Combinatorial properties of triplet covers for binary trees

It is a classical result that an unrooted tree $T$ having positive real-valued edge lengths and no vertices of degree two can be reconstructed from the induced distance between each pair of leaves. Moreover, if each non-leaf vertex of $T$ has degree 3 then the number of distance values required is linear in the number of leaves. A canonical candidate for such a set of pairs of leaves in $T$ is the following: for each non-leaf vertex $v$, choose a leaf in each of the three components of $T-v$, group these three leaves into three pairs, and take the union of this set over all choices of $v$. This forms a so-called `triplet cover' for $T$. In the first part of this paper we answer an open question (from 2012) by showing that the induced leaf-to-leaf distances for any triplet cover for $T$ uniquely determine $T$ and its edge lengths. We then investigate the finer combinatorial properties of triplet covers. In particular, we describe the structure of triplet covers that satisfy one or more of the following properties of being minimal, `sparse', and `shellable'

Noncommutative crossing partitions

We define and study noncommutative crossing partitions which are a generalization of non-crossing partitions. By introducing a new cover relation on binary trees, we show that the partially ordered set of noncommutative crossing partitions is a graded lattice. This new lattice contains the Kreweras lattice, the lattice of non-crossing partitions, as a sublattice. We calculate the M\"obius function, the number of maximal chains and the number of $k$-chains in this new lattice by constructing an explicit $EL$-labeling on the lattice. By use of the $EL$-labeling, we recover the classical results on the Kreweras lattice. We characterize two endomorphism on the Kreweras lattice, the Kreweras complement map and the involution defined by Simion and Ullman, in terms of the maps on the noncommutative crossing partitions. We also establish relations among three combinatorial objects: labeled $k+1$-ary trees, $k$-chains in the lattice, and $k$-Dyck tilings.Comment: 45 page

Combinatorics and geometry of finite and infinite squaregraphs

Squaregraphs were originally defined as finite plane graphs in which all inner faces are quadrilaterals (i.e., 4-cycles) and all inner vertices (i.e., the vertices not incident with the outer face) have degrees larger than three. The planar dual of a finite squaregraph is determined by a triangle-free chord diagram of the unit disk, which could alternatively be viewed as a triangle-free line arrangement in the hyperbolic plane. This representation carries over to infinite plane graphs with finite vertex degrees in which the balls are finite squaregraphs. Algebraically, finite squaregraphs are median graphs for which the duals are finite circular split systems. Hence squaregraphs are at the crosspoint of two dualities, an algebraic and a geometric one, and thus lend themselves to several combinatorial interpretations and structural characterizations. With these and the 5-colorability theorem for circle graphs at hand, we prove that every squaregraph can be isometrically embedded into the Cartesian product of five trees. This embedding result can also be extended to the infinite case without reference to an embedding in the plane and without any cardinality restriction when formulated for median graphs free of cubes and further finite obstructions. Further, we exhibit a class of squaregraphs that can be embedded into the product of three trees and we characterize those squaregraphs that are embeddable into the product of just two trees. Finally, finite squaregraphs enjoy a number of algorithmic features that do not extend to arbitrary median graphs. For instance, we show that median-generating sets of finite squaregraphs can be computed in polynomial time, whereas, not unexpectedly, the corresponding problem for median graphs turns out to be NP-hard.Comment: 46 pages, 14 figure

Minimum triplet covers of binary phylogenetic X-trees

Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed from the distances between the leaves (when the edges are given any strictly positive lengths). Moreover, a linear number of these pairwise distance values suffices to determine both the tree and its edge lengths. A natural set of pairs of leaves is provided by any `triplet cover' of the tree (based on the fact that each non-leaf vertex is the median vertex of three leaves). In this paper we describe a number of new results concerning triplet covers of minimum size. In particular, we characterize such covers in terms of an associated graph being a 2-tree. Also, we show that minimum triplet covers are `shellable' and thereby provide a set of pairs for which the inter-leaf distance values will uniquely determine the underlying tree and its associated branch lengths

Phylogenetic Flexibility via Hall-Type Inequalities and Submodularity

Given a collection τ of subsets of a finite set X, we say that τ is phylogenetically flexible if, for any collection R of rooted phylogenetic trees whose leaf sets comprise the collection τ , R is compatible (i.e. there is a rooted phylogenetic X-tree that displays each tree in R). We show that τ is phylogenetically flexible if and only if it satisfies a Hall-type inequality condition of being ‘slim’. Using submodularity arguments, we show that there is a polynomial-time algorithm for determining whether or not τ is slim. This ‘slim’ condition reduces to a simpler inequality in the case where all of the sets in τ have size 3, a property we call ‘thin’. Thin sets were recently shown to be equivalent to the existence of an (unrooted) tree for which the median function provides an injective mapping to its vertex set; we show here that the unrooted tree in this representation can always be chosen to be a caterpillar tree. We also characterise when a collection τ of subsets of size 2 is thin (in terms of the flexibility of total orders rather than phylogenies) and show that this holds if and only if an associated bipartite graph is a forest. The significance of our results for phylogenetics is in providing precise and efficiently verifiable conditions under which supertree methods that require consistent inputs of trees can be applied to any input trees on given subsets of species

Forward triplets and topological entropy on trees

We provide a new and very simple criterion of positive topological entropy for tree maps. We prove that a tree map f has positive entropy if and only if some iterate fk has a periodic orbit with three aligned points consecutive in time, that is, a triplet (a,b,c) such that fk(a)=b, fk(b)=c and b belongs to the interior of the unique interval connecting a and c (a forward triplet of fk). We also prove a new criterion of entropy zero for simplicial n-periodic patterns P based on the non existence of forward triplets of fk for any 1≤k<n inside P. Finally, we study the set Xn of all n-periodic patterns P that have a forward triplet inside P. For any n, we define a pattern that attains the minimum entropy in Xn and prove that this entropy is the unique real root in (1,∞) of the polynomial xn−2x−1

On embeddings of CAT(0) cube complexes into products of trees

We prove that the contact graph of a 2-dimensional CAT(0) cube complex ${\bf X}$ of maximum degree $\Delta$ can be coloured with at most $\epsilon(\Delta)=M\Delta^{26}$ colours, for a fixed constant $M$. This implies that ${\bf X}$ (and the associated median graph) isometrically embeds in the Cartesian product of at most $\epsilon(\Delta)$ trees, and that the event structure whose domain is ${\bf X}$ admits a nice labeling with $\epsilon(\Delta)$ labels. On the other hand, we present an example of a 5-dimensional CAT(0) cube complex with uniformly bounded degrees of 0-cubes which cannot be embedded into a Cartesian product of a finite number of trees. This answers in the negative a question raised independently by F. Haglund, G. Niblo, M. Sageev, and the first author of this paper.Comment: Some small corrections; main change is a correction of the computation of the bounds in Theorem 1. Some figures repaire