Phylogenetic reconciliation
Fig 6
Inter-host and intra-host horizontal gene transfers between symbionts.
Higher level of organization can shed light on lower levels reconciliation. In this example, the goal is to reconstruct the history of a gene present in a symbiont genome. A single transfer and a single loss of gene is the most parsimonious scenario for the reconciliation of the gene tree with either the host or the symbiont tree. Yet when considering the reconciliation of the symbiont and host trees, this scenario implies a gene transfer between two symbionts across branches of the host tree (left). Such an inter-host transfer should be considered unlikely because a series of hidden events are necessary for the gene to come in contact with its next recipient symbiont. Considering the three levels together puts forward a new scenario without inter-host transfer (right) which is slightly less parsimonious in two-level reconciliations, but implies a more likely event of gene transfer within host.