We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolu...

When constructing a cladogram from a data set a researcher will, as a matter of course, select the shortest possible branching diagram that will represent the data, thus minimizing the number of appearances of any character on the cladogram. This “parsimony program” is usually adopted without comment, but when arguments defending or questioning its use are put forward, they almost universally d...

A three-dimensional (3D) theoretical morphospace of gomphonemoid and cymbelloid diatoms was skeletonized using concepts from extended Reeb graph analysis and Morse theory. The resultant skeleton tree was matched to a cladogram of the same group of related taxa using adjacency matrices of the trees and ordinated with multidimensional scaling (MDS) of leaf nodes. From this, an unweighted path mat...

The alpha model, a parametrized family of probabilities on cladograms (rooted binary leaf labeled trees), is introduced. This model is Markovian self-similar, deletion-stable (sampling consistent), and passes through the Yule, Uniform and Comb models. An explicit formula is given to calculate the probability of any cladogram or tree shape under the alpha model. Sackin's and Colless' index are s...

For several historical reasons discussed herein, until recently the absolute temporal dimension of many phylogenetic trees has been relatively ignored whereas the branching (cladistic) aspect typically has been the focus of most phylogeny-reconstruction efforts. This unfortunate neglect of “timetrees” is now being remedied, as this book will attest. Many scientifi c benefi ts can emerge from su...

The genus Renilla is an interesting taxon for phylogenetic studies, which includes six species endemic to America with an anphiamerican distribution (Pacific–Atlantic Ocean). A cladistic analysis of Renilla Lamarck, 1816 using eight characters from external morphology produced one cladogram (length 14, CI = 0.92, RI = 0.87), and the characters were polarized using Echinoptilum macintoshii Hubre...

Rytidosperma s.l., wallaby grasses and allies, is in dire need of a single, unanimously accepted generic taxonomy. Motivated by the desire to establish a generic classification that complies with phylogeny, we investigated how much phylogenetic signal is contained within a plastid (cpDNA) tree, given that the nrDNA tree (ITS) was uninformative and that a phylogenetic hypothesis based on a singl...

We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observe...

Phylogenetic taxonomy, like modern Linnean taxonomy, was modeled on a phylogenetic tree rather than a cladogram and, like its predecessor, perpetuates the use of morphology as a means of recognizing clades. Both practices have generated confusion in graphical representation, operational terminology, and definitional rationale in phylogenetic taxonomy, the history of which is traced. The followi...

The terminology and principles of phylogenelic analysis (cladism) are briefly discussed. Three myths commonly ascribed to cladism are discussed and dispelled. They are; I) that cladism is completely objective, 2) that complete reliance is placed on evolutionary parsimony, and 3) that fossil evidence is not relevant. A step-by-step procedure is outlined for the phylogenetic analysis of the gener...