

 

 

 

Session 6: Phylogenetic structure of communities (afternoon)

 

This module will explore the possibilities that are available to understand if there is a phylogenetic structure in community datasets, and which consequences it could have in the interpretation of the results of analyses in community ecology.

 

 

 

 

 

Thursday – Classes from 09:00 to 17:00 - “Apply your knowledge to real world”

 

 

Session 7: Group Tasks (morning)

 

In this session, each attendee will present its research project and how molecular phylogenies could be used to address some questions in its own research agenda.

 

 

 

Session 8: Journal club (afternoon)

 

 

In this session, we will discuss three recently published papers that we selected together on Tuesday. The discussion will focus on how to present the results, potential pitfalls and problems, and how to include new methods and approaches in one’s own work.

 

The session is followed by a general discussion about the course.