Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

The evolution of genomes can be studied at at least three different scales: the nucleotide level, accounting for substitutions and indels, the gene level, accounting for gains and losses, and the genome level, accounting for rearrangements of chromosome organization. While the nucleotide and gene levels are now often integrated in a single model using reconciled gene trees, very little work integrates the genome level as well, and considers gene trees and gene orders simultaneously. In a seminal book chapter published in 2000 and entitled “Duplication, Rearrangement and Reconciliation”, Sankoff and El-Mabrouk outlined a general approach, making a step in that direction. This avenue has been poorly exploited by the community for over ten years, but recent developments allow the design of integrated methods where phylogeny informs the study of synteny and vice-versa. We review these developments and show how this influence of synteny on gene tree construction can be implemented.