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Complement Submodular Information Measures for Balanced and Robust Data Selection A Proof of a Conjecture on Positive and Negative Square Energies of Unicyclic Graphs Laplacian Spectrum of the Weakly Zero-Divisor Graph of a Finite Commutative Ring An identity for second Eulerian numbers via lattice-point counting $t$-tone edge coloring of graphs Constructing Maximal Bumpless Pipedreams for Double Grothendieck Polynomials Mubayi's Polynomial-Ideal Conjecture and Cover-Ideal Turán Methods Implicit Binarization via Complex Phase Dynamics in Combinatorial Optimization The limits of Schur multipliers in Pólya conversion problems for the $q$-permanent function Universality theorems for generalized splines Framing Triangulations for Arbitrary Integer Flow Polytopes On the Common Generalization of Gentle Algebras and Framed Directed Acyclic Graphs The complexity of frugal digraph homomorphisms Chaotic and periodic behavior of jeu de taquin on infinite Young tableaux Enumerating Pattern Avoiding Parking Functions Incidence toric ideals and three-point functions Unique Winning Opening Move in Three-Row Chomp Strong majority colorings of graphs A Balancing Theorem for Spanning Trees of Rectangular Grid Graphs Spectral radius and edge-disjoint connected factors of graphs New invariants for rank metric codes, with applications to the classification of rank two semifields of order 256 Flexible DP-4-coloring of planar graphs without 4-cycles and intersecting triangles Balanced intersection size distributions in projective planes List Reconstruction Problem with List Size Two Is Dimensionality a Barrier for Retrieval Models? The INIEP: Irreducible and Positive Realizations The number of Pfaffian orientations on punctured polygonally cellulated surfaces Explicit Construction of Polytopes whose Ehrhart Polynomials Realize any Given Sign Pattern Finite-state enumeration of adjacency-constrained 132-avoiding permutations AMDS and quantum AMDS Constacyclic codes of length $4p^ς$ over $\mathbb{F}_{{p}^{m}}$
Orthology and Near-Cographs in the Context of Phylogeneti...
Anna Lindeberg, Guillaume E. Scholz, Nicolas Wieseke, Marc Hellm · 2025-02-13 · via math.CO updates on arXiv.org

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. Here, 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.