TiLV quartet phylogenetic analysis to detect reassortment

To look for evidence of reassortment among the TiLV segments, we used the phylogenetic approach developed by Suzuki (2010) for human influenza A viruses. Using the seven TiLV isolates for which we had the full sequence of all ten segments, we selected every possible quartet (i.e. group of four isolates), 35 in total. For each quartet, we constructed ten neighbour-joining trees (one per segment) using the p-distance method with 1000 bootstrap replicates. A quartet can have only three resolved topologies (e.g. pairs A/B + C/D, or A/C + B/D, or A/D + B/C), so we then compared the tree topologies of all ten segments for each quartet and summarised them as a string of digits, representing segments 1-10, showing where the topology differed.<br>Suzuki, Y., 2010. A phylogenetic approach to detecting reassortments in viruses with segmented genomes. Gene 464, 11–16. doi:10.1016/j.gene.2010.05.002