Spatiotemporal reorganization of growth rates in the evolution of ontogeny

Abstract. Heterochrony, evolutionary changes in rate or timing of development producing parallelism between ontogeny and phylogeny, is viewed as the most common type of evolutionary change in development. Alternative hypotheses such as heterotopy, evolutionary change in the spatial patterning of development, are rarely entertained. We examine the evidence for heterochrony and heterotopy in the evolution of body shape in two clades of piranhas. One of these is the sole case of heterochrony previously reported in the group; the others were previously interpreted as cases of heterotopy. To compare ontogenies of shape, we computed ontogenetic trajectories of shape by multivariate regression of geometric shape variables (i.e., partial warp scores and shape coordinates) on centroid size. Rates of development relative to developmental age and angles between the trajectories were compared statistically. We found a significant difference in developmental rate between species of Serrasalmus , suggesting that heterochrony is a partial explanation for the evolution of body shape, but we also found a significant difference between their ontogenetic transformations; the direction of the difference between them suggests that heterotopy also plays a role in this group. In Pygocentrus we found no difference in developmental rate among species, but we did find a difference in the ontogenies, suggesting that heterotopy, but not heterochrony, is the developmental basis for shape diversification in this group. The prevalence of heterotopy as a source of evolutionary novelty remains largely unexplored and will not become clear until the search for developmental explanations looks beyond heterochrony.     

Heterochrony and allometry: the analysis of evolutionary change in ontogeny

The connection between development and evolution has become the focus of an increasing amount of research in recent years, and heterochrony has long been a key concept in this relation. Heterochrony is defined as evolutionary change in rates and timing of developmental processes; the dimension of time is therefore an essential part in studies of heterochrony. Over the past two decades, evolutionary biologists have used several methodological frameworks to analyse heterochrony, which differ substantially in the way they characterize evolutionary changes in ontogenies and in the resulting classification, although they mostly use the same terms. This review examines how these methods compare ancestral and descendant ontogenies, emphasizing their differences and the potential for contradictory results from analyses using different frameworks. One of the two principal methods uses a clock as a graphical display for comparisons of size, shape and age at a particular ontogenic stage, whereas the other characterizes a developmental process by its time of onset, rate, and time of cessation. The literature on human heterochrony provides particularly clear examples of how these differences produce apparent contradictions when applied to the same problem. Developmental biologists recently have extended the concept of heterochrony to the earliest stages of development and have applied it at the cellular and molecular scale. This extension brought considerations of developmental mechanisms and genetics into the study of heterochrony, which previously was based primarily on phenomenological characterizations of morphological change in ontogeny. Allometry is the pattern of covariation among several morphological traits or between measures of size and shape; unlike heterochrony, allometry does not deal with time explicitly. Two main approaches to the study of allometry are distinguished, which differ in the way they characterize organismal form. One approach defines shape as proportions among measurements, based on considerations of geometric similarity, whereas the other focuses on the covariation among measurements in ontogeny and evolution. Both are related conceptually and through the use of similar algebra. In addition, there are close connections between heterochrony and changes in allometric growth trajectories, although there is no one-to-one correspondence. These relationships and outline links between different analytical frameworks are discussed.     

Synchrony and heterochrony in ontogeny (of fish)

The ontogeny of an organism is a complex process that strongly depends on the timing of developmental processes. In this article, I discuss ontogeny of fish (and other organisms) in temporal terms, based on the hypothesis that organisms as self-organized entities may create their own times for their development, and that this development consists of a sequence of longer stabilized states (steps) with shorter, intermittent less-stable intervals (thresholds). If viewed within the context of structure-to-structure, organ-to-organ and/or organism-to-environment relationships, then the saltatory pattern of ontogeny emerges at each transition from one stabilized state to another. I consider two timing mechanisms essential to ontogeny - synchrony (coordinating) and heterochrony (implementing); their possible roles are discussed. Besides this, a new context and understanding for the term heterochrony is proposed. At least three levels of heterochrony should be distinguished: interspecific, intraspecific and intraindividual. However, the difference among these three types of heterochrony is not in the phenomenon itself but in the way we perceive and classify it.     

Sequence heterochrony and the evolution of development

One of the most persistent questions in comparative developmental biology concerns whether there are general rules by which ontogeny and phylogeny are related. Answering this question requires conceptual and analytic approaches that allow biologists to examine a wide range of developmental events in well-structured phylogenetic contexts. For evolutionary biologists, one of the most dominant approaches to comparative developmental biology has centered around the concept of heterochrony. However, in recent years the focus of studies of heterochrony largely has been limited to one aspect, changes in size and shape. I argue that this focus has restricted the kinds of questions that have been asked about the patterns of developmental change in phylogeny, which has narrowed our ability to address some of the most fundamental questions about development and evolution. Here I contrast the approaches of growth heterochrony with a broader view of heterochrony that concentrates on changes in developmental sequence. I discuss a general approach to sequence heterochrony and summarize newly emerging methods to analyze a variety of kinds of developmental change in explicit phylogenetic contexts. Finally, I summarize a series of studies on the evolution of development in mammals that use these new approaches.     

Mosaic Evolution of the Basicranium in <Emphasis Type="Italic">Homo</Emphasis> and its Relation to Modular Development

Mosaic evolution describes different rates of evolutionary change in different body units. Morphologically these units are described by more relationships within a unit than between different units which relates mosaic evolution with morphological integration and modularity. Recent evidence suggests mosaic evolution at the human basicranium due to different evolutionary rates of midline and lateral cranial base morphology but this hypothesis has not yet been addressed explicitly. We this hypothesis and explore how mosaic evolution relates to modular development. Evolutionary data sets on midline (N = 186) and lateral (N = 86) basicranial morphology are compared with 3D data on pre- and postnatal basicranial ontogeny (N = 71). Our results support the hypothesis of mosaic evolution and suggest a modular nature of basicranial development. Different embryological basicranial units likely became differently modified during evolution, with relatively stable midline elements and more variable lateral elements. In addition, developmental data suggests that modularity patterns change throughout ontogeny. During prenatal ontogeny lateral basicranial elements (greater sphenoid wings and petrosal pyramids) change together compared with the midline base. Close to birth the greater sphenoid wings keep a spatially stable position, while the petrosal pyramids become dissociated and shifted posteriorly. After birth the greater sphenoid wings and petrosal pyramids change again jointly and with respect to midline cranial base elements. This sequential pattern of integration and modularization and re-integration describes human basicranial ontogeny in a way that is potentially important for the understanding of evolutionary change. Phylogenetic modifications of this pattern during morphogenesis, growth, and development may underlie the mosaic evolution of the hominin basicranium.     

Why the short face? Developmental disintegration of the neurocranium drives convergent evolution in neotropical electric fishes

Convergent evolution is widely viewed as strong evidence for the influence of natural selection on the origin of phenotypic design. However, the emerging evo‐devo synthesis has highlighted other processes that may bias and direct phenotypic evolution in the presence of environmental and genetic variation. Developmental biases on the production of phenotypic variation may channel the evolution of convergent forms by limiting the range of phenotypes produced during ontogeny. Here, we study the evolution and convergence of brachycephalic and dolichocephalic skull shapes among 133 species of Neotropical electric fishes (Gymnotiformes: Teleostei) and identify potential developmental biases on phenotypic evolution. We plot the ontogenetic trajectories of neurocranial phenotypes in 17 species and document developmental modularity between the face and braincase regions of the skull. We recover a significant relationship between developmental covariation and relative skull length and a significant relationship between developmental covariation and ontogenetic disparity. We demonstrate that modularity and integration bias the production of phenotypes along the brachycephalic and dolichocephalic skull axis and contribute to multiple, independent evolutionary transformations to highly brachycephalic and dolichocephalic skull morphologies.     

A genetic basis for intraspecific differences in developmental timing?

Heterochrony, altered developmental timing between ancestors and their descendents, has been proposed as a pervasive evolutionary feature and recent analytical approaches have confirmed its existence as an evolutionary pattern. Yet, the mechanistic basis for heterochrony remains unclear and, in particular, whether intraspecific variation in the timing of developmental events generates, or has the potential to generate, future between‐species differences. Here we make a key step in linking heterochrony at the inter‐ and intraspecific level by reporting an association between interindividual variation in both the absolute and relative timing (position within the sequence of developmental events) of key embryonic developmental events and genetic distance for the pond snail, Radix balthica. We report significant differences in the genetic distance of individuals exhibiting different levels of dissimilarity in their absolute and relative timing of developmental events such as spinning activity, eyespot formation, heart ontogeny, and hatching. This relationship between genetic and developmental dissimilarity is consistent with there being a genetic basis for variation in developmental timing and so suggests that intraspecific heterochrony could provide the raw material for natural selection to produce speciation.     

Modularity of a Cambrian ptychoparioid trilobite cranidium

SUMMARY Modularity of the cranidium of Crassifimbra? metalaspis, a Cambrian ptychoparioid trilobite, is investigated using landmark‐based geometric morphometric methods to gain insight into the integration among morphogenetic processes responsible for shaping the head of an ancient arthropod. Of particular interest is the extent to which the structure of phenotypic integration was governed by direct interactions among developmental pathways, because these interactions may generate long‐term constraints on evolutionary innovation. A modified two‐way ANOVA decomposes cranidial shape variation into components representing symmetric variation among individuals and fluctuating asymmetry (FA). The structure of integration of each of these components is inferred from correlated deviations in shape among nine partitions of the cranidium. Significant correlation among partitions in FA indicates direct interactions among their respective developmental pathways. An a priori hypothesis that modularity was determined by functional association among partitions is not well supported by the among‐partition correlation structure for either component of variation. Instead, exploratory analyses reveal that phenotypic integration was strongly influenced by spatially localized morphogenetic controls. Comparison of the structures of the Individuals and FA components of variation reveals that the two share relatively few commonalities: the structure of phenotypic integration was only weakly influenced by direct interactions. The large contribution of parallel variation to phenotypic integration suggests that modularity was unlikely to have imposed a long‐term constraint on evolutionary innovation in these early trilobites.     

INTEGRATING DEVELOPMENTAL EVOLUTIONARY PATTERNS AND MECHANISMS: A CASE STUDY USING THE GASTROPOD RADULA

Determining the connection between ontogeny and phylogeny continues to be a major theme in biology. However, few studies have combined dissection of pattern and process that lead to transformation of complex morphological structures. Here we examine the patterns and processes of shape change in a model system—the gastropod radula. This system is a simple one having only two processes: initial secretion and postsecretional movement of teeth. However, it produces a tremendous amount of shape variability and fusion patterns. To determine both pattern and mechanism of shape change in an evolutionary context, we use three complementary approaches and datasets. First, we use a phylogenetic hypothesis to determine the polarity of developmental events. Second, we perform a morphometric analysis of shape change using relative warp analysis that allows us to locate and compare the direction and magnitude of ontogenetic and phylogenetic shape divergence. These comparisons are the basis for testing hyptheses of heterochrony and heterotopy, and we show how our results do not conform to expectations of pure heterochrony. The rejection of heterochrony as a hypothesis is based on empirically demonstrating (1) initial shape differs in each taxon; (2) a single dimension of shape variability does not simultaneously describe ontogenetic and evolutionary shape changes; and (3) a significantly different shape and size covariance between taxa. This rejection is probably based on spatial changes in initial conditions and not spatial changes caused by the process itself. Finally, we construct a mechanistic model that explains how shape change happens based on the sequence of events during ontogeny. By using the parameters in the model as characters in the phylogenetic dataset, we show that different parts of the system have arisen at different times and become co-opted into the process. By integrating our analyses together we show that spatial process parameters can be responsible for our nonspatial patterns and that different ontogenetic processes can create similar end morphologies.     

Mammalian organogenesis in deep time: tools for teaching and outreach

Mammals constitute a rich subject of study on evolution and development and provide model organisms for experimental investigations. They can serve to illustrate how ontogeny and phylogeny can be studied together and how the reconstruction of ancestors of our own evolutionary lineage can be approached. Likewise, mammals can be used to promote 'tree thinking' and can provide an organismal appreciation of evolutionary changes. This subject is suitable for the classroom and to the public at large given the interest and familiarity of people with mammals and their closest relatives. We present a simple exercise in which embryonic development is presented as a transformative process that can be observed, compared, and analyzed. In addition, we provide and discuss a freely available animation on organogenesis and life history evolution in mammals. An evolutionary tree can be the best tool to order and understand those transformations for different species. A simple exercise introduces the subject of changes in developmental timing or heterochrony and its importance in evolution. The developmental perspective is relevant in teaching and outreach efforts for the understanding of evolutionary theory today.     

Scute’s polymorphism as a source of evolutionary development of the turtle shell

The scute mosaic (pholidosis) of the turtle shell is a complex correlated system of the modular type. Horny scutes are separate morphological elements partially closely connected with each other and partially relatively autonomous in development. The last feature causes high variability of scutes in the shape, size, rate and direction of growth, and provides the basis of transformation of the entire mosaic. In the evolution of turtles, the horny shell changed towards a decrease in the number of elements composing it. The process of oligomerization developed through reduction and fusion of scutes or their anlages. The traces of these transformations are observed in the ontogeny of living turtles. The scutes undergoing reduction display the following developmental deviations: (1) a decrease in size of the scute anlage, (2) the temporal shift in initiation to later embryonic stages, (3) absence of an anlage of a own furrow (the boundaries of the scute are formed by the furrows of neighboring scutes), and (4) a decrease in size of the zone and rate of the scute growth. The fusion of horny scutes follows two patterns: (1) fusion of scute anlages and (2) reduction of horny furrows separating scutes before. Secondary polymerization of the scute mosaic by the appearance of additional elements usually results from abnormal development and is infrequently fixed in evolution. The main mechanism of evolutionary changes in turtle pholidosis was heterochrony, i.e., the time shift in initiation and developmental rate of scutes. The heterotopies, i.e., changes in the position of scute anlages, played a minor role in the evolution of turtles; they usually caused only scute abnormalities, which was frequently asymmetrical.     

Modularity as a source of new morphological variation in the mandible of hybrid mice

ABSTRACT: BACKGROUND: Hybridization is often seen as a process dampening phenotypic differences accumulated between diverging evolutionary units. For a complex trait comprising several relatively independent modules, hybridization may however simply generate new phenotypes, by combining into a new mosaic modules inherited from each parental groups and parts intermediate with respect to the parental groups. We tested this hypothesis by studying mandible size and shape in a set of first and second generation hybrids resulting from inbred wild-derived laboratory strains documenting two subspecies of house mice, Musmusculusdomesticus and Musmusculusmusculus. Phenotypic variation of the mandible was divided into nested partitions of developmental, evolutionary and functional modules. RESULTS: The size and shape of the modules were differently influenced by hybridization. Some modules seemed to be the result of typical additive effects with hybrids intermediate between parents, some displayed a pattern expected in the case of monogenic dominance, whereas in other modules, hybrids were transgressive. The result is interpreted as the production of novel mandible morphologies. Beyond this modularity, modules in functional interaction tended to display significant covariations. CONCLUSIONS: Modularity emerges as a source of novel morphological variation by its simple potential to combine different parts of the parental phenotypes into a novel offspring mosaic of modules. This effect is partly counterbalanced by bone remodeling insuring an integration of the mosaic mandible into a functional ensemble, adding a non-genetic component to the production of transgressive phenotypes in hybrids.     

Origin and evolution of alternative developmental strategies in amphibious sarcopterygian parasites (Platyhelminthes, Monogenea, Polystomatidae)

Most integrative studies involving phylogenetic, developmental and ecological trends showed that the diversity of developmental modifications among the Platyhelminthes was linked to transmission opportunity pressures. For parasitic flatworms with complex life cycles it was suggested that the evolutionary forces that constrained or enhanced developmental strategies implied heterochronic patterns. Similar patterns were also reported from the Monogenea with direct life cycles, especially for Polystomatidae, which infest amphibious Sarcopterygians. Polystoma, whose members are recovered almost exclusively from anuran hosts of the Neobatrachia, is capable of following two alternative developmental strategies depending on the physiological stage of its host. Processes by which parasites reach maturity are strikingly different, and lead to discrete adult phenotypes within the same parasite species. In the present study, we investigate the origin and evolution of developmental patterns of polystomatids in a phylogenetic framework, using an integrative approach of heterochrony and evolutionary ecology. The results suggest that both phenotypes have coexisted during the early stages of polystome evolution, and that neither of them can be considered as the ancestral one. The two developmental pathways, each associated with one life cycle, may have arisen independently prior to polystome diversification, when strictly aquatic sarcopterygians attempted colonization of temporary freshwater environments. The occurrence of these two patterns within species of the genus Polystoma is suggested to reflect the ancestral condition, and to have allowed both developmental strategies to be successful depending on shifts in transmission opportunities. Thus, host evolutionary ecology may be the main factor in shaping developmental strategies within polystomatids.     

Cranial modularity and sequence heterochrony in mammals

Heterochrony, the temporal shifting of developmental events relative to each other, requires a degree of autonomy among those processes or structures. Modularity, the division of larger structures or processes into autonomous sets of internally integrated units, is often discussed in relation to the concept of heterochrony. However, the relationship between the developmental modules derived from studies of heterochrony and evolutionary modules, which should be of adaptive importance and relate to the genotype-phenotype map, has not been explicitly studied. I analyzed a series of sectioned and whole cleared-and-stained embryological and neonatal specimens, supplemented with published ontogenetic data, to test the hypothesis that bones within the same phenotypic modules, as determined by morphometric analysis, are developmentally integrated and will display coordinated heterochronic shifts across taxa. Modularity was analyzed in cranial bone ossification sequences of 12 therian mammals. A dataset of 12-18 developmental events was used to assess if modularity in developmental sequences corresponds to six phenotypic modules, derived from a recent morphometric analysis of cranial modularity in mammals. Kendall's tau was used to measure rank correlations, with randomization tests for significance. If modularity in developmental sequences corresponds to observed phenotypic modules, bones within a single phenotypic module should show integration of developmental timing, maintaining the same timing of ossification relative to each other, despite differences in overall ossification sequences across taxa. Analyses did not find any significant conservation of developmental timing within the six phenotypic modules, meaning that bones that are highly integrated in adult morphology are not significantly integrated in developmental timing.     

Functional decoupling between flowers and leaves in the Ameroglossum pernambucense complex can facilitate local adaptation across a pollinator and climatic heterogeneous landscape

Decoupling between floral and leaf traits is expected in plants with specialized pollination systems to assure a precise flower–pollinator fit, irrespective of leaf variation associated with environmental heterogeneity (functional modularity). Nonetheless, developmental interactions among floral traits also decouple flowers from leaves regardless of selection pressures (developmental modularity). We tested functional modularity in the hummingbird‐pollinated flowers of the Ameroglossum pernambucense complex while controlling for developmental modularity. Using two functional traits responsible for flower–pollinator fit [floral tube length (TL) and anther–nectary distance (AN)], one floral trait not linked to pollination [sepal length (SL), control for developmental modularity] and one leaf trait [leaf length (LL)], we found evidence of flower functional modularity. Covariation between TL and AN was ca. two‐fold higher than the covariation of either of these traits with sepal and leaf lengths, and variations in TL and AN, important for a precise flower–pollinator fit, were smaller than SL and LL variations. Furthermore, we show that previously reported among‐population variation of flowers associated with local pollinator phenotypes was independent from SL and LL variations. These results suggest that TL and AN are functionally linked to fit pollinators and sufficiently decoupled from developmentally related floral traits (SL) and vegetative traits (LL). These results support previous evidences of population differentiation due to local adaptation in the A. pernambucense complex and shed light on the role of flower–leaf decoupling for local adaptation in species distributed across biotic and abiotic heterogeneous landscapes.     

An integrative approach identifies developmental sequence heterochronies in freshwater basommatophoran snails

Adopting an integrative approach to the study of sequence heterochrony, we compared the timing of developmental events encompassing a mixture of developmental stages and functional traits in the embryos of 12 species of basommatophoran snails in an explicit phylogenetic framework. PARSIMOV analysis demonstrated clear functional heterochronies associated both with basal branches within the phylogeny and with terminal speciation events. A consensus of changes inferred under both accelerated transformation and delayed transformation optimizations identified four heterochronies where the direction of movement was known plus six twin heterochronies where the relative movements of the two events could not be assigned. On average, 0.5 and 0.58 events were inferred to have changed their position in the developmental sequence on internal and terminal branches of the phylogeny, respectively; these values are comparable with frequencies of sequence heterochrony reported in mammals. Directional heterochronies such as the early occurrence of body flexing in relation to the ontogeny of the eye spots, heart beat, and free swimming events occurred convergently and/or at different levels (i.e., familial, generic, and species) within the phylogeny. Such a functional approach to the study of developmental sequences has highlighted the possibility that heterochrony may have played a prominent role in the evolution of this group of invertebrates.     

Heterochrony in plant evolutionary studies through the twentieth century

The evolution of plant morphology is the result of changes in developmental processes. Heterochrony, the evolutionary change in developmental rate or timing, is a major cause of ontogenetic modification during evolution. It is responsible for both interspecific and intraspecific morphological differences. Other causes include heterotopy, the change of structural position, and homeosis, the replacement of a structure by another. This paper discusses and reviews the role of heterochrony in plant evolution at the organismal, organ, tissue, cellular, and molecular levels, as well as the relationships among heterochrony, heterotopy, and homeosis. An attempt has been made to include all published studies through late 1999. It is likely that most heterochronic change involves more than one of the six classic pure heterochronic processes. Of these processes, we found neoteny (decreased developmental rate in descendant), progenesis (earlier offset), and acceleration (increased rate) to be more commonly reported than hypermorphosis (delayed offset) or predisplacement (earlier onset). We found no reports of postdisplacement (delayed onset). Therefore, although rate changes are common (both neoteny and acceleration), shifts in timing most commonly involve earlier termination in the descendant (progenesis). These relative frequencies may change as more kinds of structures are analyzed. Phenotypic effects of evolutionary changes in onset or offset timing can be exaggerated, suppressed, or reversed by changes in rate. Because not all developmental changes responsible for evolution result from heterochrony, however, we propose that plant evolution be studied from a viewpoint that integrates these different developmental mechanisms.     

Balancing sampling and specialization: an adaptationist model of incremental development

Development is typically a constructive process, in which phenotypes incrementally adapt to local ecologies. Here, we present a novel model in which natural selection shapes developmental systems based on the evolutionary ecology, and these systems adaptively guide phenotypic development. We assume that phenotypic construction is incremental and trades off with sampling cues to the environmental state. We computed the optimal developmental programmes across a range of evolutionary ecological conditions. Using these programmes, we simulated distributions of mature phenotypes. Our results show that organisms sample the environment most extensively when cues are moderately, not highly, informative. When the developmental programme relies heavily on sampling, individuals transition from sampling to specialization at different times in ontogeny, depending on the consistency of their sampled cue set; this finding suggests that stochastic sampling may result in individual differences in plasticity itself. In addition, we find that different selection pressures may favour similar developmental mechanisms, and that organisms may incorrectly calibrate development despite stable ontogenetic environments. We hope our model will stimulate adaptationist research on the constructive processes guiding development.     

The integrated phenotype

Proper functioning of complex phenotypes requires that multiple traits work together. Examination of relationships among traits within and between complex characters and how they interact to function as a whole organism is critical to advancing our understanding of evolutionary developmental plasticity. Phenotypic integration refers to the relationships among multiple characters of a complex phenotype, and their relationships with other functional units (modules) in an organism. In this review, I summarize a brief history of the concept of phenotypic integration in plant and animal biology. Following an introduction of concepts, including modularity, I use an empirical case-study approach to highlight recent advance in clarifying the developmental and genomic basis of integration. I end by highlighting some novel approaches to genomic and epigenetic perturbations that offer promise in further addressing the role of phenotypic integration in evolutionary diversification. In the age of the phenotype, studies that examine the genomic and developmental changes in relationships of traits across environments will shape the next chapter in our quest for understanding the evolution of complex characters.