Foundations of Phylogenetic Inference

About the course  |  Intended audience  |  Prerequisites  |  Content details  |  Scheduled events

About the course

Phylogenetic methods use molecular sequence data to reconstruct evolutionary relationships between organisms and genes. This course provides an introduction to the principles and practice of molecular phylogenetic inference, from preparing sequence data through to interpreting phylogenetic trees.

Participants will learn the fundamental concepts of phylogenetic analysis, including what phylogenetic trees represent and how to interpret them. The course covers the generation of multiple sequence alignments from DNA and protein sequences and discusses the strengths and limitations of different alignment approaches.

The course then introduces methods for phylogenetic tree reconstruction, with a particular focus on maximum likelihood inference and assessing confidence in inferred relationships using bootstrap resampling. Finally, participants will be introduced to Bayesian approaches for estimating uncertainty in phylogenetic parameters and incorporating additional information into more advanced phylogenetic analyses.

By the end of the course, participants should be able to reconstruct and critically interpret molecular phylogenies and make informed choices about phylogenetic methods and software.

Teaching is primarily hands-on, with short presentations and demonstrations introducing the concepts and methods needed to construct and interpret phylogenetic trees.

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Intended audience

This course is suitable for:

• researchers with little or no prior experience in phylogenetic analysis
• participants interested in constructing phylogenies from relatively small sequence datasets, including viral genomes and targeted regions of eukaryotic genomes
• researchers seeking practical experience with phylogenetic inference methods and software
• participants interested in interpreting evolutionary relationships using molecular data

This course does not cover topics in phylogenomics or bacterial genomics.

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Prerequisites

Participants should have:

• familiarity with the UNIX command line
• familiarity with basic concepts in evolution, including common ancestry, sequence divergence through mutation, and natural selection
• basic experience examining DNA and protein sequence data

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Content details

The course covers the following topics:

• Introduction to molecular phylogenetics
  Introduces the principles of molecular phylogenetics, what phylogenetic trees represent, and how evolutionary relationships can be inferred from molecular sequence data.
• Multiple sequence alignment
  Covers the generation of multiple sequence alignments from DNA and protein sequences and discusses the advantages and limitations of different alignment algorithms. Participants will also learn how to recognise quality issues in alignments.
• Phylogenetic tree inference
  Introduces methods for reconstructing phylogenetic trees, with a focus on maximum likelihood approaches and selecting appropriate substitution models for sequence data.
• Assessing confidence in phylogenetic trees
  Covers the use of bootstrap resampling to assess the robustness of inferred trees and discusses the interpretation and limitations of bootstrap support values.
• Sequence and tree file formats
  Introduces standard file formats used in phylogenetic analyses, including FASTA for sequence data and Newick for phylogenetic trees, and demonstrates tools for manipulating and visualising these data.
• Bayesian phylogenetic inference
  Introduces Bayesian approaches for phylogenetic analysis and demonstrates how these methods can be used to estimate uncertainty in tree parameters and infer divergence times.
• Phylogenetic applications
  Discusses applications of phylogenetic methods and how phylogenetic inference can be used to address evolutionary and biological questions.

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