Theory

Introduction

• Often, we are interested in structured populations
  • Host type
  • Country
• We would like to be able to include this information in our analyses to ask questions such as:
  • When did a virus jump host?
  • What was the geographic spread of a virus

'Mugration' models

• Most commonly, categorical traits are modelled as if they were mutations
  • No association between the tree structure and the trait
• This is for computational efficiency
• Can be very vulnerable to sampling biases
  • Example of influenza A spread and India

Structured coalescent models

• Structured coalescent models permit interactions between the tree structure and the trait
• Much slower to run
• More robust to sampling biases