The hierarchical basis of serial homology and evolutionary novelty

Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as "partial" homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a long scientific tradition, we advocate a strategy of "theoretical articulation" that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages.

Regulation of posterior Hox genes by sex steroids explains vertebral variation in inbred mouse strains

A series of elegant embryo transfer experiments in the 1950s demonstrated that the uterine environment could alter vertebral patterning in inbred mouse strains. In the intervening decades, attention has tended to focus on the technical achievements involved and neglected the underlying biological question: how can genetically homogenous individuals have a heterogenous number of vertebrae? Here I revisit these experiments and, with the benefit of knowledge of the molecular-level processes of vertebral patterning gained over the intervening decades, suggest a novel hypothesis for homeotic transformation of the last lumbar vertebra to the adjacent sacral type through regulation of Hox genes by sex steroids. Hox genes are involved in both axial patterning and development of male and female reproductive systems and have been shown to be sensitive to sex steroids in vitro and in vivo. Regulation of these genes by sex steroids and resulting alterations to vertebral patterning may hint at a deep evolutionary link between the ribless lumbar region of mammals and the switch from egg-laying to embryo implantation. An appreciation of the impact of sex steroids on Hox genes may explain some puzzling aspects of human disease, and highlights the spine as a neglected target for in utero exposure to endocrine disruptors.

Imaging With the Past: Revealing the Complexity of Chimaeroid Pelvic Musculature Anatomy and Development

Chondrichthyans are now widely adopted as models for examining the development and evolution of the stem gnathostome body plan. The fins of some cartilaginous fish are recognized for their plesiomorphic form and mode of muscular development, i.e., epithelial extension. Despite detailed molecular and descriptive examinations of these developmental mechanisms, there has been little contemporary examination of the ontogeny and morphology of the musculature in chondrichthyans including that of the paired fins. This gap represents a need for further examination of the developmental morphology of these appendicular musculatures to gain insight into their evolution in gnathostomes. The elephant shark is a Holocephalan, the sister group of all other chondrichthyans (Holocephali: Callorhinchus milii). Here, we use nano-CT imaging and 3D reconstructions to describe the development of the pelvic musculature of a growth series of elephant shark embryos. We also use historical descriptions from the nineteenth century and traditional dissection methods to describe the adult anatomy. This combined approach, using traditional methods and historical knowledge with modern imaging techniques, has enabled a more thorough examination of the anatomy and development of the pelvic musculature revealing that chimaeroid musculatures are more complex than previously thought. These data, when compared to extant and extinct sister taxa, are essential for interpreting and reconstructing fossil musculatures as well as understanding the evolution of paired fins.

Not deconstructing serial homology, but instead, the a priori assumption that it generally involves ancestral anatomical similarity: An answer to Kuznetsov's paper

I am very thankful to Kuznetsov for his comments on our recent paper about serial structures published in this journal. I hope this is just the beginning of a much wider, and holistic, discussion on the evolution of serial homologous structures, and of so-called "serial structures" in general, whether they are truly serial homologs or the secondary result of homoplasy. Strangely, Kuznetsov seems to have missed the main point of our paper, what is particularly puzzling as this point is clearly made in the very title of our paper. For instance, he states that "Siomava et al. claim that the serial homologues are false because they are ancestrally anisomeric (dissimilar)' and that" Siomava et al., (Siomava et al., Journal of Morphology, 2020, 281, 1110-1132) expected that if serial homology was true, then the serial homologs would be identical at the start and then only diverge. " However, our paper clearly did not state this. Instead, we stated that (a) serial homology is a real phenomenon, and (b) ancestral dissimilarity is actually likely the norm, and not the exception, within serial homology. In particular, our paper showed that, as clearly stated in its title and abstract, within the evolution of serial homologues these structures "many times display trends toward less similarity while in many others display trends toward more similarity, that is, one cannot say that there is a clear, overall trend to anisomerism." Serial homology is therefore a genuine and much widespread phenomenon within the evolution of life in this planet. It is clearly one of the most important issues-and paradoxically one of the less understood, precisely because of the a priori acceptance of long-standing assumptions that have never been empirically tested, some of them repeated in Kuznetsov's paper-within macroevolution and comparative anatomy.

Reconstructing serial homology with a special emphasis on the nature of limbs in vertebrates and with references to Cruveilhier, Wyman, Belogolowy, and Balinsky

This analysis was inspired by the recent paper by Siomava et al. (2020) who attempted to deconstruct the serial homology concept, but retain the special homology. The criticism against this attempt is presented based on reconsideration of the original Owen's trinitarian concept of the general, serial, and special homology, and on a number of evidence on the vertebrate limbs serial homologies and on the vertebrate occiput special homologies which are currently missed by the morphologist community. The research of Belogolowy (1911) proved that the concept of special homology can be deconstructed with the same reasoning as suggested by Siomava et al. (2020) against the serial homology concept. It is argued that the deconstruction attempts come from wrong expectations in respect of homology. It is argued, that, due to developmental singularities, such as the zygote, or spore, or bud (in vegetative reproduction), the true homogeny is possible for genes only. The organs do not arise from organs, and therefore their genetic basis, and hence homology, can be changed in the developmental singularities. Thus, the morphological homology is not static. It can be acquired and it can evolve. Genetically, the evolution of morphological homologies can be thought of as a succession of co-options. The evidence for a succession of serial homologies in vertebrate limbs is suggested. It is argued that homology and analogy have a sense only in relation to each other. When two correspondences between two organs exist simultaneously, the older (deeper in time) is homology, and the newer (more superficial) is analogy. In this conceptual framework of evolvable homology, neither of the three Owen's types of homology can be abandoned. Three respective types of analogy should be added-the general analogy, the serial analogy, and the special analogy.