In phylogenetic analysis it is useful to study the distribution of the parsimony length of a tree under the null model, by which the leaves are independently assigned letters according to prescribed probabilities. Except in one special case, this distribution is difficult to describe exactly. Here we analyze this distribution by providing a recursive and readily computable description, establis...

Swofford and Berlocher (1987) described a method for inferring trees from polymorphic character data that searches for trees that minimize the total amount of allelic frequency change as measured by the Manhattan metric. We provided three primary arguments for choosing our method over other parsimony methods proposed for polymorphic data: (1) it accommodates polymorphism without resorting to co...

Parsimony arguments are advanced in both science and philosophy. How are they related? This question is a test case for Naturalismp, which is the thesis that philosophical theories and scientific theories should be evaluated by the same criteria. In this paper, I describe the justifications that attach to two types of parsimony argument in science. In the first, parsimony is a surrogate for lik...

Though human beings are experts in the determination of aspectual relations, current models of Aspect lack principled parsimony. We show that even on a limited segment of language, determining aspectual interpretations seems to require much ad hoc information. Our suggestion is to give parsimony first priority. The model we present in this paper is limited in scope, but its complexity is bounde...

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's phil...

The proliferation of gene data from multiple loci of large multigene families has been greatly facilitated by considerable recent advances in sequence generation. The evolution of such gene families, which often undergo complex histories and different rates of change, combined with increases in sequence data, pose complex problems for traditional phylogenetic analyses, and in particular, those ...

BACKGROUND We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining ...

Parsimony and Bayesian methods have been developed for detecting positively selected amino acid sites. It has been reported that the parsimony method is generally conservative. In contrast, the Bayesian method is known to identify more positively selected sites than the parsimony method, especially when the number of sequences analyzed is small, although the interpretation of results obtained f...

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...

The accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, rearrangements lead to NP-hard problems, so that current approaches, such as the MGR tool, are limited to small...