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It was not a foregone conclusion that systematics should be phylogenetic. Several commentators on both sides of the Atlantic pointed to logistical, epistemic, and ontological reasons why a phylogenetic basis for classification was theoretically abhorrent or practically impossible. Willi Hennig, in facing these objections, offered a reading of clades as individuals in a way that solves several problems at once. As elegant as it is, this solution leads directly to difficulties with finding a theoretical basis for taxonomic ranking.

Homology, a central concept in comparative biology, has been variously understood over the last century. This chapter tracks several versions of homology over time and through the lens of the historical/mechanistic distinction one finds in Hans Spemann’s work in the early twentieth century. These various interpretations of homology are seen to converge again in the case of developmental evolution, where the differences between them, which have come from the rise of evolutionary biology in general and phylogenetic systematics in particular, again become both salient and informative.

Willi Hennig, a shy and modest entomologist, is regarded to have caused a “revolution” in systematics. A condensed description of his life and career provide the background of an evaluation of his contribution to the development of biological systematics. His main emphasis lay on a strict concept of “relationship,” as founded on genealogy, in contrast to similarity, and on a clear terminology and an explicit substantiation of hypotheses on phylogenetic relationships. He was not a revolutionary person but provided the foundation of modern cladistics, which fundamentally changed the methodology of systematics.

The New Systematics, the New Taxonomy, and the Future of Biodiversity Studies This chapter places the future practice of taxonomy in its historical and conceptual context, asking what kinds of technological investments make sense given taxonomy’s theoretical structure and the need for accelerating taxonomic studies. We defend the view that the theoretical and epistemological foundations of taxonomy point toward, rather than away from, the continued development of a new cyberinfrastructure that importantly includes morphology, even as molecular techniques become more common and more sophisticated. While we are excited and enthusiastic about developments in molecular systematics, we think comparative morphology should retain a central place in our collective attempt to understand life more fully. This is not just because of the pride of place morphology has in the history of natural history but because of what we understand the foundational ideas of contemporary taxonomy to require.

The production of phylogenies and taxonomies has long been based on personal interpretation rather than rigorous character analysis. The introduction of Hennig’s phylogenetic systematics (cladistics) has markedly improved the situation. However, not only is the amount of data derived from whatever sources (anatomy, development, and molecules) important but also the need to employ comprehensive taxon samples is critical. Any phylogeny represents one opinion (hypothesis) until tested against alternatives. A rigorous phylogeny can lead to more reliable classification schemes. Even so, phylogenies and taxonomies are only hypotheses that must remain open to consideration of alternative hypotheses. This chapter provides the framework for the structure of the rest of the book.

Thoracica, barnacles, present the most successful, most biodiverse radiation of Cirripedia, linked with a body plan wherein the carapace of the sessile adult stage develops protective calcified plates (except in the plateless species). Thoracicans also have no abdomen, lacking as they do expression of the Hox gene abdominal A. Most phylogenetic studies of barnacles have employed patterns of plate anatomy and arrangements. Recently, molecule sequences and new insights into the fossil record and deep sea fauna have resulted in a major revolution in the understanding of their evolution. All thoracicans are either stalked (pedunculated) or unstalked (sessile). They undergo a major metamorphosis from the cyprid to the adult stage. Their fossil record extends from the Cambrian to Recent time, but most fossils are separated plates, whereas articulated capitular plates are rare.