Exploring the space of gene/species reconciliations with transfers
Résumé
Reconciliations between gene and species trees have important applications
in the study of genome evolution (e.g. sequence orthology prediction or quantification
of transfer events). While numerous methods have been proposed to infer them, little
has been done to study the underlying reconciliation space. In this paper, we characterise
the reconciliation space for two evolutionary models: the DTL (duplication,
loss and transfer) model and a variant of it—the no-TL model—which does not allow
TL events (a transfer immediately followed by a loss). We provide formulae to compute
the size of the corresponding spaces and define a set of transformation operators
sufficient to explore the entire reconciliation space.We also define a distance between
two reconciliations as the minimal number of operations needed to transform one
into the other and prove that this distance is easily computable in the no-TL model.
Computing this distance in the DTL model is more difficult and it is an open question
whether it is NP-hard or not. This work constitutes an important step toward reconciliation
space characterisation and reconciliation comparison, needed to better assess
the performance of reconciliation inference methods through simulations.
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