A Unifying Model of Genome Evolution Under Parsimony

TL;DR

This paper introduces a history graph data structure that unifies the analysis of genome evolution, encompassing substitutions and rearrangements, and provides bounds and methods to explore parsimonious evolutionary histories efficiently.

Contribution

It presents a novel history graph model that simplifies genome evolution analysis and offers bounds and sampling methods for parsimonious histories.

Findings

Bounds on the minimum number of evolutionary operations are tight for AVGs.

A finite set of AVGs describes all parsimonious interpretations of a history graph.

The model unifies phylogenetic reconstruction and genome rearrangement problems.

Abstract

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.