File:Phylogenetic Reconciliation Summary.svg
This table is intended to serve as illustration to the 2-Level reconciliation section of Menet et al. (2022) Phylogenetic reconciliation. PLoS Comput Biol 18(11): e1010621. doi:10.1371/journal.pcbi.1010621 and can be read along it.
- Adding the horizontal Transfer event adds 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).
- Dynamic programming is limited by the fact that it assumes independence between sister lineages, which 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.