FIG 1.

Deducing transmitted/founder (T/F) viruses. For each dataset, we generated a multiple-sequence alignment of stock and animal Env sequences. A distance matrix computed from the alignment guided the construction of a neighbor-joining (NJ) phylogenetic tree. To identify a single T/F virus per transmission event, we selected the predominant recipient lineage from the NJ tree. The predominant lineage (orange box) was defined as the set of recipient (blue) sequences whose closest neighborhood consisted of 90% or more recipient sequences. The T/F virus was deduced as the consensus of the sequences in the predominant recipient/transmitted lineage.