Computing the minimum number of hybridization events for a consistent evolutionary history

It is now well-documented that the structure of evolutionary relationships between a set of present-day species is not necessarily tree-like. The reason for this is that reticulation events such as hybridizations mean that species are a mixture of genes from different ancestors. Since such events are relatively rare, a fundamental problem for biologists is to determine the smallest number of hybridization events required to explain a given (input) set of data in a single (hybrid) phylogeny. The main results of this paper show that computing this smallest number is APX-hard, and thus NP-hard, in the case the input is a collection of phylogenetic trees on sets of present-day species. This answers a problem which was raised at a recent conference (Phylogenetic Combinatorics and Applications, Uppsala University, 2004). As a consequence of these results, we also correct a previously published NP-hardness proof in the case the input is a collection of binary sequences, where each sequence represents the attributes of a particular present-day species. The APX-hardness of these problems means that it is unlikely that there is an efficient algorithm for either computing the result exactly or approximating it to any arbitrary degree of accuracy.     

Patching upX-trees

A fundamental problem in many areas of classification, and particularly in biology, is the reconstruction of a leaf-labeled tree from just a subset of its induced subtrees. Without loss of generality, we may assume that these induced subtrees all have precisely four leaves. Of particular interest is determining whether a collection of quartet subtrees uniquely defines a parent tree. Here, we solve this problem in the case where the collection of quartet trees is of minimal size, by studyingencodings of binary trees by such quartet trees. We obtain a characterization of minimal encodings that exploits an underlying patchwork structure. As we will show elsewhere, this allows one to obtain a polynomial time algorithm for certain instances of the problem of reconstructing trees from subtrees.Supported by DFG — Graduiertenkolleg Strukturbildungsprozesse, Forschungsschwerpunkt Mathematisierung, University of Bielefeld, Germany.Supported by the New Zealand Marsden Fund.     

A Framework for Representing Reticulate Evolution

Acyclic directed graphs (ADGs) are increasingly being viewed as more appropriate for representing certain evolutionary relationships, particularly in biology, than rooted trees. In this paper, we develop a framework for the analysis of these graphs which we call hybrid phylogenies. We are particularly interested in the problem whereby one is given a set of phylogenetic trees and wishes to determine a hybrid phylogeny that embeds each of these trees and which requires the smallest number of hybridisation events. We show that this quantity can be greatly reduced if additional species are involved, and investigate other combinatorial aspects of this and related questions.Received November 12, 2003     

The Effects of Migration on the Transmission Dynamics of Sickle Cell Anaemia

Among the factors which should be considered in the formulation of a model representing a phenomenon in population dynamics, migration has always been the most difficult to treat mathematically and, hence, it has not been given prominence by researchers over the years. Nevertheless, in this paper we shall analyze its role in the transmission dynamics of a genetically transmitted disease, the Sickle-Cell Anaemia.     

On the maximal energy tree with two maximum degree vertices

For a simple graph G, the energy E(G) is defined as the sum of the absolute values of all eigenvalues of its adjacent matrix.For Δ?3 and t?3, denote by T_a(Δ,t) (or simply T_a) the tree formed from a path P_t on t vertices by attaching Δ-1P₂’s on each end of the path P_t, and T_b(Δ,t) (or simply T_b) the tree formed from P_t+2 by attaching Δ-1P₂’s on an end of the P_t+2 and Δ-2P₂’s on the vertex next to the end.In Li et al.(2009) [16] proved that among trees of order n with two vertices of maximum degree Δ, the maximal energy tree is either the graph T_a or the graph T_b, where t=n+4-4Δ?3.However, they could not determine which one of T_a and T_b is the maximal energy tree.This is because the quasi-order method is invalid for comparing their energies.In this paper, we use a new method to determine the maximal energy tree.It turns out that things are more complicated.We prove that the maximal energy tree is T_b for Δ?7 and any t?3, while the maximal energy tree is T_a for Δ=3 and any t?3.Moreover, for Δ=4, the maximal energy tree is T_a for all t?3 but one exception that t=4, for which T_b is the maximal energy tree.For Δ=5, the maximal energy tree is T_b for all t?3 but 44 exceptions that t is both odd and 3?t?89, for which T_a is the maximal energy tree.For Δ=6, the maximal energy tree is T_b for all t?3 but three exceptions that t=3,5,7, for which T_a is the maximal energy tree.One can see that for most cases of Δ, T_b is the maximal energy tree,Δ=5 is a turning point, and Δ=3 and 4 are exceptional cases, which means that for all chemical trees (whose maximum degrees are at most 4) with two vertices of maximum degree at least 3, T_a has maximal energy, with only one exception T_a(4,4).     

Polyhedral combinatorics of UPGMA cones

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm. The partition lattice informs the study of UPGMA trees. We give a closed form for the extreme rays of UPGMA cones on n taxa, and compute the spherical volumes of the UPGMA cones for small n.     

COMPUTATIONAL COMPLEXITY OF（2,2） PATH CHROMATIC NUMBER PROBLEM

Is there a normal Pk coloring using r colors for a given graph ? This problem is called the (k, r) path chromatic number problem of graphs. This paper proves that the (2, 2) path chromatic number problem of graphs with maximum degree 4 is NP-complete.     

Analysis of competitive chemostat models with the Beddington–DeAngelis functional response and impulsive effect

In this paper, we introduce and study a competitive system with Beddington–DeAngelis type functional response in periodic pulsed chemostat conditions. We investigate the subsystem with substrate and one of the microorganisms and study the stability of the periodic solutions, which are the boundary periodic solution of the system. The stability analysis of the boundary periodic solution yields an invasion threshold. By use of standard techniques of bifurcation theory, we prove that above this threshold there are periodic oscillations in substrate and one of the microorganism. Further, we prove that the system is permanent if the impulsive period less than some critical value. Therefore, our results are valuable for the manufacture of products by genetically altered organisms.     

Expected length of the longest common subsequence for large alphabets

We consider the length L of the longest common subsequence of two randomly uniformly and independently chosen n character words over a k-ary alphabet. Subadditivity arguments yield that E[L]/n converges to a constant γ_k. We prove a conjecture of Sankoff and Mainville from the early 1980s claiming that as k→∞.     

On multiplicative graphs and the product conjecture

We study the following problem: which graphsG have the property that the class of all graphs not admitting a homomorphism intoG is closed under taking the product (conjunction)? Whether all undirected complete graphs have the property is a longstanding open problem due to S. Hedetniemi. We prove that all odd undirected cycles and all prime-power directed cycles have the property. The former result provides the first non-trivial infinite family of undirected graphs known to have the property, and the latter result verifies a conjecture of Ne?et?il and Pultr These results allow us (in conjunction with earlier results of Ne?et?il and Pultr [17], cf also [7]) to completely characterize all (finite and infinite, directed and undirected) paths and cycles having the property. We also derive the property for a wide class of 3-chromatic graphs studied by Gerards, [5].     

On minors of the compound matrix of a Laplacian

Let L   be an n×n$n\times n$ matrix with zero row and column sums, n?3$n?3$. We obtain a formula for any minor of the (n−2)$(n-2)$-th compound of L. An application to counting spanning trees extending a given forest is given.     

Exact Distribution of the Occurrence Number for K-tuples Over an Alphabet of Non-Equal Probability Letters

A nucleotide sequence can be considered as a realization of the non-equal-probability independently and identically distributed (niid) model. In this paper we derive the exact distribution of the occurrence number for each K-tuple with respect to the niid model by means of the Goulden-Jackson cluster method. An application of the probability function to get exact expectation curves [9] is presented, accompanied by comparison between the exact approach and the approximate solution.Received October 31, 2004     

On the conjecture of hajós

Hajós conjectured that everys-chromatic graph contains a subdivision ofK _s, the complete graph ons vertices. Catlin disproved this conjecture. We prove that almost all graphs are counter-examles in a very strong sense.     

On the fractional matching polytope of a hypergraph

For a hypergraph andb:⁺ define Conjecture. There is a matching of such that For uniform andb constant this is the main theorem of [4]. Here we prove the conjecture if is uniform or intersecting, orb is constant.The research was done while the author visited the Department of Mathematics at Rutgers University. Research supported in part by the Hungarian National Science Foundation under grant No. 1812Supported in party by NSF and AFOSR grants and by a Sloan Research Fellowship     

On the Number of Latin Squares

We (1) determine the number of Latin rectangles with 11 columns and each possible number of rows, including the Latin squares of order 11, (2) answer some questions of Alter by showing that the number of reduced Latin squares of order n is divisible by f! where f is a particular integer close to (3) provide a formula for the number of Latin squares in terms of permanents of (+1, −1)-matrices, (4) find the extremal values for the number of 1-factorisations of k-regular bipartite graphs on 2n vertices whenever 1 ≤ k ≤ n ≤ 11, (5) show that the proportion of Latin squares with a non-trivial symmetry group tends quickly to zero as the order increases. Received September 3, 2004     

Extremal Problems For Transversals In Graphs With Bounded Degree

We introduce and discuss generalizations of the problem of independent transversals. Given a graph property , we investigate whether any graph of maximum degree at most d with a vertex partition into classes of size at least p admits a transversal having property . In this paper we study this problem for the following properties : “acyclic”, “H-free”, and “having connected components of order at most r”. We strengthen a result of [13]. We prove that if the vertex set of a d-regular graph is partitioned into classes of size d+⌞d/r⌟, then it is possible to select a transversal inducing vertex disjoint trees on at most r vertices. Our approach applies appropriate triangulations of the simplex and Sperner’s Lemma. We also establish some limitations on the power of this topological method. We give constructions of vertex-partitioned graphs admitting no independent transversals that partially settles an old question of Bollobás, Erdős and Szemerédi. An extension of this construction provides vertex-partitioned graphs with small degree such that every transversal contains a fixed graph H as a subgraph. Finally, we pose several open questions. * Research supported by the joint Berlin/Zurichgrad uate program Combinatorics, Geometry, Computation, financed by the German Science Foundation (DFG) and ETH Zürich. † Research partially supported by Hungarian National Research Fund grants T-037846, T-046234 and AT-048826.     

On the null-spaces of acyclic and unicyclic singular graphs

For acyclic and unicyclic graphs we determine a necessary and sufficient condition for a graph G to be singular. Further, it is shown that this characterization can be used to construct a basis for the null-space of G.     

On the existence of two non-neighboring subgraphs in a graph

Does there exist a functionf(r, n) such that each graphG with _Z (G)≧f(r, n) contains either a complete subgraph of orderr or else two non-neighboringn-chromatic subgraphs? It is known thatf(r, 2) exists and we establish the existence off(r, 3). We also give some interesting results about graphs which do not contain two independent edges.