Concentration ratios (CRs) are used to derive activity concentrations in wild plants and animals. Usually, compilations of CR values encompass a wide range of element-organism combinations, extracted from different studies with statistical information reported at varying degrees of detail. To produce a more robust estimation of distribution parameters, data from different studies are normally p...

Reliability assessment of upgraded legacy systems is an important problem in many safety-related industries. Some parts of the equipment used in the original design of such systems are either not available off-the-shelf (OTS) or have become extremely expensive as a result of being discontinued as mass production components. Maintaining a legacy system, therefore, demands using different OTS com...

Haeckel created much of our current vocabulary in evolutionary biology, such as the term phylogeny, which is currently used to designate trees. Assuming that Haeckel gave the same meaning to this term, one often reproduces Haeckel's trees as the first illustrations of phylogenetic trees. A detailed analysis of Haeckel's own evolutionary vocabulary and theory revealed that Haeckel's trees were g...

IV. Methods of Analysis of Molecular Data A. Phylogenetic Analysis 1. Tree-Building Methods 2. Statistical Methods for Testing the Reliability of a Tree 3. Other Methods B. Phylogenetics versus Population Genetics V. Application of Molecular Methods in Amphibian Systematics A. Determination and Identification of Species and Species Hybrids B. Molecular Phylogeny of Living Amphibians 1. The Phyl...

A phylogeny is a tree that relates taxonomic units, based on their similarity over a set of characters. The phylogeny problem consists in finding a phylogeny with the minimum number of evolutionary steps. We propose a new neighborhood structure for the phylogeny problem. A greedy randomized adaptive search procedure heuristic based on this neighborhood structure and using variable neighborhood ...

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching...

In the eleven years since Harvey and Pagel (1991), evolutionary biologists committed considerable methodological effort into the relationship between phylogeny and numerous types of patterns. Morphology , Shape and Phylogeny and Fossils, Phylogeny, and Form both concern themselves with these issues. The former book deals primarily with the relationship between phylogeny and continuous mor-phome...

A malware phylogeny model is an estimation of the derivation relationships between a set of species of malware. Systems that construct phylogeny models are expected to be useful for malware analysts. While several different phylogeny construction systems have been proposed, little is known about effective ways of evaluating and comparing them. Little is also known about the consistency of their...

Lam, Gusfield, and Sridhar (2009) showed that a set of three-state characters has a perfect phylogeny if and only if every subset of three characters has a perfect phylogeny. They also gave a complete characterization of the sets of three three-state characters that do not have a perfect phylogeny. However, it is not clear from their characterization how to find a subset of three characters tha...

Computational methods for inferring haplotype information from genotype data are used in studying the association between genomic variation and medical condition. Recently, Gusfield proposed a haplotype inference method that is based on perfect phylogeny principles. A fundamental problem arises when one tries to apply this approach in the presence of missing genotype data, which is common in pr...