Cursos de Postgrado

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Phylogenetic Approaches to Biodiversity II

Curso de Postgrado
2 – 4 noviembre 2016

Auspician:   Sociedad Chilena de Evolución.
Facultad de Ecología y Recursos Naturales.
Universidad Andrés Bello.

Organiza:    Doctorado en Medicina de la Conservación.

Patrocina:   FONDECYT 1130266.

Profesor encargado

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

Colaboradores:

Dr. Christian M. Ibáñez (Universidad Andres Bello)
Dr. Eduardo Castro-Nallar (Universidad Andres 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

Miércoles 2 de noviembre
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.


Jueves 3 de noviembre
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.


Viernes 4 de noviembre
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.

EVALUACIÓN
Los estudiantes que requieran evaluación deben especificarlo en la carta de intenciones.

LUGAR
El taller tendrá lugar en la Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, República 440, Santiago.

PRERREQUISITOS
Se sugiere que cada uno de los alumnos traiga su computadora con los paquetes de R ya instalados, así como los softwares que se emplearán durante las actividades prácticas: Diversitree, Phytools, Caper, Geiger, BAMM, entre los más comunes.
Si bien como prerrequisito no se solicita ningún curso, es preferible que los alumnos participantes tengan amplios conocimientos en estadística probabilística y bayesiana, Biología Evolutiva Avanzada con énfasis en Sistemática Molecular, manejo del software R y uso de los paquetes requeridos, así como dominio del idioma inglés.

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