A computational model of teeth and the developmental origins of morphological variation

The dental phenotype of hairless dogs with FOXI3 haploinsufficiency

Hairless dog breeds show a form of ectodermal dysplasia characterised by a lack of hair and abnormal tooth morphology. This has been attributed to a semi-dominant 7-base-pair duplication in the first exon of the forkhead box I3 gene (FOXI3) shared by all three breeds. Here, we identified this FOXI3 variant in a historical museum sample of pedigreed hairless dog skulls by using ancient DNA extraction and present the associated dental phenotype. Unlike in the coated wild type dogs, the hairless dogs were characterised in both the mandibular and maxillary dentition by a loss of the permanent canines, premolars and to some extent incisors. In addition, the deciduous fourth premolars and permanent first and second molars consistently lacked the distal and lingual cusps; this resulted in only a single enlarged cusp in the basin-like heel (talonid in lower molars, talon in upper molars). This molar phenotype is also found among several living and fossil carnivorans and the extinct order Creodonta in which it is associated with hypercarnivory. We therefore suggest that FOXI3 may generally be involved in dental (cusp) development within and across mammalian lineages including the hominids which are known to exhibit marked variability in the presence of lingual cusps.

Approaches to Macroevolution: 1. General Concepts and Origin of Variation

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.

The gastropod foregut — evolution viewed through a developmental lens

Comparative data on the developing gastropod foregut suggest that this multicomponent feeding complex consists of two developmental modules. Modularity is revealed by delayed development of the buccal cavity and radular sac (“ventral module”) relative to the dorsal food channel (“dorsal module”) in gastropods with feeding larvae compared with those that may have never had a feeding larval stage. If nonfeeding larvae like those of extant patellogastropods and vetigastropods are ancestral for gastropods, then the uncoupling and heterochronic offset of dorsal and ventral foregut modules allowed the post-metamorphic dorsal food channel to be co-opted as a simple but functional esophagus for feeding larvae. Furthermore, by reducing energy cost per ovum, the heterochronic offset may have given mothers the evolutionary option of increasing fecundity or investing in protective egg encapsulation material. A second developmental innovation was spatial separation of the dorsal and ventral foregut modules, as illustrated by distal foregut development in buccinid neogastropods and venom gland development in cone snails. Spatial uncoupling may have enhanced the evolvability of gastropod foreguts by allowing phenotypic variants of ventral module components to be selected within post-metamorphic ecological settings, without needing to be first tested for compatibility with larval feeding. Finally, we describe a case in which foregut modularity has helped facilitate a highly derived life history in which encapsulated embryos ingest nurse eggs.

Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

Background

Comparative transcriptomics can answer many questions in developmental and evolutionary developmental biology. Most transcriptomic studies start by showing global patterns of variation in transcriptomes that differ between species or organs through developmental time. However, little is known about the kinds of expression differences that shape these patterns.

Results

We compared transcriptomes during the development of two morphologically distinct serial organs, the upper and lower first molars of the mouse. We found that these two types of teeth largely share the same gene expression dynamics but that three major transcriptomic signatures distinguish them, all of which are shaped by differences in the relative abundance of different cell types. First, lower/upper molar differences are maintained throughout morphogenesis and stem from differences in the relative abundance of mesenchyme and from constant differences in gene expression within tissues. Second, there are clear time-shift differences in the transcriptomes of the two molars related to cusp tissue abundance. Third, the transcriptomes differ most during early-mid crown morphogenesis, corresponding to exaggerated morphogenetic processes in the upper molar involving fewer mitotic cells but more migrating cells. From these findings, we formulate hypotheses about the mechanisms enabling the two molars to reach different phenotypes. We also successfully applied our approach to forelimb and hindlimb development.

Conclusions

Gene expression in a complex tissue reflects not only transcriptional regulation but also abundance of different cell types. This knowledge provides valuable insights into the cellular processes underpinning differences in organ development. Our approach should be applicable to most comparative developmental contexts.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1157-7) contains supplementary material, which is available to authorized users.

Evolutionary aspects of the development of teeth and baleen in the bowhead whale

In utero, baleen whales initiate the development of several dozens of teeth in upper and lower jaws. These tooth germs reach the bell stage and are sometimes mineralized, but toward the end of prenatal life they are resorbed and no trace remains after birth. Around the time that the germs disappear, the keratinous baleen plates start to form in the upper jaw, and these form the food-collecting mechanism. Baleen whale ancestors had two generations of teeth and never developed baleen, and the prenatal teeth of modern fetuses are usually interpreted as an evolutionary leftover. We investigated the development of teeth and baleen in bowhead whale fetuses using histological and immunohistochemical evidence. We found that upper and lower dentition initially follow similar developmental pathways. As development proceeds, upper and lower tooth germs diverge developmentally. Lower tooth germs differ along the length of the jaw, reminiscent of a heterodont dentition of cetacean ancestors, and lingual processes of the dental lamina represent initiation of tooth bud formation of replacement teeth. Upper tooth germs remain homodont and there is no evidence of a secondary dentition. After these germs disappear, the oral epithelium thickens to form the baleen plates, and the protein FGF-4 displays a signaling pattern reminiscent of baleen plates. In laboratory mammals, FGF-4 is not involved in the formation of hair or palatal rugae, but it is involved in tooth development. This leads us to propose that the signaling cascade that forms teeth in most mammals has been exapted to be involved in baleen plate ontogeny in mysticetes.

Building and maintaining joints by exquisite local control of cell fate

We owe the flexibility of our bodies to sophisticated articulations between bones. Establishment of these joints requires the integration of multiple tissue types: permanent cartilage that cushions the articulating bones, synovial membranes that enclose a lubricating fluid-filled cavity, and a fibrous capsule and ligaments that provide structural support. Positioning the prospective joint region involves establishment of an "interzone" region of joint progenitor cells within a nascent cartilage condensation, which is achieved through the interplay of activators and inhibitors of multiple developmental signaling pathways. Within the interzone, tight regulation of BMP and TGFβ signaling prevents the hypertrophic maturation of joint chondrocytes, in part through downstream transcriptional repressors and epigenetic modulators. Synovial cells then acquire further specializations through expression of genes that promote lubrication, as well as the formation of complex structures such as cavities and entheses. Whereas genetic investigations in mice and humans have uncovered a number of regulators of joint development and homeostasis, recent work in zebrafish offers a complementary reductionist approach toward understanding joint positioning and the regulation of chondrocyte fate at joints. The complexity of building and maintaining joints may help explain why there are still few treatments for osteoarthritis, one of the most common diseases in the human population. A major challenge will be to understand how developmental abnormalities in joint structure, as well as postnatal roles for developmental genes in joint homeostasis, contribute to birth defects and degenerative diseases of joints. WIREs Dev Biol 2017, 6:e245. doi: 10.1002/wdev.245 For further resources related to this article, please visit the WIREs website.

Computational identification of genes modulating stem height-diameter allometry

The developmental variation in stem height with respect to stem diameter is related to a broad range of ecological and evolutionary phenomena in trees, but the underlying genetic basis of this variation remains elusive. We implement a dynamic statistical model, functional mapping, to formulate a general procedure for the computational identification of quantitative trait loci (QTLs) that control stem height-diameter allometry during development. Functional mapping integrates the biological principles underlying trait formation and development into the association analysis of DNA genotype and endpoint phenotype, thus providing an incentive for understanding the mechanistic interplay between genes and development. Built on the basic tenet of functional mapping, we explore two core ecological scenarios of how stem height and stem diameter covary in response to environmental stimuli: (i) trees pioneer sunlit space by allocating more growth to stem height than diameter and (ii) trees maintain their competitive advantage through an inverse pattern. The model is equipped to characterize 'pioneering' QTLs (piQTLs) and 'maintaining' QTLs (miQTLs) which modulate these two ecological scenarios, respectively. In a practical application to a mapping population of full-sib hybrids derived from two Populus species, the model has well proven its versatility by identifying several piQTLs that promote height growth at a cost of diameter growth and several miQTLs that benefit radial growth at a cost of height growth. Judicious application of functional mapping may lead to improved strategies for studying the genetic control of the formation mechanisms underlying trade-offs among quantities of assimilates allocated to different growth parts.

The mandibular molar pit-tubercle (MMPT) dental nonmetric trait: Comprehensive analysis of a large sample

Dental nonmetric traits are quasicontinous variables, mostly of genetic origin. Thus, sets of such traits allow biological distance estimation between samples. Mandibular molar pit-tubercle (MMPT) is a buccal trait defined by Weets (2009) in Irish samples. This study aims to analyze (a) trait frequencies, (b) grade definitions, (c) intraobserver error, (d) sexual dimorphism, (e) asymmetry, and (f) trait associations for MMPT in a Portuguese sample. The first (LM1), second (LM2) and third (LM3) lower molars of 600 identified individuals from the Coimbra collections were scored for MMPT in three scoring sessions. Intraobserver error, bilateral asymmetry and trait correlations were tested using Kendall's τ-b, while sexual dimorphism was verified using Pearson's χ². Frequencies (LM1: 2.1%; LM2: 3.5%; LM3: 30.3%) were similar to previous reports. However, a new free apex cusp form (grade 3+) was detected. Considering three scoring sessions, intraobserver precision was above 85%, and correlation coefficients between observations were positive and moderate to very strong (0.291<τ-b<0.835). Intrasample variation was low, since only LM3 showed sexual dimorphism (female: 30.2%; males: 16.2%; χ²=15.512; p<0.001; df=1; n=556) and large asymmetry (27.1%). There were no strong (τ-b>0.3) intertrait associations involving MMPT. MMPT shows low trait presence, sexual dimorphism and asymmetry in stable teeth (LM1 and LM2). Intraobserver precision is high, so scoring should be reliable, although a plaque and better threshold grade definition is needed. After further research on non-European samples, MMPT can be useful in biodistance research.

Fine tuning of Rac1 and RhoA alters cuspal shapes by remolding the cellular geometry

The anatomic and functional combinations of cusps and lophs (ridges) define the tooth shape of rodent molars, which distinguishes species. The species-specific cusp patterns result from the spatiotemporal induction of enamel knots (EKs), which require precisely controlled cellular behavior to control the epithelial invagination. Despite the well-defined roles of EK in cusp patterning, the determinants of the ultimate cuspal shapes and involvement of epithelial cellular geometry are unknown. Using two typical tooth patterns, the lophodont in gerbils and the bunodont in mice, we showed that the cuspal shape is determined by the dental epithelium at the cap stage, whereas the cellular geometry in the inner dental epithelium (IDE) is correlated with the cuspal shape. Intriguingly, fine tuning Rac1 and RhoA interconvert cuspal shapes between two species by remolding the cellular geometry. Either inhibition of Rac1 or ectopic expression of RhoA could region-distinctively change the columnar shape of IDE cells in gerbils to drive invagination to produce cusps. Conversely, RhoA reduction in mice inhibited invagination and developed lophs. Furthermore, we found that Rac1 and RhoA modulate the choices of cuspal shape by coordinating adhesion junctions, actin distribution, and fibronectin localization to drive IDE invagination.

Modularity: genes, development and evolution

Modularity has emerged as a central concept for evolutionary biology, providing the field with a theory of organismal structure and variation. This theory has reframed long standing questions and serves as a unified conceptual framework for genetics, developmental biology and multivariate evolution. Research programs in systems biology and quantitative genetics are bridging the gap between these fields. While this synthesis is ongoing, some major themes have emerged and empirical evidence for modularity has become abundant. In this review, we look at modularity from an historical perspective, highlighting its meaning at different levels of biological organization and the different methods that can be used to detect it. We then explore the relationship between quantitative genetic approaches to modularity and developmental genetic studies. We conclude by investigating the dynamic relationship between modularity and the adaptive landscape and how this potentially shapes evolution and can help bridge the gap between micro- and macroevolution.

Mathematical study on robust tissue pattern formation in growing epididymal tubule

Tissue pattern formation during development is a reproducible morphogenetic process organized by a series of kinetic cellular activities, leading to the building of functional and stable organs. Recent studies focusing on mechanical aspects have revealed physical mechanisms on how the cellular activities contribute to the formation of reproducible tissue patterns; however, the understanding for what factors achieve the reproducibility of such patterning and how it occurs is far from complete. Here, I focus on a tube pattern formation during murine epididymal development, and show that two factors influencing physical design for the patterning, the proliferative zone within the tubule and the viscosity of tissues surrounding to the tubule, control the reproducibility of epididymal tubule pattern, using a mathematical model based on experimental data. Extensive numerical simulation of the simple mathematical model revealed that a spatially localized proliferative zone within the tubule, observed in experiments, results in more reproducible tubule pattern. Moreover, I found that the viscosity of tissues surrounding to the tubule imposes a trade-off regarding pattern reproducibility and spatial accuracy relating to the region where the tubule pattern is formed. This indicates an existence of optimality in material properties of tissues for the robust patterning of epididymal tubule. The results obtained by numerical analysis based on experimental observations provide a general insight on how physical design realizes robust tissue pattern formation.

Unique pattern of dietary adaptation in the dentition of Carnivora: its advantage and developmental origin

Carnivora is a successful taxon in terms of dietary diversity. We investigated the dietary adaptations of carnivoran dentition and the developmental background of their dental diversity, which may have contributed to the success of the lineage. A developmental model was tested and extended to explain the unique variability and exceptional phenotypes observed in carnivoran dentition. Carnivorous mammalian orders exhibited two distinct patterns of dietary adaptation in molars and only Carnivora evolved novel variability, exhibiting a high correlation between relative molar size and the shape of the first molar. Studies of Bmp7-hetero-deficient mice, which may exhibit lower Bmp7 expression, suggested that Bmp7 has pleiotropic effects on these two dental traits. Its effects are consistent with the pattern of dietary adaptation observed in Carnivora, but not that observed in other carnivorous mammals. A molecular evolutionary analysis revealed that Bmp7 sequence evolved by natural selection during ursid evolution, suggesting that it plays an evolutionary role in the variation of carnivoran dentition. Using mouse experiments and a molecular evolutionary analysis, we extrapolated the causal mechanism of the hitherto enigmatic ursid dentition (larger M₂ than M₁ and M₃). Our results demonstrate how carnivorans acquired novel dental variability that benefits their dietary divergence.

Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues

The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss in vitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas.

Exploring metameric variation in human molars: a morphological study using morphometric mapping

Human molars exhibit a type of metameric variation, which is the difference in serially repeated morphology within an organism. Various theories have been proposed to explain how this variation is brought about in the molars. Actualistic data that support the theories, however, are still relatively scarce because of methodological limitations. Here we propose new methods to analyse detailed tooth crown morphologies. We applied morphometric mapping to the enamel-dentine junction of human maxillary molars and examined whether odontogenetic models were adaptable to human maxillary molars. Our results showed that the upper first molar is phenotypically distinct among the maxillary molars. The average shape of the upper first molar is characterized by four well-defined cusps and precipitous surface relief of the occlusal table. On the other hand, upper third molar is characterized by smooth surface relief of the occlusal table and shows greater shape variation and distinct distribution patterns in morphospace. The upper second molar represents an intermediate state between first and third molar. Size-related shape variation was investigated by the allometric vector analysis, and it appeared that human maxillary molars tend to converge toward the shape of the upper first molar as the size increases. Differences between the upper first molar and the upper second and third molar can thus be largely explained as an effect of allometry. Collectively, these results indicate that the observed pattern of metameric variation in human molars is consistent with odontogenetic models of molar row structure (inhibitory cascade model) and molar crown morphology (patterning cascade model). This study shows that morphometric mapping is a useful tool to visualize and quantify the morphological features of teeth, which can provide the basis for a better understanding of tooth evolution linking morphology and development.

Toward a study of gene regulatory constraints to morphological evolution of the Drosophila ocellar region

The morphology and function of organs depend on coordinated changes in gene expression during development. These changes are controlled by transcription factors, signaling pathways, and their regulatory interactions, which are represented by gene regulatory networks (GRNs). Therefore, the structure of an organ GRN restricts the morphological and functional variations that the organ can experience—its potential morphospace. Therefore, two important questions arise when studying any GRN: what is the predicted available morphospace and what are the regulatory linkages that contribute the most to control morphological variation within this space. Here, we explore these questions by analyzing a small “three-node” GRN model that captures the Hh-driven regulatory interactions controlling a simple visual structure: the ocellar region of Drosophila. Analysis of the model predicts that random variation of model parameters results in a specific non-random distribution of morphological variants. Study of a limited sample of drosophilids and other dipterans finds a correspondence between the predicted phenotypic range and that found in nature. As an alternative to simulations, we apply Bayesian networks methods in order to identify the set of parameters with the largest contribution to morphological variation. Our results predict the potential morphological space of the ocellar complex and identify likely candidate processes to be responsible for ocellar morphological evolution using Bayesian networks. We further discuss the assumptions that the approach we have taken entails and their validity.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

Tooth and scale morphogenesis in shark: an alternative process to the mammalian enamel knot system

BACKGROUND

The gene regulatory network involved in tooth morphogenesis has been extremely well described in mammals and its modeling has allowed predictions of variations in regulatory pathway that may have led to evolution of tooth shapes. However, very little is known outside of mammals to understand how this regulatory framework may also account for tooth shape evolution at the level of gnathostomes. In this work, we describe expression patterns and proliferation/apoptosis assays to uncover homologous regulatory pathways in the catshark Scyliorhinus canicula.

RESULTS

Because of their similar structural and developmental features, gene expression patterns were described over the four developmental stages of both tooth and scale buds in the catshark. These gene expression patterns differ from mouse tooth development, and discrepancies are also observed between tooth and scale development within the catshark. However, a similar nested expression of Shh and Fgf suggests similar signaling involved in morphogenesis of all structures, although apoptosis assays do not support a strictly equivalent enamel knot system in sharks. Similarities in the topology of gene expression pattern, including Bmp signaling pathway, suggest that mouse molar development is more similar to scale bud development in the catshark.

CONCLUSIONS

These results support the fact that no enamel knot, as described in mammalian teeth, can be described in the morphogenesis of shark teeth or scales. However, homologous signaling pathways are involved in growth and morphogenesis with variations in their respective expression patterns. We speculate that variations in this topology of expression are also a substrate for tooth shape evolution, notably in regulating the growth axis and symmetry of the developing structure.

Suppression of epithelial differentiation by Foxi3 is essential for molar crown patterning

Epithelial morphogenesis generates the shape of the tooth crown. This is driven by patterned differentiation of cells into enamel knots, root-forming cervical loops and enamel-forming ameloblasts. Enamel knots are signaling centers that define the positions of cusp tips in a tooth by instructing the adjacent epithelium to fold and proliferate. Here, we show that the forkhead-box transcription factor Foxi3 inhibits formation of enamel knots and cervical loops and thus the differentiation of dental epithelium in mice. Conditional deletion of Foxi3 (Foxi3 cKO) led to fusion of molars with abnormally patterned shallow cusps. Foxi3 was expressed in the epithelium, and its expression was reduced in the enamel knots and cervical loops and in ameloblasts. Bmp4, a known inducer of enamel knots and dental epithelial differentiation, downregulated Foxi3 in wild-type teeth. Using genome-wide gene expression profiling, we showed that in Foxi3 cKO there was an early upregulation of differentiation markers, such as p21, Fgf15 and Sfrp5. Different signaling pathway components that are normally restricted to the enamel knots were expanded in the epithelium, and Sostdc1, a marker of the intercuspal epithelium, was missing. These findings indicated that the activator-inhibitor balance regulating cusp patterning was disrupted in Foxi3 cKO. In addition, early molar bud morphogenesis and, in particular, formation of the suprabasal epithelial cell layer were impaired. We identified keratin 10 as a marker of suprabasal epithelial cells in teeth. Our results suggest that Foxi3 maintains dental epithelial cells in an undifferentiated state and thereby regulates multiple stages of tooth morphogenesis.

Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development

How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb.

From limbs to leaves: common themes in evolutionary diversification of organ form

An open problem in biology is to derive general principles that capture how morphogenesis evolved to generate diverse forms in different organisms. Here we discuss recent work investigating the morphogenetic basis for digit loss in vertebrate limbs and variation in form of marginal outgrowths of angiosperm (flowering plant) leaves. Two pathways underlie digit loss in vertebrate limbs. First, alterations to digit patterning arise through modification of expression of the Patched 1 receptor, which senses the Sonic Hedgehog morphogen and limits its mobility in the limb bud. Second, evolutionary changes to the degree of programmed cell death between digits influence their development after their initiation. Similarly, evolutionary modification of leaf margin outgrowths occurs via two broad pathways. First, species-specific transcription factor expression modulates outgrowth patterning dependent on regulated transport of the hormone auxin. Second, species-specific expression of the newly discovered REDUCED COMPLEXITY homeodomain transcription factor influences growth between individual outgrowths after their initiation. These findings demonstrate that in both plants and animals tinkering with either patterning or post-patterning processes can cause morphological change. They also highlight the considerable flexibility of morphological evolution and indicate that it may be possible to derive broad principles that capture how morphogenesis evolved across complex eukaryotes.

Evolutionary quantitative genetics of nonlinear developmental systems

In quantitative genetics, the effects of developmental relationships among traits on microevolution are generally represented by the contribution of pleiotropy to additive genetic covariances. Pleiotropic additive genetic covariances arise only from the average effects of alleles on multiple traits, and therefore the evolutionary importance of nonlinearities in development is generally neglected in quantitative genetic views on evolution. However, nonlinearities in relationships among traits at the level of whole organisms are undeniably important to biology in general, and therefore critical to understanding evolution. I outline a system for characterizing key quantitative parameters in nonlinear developmental systems, which yields expressions for quantities such as trait means and phenotypic and genetic covariance matrices. I then develop a system for quantitative prediction of evolution in nonlinear developmental systems. I apply the system to generating a new hypothesis for why direct stabilizing selection is rarely observed. Other uses will include separation of purely correlative from direct and indirect causal effects in studying mechanisms of selection, generation of predictions of medium-term evolutionary trajectories rather than immediate predictions of evolutionary change over single generation time-steps, and the development of efficient and biologically motivated models for separating additive from epistatic genetic variances and covariances.

The significance and scope of evolutionary developmental biology: a vision for the 21st century

Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.

Tooth germ invagination from cell-cell interaction: Working hypothesis on mechanical instability

In the early stage of tooth germ development, the bud of the dental epithelium is invaginated by the underlying mesenchyme, resulting in the formation of a cap-like folded shape. This bud-to-cap transition plays a critical role in determining the steric design of the tooth. The epithelial-mesenchymal interaction within a tooth germ is essential for mediating the bud-to-cap transition. Here, we present a theoretical model to describe the autonomous process of the morphological transition, in which we introduce mechanical interactions among cells. Based on our observations, we assumed that peripheral cells of the dental epithelium bound tightly to each other to form an elastic sheet, and mesenchymal cells that covered the tooth germ would restrict its growth. By considering the time-dependent growth of cells, we were able to numerically show that the epithelium within the tooth germ buckled spontaneously, which is reminiscent of the cap-stage form. The difference in growth rates between the peripheral and interior parts of the dental epithelium, together with the steric size of the tooth germ, were determining factors for the number of invaginations. Our theoretical results provide a new hypothesis to explain the histological features of the tooth germ.

Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration

Transformative applications in biomedicine require the discovery of complex regulatory networks that explain the development and regeneration of anatomical structures, and reveal what external signals will trigger desired changes of large-scale pattern. Despite recent advances in bioinformatics, extracting mechanistic pathway models from experimental morphological data is a key open challenge that has resisted automation. The fundamental difficulty of manually predicting emergent behavior of even simple networks has limited the models invented by human scientists to pathway diagrams that show necessary subunit interactions but do not reveal the dynamics that are sufficient for complex, self-regulating pattern to emerge. To finally bridge the gap between high-resolution genetic data and the ability to understand and control patterning, it is critical to develop computational tools to efficiently extract regulatory pathways from the resultant experimental shape phenotypes. For example, planarian regeneration has been studied for over a century, but despite increasing insight into the pathways that control its stem cells, no constructive, mechanistic model has yet been found by human scientists that explains more than one or two key features of its remarkable ability to regenerate its correct anatomical pattern after drastic perturbations. We present a method to infer the molecular products, topology, and spatial and temporal non-linear dynamics of regulatory networks recapitulating in silico the rich dataset of morphological phenotypes resulting from genetic, surgical, and pharmacological experiments. We demonstrated our approach by inferring complete regulatory networks explaining the outcomes of the main functional regeneration experiments in the planarian literature; By analyzing all the datasets together, our system inferred the first systems-biology comprehensive dynamical model explaining patterning in planarian regeneration. This method provides an automated, highly generalizable framework for identifying the underlying control mechanisms responsible for the dynamic regulation of growth and form.

Developmental and regenerative biology experiments are producing a huge number of morphological phenotypes from functional perturbation experiments. However, existing pathway models do not generally explain the dynamic regulation of anatomical shape due to the difficulty of inferring and testing non-linear regulatory networks responsible for appropriate form, shape, and pattern. We present a method that automates the discovery and testing of regulatory networks explaining morphological outcomes directly from the resultant phenotypes, producing network models as testable hypotheses explaining regeneration data. Our system integrates a formalization of the published results in planarian regeneration, an in silico simulator in which the patterning properties of regulatory networks can be quantitatively tested in a regeneration assay, and a machine learning module that evolves networks whose behavior in this assay optimally matches the database of planarian results. We applied our method to explain the key experiments in planarian regeneration, and discovered the first comprehensive model of anterior-posterior patterning in planaria under surgical, pharmacological, and genetic manipulations. Beyond the planarian data, our approach is readily generalizable to facilitate the discovery of testable regulatory networks in developmental biology and biomedicine, and represents the first developmental model discovered de novo from morphological outcomes by an automated system.

Gene networks, occlusal clocks, and functional patches: new understanding of pattern and process in the evolution of the dentition

Our understanding of the evolution of the dentition has been transformed by advances in the developmental biology, genetics, and functional morphology of teeth, as well as the methods available for studying tooth form and function. The hierarchical complexity of dental developmental genetics combined with dynamic effects of cells and tissues during development allow for substantial, rapid, and potentially non-linear evolutionary changes. Studies of selection on tooth function in the wild and evolutionary functional comparisons both suggest that tooth function and adaptation to diets are the most important factors guiding the evolution of teeth, yet selection against random changes that produce malocclusions (selectional drift) may be an equally important factor in groups with tribosphenic dentitions. These advances are critically reviewed here.

Making quantitative morphological variation from basic developmental processes: Where are we? The case of the Drosophila wing

One of the aims of evolutionary developmental biology is to discover the developmental origins of morphological variation. The discipline has mainly focused on qualitative morphological differences (e.g., presence or absence of a structure) between species. Studies addressing subtle, quantitative variation are less common. The Drosophila wing is a model for the study of development and evolution, making it suitable to investigate the developmental mechanisms underlying the subtle quantitative morphological variation observed in nature. Previous reviews have focused on the processes involved in wing differentiation, patterning and growth. Here, we investigate what is known about how the wing achieves its final shape, and what variation in development is capable of generating the variation in wing shape observed in nature. Three major developmental stages need to be considered: larval development, pupariation, and pupal development. The major cellular processes involved in the determination of tissue size and shape are cell proliferation, cell death, oriented cell division and oriented cell intercalation. We review how variation in temporal and spatial distribution of growth and transcription factors affects these cellular mechanisms, which in turn affects wing shape. We then discuss which aspects of the wing morphological variation are predictable on the basis of these mechanisms. Developmental Dynamics 244:1058-1073, 2015. © 2015 Wiley Periodicals, Inc.

The macroevolutionary consequences of phenotypic integration: from development to deep time

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.

The Comet Cometh: Evolving Developmental Systems

In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule’s prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach—which is based on reverse engineering, simulation, and mathematical analysis—the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.

Impact of the terrestrial-aquatic transition on disparity and rates of evolution in the carnivoran skull

Background

Which factors influence the distribution patterns of morphological diversity among clades? The adaptive radiation model predicts that a clade entering new ecological niche will experience high rates of evolution early in its history, followed by a gradual slowing. Here we measure disparity and rates of evolution in Carnivora, specifically focusing on the terrestrial-aquatic transition in Pinnipedia. We analyze fissiped (mostly terrestrial, arboreal, and semi-arboreal, but also including the semi-aquatic otter) and pinniped (secondarily aquatic) carnivorans as a case study of an extreme ecological transition. We used 3D geometric morphometrics to quantify cranial shape in 151 carnivoran specimens (64 fissiped, 87 pinniped) and five exceptionally-preserved fossil pinnipeds, including the stem-pinniped Enaliarctos emlongi. Range-based and variance-based disparity measures were compared between pinnipeds and fissipeds. To distinguish between evolutionary modes, a Brownian motion model was compared to selective regime shifts associated with the terrestrial-aquatic transition and at the base of Pinnipedia. Further, evolutionary patterns were estimated on individual branches using both Ornstein-Uhlenbeck and Independent Evolution models, to examine the origin of pinniped diversity.

Results

Pinnipeds exhibit greater cranial disparity than fissipeds, even though they are less taxonomically diverse and, as a clade nested within fissipeds, phylogenetically younger. Despite this, there is no increase in the rate of morphological evolution at the base of Pinnipedia, as would be predicted by an adaptive radiation model, and a Brownian motion model of evolution is supported. Instead basal pinnipeds populated new areas of morphospace via low to moderate rates of evolution in new directions, followed by later bursts within the crown-group, potentially associated with ecological diversification within the marine realm.

Conclusion

The transition to an aquatic habitat in carnivorans resulted in a shift in cranial morphology without an increase in rate in the stem lineage, contra to the adaptive radiation model. Instead these data suggest a release from evolutionary constraint model, followed by aquatic diversifications within crown families.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0285-5) contains supplementary material, which is available to authorized users.

Empirically founded genotype-phenotype maps from mammalian cyclic nucleotide-gated ion channels

A major barrier between evolutionary and functional biology is the difficulty of determining appropriate genotype-phenotype-fitness maps, particularly in metazoans. Concrete perspectives towards unifying these approaches are offered by studies on the physiological systems that depend on ion channel dynamics. I focus on the cyclic nucleotide-gated (CNG) channels implicated in the photoreceptor's response to light. From an evolutionary standpoint, sensory systems offers interpretative advantages, as the relation between the sensory response and environment is relatively straightforward. For CNG and other ion channels, extensive data are available about the physiological consequences of scanning mutagenesis on sensitive protein domains, such as the conduction pore. Mutant ion channels can be easily studied in living cells, so that the relation between genotypes and phenotypes is less speculative than usual. By relying on relatively simple theoretical frameworks, I used these data to relate the sequence space with phenotypes at increasing hierarchical levels. These empirical genotype-phenotype and phenotype-phenotype landscapes became smoother at higher integration levels, especially in heterozygous condition. The epistatic interaction between sites was analyzed from double mutant constructs. Magnitude epistasis was common. Moreover, evidence of reciprocal sign epistasis and the presence of permissive mutations were also observed, which suggest how adaptive regions can be connected across maladaptive valleys. The approach I describe suggests a way to better relate the evolutionary dynamics with the underlying physiology.

Limb, tooth, beak: three modes of development and evolutionary innovation of form

The standard model of evolutionary change of form, deriving from Darwin's theory via the Modern Synthesis, assumes a gradualistic reshaping of anatomical structures, with major changes only occurring by many cycles of natural selection for marginal adaptive advantage. This model, with its assertion that a single mechanism underlies both micro- and macroevolutionary change, contains an implicit notion of development which is only applicable in some cases. Here we compare the embryological processes that shape the vertebrate limb bud, the mammalian tooth and the avian beak. The implied notion of development in the standard evolutionary picture is met only in the case of the vertebrate limb, a single-primordium organ with morphostatic shaping, in which cells rearrange in response to signalling centres which are essentially unchanged by cell movement. In the case of the tooth, a single-primordium organ with morphodynamic shaping in which the strengths and relationships between signalling centres is influenced by the cell and tissue movements they induce, and the beak, in which the final form is influenced by the collision and rearrangement of multiple tissue primordia, abrupt appearance of qualitatively different forms (i.e. morphological novelties) can occur with small changes in system parameters induced by a genetic change, or by an environmental factor whose effects can be subsequently canalized genetically. Bringing developmental mechanisms and, specifically, the material properties of tissues as excitable media into the evolutionary picture, demonstrates that gradualistic change for incremental adaptive advantage is only one of the possible modes of morphological evolution.

Modeling the dental development of fossil hominins through the inhibitory cascade

The inhibitory cascade is a mathematical model for interpreting the relative size of the occlusal surfaces of mammalian molars in terms of developmental mechanisms. The cascade is derived from experimental studies of mouse molars developed in culture, and has been tested and applied to the dentitions of rodents, ungulates, carnivores, and platyrrhines. Results from such applications have provided new information regarding the origins of plesiomorphic traits in mammalian clade and how derived morphologies may arise. In this study we apply the inhibitory cascade model to the postcanine dentition of a sample of Old World primates that includes fossil hominins. The results of this study suggest that the inhibitory cascade (i.e. M1 < M2 < M3 ) describes the relative sizes of the molar occlusal areas of Old World primates and is likely the plesiomorphic condition for this clade. Within that clade, whereas most Old World monkeys have a M1 < M2 < M3 pattern, most apes have a M1 < M2 ≈ M3 pattern. This modified cascade suggests that greater levels of inhibition (or less activation) are acting on the posterior molars of apes, thus facilitating the reduction of M3 s within the apes. With the exception of the baboon genus Papio, extant congeners typically share the same molar inhibitory cascade. The differences in the relative size relationships observed in the molar and premolar-molar cascades of the species included in the fossil hominin genus Paranthropus suggest that although large postcanine teeth are a shared derived trait within this genus, the developmental basis for postcanine megadontia may not be the same in these two Paranthropus taxa. Our results show that phenotypic characters such as postcanine megadontia may not reflect common development.

Manipulation of Fgf and Bmp signaling in teleost fishes suggests potential pathways for the evolutionary origin of multicuspid teeth

Teeth with two or more cusps have arisen independently from an ancestral unicuspid condition in a variety of vertebrate lineages, including sharks, teleost fishes, amphibians, lizards, and mammals. One potential explanation for the repeated origins of multicuspid teeth is the existence of multiple adaptive pathways leading to them, as suggested by their different uses in these lineages. Another is that the addition of cusps required only minor changes in genetic pathways regulating tooth development. Here we provide support for the latter hypothesis by demonstrating that manipulation of the levels of Fibroblast growth factor (Fgf) or Bone morphogenetic protein (Bmp) signaling produces bicuspid teeth in the zebrafish (Danio rerio), a species lacking multicuspid teeth in its ancestry. The generality of these results for teleosts is suggested by the conversion of unicuspid pharyngeal teeth into bicuspid teeth by similar manipulations of the Mexican Tetra (Astyanax mexicanus). That these manipulations also produced supernumerary teeth in both species supports previous suggestions of similarities in the molecular control of tooth and cusp number. We conclude that despite their apparent complexity, the evolutionary origin of multicuspid teeth is positively constrained, likely requiring only slight modifications of a pre-existing mechanism for patterning the number and spacing of individual teeth.

Quantifying the impact of development on phenotypic variation and evolution

A primary goal of evolutionary biology is to identify the factors that shape phenotypic evolution. According to the theory of natural selection, phenotypic evolution occurs through the differential survival and reproduction of individuals whose traits are selectively advantageous relative to other individuals in the population. This implies that evolution by natural selection is contingent upon the distribution and magnitude of phenotypic variation among individuals, which are in turn the products of developmental processes. Development therefore has the potential to affect the trajectory and rate of phenotypic evolution. Recent research in diverse systems (e.g., mammalian teeth, cichlid skulls, butterfly wings, and marsupial limbs) supports the hypothesis that development biases phenotypic variation and evolution, but suggests that these biases might be system-specific.