Theory

Introduction

• Phylogenetic reconstruction typically involves assuming that the sequences have evolved in a tree like way
• Recombination can lead to different regions of the genome having different evolutionary histories
  • Different trees for different regions
  • Overall, a phylogenetic network

The impact of recombination

• Recombination can lead to (incorrect) 'star-like' trees
• Recombination can lead to incorrect estimates of evolutionary rates

Recombination clues

• Outlying sequences
• Sequences isolated between clusters of similar sequences
• Significantly different trees from different parts of the genome

Testing for recombination

• A comprehensive list of recombination analysis/detection software is maintained by David Robertson's lab here

Approaches for recombination

• The best way to detect recombination depends on the pattern of recombination
  • Single recombinant sequence or several
  • Single breakpoint
  • Recombinant segment

Examples of recombinant structures in HIV

• Take a look at this list of recombinant forms of HIV
• This shows how rich recombinant structure can be