Cursos de Postgrado

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Phylogenetic Approaches to Biodiversity II

Postgraduate course
2 - 4 November 2016

Sponsored by: Sociedad Chilena de evolution.
Faculty of ecology and natural resources.
Universidad Andrés Bello.

It organizes: Doctorate in Conservation Medicine.

It sponsors: FONDECYT 1130266.

Professor in charge

DRA. Samantha A. Price (University of California Davis)

Collaborators:

Dr. Christian M. Ibanez (Universidad Andrés Bello)
Dr. Eduardo Castro-Nallar (Universidad Andrés Bello)

DESCRIPCIÓN

This hands-on workshop will cover the primary phylogenetic comparative methods used to study the evolution of biodiversity. By the end of the workshop students will 1) Understand the fundamental models of character and lineage diversification 2) Know how to implement these models to test hypotheses using the R statistical framework 3) Understand some of the limitations of these methods and how to assess the appropriateness of the model. The workshop will integrate lectures, with hands-on demonstrations and in-depth exercises.

OBJETIVOS GENERALES

1. Understand the fundamental models of character and lineage diversification.
2. Know how to implement these models to test hypotheses using the R software.
3. Understand some of the limitations of these methods and how to assess the appropriateness of the model.


CONTENIDOS Y ACTIVIDADES

Wednesday 2 November
9:00 - 12:30
Basic tree and data manipulation and visualization in R. This is an introductory session covering the tree and basic data structures in R as well as the visualization of phylogenies and data.

  • Coffee Break
  • 12:30 - 14:00 almuerzo

14:00 - 16:00
Models of discrete character evolution. We will learn about continuous-time Markov models – what the assumptions of these models are and the effect of changing parameter values through simulation. We will also cover practical considerations when applying these models and their limitations.


Thursday 3 November
9:00 - 12:30
Models of continuous character evolution. Using simple simulations in R we will learn about Brownian motion, early burst and Ornstein-Uhlenbeck models of continuous character evolution – what the assumptions of these models are and the effect of changing parameter values. We will then learn how to fit these models to real trait data using several different R and estimate rates of evolution.

  • Coffee Break
  • 12:30 - 14:00 almuerzo

14:00 - 16:00
Models of lineage diversification. We will learn about Yule and Birth-Death models of lineage diversification using simulations and discuss diversity- dependent modifications to these models. We will then learn how to fit these models to real phylogenies data using several different R packages as well as BAMM.


Friday 4 November
9:00 - 12:30
Complex hypothesis testing. Many of the most interesting hypotheses concern how a particular ecological trait or environmental variable has influenced diversification rates of lineages or characters. We will discuss and implement the latest methods to test these hypotheses including state-dependent continuous trait evolution in the R package OUwie.

  • Coffee Break
  • 12:30 - 14:00 almuerzo

14:00 - 16:00
Using simulation to critically assess power and model-fit. Evolutionary models of diversification are necessarily simplistic, it is therefore important to understand the limitations these models, when they may be misleading or inappropriate, including when our datasets lack the power to detect the pattern we are interested in. Simulation and careful thought can help with these issues; we will cover the basic concepts of parametric-bootstrapping.


ESTRATEGIA DIDÁCTICA
El taller integrará conferencias, lecturas, demostraciones prácticas y desarrollo de ejercicios. Todo trabajo práctico será desarrollado en el ambiente estadístico R, empleando los paquetes ape, diversitree, caper, corHMM, expoTree, Geiger, phytools, Pmc, OUwie, TreeSim.

Evaluation
Students requiring evaluation should specify it in the letter of intent.

PLACE
The workshop will take place at the Faculty of ecology and natural resources, Universidad Andrés Bello, Republic 440, Santiago.

Prerequisites
It is suggested that each student bring their computer with the R packages already installed, as well as the software to be used during the practical activities: Diversitree, Phytools, Caper, Geiger, Bamm, among the most common.
While no course is requested as a prerequisite, it is preferable for participating students to have extensive knowledge in probabilistic and Bayesian statistics, Advanced Evolutionary Biology with Emphasis on Molecular Systematics, handling R software and using the required packages, as well as English language proficiency.

Inscriptions:
Para inscribirse enviar CV y carta de intención antes del 21 de octubre.
Dr. Christian Ibañez (UNAB) ibanez.christian@gmail.com
Consultas:
Elfego Cuevas (UNAB) elfcuevas@gmail.com
Mario Alvarado (UNAB) maalry@gmail.com