Approximation algorithms for the fixed-topology phylogenetic number problem

In the l-phylogeny problem, one wishes to construct an evolutionary tree for a. set of species represented by characters, in which each state of each character induces no more than l connected components. We consider the fixed-topology version of this problem for fixed-topologies of arbitrary degree. This version of the problem is known to be NP-complete for l greater than or equal to 3 even for degree-3 trees in which no state labels more than l + 1 leaves (and therefore there is a trivial l + 1 phylogeny) We give a 2-approximation algorithm for all l greater than or equal to 3 for arbitrary input topologies and we give an optimal approximation algorithm that constructs a 4-phylogeny when a 3-phylogeny exists. Dynamic programming techniques, which are typically used in fixed-toplogy problems, cannot be applied to l-phylogeny problems. Our 2-approximation algorithm is the first application of linear programming to approximation algorithms for phylogeny problems. We extend our results to a related problem in which characters are polymorphic

Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects

PHYLO-ASP: Phylogenetic Systematics with Answer Set Programming

This note summarizes the use of Answer Set Programming to solve various computational problems to infer phylogenetic trees and phylogenetic networks, and discusses its applicability and effectiveness on some real taxa

ZARAMIT: A System for the Evolutionary Study of Human Mitochondrial DNA

Abstract. ZARAMIT is an information system capable of fully auto-mated phylogeny reconstruction. Methods have been tailored to mito-chondrial DNA sequences, with focus on subproblem partitioning. We have built exhaustive human mitochondrial phylogenies (∼5500 sequences) and detected problems in existing haplogroup hierarchies through data-driven classification. Information on the project can be found on zaramit.org. 1 The case for mitochondrial DNA Mitochondria, organelles present in most eukaryotic cells, are responsible for the generation of most of the cell’s chemical energy. They are also remarkable for possessing their own, separate genome, which coexists with nuclear DNA and is inherited independently. Further, mitochondrial DNA (mtDNA) has several features which make it an ideal candidate for conducting evolutionary studies. Firstly, it is small in mammals (15000 to 17000 base pairs) and encodes a homogeneous set of gene

Efficiently Calculating Evolutionary Tree Measures Using SAT

We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers. Comparing evolutionary trees is a necessary step in tree reconstruction algorithms, locating recombination and lateral gene transfer, and in analyzing and visualizing sets of trees. We focus on two popular comparison measures for trees: the hybridization number and the rooted subtree-prune-and-regraft (rSPR) distance. Both have recently been shown to be NP-hard, and effcient algorithms are needed to compute and approximate these measures. We encode these as a Boolean formula such that two trees have hybridization number k (or rSPR distance k) if and only if the corresponding formula is satisfiable. We use state-of-the-art SAT solvers to determine if the formula encoding the measure has a satisfying assignment. Our encoding also provides a rich source of real-world SAT instances, and we include a comparison of several recent solvers (minisat, adaptg2wsat, novelty+p, Walksat, March KS and SATzilla).Postprint (author’s final draft