English: 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.

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, the interacting history of transposable elements and species, the evolution of protein complex among species. The scale of evolutionary events considered can go from population events such as geographical diversification to nucleotids levels one inside genes, including for instance chromosome levels events inside genomes such as whole genome duplication.