On distinguishing trees by their chromatic symmetric functions

Let $T$ be an unrooted tree. The \emph{chromatic symmetric function} $X_T$, introduced by Stanley, is a sum of monomial symmetric functions corresponding to proper colorings of $T$. The \emph{subtree polynomial} $S_T$, first considered under a different name by Chaudhary and Gordon, is the bivariate generating function for subtrees of $T$ by their numbers of edges and leaves. We prove that $S_T =$, where $$ is the Hall inner product on symmetric functions and $\Phi$ is a certain symmetric function that does not depend on $T$. Thus the chromatic symmetric function is a stronger isomorphism invariant than the subtree polynomial. As a corollary, the path and degree sequences of a tree can be obtained from its chromatic symmetric function. As another application, we exhibit two infinite families of trees (\emph{spiders} and some \emph{caterpillars}), and one family of unicyclic graphs (\emph{squids}) whose members are determined completely by their chromatic symmetric functions.Comment: 16 pages, 3 figures. Added references [2], [13], and [15

On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure

Generalized centrality in trees

In 1982, Slater defined path subgraph analogues to the center, median, and (branch or branchweight) centroid of a tree. We define three families of central substructures of trees, including three types of central subtrees of degree at most D that yield the center, median, and centroid for D = 0 and Slater's path analogues for D = 2. We generalize these results concerning paths and include proofs that each type of generalized center and generalized centroid is unique. We also present algorithms for finding one or all generalized central substructures of each type.

On distinguishing trees by their chromatic symmetric functions

This is the author's accepted manuscript

Relaxed Agreement Forests

There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf labels X but with distinct topologies. This leads naturally to the goal of quantifying the difference between two such trees T_1 and T_2. Here we introduce the problem of computing a 'maximum relaxed agreement forest' (MRAF) and use this as a proxy for the dissimilarity of T_1 and T_2, which in this article we assume to be unrooted binary phylogenetic trees. MRAF asks for a partition of the leaf labels X into a minimum number of blocks S_1, S_2, ... S_k such that for each i, the subtrees induced in T_1 and T_2 by S_i are isomorphic up to suppression of degree-2 nodes and taking the labels X into account. Unlike the earlier introduced maximum agreement forest (MAF) model, the subtrees induced by the S_i are allowed to overlap. We prove that it is NP-hard to compute MRAF, by reducing from the problem of partitioning a permutation into a minimum number of monotonic subsequences (PIMS). Furthermore, we show that MRAF has a polynomial time O(log n)-approximation algorithm where n=|X| and permits exact algorithms with single-exponential running time. When at least one of the two input trees has a caterpillar topology, we prove that testing whether a MRAF has size at most k can be answered in polynomial time when k is fixed. We also note that on two caterpillars the approximability of MRAF is related to that of PIMS. Finally, we establish a number of bounds on MRAF, compare its behaviour to MAF both in theory and in an experimental setting and discuss a number of open problems.Comment: 14 pages plus appendi

Automorphism Groups of Geometrically Represented Graphs

We describe a technique to determine the automorphism group of a geometrically represented graph, by understanding the structure of the induced action on all geometric representations. Using this, we characterize automorphism groups of interval, permutation and circle graphs. We combine techniques from group theory (products, homomorphisms, actions) with data structures from computer science (PQ-trees, split trees, modular trees) that encode all geometric representations. We prove that interval graphs have the same automorphism groups as trees, and for a given interval graph, we construct a tree with the same automorphism group which answers a question of Hanlon [Trans. Amer. Math. Soc 272(2), 1982]. For permutation and circle graphs, we give an inductive characterization by semidirect and wreath products. We also prove that every abstract group can be realized by the automorphism group of a comparability graph/poset of the dimension at most four