Phylogenetic reconciliation
Fig 4
Reconciliation methods and summary.
Illustration of reconciliation events, inputs, outputs, and computational difficulties. This table is intended to serve as illustration to Development of phylogenetic reconciliation models section and can be read along it. Inputs are on the left of entries, output on the right. Upper trees are drawn in blue, lower trees in red. Adding the horizontal Transfer event add new more parsimonious solutions compared to the previous DL model (A). With this new event, costs must be assigned to D,T and L events, and different costs give different solutions (B). Not all scenarios including transfers are time feasible. Some might include time constraints incompatible with the upper tree (C). Transfer can go from a species to one of its descendant via a sister lineages that went extinct (D). In biogeography, a tree like structure can be constructed to account for the possible migrations between different geographical areas (E). In some cases, an exponential number of scenarios might be most parsimonious, for example when two equivalent patterns have the same cost (F). The lower tree can be unrooted (G), multifurcating (H), or given as a sample of potential trees (I) and reconciliation can be used to resolve those uncertainties to get a binary rooted lower tree. Reconciliation score can also be used to help construct an upper tree (J). The dynamic programming is limited, by the fact it assume independence between sister lineages, that makes it unable to consider replacing transfers or gene conversion (K), as well as Failure to diverge (L) and Incomplete Lineage Sorting (M), two population level events.