How many processes are responsible for phenotypic evolution?

Multiple evolutionary pressures shape identical consonant avoidance in the world's languages

Languages disfavor word forms containing sequences of similar or identical consonants, due to the biomechanical and cognitive difficulties posed by patterns of this sort. However, the specific evolutionary processes responsible for this phenomenon are not fully understood. Words containing sequences of identical consonants may be more likely to arise than those without; processes of word form mutation may be more likely to remove than create sequences of identical consonants in word forms; finally, words containing identical consonants may die out more frequently than those without. Phylogenetic analyses of the evolution of homologous word forms indicate that words with identical consonants arise less frequently than those without. However, words with identical consonants do not die out more frequently than those without. Further analyses reveal that forms with identical consonants are replaced in basic meaning functions more frequently than words without. Taken together, results suggest that the underrepresentation of sequences of identical consonants is overwhelmingly a by-product of constraints on word form coinage, though processes related to word usage also serve to ensure that such patterns are infrequent in more salient vocabulary items. These findings clarify aspects of processes of lexical evolution and competition that take place during language change, optimizing communicative systems.

Investigation of the highly endangered Pinna nobilis' mass mortalities: Seasonal and temperature patterns of health status, antioxidant and heat stress responses

Recently, P. nobilis populations have suffered a tremendous reduction, with pathogens potentially playing a crucial role. Considering its highly endangered status, mechanisms leading to mass mortalities were examined in one or multiple pathogens infected populations. Thus, seasonal antioxidant enzymatic activities, hsp70 and catalase mRNA levels, were investigated in two different Greek populations, during mass mortality events in summer of 2020. Samples were collected from Fthiotis and Lesvos during February (T^oC 14 ± 1.2 and 15 ± 1 respectively), April (T^oC 18 ± 1.2 and 17 ± 1.3 respectively), and June (T^oC 24.5 ± 1.5 and 21.5 ± 1.5 respectively) 2020. In July of the same year (T^oC 26.5 ± 1.7 in Fthiotis and 24.5 ± 1.7 in Lesvos), no live specimens were found. All biochemical parameters and phylogenetic analysis suggest that pathogen infection increases P. nobilis sensitivity to water temperature, subsequently leading to mass mortality. The latter was obvious in Fthiotis individuals, in which Haplosporidium pinnae was also observed with Mycobacterium spp., compared to Lesvos individuals.

Growth Regulation in the Larvae of the Lepidopteran Pieris brassicae: A Field Study

Size and shape are important determinants of fitness in most living beings. Accordingly, the capacity of the organism to regulate size and shape during growth, containing the effects of developmental disturbances of different origin, is considered a key feature of the developmental system. In a recent study, through a geometric morphometric analysis on a laboratory-reared sample of the lepidopteran Pieris brassicae, we found evidence of regulatory mechanisms able to restrain size and shape variation, including bilateral fluctuating asymmetry, during larval development. However, the efficacy of the regulatory mechanism under greater environmental variation remains to be explored. Here, based on a field-reared sample of the same species, by adopting identical measurements of size and shape variation, we found that the regulatory mechanisms for containing the effects of developmental disturbances during larval growth in P. brassicae are also effective under more natural environmental conditions. This study may contribute to better characterization of the mechanisms of developmental stability and canalization and their combined effects in the developmental interactions between the organism and its environment.

A global meta-analysis reveals higher variation in breeding phenology in urban birds than in their non-urban neighbours

Cities pose a major ecological challenge for wildlife worldwide. Phenotypic variation, which can result from underlying genetic variation or plasticity, is an important metric to understand eco-evolutionary responses to environmental change. Recent work suggests that urban populations might have higher levels of phenotypic variation than non-urban counterparts. This prediction, however, has never been tested across species nor over a broad geographical range. Here, we conducted a meta-analysis of the avian literature to compare urban versus non-urban means and variation in phenology (i.e. lay date) and reproductive effort (i.e. clutch size, number of fledglings). First, we show that urban populations reproduce earlier and have smaller broods than non-urban conspecifics. Second, we show that urban populations have higher phenotypic variation in laying date than non-urban populations. This result arises from differences between populations within breeding seasons, conceivably due to higher landscape heterogeneity in urban habitats. These findings reveal a novel effect of urbanisation on animal life histories with potential implications for species adaptation to urban environments (which will require further investigation). The higher variation in phenology in birds subjected to urban disturbance could result from plastic responses to a heterogeneous environment, or from higher genetic variation in phenology, possibly linked to higher evolutionary potential.

Size and shape regulation during larval growth in the lepidopteran Pieris brassicae

By adopting a longitudinal study design and through geometric morphometrics methods, we investigated size and shape regulation in the head capsule during the larval development of the cabbage butterfly Pieris brassicae under laboratory conditions. We found evidence of size regulation by compensatory growth, although not equally effective in all larval stages. Size compensation is not attained through the regulation of developmental timing, but rather through the modulation of per-time growth rate. As for the shape, neither the variance of the symmetric component of shape, nor the level of fluctuating asymmetry show any evidence of increase across stages, either at the population or individual level, which is interpreted as a mark of ontogenetic shape regulation. In addition, also the geometry of individual asymmetry is basically conserved across stages. While providing specific documentation on the ontogeny of size and shape variation in this insect, this study may contribute to a more general understanding of developmental regulation and its influence on phenotypic evolution.

The dynamic mosaic phenotypes of flowering plants

Ecological interaction and adaptation both depend on phenotypic characteristics. In contrast with the common conception of the 'adult' phenotype, plant bodies develop continuously during their lives. Furthermore, the different units (metamers) that comprise plant bodies are not identical copies, but vary extensively within individuals. These characteristics foster recognition of plant phenotypes as dynamic mosaics. We elaborate this conception based largely on a wide-ranging review of developmental, ecological and evolutionary studies of plant reproduction, and identify its utility in the analysis of plant form, function and diversification. An expanded phenotypic conception is warranted because dynamic mosaic features affect plant performance and evolve. Evidence demonstrates that dynamic mosaic phenotypes enable functional ontogeny, division of labour, resource and mating efficiency. In addition, dynamic mosaic features differ between individuals and experience phenotypic selection. Investigation of the characteristics and roles of dynamic and mosaic features of plant phenotypes benefits from considering within-individual variation as a function-valued trait that can be analysed with functional data methods. Phenotypic dynamics and within-individual variation arise despite an individual's genetic uniformity, and develop largely by heterogeneous gene expression and associated hormonal control. These characteristics can be heritable, so that dynamic mosaic phenotypes can evolve and diversify by natural selection.

Are developmental shifts the main driver of phenotypic evolution in Diplodus spp. (Perciformes: Sparidae)?

Background

Sparid fishes of the genus Diplodus show a complex life history. Juveniles have adaptations well suited to life in the water column. When fishes recruit into the adult population, individuals develop a radically differentiated shape that reflects their adaptation to the new benthic environment typical of the adult.

A comparative analysis of ontogenetic trajectories was performed to assess the presence of divergence in the developmental pattern. By using a geometric morphometric approach, we investigated the pattern of shape variation across ontogenetic stages that span from early settlement to the adult stage in four species of the genus Diplodus. Landmarks were collected on the whole body of fishes to quantify the phenotypic variation along two well defined life stages, i.e. juvenile and adult.

A comparative analysis of ontogenetic trajectories was performed to assess the presence of divergence in the developmental pattern. Subsequently, we investigated the patterns of integration and modularity as proxy for the alteration of the developmental processes. This have allowed to give an insight in morphological developmental patterns across ecologically and ontogenetically differentiated life stages and to investigate the process leading to the adult shape.

Result

Our results suggest that the origin of morphological novelties in Diplodus spp. arise from shifts of the ontogenetic trajectories during development. During the settlement phase, the juveniles’ morphological shapes converge towards similar regions of the morphospace. When the four species approach the transition between settlement and recruitment, we observe the lowest level of inter- and intra-specific disparity. After this transition we detect an abrupt shift of ontogenetic trajectories, i.e. the path taken by species during development, that led to highly divergent adult phenotypes.

Discussion

We suggest that the evolution of new ecomorphologies, better suited to exploit different niches (pelagic vs. benthonic) and reduce inter-specific competition in Diplodus spp., are related to the shift in the ontogenetic trajectory that in turn is associated to changes in modularity and integration pattern.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1424-1) contains supplementary material, which is available to authorized users.

Spandrels and trait delimitation: No such thing as "architectural constraint"

Forty years ago, Gould and Lewontin used the metaphor of a building's "spandrels" to highlight that organismal traits could be the inevitable consequence of organismal construction, with no alternative configurations possible. Because adaptation by natural selection requires variation, regarding a trait incapable of variation as an adaptation could be a serious error. Gould and Lewontin's exhortation spurred biologists' efforts to investigate biases and limitations in development in their studies of adaptation, a major methodological advance. But in terms of the metaphor itself, over the past 40 years there are virtually no examples of "spandrels" in the primary literature. Moreover, multiple serious confusions in the metaphor have been identified and clarified, for example, that the "spandrels" of San Marco are pendentives, and pendentives are perfect examples of adaptation. I look back over the sparse empirical fruits of the "spandrels" metaphor, and ask what the clarifications of the past 40 years mean for biological theory and practice. I conclude that if there is anything to be rescued from the clarified spandrels metaphor, it is not "constraint" at all. Instead, it is the still-unresolved issue of trait delimitation, which is how to parse organisms into subsets that are tractable and biologically appropriate for study.

Nearly 200 years of sustained selection have not overcome the leaf area-stem size relationship in the poinsettia

Organismal parts often covary in their proportions, a phenomenon known as allometry. One way of exploring the causes of widespread allometric patterns is with artificial selection, to test whether or not it is possible to move populations into "empty" allometric space not occupied by the wild type. Domesticated organisms have been subject to many generations of selection, making them ideal model systems. We used the domesticated Christmas poinsettia Euphorbia pulcherrima in combination with wild populations to examine the origin of the proportionality between leaf area and stem size, which scales predictably across nearly all plants. In accordance with the stated aims of breeders to produce more compact plants, we predicted that domesticated poinsettias would have greater leaf area for a given stem volume than the tall, lanky wild ancestors. Our data rejected this prediction, showing instead that domesticates have leaf area-stem volume relationships identical to the wild ancestors. Presumably the metabolic dependence between stems and leaves makes the leaf area-stem volume relationship difficult to overcome. The relative fixity of this relationship leads to predictable covariation in other traits: The fuller outlines of domestic poinsettias involve significantly shorter internodes, and given a constant leaf area-stem volume relationship, smaller individual leaf areas. At the same time, domestic poinsettias are subject to selection favoring breakage resistance, which is achieved via thicker stems for a given length rather than stiffer stem tissue resistance to bending. Our results show that domesticated poinsettias differ from wild plants in a suite of traits including leaf size, internode distances, and stem length-diameter relations, but despite over 200 years of selection favoring rounded outlines, there has been no change in the total leaf area-stem volume relationship, helping to predict which changes are likely achievable and which will not be under continued artificial selection and in the wild.

Heredity and self-organization: partners in the generation and evolution of phenotypes

In this review we examine the role of self-organization in the context of the evolution of morphogenesis. We provide examples to show that self-organized behavior is ubiquitous, and suggest it is a mechanism that can permit high levels of biodiversity without the invention of ever-increasing numbers of genes. We also examine the implications of self-organization for understanding the "internal descriptions" of organisms and the concept of a genotype-phenotype map.

Evolution of Drosophila sex comb length illustrates the inextricable interplay between selection and variation

In spite of the diversity of possible biological forms observed in nature, a limited range of morphospace is frequently occupied for a given trait. Several mechanisms have been proposed to explain this bias in the distribution of phenotypes including selection, drift, and developmental constraints. Despite extensive work on phenotypic bias, the underlying developmental mechanisms explaining why particular regions of morphological space remain unoccupied are poorly understood. To address this issue, we studied the sex comb, a group of modified bristles used in courtship that shows marked morphological diversity among Drosophila species. In many Drosophila species including Drosophila melanogaster, the sex comb rotates 90° to a vertical position during development. Here we analyze the effect of changing D. melanogaster sex comb length on the process of rotation. We find that artificial selection changes the number of bristles per comb without a proportional change in the space available for rotation. As a result, when increasing sex comb length, rather than displaying a similar straight vertical shape observed in other Drosophila species, long sex combs bend because rotation is blocked by a neighboring row of bristles. Our results show ways in which morphologies that would be favored by natural selection are apparently impossible to achieve developmentally. These findings highlight the potential role of development in modifying selectable variation in the evolution of Drosophila sex comb length.

Evolution of early development in dipterans: reverse-engineering the gap gene network in the moth midge Clogmia albipunctata (Psychodidae)

Understanding the developmental and evolutionary dynamics of regulatory networks is essential if we are to explain the non-random distribution of phenotypes among the diversity of organismic forms. Here, we present a comparative analysis of one of the best understood developmental gene regulatory networks today: the gap gene network involved in early patterning of insect embryos. We use gene circuit models, which are fitted to quantitative spatio-temporal gene expression data for the four trunk gap genes hunchback (hb), Krüppel (Kr), giant (gt), and knirps (kni)/knirps-like (knl) in the moth midge Clogmia albipunctata, and compare them to equivalent reverse-engineered circuits from our reference species, the vinegar fly Drosophila melanogaster. In contrast to the single network structure we find for D. melanogaster, our models predict four alternative networks for C. albipunctata. These networks share a core structure, which includes the central regulatory feedback between hb and knl. Other interactions are only partially determined, as they differ between our four network structures. Nevertheless, our models make testable predictions and enable us to gain specific insights into gap gene regulation in C. albipunctata. They suggest a less central role for Kr in C. albipunctata than in D. melanogaster, and show that the mechanisms causing an anterior shift of gap domains over time are largely conserved between the two species, although shift dynamics differ. The set of C. albipunctata gene circuit models presented here will be used as the starting point for data-constrained in silico evolutionary simulations to study patterning transitions in the early development of dipteran species.

Classification of transient behaviours in a time-dependent toggle switch model

BACKGROUND

Waddington's epigenetic landscape is an intuitive metaphor for the developmental and evolutionary potential of biological regulatory processes. It emphasises time-dependence and transient behaviour. Nowadays, we can derive this landscape by modelling a specific regulatory network as a dynamical system and calculating its so-called potential surface. In this sense, potential surfaces are the mathematical equivalent of the Waddingtonian landscape metaphor. In order to fully capture the time-dependent (non-autonomous) transient behaviour of biological processes, we must be able to characterise potential landscapes and how they change over time. However, currently available mathematical tools focus on the asymptotic (steady-state) behaviour of autonomous dynamical systems, which restricts how biological systems are studied.

RESULTS

We present a pragmatic first step towards a methodology for dealing with transient behaviours in non-autonomous systems. We propose a classification scheme for different kinds of such dynamics based on the simulation of a simple genetic toggle-switch model with time-variable parameters. For this low-dimensional system, we can calculate and explicitly visualise numerical approximations to the potential landscape. Focussing on transient dynamics in non-autonomous systems reveals a range of interesting and biologically relevant behaviours that would be missed in steady-state analyses of autonomous systems. Our simulation-based approach allows us to identify four qualitatively different kinds of dynamics: transitions, pursuits, and two kinds of captures. We describe these in detail, and illustrate the usefulness of our classification scheme by providing a number of examples that demonstrate how it can be employed to gain specific mechanistic insights into the dynamics of gene regulation.

CONCLUSIONS

The practical aim of our proposed classification scheme is to make the analysis of explicitly time-dependent transient behaviour tractable, and to encourage the wider use of non-autonomous models in systems biology. Our method is applicable to a large class of biological processes.

The generation of variation and the developmental basis for evolutionary novelty

Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the "obvious" case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation- or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We propose instead that for a feature to be novel, it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low-probability evolutionary transitions and highlights how the integration of developmental and functional considerations are necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., "evo-devo") but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle.

The developmental renaissance in adaptationism

From an adaptation perspective, unoccupied patches of morphological space are inferred to be empty because they are of low fitness and selected against. These inferences hinge on venturesome assumptions, because emptiness is explained by low fitness and low fitness is inferred from emptiness. Moreover, non-adaptive factors, such as developmental constraint, could also plausibly account for empty morphospace. In response, biologists increasingly study ontogeny to test the assumption that unobserved phenotypes could be produced if selection were to favor them; finding that empty space morphologies can be readily produced in development helps reject constraint and lends support to adaptive hypotheses. This developmental approach to adaptation calls on manifold techniques, including embryology, artificial selection and comparative methods. Belying their diversity, all of these methods examine the causes of empty morphospace and mark a return of development, long excluded from traditional evolutionary biology, to adaptationist practice.

Quantitative genetics of shape in cricket wings: developmental integration in a functional structure

The role of developmental and genetic integration for evolution is contentious. One hypothesis states that integration acts as a constraint on evolution, whereas an alternative is that developmental and genetic systems evolve to match the functional modularity of organisms. This study examined a morphological structure, the cricket wing, where developmental and functional modules are discordant, making it possible to distinguish the two alternatives. Wing shape was characterized with geometric morphometrics, quantitative genetic information was extracted using a full-sibling breeding design, and patterns of developmental integration were inferred from fluctuating asymmetry of wing shape. The patterns of genetic, phenotypic, and developmental integration were clearly similar, but not identical. Heritabilities for different shape variables varied widely, but no shape variables were devoid of genetic variation. Simulated selection for specific shape changes produced predicted responses with marked deflections due to the genetic covariance structure. Three hypotheses of modularity according to the wing structures involved in sound production were inconsistent with the genetic, phenotypic, or developmental covariance structure. Instead, there appears to be strong integration throughout the wing. The hypothesis that genetic and developmental integration evolve to match functional modularity can therefore be rejected for this example.

Phenotypic plasticity in development and evolution: facts and concepts. Introduction

This theme issue pursues an exploration of the potential of taking into account the environmental sensitivity of development to explaining the evolution of metazoan life cycles, with special focus on complex life cycles and the role of developmental plasticity. The evolution of switches between alternative phenotypes as a response to different environmental cues and the evolution of the control of the temporal expression of alternative phenotypes within an organism's life cycle are here treated together as different dimensions of the complex relationships between genotype and phenotype, fostering the emergence of a more general and comprehensive picture of phenotypic evolution through a quite diverse sample of case studies. This introductory article reviews fundamental facts and concepts about phenotypic plasticity, adopting the most authoritative terminology in use in the current literature. The main topics are types and components of phenotypic variation, the evolution of organismal traits through plasticity, the origin and evolution of phenotypic plasticity and its adaptive value.

Trunk anomalies in the centipede Stigmatogaster subterranea provide insight into late-embryonic segmentation

We describe and analyze naturally occurring anomalies in the segmental structures of the trunk in an isolated population of the geophilomorph centipede Stigmatogaster subterranea. Recorded anomalies include mispaired tergites, shrunk segments, variously deformed sclerites, bifurcated trunk, and defects of spiracles and sternal pore areas. One specimen has a perfect segmentally patterned trunk, but with an even number of leg-bearing segments, representing the first record of such a phenotype in adult centipedes. We interpret these anomalies as the effects of perturbation of specific morphogenetic processes in trunk segmentation, occurring at different embryonic stages. The variety of segmental anomalies found in this population provides insights into the developmental process of segmentation and its evolution in geophilomorph centipedes. Variation in dorsal mispairing anomalies demonstrates that segments, as traditionally defined in arthropod morphology, are not the effective developmental units throughout embryogenesis.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

Developmental constraints vs. variational properties: How pattern formation can help to understand evolution and development

This article suggests that apparent disagreements between the concept of developmental constraints and neo-Darwinian views on morphological evolution can disappear by using a different conceptualization of the interplay between development and selection. A theoretical framework based on current evolutionary and developmental biology and the concepts of variational properties, developmental patterns and developmental mechanisms is presented. In contrast with existing paradigms, the approach in this article is specifically developed to compare developmental mechanisms by the morphological variation they produce and the way in which their functioning can change due to genetic variation. A developmental mechanism is a gene network, which is able to produce patterns in space though the regulation of some cell behaviour (like signalling, mitosis, apoptosis, adhesion, etc.). The variational properties of a developmental mechanism are all the pattern transformations produced under different initial and environmental conditions or IS-mutations. IS-mutations are DNA changes that affect how two genes in a network interact, while T-mutations are mutations that affect the topology of the network itself. This article explains how this new framework allows predictions not only about how pattern formation affects variation, and thus phenotypic evolution, but also about how development evolves by replacement between pattern formation mechanisms. This article presents testable inferences about the evolution of the structure of development and the phenotype under different selective pressures. That is what kind of pattern formation mechanisms, in which relative temporal order, and which kind of phenotypic changes, are expected to be found in development.

Conserved versus innovative features in animal body organization

The origin of evolutionary novelties is a central topic in evolutionary developmental biology (evo-devo) studies. In any new feature, there is a conserved component that is either structural or related to the underlying genetic control, but it is not always obvious what is really new and what is conserved. Nevertheless, disentangling this blending of old and new features is basic to understanding mechanisms of evolutionary change. The origin of arthropod appendages illustrates the complexity in tracing the origin of evolutionary novelties. At the base of the lineage, the main body axis was already segmented and antero-posteriorly patterned, and the genetic tool kit required to form lateral outgrowths was already available. The novelty was possibly the developmental decision to "read" the available axial information and to exploit it for differentiating segmentally patterned and axially segmented appendages. Some important novelties bridge the gap between what have been traditionally distinguished as systemic and local changes. For example, the origin of the body cavities evolved by several animal groups may have been initiated by simple changes in cell-to-cell adhesive properties. Any possible change in an existing ontogenetic pathway has the potential to generate novelties.

Complexity and integration in sexual ornamentation: an example with carotenoid and melanin plumage pigmentation

Sexual ornaments often consist of several components produced by distinct developmental processes. The complexity of sexual ornaments might be favoured by mate choice of individual components in different environments which ultimately results in weak interrelationships (integration) among the developmental processes that produce these components. At the same time, sexual selection for greater exaggeration of individual components favours their stronger co-dependence on organismal resources. This should ultimately produce stronger condition-mediated integration among ornaments' components in individuals with the most exaggerated ornamentation. Here we distinguish between these two sources of integration by examining the relationship between integration and elaboration of sexual ornamentation in three bird species: two with carotenoid-based sexual ornamentation (the house finch, Carpodacus mexicanus and common redpoll, Carduelis flammea) and a species with melanin-based sexual ornamentation (house sparrow, Passer domesticus). We found that integration of components varied with elaboration of carotenoid-based ornamentation but not of melanin ornamentation. In the house finches, integration was the highest in individuals with small ornaments and decreased with ornament elaboration whereas the pattern was the opposite in common redpolls. These results suggest that in these species integration and complexity of carotenoid-based ornamental components are due to shared condition-dependence of distinct developmental pathways, whereas integration and complexity of the melanin ornamentation is due to organismal integration of developmental pathways and is largely condition- and environment-invariant. Thus, functionally, ornamentation of the house sparrows can be considered a single trait, whereas complexity of the house finch and redpoll ornamentation varies with ornament elaboration and individual condition.

Evolution of morphological integration. I. Functional units channel stress-induced variation in shrew mandibles

Stress-induced deviations from normal development are often assumed to be random, yet their accumulation and expression can be influenced by patterns of morphological integration within an organism. We studied within-individual developmental variation (fluctuating asymmetry) in the mandible of four shrew species raised under normal and extreme environments. Patterns of among-individual variation and fluctuating asymmetry were strongly concordant in traits that were involved in the attachment of the same muscles (i.e., functionally integrated traits), and fluctuating asymmetry was closely integrated among these traits, implying direct developmental interactions among traits involved in the same function. Stress-induced variation was largely confined to the directions delimited by functionally integrated groups of traits in the pattern that was concordant with species divergence--species differed most in the same traits that were most sensitive to stress within each species. These results reveal a strong effect of functional complexes on directing and incorporating stress-induced variation during development and might explain the historical persistence of sets of traits involved in the same function in shrew jaws despite their high sensitivity to environmental variation.

Developmental constraints in a comparative framework: a test case using variations in phalanx number during amniote evolution

Constraints are factors that limit evolutionary change. A subset of constraints is developmental, and acts during embryonic development. There is some uncertainty about how to define developmental constraints, and how to formulate them as testable hypotheses. Furthermore, concepts such as constraint-breaking, universal constraints, and forbidden morphologies present some conceptual difficulties. One of our aims is to clarify these issues. After briefly reviewing current classifications of constraint, we define developmental constraints as those affecting morphogenetic processes in ontogeny. They may be generative or selective, although a clear distinction cannot always be drawn. We support the idea that statements about constraints are in fact statements about the relative frequency of particular transformations (where 'transformation' indicates a change from the ancestral condition). An important consequence of this is that the same transformation may be constrained in one developmental or phylogenetic context, but evolutionarily plastic in another. In this paper, we analyse developmental constraints within a phylogenetic framework, building on similar work by previous authors. Our approach is based on the following assumptions from the literature: (1) constraints are identified when there is a discrepancy between the observed frequency of a transformation, and its expected frequency; (2) the 'expected' distribution is derived by examining the phylogenetic distribution of the transformation and its associated selection pressures. Thus, by looking for congruence between these various phylogenetic distribution patterns, we can test hypotheses about constraint. We critically examine this approach using a test case: variation in phalanx-number in the amniote limb.

The interaction between developmental bias and natural selection: from centipede segments to a general hypothesis

Do limitations to the ways in which mutations can alter developmental processes help to determine the direction of phenotypic evolution? In the early days of neo-Darwinism, the answer given to this question was an emphatic 'no'. However, recent work, both theoretical and empirical, argues that the answer should at least be 'sometimes', and possibly even a straightforward 'yes'. Here, I examine the key concept of developmental bias, which encompasses both developmental constraint and developmental drive. I review the case of centipede segment number, which is a particularly clear example of developmental bias, but also a rather unusual one. I then consider how, in general terms, developmental bias and natural selection might interact, with the result that it is their interaction, rather than either process on its own, that determines evolutionary direction. Essentially, the whole argument is about the extent to which phenotypic variation is developmentally structured as opposed to amorphous or random. This issue can be traced back to the very beginning of evolutionary biology, and in particular to a difference of opinion between Darwin and Wallace, who emphasized, respectively, character correlation and character independence.

Developmental drive: an important determinant of the direction of phenotypic evolution

Over any period of evolutionary time, the prevailing ontogenetic trajectory within a lineage may either recur unchanged from generation to generation (stasis) or alter (developmental reprogramming). A key question about reprogramming is whether it exhibits intrinsic biases in favor of some sorts of change and against others, which may be referred to respectively as "drive" and "constraint." A simple logical argument suggests that both drive and constraint should be common, and conversely that cases of equiprobable modification in various phenotypic directions should be relatively rare. These proposals, that drive and constraint exist and that they are common, appear to be widely accepted, even among neo-Darwinians, who are sometimes portrayed as rejecting them. What is more controversial is that developmental drive (and constraint) can have a powerful influence on the direction of evolutionary change. It is argued that such an influence will occur, and indeed may be pervasive.