Systematic and biogeographical relationships within the Hawaiian clade of the pantropical understory shrub genus Psychotria (Rubiaceae) were investigated using phylogenetic analysis of 18S-26S ribosomal DNA internal (ITS) and external (ETS) transcribed spacers. Phylogenetic analyses strongly suggest that the Hawaiian Psychotria are monophyletic and the result of a single introduction to the Haw...

We examined phylogenetic relationships among the Namib day geckos (genus Rhoptropus) using DNA sequence data from the mitochondrial cytochrome b (cytb) and 16S ribosomal RNA genes. Maximum-parsimony analysis of the cytb, 16S, and combined (cytb/16S) datasets each recovered an identical single most-parsimonious tree, revealing two well-supported clades: (1) Rhoptropus afer 1 Rhoptropus bradfield...

An assignment of colors to objects induces a natural integer weight on each tree that has these objects as leaves. This weight is called “parsimony length” in biostatistics and is the basis of the “maximum parsimony” technique for reconstructing evolutionary trees. Equations for the average value (over all binary trees) of the parsimony length of both fixed and random colorations are derived us...

Our research was motivated by the pure parsimony haplotyping problem: Given a set G of genotypes, the haplotyping problem consists in finding a set H of haplotypes that explains G. In the pure parsimony haplotyping problem (PPH) we are interested in finding a set H of smallest possible cardinality. The pure parsimony haplotyping problem can be described as a graph colouring problem as follows: ...

We introduce a technique called lexicographic parsimony pressure, for controlling the significant growth of genetic programming trees during the course of an evolutionary computation run. Lexicographic parsimony pressure modifies selection to prefer smaller trees only when fitnesses are equal (or equal in rank). This technique is simple to implement and is not affected by specific differences i...

Maximum Parsimony (MP) is a character-based approach that relies on the work of the german entomologist Willy Hennig (1913-1976). Although Hennig’s work has generated significant controversy, the principles that underlie what was later called cladistics, laid the basis for a convenient and powerful method for the analysis of molecular data with the use of computers. For more details about the h...

Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior ...

The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA, RNA or protein sequences while minimizing the number of evolutionary changes. Much work has been devoted by the research community to solve this NP-complete problem and many algorithms and techniques have been devised in order to find high quality solution with reasonable computational resources. In this paper we...