Phylogenetic reconciliation
Fig 5
Illustration of input, output and events, of published methods which can be identified with 3-level methods. The formalism is similar to the one on Fig 4. Multiple gene lineages can undergo joint events like whole genome duplication (A) or segmental events (B), some events might be more probable than others, like specific horizontal transfers with highway of transfers or hybridization (C). Cophylogenetic patterns can be compared, to see for instance if the common pattern of a host and a symbiont are not just the common pattern of the symbiont and the geography (D). Characters can evolve on reconciled phylogeny, like gene synteny (E), or two levels can be reconciled with the constraint of an upper one (F). Transfers can be upper dependent, more likely between two intermediate entities that belong to a same upper one (G). Three levels can be reconciled together, sequentially, the intermediate in the upper before adding the lower, or trying to find a joint most parsimonious scenario for the two reconciliations (H). These multi-level models can also be used to reconstruct the intermediate phylogeny (I).