Content area

Abstract

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying gene or species trees. This results in orthology graphs, where each vertex represents a gene, and an edge exists between two vertices if the corresponding genes are estimated to be orthologs. Orthology graphs inferred under a tree-like evolutionary model must be cographs. However, real-world data often deviate from this property, either due to noise in the data, errors in inference methods or, simply, because evolution follows a network-like rather than a tree-like process. The latter, in particular, raises the question of whether and how orthology graphs can be derived from or, equivalently, are explained by phylogenetic networks. In this work, we study the constraints imposed on orthology graphs when the underlying evolutionary history follows a phylogenetic network instead of a tree. We show that any orthology graph can be represented by a sufficiently complex level-k network. However, such networks lack biologically meaningful constraints. In contrast, level-1 networks provide a simpler explanation, and we establish characterizations for level-1 explainable orthology graphs, i.e., those derived from level-1 evolutionary histories. To this end, we employ modular decomposition, a classical technique for studying graph structures. Specifically, an arbitrary graph is level-1 explainable if and only if each primitive subgraph is a near-cograph (a graph in which the removal of a single vertex results in a cograph). Additionally, we present a linear-time algorithm to recognize level-1 explainable orthology graphs and to construct a level-1 network that explains them, if such a network exists. Finally, we demonstrate the close relationship of level-1 explainable orthology graphs to the substitution operation, weakly chordal and perfect graphs, as well as graphs with twin-width at most 2.

Details

1009240
Title
Orthology and near-cographs in the context of phylogenetic networks
Publication title
Volume
20
Pages
1-27
Number of pages
28
Publication year
2025
Publication date
2025
Section
Research
Publisher
Springer Nature B.V.
Place of publication
London
Country of publication
Netherlands
Publication subject
e-ISSN
1748-7188
Source type
Scholarly Journal
Language of publication
English
Document type
Journal Article
Publication history
 
 
Online publication date
2025-10-02
Milestone dates
2025-02-10 (Received); 2025-05-22 (Accepted); 2025-10-02 (Published)
Publication history
 
 
   First posting date
02 Oct 2025
ProQuest document ID
3257226982
Document URL
https://www.proquest.com/scholarly-journals/orthology-near-cographs-context-phylogenetic/docview/3257226982/se-2?accountid=208611
Copyright
© 2025. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Last updated
2025-10-05
Database
ProQuest One Academic