Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies

TL;DR

This paper evaluates the robustness of parsimonious gene adjacency predictions from reconciled phylogenies, revealing insights into gene evolution and the stability of the DeCo model across different cost schemes.

Contribution

It introduces a method to assess the robustness of parsimonious gene adjacency predictions to cost scheme variations in the DeCo algorithm.

Findings

Robustness analysis uncovers stable gene adjacency predictions.

Application to mammalian gene families reveals evolutionary insights.

Method enhances understanding of model sensitivity to cost parameters.

Abstract

The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Following the approach pioneered by Sturmfels and Pachter, we describe how to modify the DeCo dynamic programming algorithm to identify classes of cost schemes that generates similar parsimonious evolutionary scenarios for gene adjacencies, as well as the robustness to changes to the cost scheme of evolutionary events of the presence or absence of specific ancestral gene adjacencies. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes to cost schemes provides new and interesting insights on the evolution of gene adjacencies and the DeCo model.