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The concept of character and the definition of the attribute are two major theoretical issues of phylogenetics. Lately, great progress has been made in the conceptual development of attributes as historical individuals undergoing series of transformations. While operational application of this ideographic concept of character has been possible since the publication of the direct optimization algorithm and POY software, it has been restricted to molecular characters only. The present paper proposes the first application of direct optimization to morphological characters, in the case study of the phylogeny of Odontellidae. This new homology regime is compared to the traditional homology scheme. The theoretical and operational limitations of the application of direct optimization to morphological characters are discussed. Some thoughts on the basics of its generalization to all morphological characters analyzed in a dynamic homology phylogenetic framework are given. © The Willi Hennig Society 2009;., (© The Willi Hennig Society 2009.)

New Caledonia is well known as a hot spot of biodiversity whose origin as a land mass can be traced back to the Gondwanan supercontinent. The local flora and fauna, in addition to being remarkably rich and endemic, comprise many supposedly relictual groups. Does the New Caledonian biota date back to Gondwanan times, building up its richness and endemism over 100 Myr or does it result from recent diversifications after Tertiary geological catastrophic events? Here we use a molecular phylogenetic approach to answer this question with the study of the Neocaledonian cockroach genus Angustonicus belonging to the subfamily Tryonicinae from Australia and New Caledonia. Both geological and molecular dating show that the diversification of this group is less than two million years old, whatever the date of its origin itself. This dating is not consistent with hypotheses of Gondwanan richness and endemism in New Caledonian biota. In other terms, local richness and endemism at the specific level are not necessarily related to an old Gondwanan origin of the Neocaledonian groups., (© The Willi Hennig Society 2005.)

A character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non-exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest., (© The Willi Hennig Society 2004.)

An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds., (© The Willi Hennig Society 2004.)

The geometric mean length (GML) is proposed as a new statistic aimed at describing the evenness of character changes on a tree for a given set of character optimizations. It is the geometric mean of the number of steps on each branch of the tree, varying between a maximum value when all branch lengths are equal, and a minimum value when all branches but one have only one character step. It can be scaled according to its theoretical maximum value, thus indicating a relative GML that allows a comparison of the evenness of character steps between different tree topologies.

The law of the unspecialized states that specialized taxa have evolved from more generalized ancestors. Moreover, it is usually assumed that ecological specialization is irreversible and hence leads to extinction. This study aims to test these assumptions using a phylogenetic framework in a case study within the springtail genus Willemia and its diverse life habits. This genus is represented mostly by loam-dwelling species (generalized condition), but some species are psammophilous, living in sandy habitats (specialized condition). Fifty-two morphological characters were examined in 34 of the 36 species of the genus and in three outgroups. The cladistic analysis yielded two most parsimonious trees (tree length 124 steps; consistency index 0.56; retention index 0.86). The evolution of psammophily versus loam-confined life is compared to the cladogram: unexpectedly, psammophily is not an evolutionary innovation that occurred once in a monophyletic group; the evolutionary scenario that parsimoniously fits the phylogeny suggests that psammophily is ancestral to the genus Willemia and reversed twice to loam-confined life. These results demonstrate that habitat generalists can evolve from habitat specialists and therefore that habitat specializations are not necessarily an evolutionary dead end. Many other seemingly specialized characters may be shown to be equally malleable.