Abstract: Classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is clearly not suited for genes grouped in syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation model, which extends the traditional Duplication-Loss model to the reconciliation of a set of trees, accounting for segmental duplications and losses. From a complexity point of view, we show the associated decision problem is NP-hard. We then give an exact exponential-time algorithm for this problem, test its time efficiency on simulated datasets, and give a proof of concept on the opioid receptor genes.
Reconstructing the history of syntenies through Super-Reconciliation