# Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

## TL;DR

This paper improves a method for reconstructing evolutionary scenarios of gene adjacencies, leading to fewer conflicts in ancestral genome arrangements.

## Contribution

The paper introduces an extension of the DeCo algorithm to sample evolutionary scenarios using the Boltzmann distribution and compute probabilities for ancestral adjacencies.

## Key findings

- The extended DeCo algorithm samples evolutionary scenarios from the solution space under the Boltzmann distribution.
- Applying the method to mammalian data reduced syntenic conflicts in inferred ancestral gene adjacencies.

## Abstract

The reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bérard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered.

We extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.

We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.