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.     

Rebuilding ships while at sea—Character individuality,homology, and evolutionary innovation

How novel traits originate in evolution is still one of the most perplexing questions in Evolutionary Biology. Building on a previous account of evolutionary innovation, I here propose that evolutionary novelties are those individualized characters that are not homologous to any characters in the ancestor. To clarify this definition, I here provide a detailed analysis of the concepts of “character individuality” and “homology” first, before addressing their role for our understanding of evolutionary innovation. I will argue (1) that functional as well as structural considerations are important for character individualization; and (2) that compositional (structural) and positional homology need to be clearly distinguished to properly describe the evolutionary transformations of hierarchically structured characters. My account will therefore integrate functional and structural perspectives and put forward a new multi-level view of character identity and transformation.     

Developmental and evolutionary hypotheses for the origin of double fertilization and endosperm.

The discovery of a second fertilization event that initiates endosperm in flowering plants, just over a century ago, stimulated intense interest in the evolutionary history and homology of endosperm, the genetically biparental embryo-nourishing tissue that is found only in angiosperms. Two alternative hypotheses for the origin of double fertilization and endosperm have been invoked to explain the origin of the angiosperm reproductive syndrome from a typical non-flowering seed plant reproductive syndrome. Endosperm may have arisen from a developmental transformation of a supernumerary embryo derived from a rudimentary second fertilization event that first evolved in the ancestors of angiosperms (endosperm homologous with an embryo). Conversely, endosperm may represent the developmental transformation of the cellular phase of non-flowering seed plant female gametophyte ontogeny that was later sexualized by the addition of a second fertilization event in a strongly progenetic female gametophyte (endosperm homologous with a female gametophyte). For the first time, explicit developmental and evolutionary transitions for both of these hypotheses are examined and compared. In addition, current data that may be congruent with either of these hypotheses are discussed. It is clear that much remains to be accomplished if the evolutionary significance of the process of double fertilization and the formation of endosperm is to be fully understood.     

Hox genes, homology and axis formation—The application of morphological concepts to evolutionary developmental biology

This article focuses on the interphyletic comparison of gene expression patterns. By means of the hypothesis of the inversion of the dorsoventral axis during the evolution of the Bilateria, it is demonstrated, that evolutionary developmental biologists use similarities in spatial and temporal gene expression patterns as evidence for the formulation of hypotheses of homology concerning either developing structures or body regions. The molecular genetic and morphogenetic evidence used is discussed within the framework of a cladistic-phylogenetic analysis based on the phylogenetic tree of the Bilateria. I argue that similarity of spatial and temporal gene expression patterns is not a sufficient criterion for homology inference. Therefore, gene expression patterns should be coded as characters. Their homology should be tested in concert with other characters.

Furthermore, it is demonstrated, that spatial and temporal similar gene expression patterns, indicating similar molecular genetic mechanisms, were interpreted as an analytical criterion of homology, offering the possibility to identify similar structures. In contrast to this, the evolutionary developmental biolgists have not developed a causal-analytically extended concept of shape, from which a causal-analytical concept of homology could be deduced. Instead, the homology concept from evolutionary morphology is used.     

Deconstructing morphology

Scholtz, G. 2010. Deconstructing morphology. —Acta Zoologica (Stockholm) 91 : 44–63 Morphology as the science of form is, in particular, related to the overwhelming diversity of animal forms. Due to its long pre‐Darwinian tradition, organismic morphology is partly burdened by ahistorical typological views. On the other hand, the study of organismic form has always implied concepts of transformation, which helped to pave the way for evolutionary theories. This contradictory history and the fact that we need words to describe organismic form lead in many cases to morphological concepts implying a mixture of structural, functional, developmental, ecological, typological, and evolutionary aspects in current morphological approaches. Because these mixed views lead to contradictory and misleading interpretations of animal form, I stress the need to deconstruct morphological concepts at all levels. I propose a morphology that analyses transformation of animal forms strictly at the structural level in combination with genealogical thinking. Function and other biological aspects of form should be considered in an independent second analytical step. A comparative pattern approach, including developmental patterns, of animal structure in an evolutionary framework allows for the analysis of morphological change, in particular, phylogenetic reconstructions, homology assessment, and the recognition of evolutionary independent morphological units.     

Homology and ontogeny: pattern and process in comparative developmental biology

In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologised. These two approaches must not be conflated. This distinction leads to the conclusion that there is no ontogenetic homology “criterion”.     

Homology in Development and the Development of the Homology Concept

Homology is a central concept for Developmental Evolution. HereI argue that homology should be explained within the referenceprocesses of development and evolution; development becauseit is the proximate cause of morphological characters and evolutionbecause it deals with organic transformations and stability.This was already recognized by Hans Spemann in 1915. In a seminalessay "A history and critique of the homology concept" Spemannanalyzed the history and present problems of the homology concept.Here I will continue Spemann's project and analyze some of the20th century contributions to homology. I will end with a fewreflections about the connections between developmental processesand homology and conclude that developmental processes are inherentin (i) the assessment of homology, (ii) the explanation of homology,(iii) the origin of evolutionary innovations (incipient homologues),and (iv) can be considered homologous themselves.     

The Engrailed-expressing secondary head spots in the embryonic crayfish brain: examples for a group of homologous neurons in Crustacea and Hexapoda?

Hexapoda have been traditionally seen as the closest relatives of the Myriapoda (Tracheata hypothesis) but molecular studies have challenged this hypothesis and rather have suggested a close relationship of hexapods and crustaceans (Tetraconata hypothesis). In this new debate, data on the structure and development of the arthropod nervous system contribute important new data ("neurophylogeny"). Neurophylogenetic studies have already provided several examples for individually identifiably neurons in the ventral nerve cord that are homologous between insects and crustaceans. In the present report, we have analysed the emergence of Engrailed-expressing cells in the embryonic brain of a parthenogenetic crayfish, the marbled crayfish (Marmorkrebs), and have compared our findings to the pattern previously reported from insects. Our data suggest that a group of six Engrailed-expressing neurons in the optic anlagen, the so-called secondary head spot cells can be homologised between crayfish and the grasshopper. In the grasshopper, these cells are supposed to be involved in establishing the primary axon scaffold of the brain. Our data provide the first example for a cluster of brain neurons that can be homologised between insects and crustaceans and show that even at the level of certain cell groups, brain structures are evolutionary conserved in these two groups.     

The "eyespot module" and eyespots as modules: development, evolution, and integration of a complex phenotype

Organisms are inherently modular, yet modules also evolve in response to selection for functional integration or functional specialization of traits. For serially repeated homologous traits, there is a clear expectation that selection on the function of individual traits will reduce the integration between traits and subdivide a single ancestral module. The eyespots on butterfly wings are one example of serially repeated morphological traits that share a common developmental mechanism but are subject to natural and sexual selection for divergent functions. Here, I test two hypotheses about the organization of the eyespot pattern into independent dorsal-ventral and anterior-posterior modules, using a graphical modeling technique to examine patterns of eyespot covariation among and within wing surfaces in the butterfly Bicyclus anynana. Although there is a hierarchical and complex pattern of integration among eyespots, the results show a surprising mismatch between patterns of eyespot integration and the developmental and evolutionary eyespot units identified in previous empirical studies. These results are discussed in light of the relationships between developmental, functional, and evolutionary modules, and they suggest that developmental sources of independent trait variation are often masked by developmental sources of trait integration.     

Adaptations and history

The historical definition of adaptations has come into wide use as comparative biologists have applied methods of phylogenetic analysis to a variety of evolutionary problems. Here we point out a number of difficulties in applying historical methods to the study of adaptation, especially in cases where a trait has arisen but once. In particular, the potential complexity of the genetic correlations among phenotypic traits, performance variables and fitness makes inferring past patterns of selection from comparative data difficult. A given pattern of character distribution may support many alternative hypotheses of mechanism. While phylogenetic data are limited in their ability to reveal evolutionary mechanisms, they have always been an important source of adaptive hypotheses and will continue to be so.     

Using genetic networks and homology to understand the evolution of phenotypic traits

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, "biological homology" emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as "the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features." Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its "essential identity" (a Character Identity Network or "ChIN") must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.     

Transformation Series as an Ideographic Character Concept

An ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as “transformation series”, a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennig's definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical/transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing.     

Homologies in phylogenetic analyses—concept and tests

Analyzing morphological characters in a phylogenetic context comprises two steps, character analysis and cladistic analysis, which are equivalent to two independent tests for hypotheses on homology. The concept of homology concerns comparable parts of the same or different organisms if their correspondences are the consequence of the same genetic or epigenetic information, and consequently of the same origin. The concept of homology is more inclusive than the character concept. Characters are seen as parts of transformation series. In the first step of morphological character analyses correspondences and non-correspondences between two characters are analyzed. A range of different examination methods and accurate study contribute to the severity of test. The hypothesis that two characters are homologous is corroborated if the correspondences outweigh the non-correspondences because the non-correspondences contradict the homology hypothesis whereas the correspondences contradict the analogy hypothesis. Complex characters possess a higher empirical content than less complex characters because they are more severely testable. The cladistic analysis tests characters against other characters which have all passed the first test. Characters which are congruent with the most parsimonious topology are further corroborated; incongruent characters are not seen as ‘falsified’ but as not further corroborated and subject to re-analysis. To test both homologies and topologies repeatedly is consistent with Popperian testability, and it is in such cycles of research that hypotheses will be critically re-evaluated.     

Evolutionary transformations of the fetal membranes of viviparous reptiles: a case study of two lineages

The reptilian placenta is a composite structure formed by a functional interaction between extraembryonic membranes and the maternal uterus. Study of placental structure of squamate reptiles over the past century has established that each of the multiple independent origins of placentation, which characterize the reproductive diversity of squamates, has resulted from the evolutionary transformation of these homologous structures. Because each evolutionary transformation is an independent novel relationship between maternal and embryonic tissues, the resulting placentae are not homologous, even though the individual components may be. The evolution of reptilian placentation should reveal much about evolutionary patterns and mechanisms because similar structural-functional systems have been transformed along parallel trajectories on multiple occasions. We compared extraembryonic membrane and placental development and pattern of embryonic nutrition in thamnophiine snakes and Pseudemoia lizards in the context of recent hypotheses of phylogenetic relationships. Two primary types of placentation, chorioallantoic and yolk sac, evolved in each lineage. Smooth, highly vascular regions of chorioallantoic placentation are indistinguishable homoplasies that evolved in parallel, likely to facilitate respiratory exchange. The yolk sac placenta of each lineage is specialized for histotrophic nutrient transfer, yet composition of these structures differs because of variation in the ancestral snakes and lizards. In addition, the omphalopleure that contributes to yolk sac placentation persists to later embryonic stages compared to oviparous outgroups, but the two lineages have evolved different structures that prevent replacement of the omphalopleure by the allantois. Each lineage has also evolved unique structural specializations of the chorioallantoic placenta.     

Field homology: a meaningless concept.

Most biological homologues involve comparison of single characters in two or more taxa. It is possible, however, to recognize homologous characters between two or more taxa that involve the transformation of one character into many characters or many characters into one character. This type of homology is recognized as field homology and it has been widely used in comparative neuroanatomy. The emergence of the cladistic analysis of embryonic stages in the development of neural characters, however, strongly suggests that field homology is a meaningless concept. When it appears necessary to recognize field homologues, it is because comparisons are being made at an inappropriate level within a given biological hierarchy. Furthermore, recognition of field homologues restricts evolutionary mechanisms to a single mechanism of parcellation as defined by Ebbesson.     

Internodons as equivalence classes in genealogical networks: building-blocks for a rigorous species concept

Among the options suggested in phylogenetic systematics to solve the species problem is the Hennigian or internodal species concept. This concept interprets species as parts of the genealogical network of individual organisms between two successive permanent splits or between a permanent split and an extinction event. Though this option is at present not favoured by phylogeneticists, we believe that, to solve the species problem, there is no alternative to finding a satisfactory partition of the genealogical network. In previous work a formal definition has been developed of Hennigian or internodal species (called internodons here), based on a logical relation between individual organisms. In this paper, we prove that this definition indeed partitions genealogical networks exhaustively into mutually exclusive entities, by showing that the defining relation is an equivalence relation. Although internodons should not themselves be seen as species, they are essential building-blocks for any satisfying species concept.     

Homology and synapomorphy‐symplesiomorphy—neither synonymous nor equivalent but different perspectives on the same phenomenon

In a recent debate, either synapomorphy and symplesiomorphy or only synapomorphy have been claimed to be synonymous or equivalent to homology. In my view, exactly the same relationship exists between homology supported by a congruence test on the one hand and synapomorphy as well as symplesiomorphy on the other hand. Both conditions become established at the same time with the process of rooting of an unrooted topology. I, however, do not consider the concept of homology equal or synonymous to that of synapomorphy and symplesiomorphy. In my view, they represent different perspectives on the same phenomenon, i.e. correspondence by common origin. Homology has no implication on the direction of transformation, whereas symplesiomorphy as “primitive” condition and synapomorphy as “derived” condition refer directly to phylogenesis, the real historical evolutionary process of speciation and transformation. In addition, synapomorphy and symplesiomorphy might also refer to a character state that refers to the absence of a structure/organ, which creates problems with traditional homology concepts. Hennig's terms synapomorphy and symplesiomorphy are necessary and sufficient for the evolutionary interpretation of character states. For what is corroborated in an unrooted topology as the result of a congruence test, I suggest as a new term “synmorphy” because it can well be applied also to those characters where one state represents the absence of a structure/organ. The place for homology in morphological cladistics, however, is restricted to the characterization of the relationship between different character states of one transformation series (i.e. character).