A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work and are publicly available. We also apply our methods to real data

A Duality Based 2-Approximation Algorithm for Maximum Agreement Forest

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree Prune-and-Regraft (rSPR) distance between two phylogenetic trees. Our algorithm is combinatorial and its running time is quadratic in the input size. To prove the approximation guarantee, we construct a feasible dual solution for a novel linear programming formulation. In addition, we show this linear program is stronger than previously known formulations, and we give a compact formulation, showing that it can be solved in polynomial tim

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

Analyzing tree distribution and abundance in Yukon-Charley Rivers National Preserve: developing geostatistical Bayesian models with count data

Master's Project (M.S.) University of Alaska Fairbanks, 2018Species distribution models (SDMs) describe the relationship between where a species occurs and underlying environmental conditions. For this project, I created SDMs for the five tree species that occur in Yukon-Charley Rivers National Preserve (YUCH) in order to gain insight into which environmental covariates are important for each species, and what effect each environmental condition has on that species' expected occurrence or abundance. I discuss some of the issues involved in creating SDMs, including whether or not to incorporate spatially explicit error terms, and if so, how to do so with generalized linear models (GLMs, which have discrete responses). I ran a total of 10 distinct geostatistical SDMs using Markov Chain Monte Carlo (Bayesian methods), and discuss the results here. I also compare these results from YUCH with results from a similar analysis conducted in Denali National Park and Preserve (DNPP)

Approximating subtree distances between Phylogenies

We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete by Bordewich and Semple [5]. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances such as Rodrigues et al. [24] and Hein et al. [13]. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a \cascading" scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

Background. A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the same method can support both data types. Results. We introduce TRaIT, a computational framework to infer mutational graphs that model the accumulation of multiple types of somatic alterations driving tumour evolution. Compared to other tools, TRaIT supports multi-region and single-cell sequencing data within the same statistical framework, and delivers expressive models that capture many complex evolutionary phenomena. TRaIT improves accuracy, robustness to data-specific errors and computational complexity compared to competing methods. Conclusions. We show that the application of TRaIT to single-cell and multi-region cancer datasets can produce accurate and reliable models of single-tumour evolution, quantify the extent of intra-tumour heterogeneity and generate new testable experimental hypotheses

Renormalization group approach to chaotic strings

Coupled map lattices of weakly coupled Chebychev maps, so-called chaotic strings, may have a profound physical meaning in terms of dynamical models of vacuum fluctuations in stochastically quantized field theories. Here we present analytic results for the invariant density of chaotic strings, as well as for the coupling parameter dependence of given observables of the chaotic string such as the vacuum expectation value. A highly nontrivial and selfsimilar parameter dependence is found, produced by perturbative and nonperturbative effects, for which we develop a mathematical description in terms of suitable scaling functions. Our analytic results are in good agreement with numerical simulations of the chaotic dynamics.Comment: 36 pages, 18 figures - v2 contains slightly more than the published versio

Improved Bounds for the Excluded-Minor Approximation of Treedepth

Treedepth, a more restrictive graph width parameter than treewidth and pathwidth, plays a major role in the theory of sparse graph classes. We show that there exists a constant C such that for every integers a,b >= 2 and a graph G, if the treedepth of G is at least Cab log a, then the treewidth of G is at least a or G contains a subcubic (i.e., of maximum degree at most 3) tree of treedepth at least b as a subgraph. As a direct corollary, we obtain that every graph of treedepth Omega(k^3 log k) is either of treewidth at least k, contains a subdivision of full binary tree of depth k, or contains a path of length 2^k. This improves the bound of Omega(k^5 log^2 k) of Kawarabayashi and Rossman [SODA 2018]. We also show an application for approximation algorithms of treedepth: given a graph G of treedepth k and treewidth t, one can in polynomial time compute a treedepth decomposition of G of width O(kt log^{3/2} t). This improves upon a bound of O(kt^2 log t) stemming from a tradeoff between known results. The main technical ingredient in our result is a proof that every tree of treedepth d contains a subcubic subtree of treedepth at least d * log_3 ((1+sqrt{5})/2)