Researchers interested in the history of the Indo-European family of languages have used a variety of methods to estimate the phylogeny of the family, and have obtained widely differing results. In this paper we explore the reconstructions of the IndoEuropean phylogeny obtained by using the major phylogeny estimation procedures on an existing database of 336 characters (including lexical, phono...

Given an acyclic digraph D, the phylogeny graph P (D) is defined to be the undirected graph with V (D) as its vertex set and with adjacencies as follows: two vertices x and y are adjacent if one of the arcs (x, y) or (y, x) is present in D, or if there exists another vertex z such that the arcs (x, z) and (y, z) are both present in D. Phylogeny graphs were introduced by Roberts and Sheng [6] fr...

Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of 'core groups' with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However...

A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn...

There are suggestions that the phylogeny of Streptococcus mutans, a member of the human indigenous biota that is transmitted mostly mother to child, might parallel the evolutionary history of its human host. The relatedness and phylogeny of plasmid-containing strains of S. mutans were examined based on chromosomal DNA fingerprints (CDF), a hypervariable region (HVR) of a 5.6-kb plasmid, the rRN...

We consider the problem of finding a Steiner minimum tree in a hypercube. Specifically, given n terminal vertices in an m dimensional cube and a parameter q, we compute the Steiner minimum tree in time O(72 + 8nm), under the assumption that the length of the minimum Steiner tree is at most m+ q. This problem has extensive applications in taxonomy and biology. The Steiner tree problem in hypercu...

Diaspore characteristics of 22 families, including 102 genera and 150 species (55 represented by seeds and 95 by fruits) from the Gurbantunggut Desert were analyzed for diaspore biological characteristics (mass, shape, color, and appendage type). The diaspore mass and shape were significantly different in phylogeny group (APG) and dispersal syndromes; vegetative periods significantly affected d...

Seed germination strongly affects plant population growth and persistence, and it can be dramatically influenced by phylogeny, seed traits, and ecological factors. In this study, we examined the relationships among seed mass, seed shape, and germination percentage (GP), and assessed the extent to which phylogeny, seed traits (seed mass, shape, and color) and ecological factors (ecotype, life fo...

Infection with the endosymbiotic bacteria Wolbachia is widespread in filarial nematodes. Previous studies have suggested concordance between the phylogeny of Wolbachia with that of their nematode hosts. However, there is only one published molecular phylogenetic study of filarial species, based on the 5S rRNA gene spacer. The phylogeny proposed by this study is partially incongruent with previo...

Haplotyping via perfect phylogeny is a method for retrieving haplotypes from genotypes. Fast algorithms are known for computing perfect phylogenies from complete and error-free input instances—these instances can be organized as a genotype matrix whose rows are the genotypes and whose columns are the single nucleotide polymorphisms under consideration. Unfortunately, in the more realistic setti...