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