Fig. 1

Our approach. Left: The red and blue areas represent regions of the sequence landscape of sequences with “good” affinity (i.e. sufficient to carry the associated function) to the target structures \(\mathcal {S}\) (red) and \(\mathcal {S}'\) (blue). Here, α and α ^′ are paralogous sequences, as well as β and β ^′, γ and γ ^′ and δ and δ ^′. Using classical reconstruction approaches, \(\mathcal {A}\) would be the inferred ancestor of the orthologous sequences α, β, γ and δ, and \(\mathcal {A}'\) would be the inferred ancestor of the orthologous sequences α ^′, β ^′, γ ^′ and δ ^′. Shaded trees represent the classical ancestral reconstructions performed separately, while the main tree rooted at \(\mathcal {A}\mathcal {A}'\) represents the simultaneous ancestral reconstruction approach introduced in this contribution. The rationale of this work is that ancestors inferred from a single family and structure may have a tendency to be located in the core of the affinity regions, and might end up with ancestral sequences that would be hard to reconcile. By contrast, a simultaneous reconstruction of orthologous families ensures the coherency of the process and a better inference of the ancestors (which are not necessarily located in the core of the affinity regions). Right: An example of a species tree T (dashed lines) of four species A, B, Γ and Δ corresponding to the neutral networks shown on the left. A duplication event is shown at the root, creating the two ncRNA families (represented by colored lines). Each node of the species tree contains a copy of each ncRNA family (one red, one blue). At the leaves of the species tree T, we find the two extant ncRNAs for which we have the sequence and the structure information. The linear gradient G is also shown: it represents the weight that is given to each structure when calculating the costs (G for one structure and 100 %-G for the other)