Modeling the selection pressure on miRNA target sites. a. The phylogenetic tree of the species in the clade (here flies) is rooted at the reference species (here melanogaster) and selection is modeled starting from the root and moving down the tree (see Methods for details). At each internal node k there are probabilities for selection to be maintained in one or both children of the node (see Methods for details). b. Relationship between selection and conservation patterns: Example of a selection pattern on a particular set of orthologous target sites in flies. Open circles indicate absence of selection pressure, closed circles indicate presence of selection pressure. Selection pressure is absent in Drosophila ananassae, mojavensis and virilis (D.ananassae, D.mojavensis, and D.virilis). The possible conservation patterns consistent with the selection pattern for this target site are listed in the table. The site needs to be conserved in all species in which selection pressure operates, namely Drosophila simulans, yakuba and pseudoobscura (D.simulans, D.yakuba, D.Pseudoobscura). In the species in which selection pressure does not operate, the site may or may not be conserved.