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Module 14: Phylogenetic analysis

2024-01-27

Overview

Module 14 introduces students to the field of phylogenetic analysis, a method used to infer the evolutionary relationships among various biological species or entities based on genetic information. This module will cover the principles of phylogenetics, the types of data used for constructing phylogenetic trees, and the different algorithms and software tools available for tree construction and analysis. Students will learn how to draw phylogenetic trees and interpret them to understand the evolutionary history and relationships of organisms. Practical labs will provide hands-on experience in phylogenetic tree construction and analysis, reinforcing the theoretical concepts taught.

Introduction

  • The concept of phylogenetics and its significance in understanding evolutionary biology
  • An overview of the types of phylogenetic trees, including rooted and unrooted trees
  • The role of molecular data in reconstructing the evolutionary history of organisms

Topics

Fundamentals of Phylogenetic Analysis

  • Understanding the basic concepts of phylogenetics, such as homology, convergence, and divergence
  • The use of molecular sequences (DNA, RNA, proteins) in phylogenetic studies
  • The criteria for selecting appropriate genetic markers for phylogenetic analysis

Data Preparation for Phylogenetic Analysis

  • Methods for sequence alignment and the importance of accurate alignment in phylogenetic inference
  • The selection of outgroups and the determination of ingroup taxa
  • Dealing with missing data and sequence variability

Phylogenetic Tree Construction Methods

  • Overview of the different methods for tree construction, including distance-based, maximum parsimony, maximum likelihood, and Bayesian inference
  • The strengths and limitations of each method and their appropriate applications
  • Introduction to software tools for phylogenetic analysis, such as MEGA, RAxML, and BEAST

Drawing Phylogenetic Trees

  • Step-by-step guide to constructing phylogenetic trees from molecular data
  • Understanding tree topologies and branch lengths
  • The use of tree visualization software like FigTree and iTOL

Interpreting Phylogenetic Trees

  • How to read and interpret phylogenetic trees, including the significance of tree branches, nodes, and support values
  • The application of phylogenetic trees in taxonomy, systematics, and comparative genomics
  • The use of phylogenetic trees in studying population structure, gene flow, and evolutionary processes

Labs

  • Lab 1: Sequence Alignment and Preparation for Phylogenetic Analysis
  • Lab 2: Constructing Phylogenetic Trees Using Different Methods
  • Lab 3: Visualization and Interpretation of Phylogenetic Trees

Learning Outcomes

By the end of this module, students will be able to:

  • Explain the principles of phylogenetic analysis and its importance in evolutionary biology research.
  • Prepare molecular sequence data for phylogenetic analysis, ensuring accurate alignment and selection of genetic markers.
  • Construct phylogenetic trees using various methods and software tools.
  • Draw and visualize phylogenetic trees, understanding the information conveyed by tree topologies and branch lengths.
  • Interpret phylogenetic trees to infer evolutionary relationships and historical events.
  • Apply phylogenetic analysis to address questions in taxonomy, systematics, and evolutionary biology.
  • Communicate the results of phylogenetic analyses effectively in both written and oral formats.