Functional homology and homology of function: biological concepts and philosophical consequences

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology.

How development changes evolution: conceptual and historical issues in evolutionary developmental biology

Evolutionary developmental biology (Evo-Devo) is a new and rapidly developing field of biology which focuses on questions in the intersection of evolution and development and has been seen by many as a potential synthesis of these two fields. This synthesis is the topic of the books reviewed here. Integrating Evolution and Development (edited by Roger Sansom and Robert Brandon), is a collection of papers on conceptual issues in Evo-Devo, while From Embryology to Evo-Devo (edited by Manfred Laubichler and Jane Maienschein) is a history of the problem of the relations between ontogeny and phylogeny.

The nature of developmental constraints and the difference-maker argument for externalism

One current version of the internalism/externalism debate in evolutionary theory focuses on the relative importance of developmental constraints in evolutionary explanation. The received view of developmental constraints sees them as an internalist concept that tend to be shared across related species as opposed to selective pressures that are not. Thus, to the extent that constraints can explain anything, they can better explain similarity across species, while natural selection is better able to explain their differences. I challenge both of these aspects of the received view and propose a hierarchical view of constraints.

Discussion: Three Ways to Misunderstand Developmental Systems Theory

Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.     

Characterizing morphological (co)variation using structural equation models: Body size,allometric relationships and evolvability in a house sparrow metapopulation

Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta‐population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable “body size,” causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. Although on islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.     

The influence of variation and of developmental constraints on the rate of multivariate phenotypic evolution

A model of multivariate phenotypic evolution is analysed under the assumption that all characters have the same variance or at least constant ratios of variance. The rate of evolution is examined as a function of the amount of phenotypic variance in a variety of adaptive landscapes (fitness functions). It is demonstrated that the effect of variation depends on the type of adaptive landscape. In “well behaved” adaptive landscapes the rate of evolution can theoretically increase without limits, depending on the amount of heritable phenotypic variation. However, in other adaptive landscapes there are upper limits to the rate of evolution which cannot be exceeded if phenotypic variation is developmentally unconstrained, i. e. if it is the same for all characters. Further it is shown that the maximal rate of evolution becomes small if the number of characters becomes large. Fitness functions of this type are called malignant. It is argued that malignant fitness functions are more adequate models for the evolution of typical organismic systems, because they are models of functionally interdependent characters. It is concluded that there are upper limits to the rate of phenotypic evolution if the variation of functionally interdependent characters is developmentally unconstrained. The possible role of developmental constraints in adaptive phenotypic evolution is discussed.     

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.     

How to be an anti-reductionist about developmental biology: Response to Laubichler and Wagner

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example.     

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.     

Patterns in stage duration and development among marine and freshwater calanoid and cyclopoid copepods: a review of rules,physiological constraints,and evolutionary significance

Studies of development time of marine and freshwater copepods have taken separate tracks. Most studies on marine copepods report development time of each individual development stage, whereas studies on freshwater copepods report only development time, from egg to nauplius and nauplius to adult. This bias allows comparison of total development time but prevents detailed comparisons of patterns in stage-specific developmental schedules. With respect to egg to adult development time, three general relationships are known: developmental rates are dependent upon temperature and food concentration but independent of terminal body size; freshwater calanoids develop significantly slower than marine calanoids; freshwater cyclopoids develop at the same rate as marine calanoids. Two rules describe stage-specific developmental rates: the equiproportional rule and the isochronal rule. The first rule states that the duration of a given life history stage is a constant proportion of the embryonic development time; the second rule states that the time spent in each stage is the same for all stages. This review focuses on the second rule. From the 80+ published studies of copepod stage-specific developmental times, no species follows the isochronal rule strictly: Acartia spp. come closest with isochronal development from third nauplius (N3) to fourth copepodite (C4). The only pattern followed by all species is rapid development of the first and/or second naupliar stages, slow development of the second and/or third nauplius and prolonged development of the final copepodite stage. Once adulthood is reached, males are usually short-lived, but females can live for weeks to months in the laboratory. Adult longevity in the sea is, however, on the order of only a few days. The evolution of developmental patterns is discussed in the context of physiological constraints, along with consideration of possible relationships between stage-specific mortality rates and life history strategies. Physiological constraints may operate at critical bottlenecks in development (e.g. at the first feeding nauplius, N6, and the fifth copepodite stage). High mortality of eggs may explain why broadcast eggs hatch 2–3 times faster than eggs carried by females in a sac; high mortality of adults may explain why adults do not grow rather they maximize their reproductive effort by partitioning all energy for growth into egg production.     

Modularity, comparative embryology and evo-devo: Developmental dissection of evolving body plans

Modules can be defined as quasi-autonomous units that are connected loosely with each other within a system. A need for the concept of modularity has emerged as we deal with evolving organisms in evolutionary developmental research, especially because it is unknown how genes are associated with anatomical patterns. One of the strategies to link genotypes with phenotypes could be to relate developmental modules with morphological ones. To do this, it is fundamental to grasp the context in which certain anatomical units and developmental processes are associated with each other specifically. By identifying morphological modularities as units recognized by some categories of general homology as established by comparative anatomy, it becomes possible to identify developmental modules whose genetic components exhibit coextensive expressions. This permits us to distinguish the evolutionary modification in which the identical morphological module simply alters its shape for adaptation, without being decoupled from the functioning gene network (‘coupled modularities’), from the evolution of novelty that involves a heterotopic shift between the anatomical and developmental modules. Using this formulation, it becomes possible, within the realm of Geoffroy's homologous networks, to reduce morphological homologies to developmental mechanistic terms by dissociating certain classes of modules that are often associated with actual shapes and functions.     

Biting through constraints: cranial morphology, disparity and convergence across living and fossil carnivorous mammals

Carnivory has evolved independently several times in eutherian (including placental) and metatherian (including marsupial) mammals. We used geometric morphometrics to assess convergences associated with the evolution of carnivory across a broad suite of mammals, including the eutherian clades Carnivora and Creodonta and the metatherian clades Thylacoleonidae, Dasyuromorphia, Didelphidae and Borhyaenoidea. We further quantified cranial disparity across eutherians and metatherians to test the hypothesis that the marsupial mode of reproduction has constrained their morphological evolution. This study, to our knowledge the first to extensively sample pre-Pleistocene taxa, analysed 30 three-dimensional landmarks, focused mainly on the facial region, which were digitized on 130 specimens, including 36 fossil taxa. Data were analysed with principal components (PC) analysis, and three measures of disparity were compared between eutherians and metatherians. PC1 showed a shift from short to long faces and seemed to represent diet and ecology. PC2 was dominated by the unique features of sabre-toothed forms: dramatic expansion of the maxilla at the expense of the frontal bones. PC3, in combination with PC1, distinguished metatherians and eutherians. Metatherians, despite common comparisons with felids, were more similar to caniforms, which was unexpected for taxa such as the sabre-toothed marsupial Thylacosmilus. Contrary to previous studies, metatherian carnivores consistently exhibited disparity which exceeded that of the much more speciose eutherian carnivore radiations, refuting the hypothesis that developmental constraints have limited the morphological evolution of the marsupial cranium.     

Morphological integration in the hominin dentition: evolutionary, developmental, and functional factors

As the most common and best preserved remains in the fossil record, teeth are central to our understanding of evolution. However, many evolutionary analyses based on dental traits overlook the constraints that limit dental evolution. These constraints are diverse, ranging from developmental interactions between the individual elements of a homologous series (the whole dentition) to functional constraints related to occlusion. This study evaluates morphological integration in the hominin dentition and its effect on dental evolution in an extensive sample of Plio- and Pleistocene hominin teeth using geometric morphometrics and phylogenetic comparative methods. Results reveal that premolars and molars display significant levels of covariation; that integration is stronger in the mandibular dentition than in the maxillary dentition; and that antagonist teeth, especially first molars, are strongly integrated. Results also show an association of morphological integration and evolution. Stasis is observed in elements with strong functional and/or developmental interactions, namely in first molars. Alternatively, directional evolution (and weaker integration) occurs in the elements with marginal roles in occlusion and mastication, probably in response to other direct or indirect selective pressures. This study points to the need to reevaluate hypotheses about hominin evolution based on dental characters, given the complex scenario in which teeth evolve.     

Evolution of a developmental mechanism: Species-specific regulation of the cell cycle and the timing of events during craniofacial osteogenesis

Neural crest mesenchyme (NCM) controls species-specific pattern in the craniofacial skeleton but how this cell population accomplishes such a complex task remains unclear. To elucidate mechanisms through which NCM directs skeletal development and evolution, we made chimeras from quail and duck embryos, which differ markedly in their craniofacial morphology and maturation rates. We show that quail NCM, when transplanted into duck, maintains its faster timetable for development and autonomously executes molecular and cellular programs for the induction, differentiation, and mineralization of bone, including premature expression of osteogenic genes such as Runx2 and Col1a1. In contrast, the duck host systemic environment appears to be relatively permissive and supports osteogenesis independently by providing circulating minerals and a vascular network. Further experiments reveal that NCM establishes the timing of osteogenesis by regulating cell cycle progression in a stage- and species-specific manner. Altering the time-course of D-type cyclin expression mimics chimeras by accelerating expression of Runx2 and Col1a1. We also discover higher endogenous expression of Runx2 in quail coincident with their smaller craniofacial skeletons, and by prematurely over-expressing Runx2 in chick embryos we reduce the overall size of the craniofacial skeleton. Thus, our work indicates that NCM establishes species-specific size in the craniofacial skeleton by controlling cell cycle, Runx2 expression, and the timing of key events during osteogenesis.     

Ontogeny, anatomy, and the problem of homology: Carl Gegenbaur and the American tradition of cell lineage studies

Summary In this paper we analyze Carl Gegenbaur’s conception of the relationship between embryology (“Ontogenie”) and comparative anatomy and his related ideas about homology. We argue that Gegenbaur’s conviction of the primacy of comparative anatomy and his careful consideration of caenogenesis led him to a more balanced view about the relationship between ontogeny and phylogeny than his good friend Ernst Haeckel. We also argue that Gegenbaur’s ideas about the centrality of comparative anatomy and his definitions of homology actually laid the conceptual foundations for Hans Spemann’s (1915) later analysis of homology. We also analyze Gegenbaur’s reception in the United States and how the discussions between E.B. Wilson and Edwin Conklin about the role of the “embryological criterion of homology” and the latter’s argument for an even earlier concept of cellular homology reflect the recurring theme of preformism in ontogeny, a theme that finds its modern equivalent in various genetic definitions of homology, only recently challenged by the emerging synthesis of evolutionary developmental biology. Finally, we conclude that Gegenbaur’s own careful methodological principles can serve as an important model for proponents of present day “evo-devo”, especially with respect to the integration of ontogeny with phylogeny embedded in comparative anatomy.     

Petrosal orientation and mandibular ramus breadth: evidence for an integrated petroso-mandibular developmental unit

The absolute and relative breadths of the mandibular ramus (MRB) display substantial variation in modern humans, and are of analytical value in paleoanthropology. According to Enlow et al. ([1969] Am. J. Orthod. 56:6-23), the ramus is the growth counterpart of the middle cranial fossa (MCF) and the pharynx. Such counterpart principles state that variation in ramus breadth is a frequent function of the horizontal alignment of the MCF, and both structures tend to covary within and between populations. These authors also suggested that lateral parts of the basicranium have a particular importance in the positioning of facial components. In the present study, this hypothesis is tested, and relationships between midline and lateral basicranial elements and ramus breadth variation are explored. Two-dimensional landmarks taken from lateral radiographs of adult crania representative of three modern human populations (Europeans, West Africans, and Japanese) were analyzed by geometric morphometry. Our results are consistent with previous counterpart analyses. Furthermore, our findings highlight the significance of the orientation of the petrous temporal to modern human mandibular ramus variation. Variation in the orientation of the petrosal bone appears to alter the spatial position of the mandible and influences MRB. Developmental integration of a petroso-mandibular unit may have important paleoanthropological implications.     

Variation in developmental biology and microsatellite DNA in reproductive ecotypes of kokanee, Oncorhynchus nerka: Implications for declining populations in a large British Columbia lake

Kokanee are the nonanadromous (freshwater resident) form of sockeyesalmon (Oncorhynchus nerka) found in lake ecosystems throughoutthe North Pacific region. Kokanee commonly exhibit two reproductiveecotypes; `stream-spawners' that reproduce in streams tributary tolakes, and `beach-spawners' that reproduce on submerged lakeshore gravelbeaches. Okanagan Lake, in the southcentral interior of BritishColumbia, Canada, contains beach- and stream-spawning kokanee and bothecotypes have declined dramatically in abundance over the last 20 years.We examined developmental biology (developmental rate to hatching andemergence) and genetic divergence at eight microsatellite loci toinvestigate phenotypic and genetic differentiation between ecotypes tounderstand selective and demographic factors that might influence therecovery of depressed populations. Beach-spawning female kokanee weresmaller and produced smaller eggs than females from stream-spawningpopulations. There was no striking difference in time to 50%hatching between ecotypes, but beach-spawning kokanee developed fasterfrom hatching to emergence. Microsatellite loci were highly polymorphicin kokanee (between 5 and 23 alleles per locus) and showed significantdifferentiation among populations (average = 0.018). There was,however, no significant variation attributable to spawning ecotype afteraccounting for variation within ecotypes. Simulated population-mixtureanalyses indicated good potential for genetic classification of kokaneeas beach- or stream-spawners; estimated mixture proportions were within11% of actual proportions averaged over 50 replications. Our datasuggest that Okanagan Lake kokanee constitute at least two managementunits within a single watershed; the ecotypes appear adapted to distinctthermal reproductive environments and show modest moleculardifferentiation from one another. Persistence of kokanee within OkanaganLake may depend, in part, on management plans that recognize thedistinctions between the sympatric reproductive ecotypes.     

Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification

Background Various groups of flowering plants reveal profound (‘saltational’) changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps ‘hopeful monsters’) that gave rise to new evolutionary lines of organisms, based on (major) genetic changes.Scope This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized.Conclusions Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves – as still distinguishable in related flowering plants – are blurred (‘fuzzy’). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.