Fig 1.
A phylogenetic reconciliation between an upper, blue, and a lower, red, tree, with the most often used evolutionary events (S,D,T,L), and their name in phylogeography, host/symbiont and gene/species frameworks. For instance S event is called allopatric speciation when reconciling geographical areas and species, cospeciation between host and symbiont, and speciation for gene and species, but always correspond to the same co-diversification pattern.
Fig 2.
Reconciliation and biological levels of organization.
Phylogenetic trees are intertwined at all levels of organization, integrating conflicts and dependencies within and between levels. Macro-organism populations migrate between continents, their microbe symbionts switch between populations, the genes of their symbionts transfer between microbe species, and domains are exchanged between genes (left third). This list of organization levels is not representative or exhaustive, but give a view of levels where reconciliation methods have been used. As a generic method, reconciliation could take into account numerous other levels, for instance it could consider the syntenic organization of genes [155,160], the interacting history of transposable elements and species [180], the evolution of protein complex among species [181]. The scale of evolutionary events considered can go from population events such as geographical diversification to nucleotides levels one inside genes [34], including for instance chromosome levels events inside genomes such as whole genome duplication [155].
Fig 3.
Pocket gophers and chewing lices.
Tanglegrams and two proposed reconciliation scenario for pocket gophers and their chewing lices symbionts. For the host, O. stands for Orthogeomys, G. for Geomys and T. for Thomomys; for the symbiont G. stands for Geomydoecus and T. for Thomoydoecus.
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.
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).
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.
Fig 7.
Reconciliation inference software.
Reconciliation software that aim at inferring reconciliation scenarios.
Fig 8.
Reconciliation software which primary goal is not to infer reconciliation scenarios. Most of them are used for tree correction using reconciliation score, some are used for rates inference or graphical visualization of scenarios.