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This chapter proposes a conceptual roadmap to homology, with the goal of supporting the research program of developmental evolution that seeks to explain the patterns of phenotypic diversity. It offers a mechanistic developmental and evolutionary explanation of the evolution of body plans and the origin of character identities. It also examines the difference between the origin of homologs (that is, novelties) and their modification by natural selection (that is, adaptation); the limits of homology, focusing on the lack of individuality of body parts; homologous genes; characters and character states; variational modalities; character identity and repeated body parts; and character swarms. Finally, it considers alternative conceptualizations of homology, conceptual liberalism, and how to sort patterns of morphological variation.

This chapter presents a genetic theory of homology that addresses the most challenging problem when attempting to explain character identity; namely, unquestionable homologies (that is, character identities across species) are often associated with extensive variations in the developmental pathways and mechanisms that produce these characters. To resolve this problem, the chapter reviews some of the relevant facts from developmental genetics and then proposes a model that explains these patterns and serves as a guide for further research into the developmental evolution of morphological characters. It shows that the function of homeotic genes offers insights into what might be the developmental genetic basis of character identity. It argues that the distinction between character identity and character states is reflected in the genetic architecture of development in which character identity has a different genetic substrate than character states. This approach leads to the concept of character identity networks.

This chapter examines the theory and methods that allow systematists to recognize characters, character states, and the taxa they delimit. In systematics, similarity is a relative relation that exists among at least three things. For a given attribute, two things are more similar to one another than either of them is to a third thing, and when multiple attributes are assessed together, the nested degrees of similarity across the range of attributes provide evidence for hypothesizing phylogenetic relationships. Yet things can be similar in one aspect but not similar in other aspects. Once recognized and characterized in words, a theory of similarity of a feature shared among taxa may be tested in three (often interconnected) ways: (1) conjunction, (2) similarity of structure, and (3) similarity of position. Although the distinction between characters and states may be semantic, treatment of features as alternate states of the same character versus different characters is necessary for the construction of data matrices. How this is done can have important implications for character weights, and potentially the outcome of analyses.

Under the extreme selective pressures imposed by meso- and bathypelagic environments, a vast array of bizarre and wonderful creatures has evolved, displaying behaviors and associated morphological adaptations that are almost beyond our ability to imagine. Among the highly diverse products of this evolution in the great oceanic depths, few are as surprising and spectacular as the deep-sea anglerfishes. A rigorously tested systematic hypothesis of relationships allows for a precise reconstruction of aspects of character evolution, which in turn will cast light on broader evolutionary processes that have taken place within the Ceratioidei, and perhaps within the deep-ocean ecosystem as a whole. This chapter is devoted to that effort. It discusses ordinal relationships, subordinal and familial relationships, giving a key to the major subgroups of the Lophiiformes, looking at the relationships of Ceratioid families and genera, characters and character states, characters restricted to metamorphosed males, characters restricted to larvae, and sexual parasitism.

This chapter describes Heterorhabdidae which can be distinguished not only from the other families of the superfamily Arietelloidea but also from all other calanoid families by these three characters: the left caudal ramus is normally fused to the anal segment, and it is longer than the right ramus; the fourth marginal seta (counted from the lateral) of the left ramus is naked and greatly elongated; and finally the basis of the male right P5 has a large, plumose inner lobe, which in some taxa is extremely large. It notes that these three characters are highly pronounced in all species examined in the study except for Paraheterorhabdus (Antirhabdus) compactus, in which the left caudal ramus is only slightly longer than the other marginal setae but not greatly elongated. It further notes that these character states of this species are believed to be reductive rather than primitive because the species shows an advanced stage of evolution in all other morphological features.