Molecular phylogenies in biodiversity
Dates 9-13 April 2018
Dr. Diego Fontaneto (CNR, ITALY)
This course will introduce ecologists interested in biodiversity to the use of molecular phylogenies to address questions that cannot be addressed by using only ecological data in their studies. After a short introduction on how to obtain reliable molecular phylogenies, the focus of the questions that could be addressed will be on taxonomy, community ecology, and comparative methods.
TARGETED AUDIENCE & ASSUMED BACKGROUND
The course is aimed at early-career researchers (PhD students, early postdocs) in ecology interested in widening their analytical toolbox. The course is structured in a way that even an inexperienced and naïve attendee could take advantage of the possibilities offered by the inclusion of molecular phylogenies in its analyses. There will be a mix of lectures and hands-on practical exercises using freely available software and online resources. Most of the steps will be performed in R, but no previous knowledge on this statistical platform is required. All scripts will be carefully explained to allow all attendees understanding the rationale and usage of the statistical approaches.
- Understand how to read, interpret and obtain molecular phylogenies, with a focus on the concepts and rationale behind phylogenetic methods
- Learn tools from DNA taxonomy
- Learn how to include phylogenies in the analyses of community ecology and in comparative analyses
- Hand-on experience on all the steps
- Being comfortable with using R when including molecular phylogenies in ecological analyses
Monday – Classes from 09:30 to 17:30 - “Molecular phylogenies”
Session 1: Introduction (morning)
In this session I will kick off with an introduction lecture about the rationale of including molecular phylogenies in ecological studies. I will use this introduction to motivate the five-day 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, 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 09:30 to 17:30 - “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, Automatic Barcode Gap Discovery, K/theta, Poisson Tree Process, Generalised Mixed Yule-Coalescent model, haplowebs, and then move to more sophisticated multi-locus methods. The module will be a mix of theory and hands-on practical exercises for each approach.
Wednesday – Classes from 09:30 to 17:30 - “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 09:30 to 17:30 - “Apply your knowledge to real world”
Session 7: Group Tasks (morning)
Students will work in groups on a specific question they choose to analyse. Then, they will explain to all the others what analysis they would do, which data is required, and why. Then, they will perform the analyses.
Session 8: Group Tasks continues (afternoon)
For the rest of the day, groups are going to finish the analyses, and then explain to the others which problems they encountered and which results they obtained.
Friday – Classes from 09:30 to 17:30 - "Already an expert?"
Session 9: Who we are and what we do (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 10: Journal club (afternoon)
In this session, we will discuss three recently published papers that we selected together on Wednesday. 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. This is followed by a general discussion about the course and the group tasks.
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