Partial Homology Relations - Satisfiability in terms of Di-Cographs

TL;DR

This paper characterizes when partial homology relations, derived from gene sequence comparisons, can be explained by evolutionary gene trees using di-cographs, and provides efficient algorithms for their recognition and cotree construction.

Contribution

It introduces a characterization and quadratic-time algorithms for recognizing partial satisfiable homology relations with forbidden pairs, explained via di-cographs and cotrees.

Findings

Provides a quadratic-time recognition algorithm.

Characterizes partial homology relations with forbidden pairs.

Ensures relations can be explained by event-labeled gene trees.

Abstract

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations.