L. Vigilant et al. [1] recently presented "the strongest support yet for the placement of [their] common mtDNA [mitochondrial DNA] ancestor in Africa some 200,000 years ago." This support stems from a tree estimated by maximum parsimony from mtDNA sequence data with the use of the computer program PAUP [2]. The African origin is inferred from this tree because (i) the most basal splits are amon...

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 Computer Science community to solve this NP-complete problem and many techniques have been used or designed in order to decrease the computation time necessary to obtain an acceptable solution. In this ...

A recent study of early dinosaur evolution using equal-weights parsimony recovered a scheme of dinosaur interrelationships and classification that differed from historical consensus in a single, but significant, respect; Ornithischia and Saurischia were not recovered as monophyletic sister-taxa, but rather Ornithischia and Theropoda formed a novel clade named Ornithoscelida. However, these anal...

Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral states of a single character have received less attention than the much less challenging endeavor of reconstructing phylogenetic trees from many c...

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It NP-hard compute, and very few positive algorithmic results are known due its complex combinatorial structure. Here we address this shortcoming by showing that problem fixed parameter tractable. We do establishing linear kernel i.e., after applying certain reduction rules resulting i...

The use of likelihood as an optimality criterion is explored in the context of dynamic homology. Simple models and procedures are described to allow the analysis of large variable length sequence data sets, alone and in combination with qualitative information (such as morphology). Several approaches are discussed that have different likelihood interpretations in terms of maximum parsimony like...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence align...

L. Vigilant et al. (1) recently presented "the strongest support yet for the placement of [their] common mtDNA [mitochondrial DNA] ancestor in Africa some 200,000 years ago." This support stems from a tree estimated by maximum parsimony from mtDNA sequence data with the use of the computer program PAUP (2). The African origin is inferred from this tree because (i) the most basal splits are amon...