Abelian permutation groups with graphical representations

In this paper we characterize those automorphism groups of colored graphs and digraphs that are abelian as abstract groups. This is done in terms of basic permutation group properties. Using Schur’s classical terminology, what we provide is characterizations of the classes of 2-closed and $$2^*$$ 2 ∗ -closed abelian permutation groups. This is the first characterization concerning these classes since they were defined.

Turán Density of $2$-Edge-Colored Bipartite Graphs with Application on $\{2, 3\}$-Hypergraphs

We consider the Turán problems of $2$-edge-colored graphs. A $2$-edge-colored graph $H=(V, E_r, E_b)$ is a triple consisting of the vertex set $V$, the set of red edges $E_r$ and the set of blue edges $E_b$ where $E_r$ and $E_b$ do not have to be disjoint. The Turán density $\pi(H)$ of $H$ is defined to be $\lim_{n\to\infty} \max_{G_n}h_n(G_n)$, where $G_n$ is chosen among all possible $2$-edge-colored graphs on $n$ vertices containing no $H$ as a sub-graph and $h_n(G_n)=(|E_r(G)|+|E_b(G)|)/\binom{n}{2}$ is the formula to measure the edge density of $G_n$. We will determine the Turán densities of all $2$-edge-colored bipartite graphs. We also give an important application on the Turán problems of $\{2, 3\}$-hypergraphs.

The Action of the Weyl Group on the $$E_8$$ Root System

Let $$\varGamma $$ Γ be the graph on the roots of the $$E_8$$ E 8 root system, where any two distinct vertices e and f are connected by an edge with color equal to the inner product of e and f. For any set c of colors, let $$\varGamma _c$$ Γ c be the subgraph of $$\varGamma $$ Γ consisting of all the 240 vertices, and all the edges whose color lies in c. We consider cliques, i.e., complete subgraphs, of $$\varGamma $$ Γ that are either monochromatic, or of size at most 3, or a maximal clique in $$\varGamma _c$$ Γ c for some color set c, or whose vertices are the vertices of a face of the $$E_8$$ E 8 root polytope. We prove that, apart from two exceptions, two such cliques are conjugate under the automorphism group of $$\varGamma $$ Γ if and only if they are isomorphic as colored graphs. Moreover, for an isomorphism f from one such clique K to another, we give necessary and sufficient conditions for f to extend to an automorphism of $$\varGamma $$ Γ , in terms of the restrictions of f to certain special subgraphs of K of size at most 7.

Indirect identification of horizontal gene transfer

Several implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

Chromatic spectrum of some classes of 2-regular bipartite colored graphs

Chromatic spectrum of a colored graph G is a multiset of eigenvalues of colored adjacency matrix of G. The nullity of a disconnected graph is equal to sum of nullities of its components but we show that this result does not hold for colored graphs. In this paper, we investigate the chromatic spectrum of three different classes of 2-regular bipartite colored graphs. In these classes of graphs, it is proved that the nullity of G is not sum of nullities of components of G. We also highlight some important properties and conjectures to extend this problem to general graphs.