What does modularity mean?

Extreme range in adult body size reveals hidden trade-offs among sexually selected traits

Sexually selected weapons used to monopolize mating opportunities are predicted to trade-off with traits used in competition for fertilization. Yet, the limited size range typically found among adults of a species often precludes clear comparisons between population-level and individual-level relative trait investment. The jousting weevil, Brentus anchorago (Coleoptera: Brentidae), varies more than 26-fold in body mass, which is among the most extreme adult body size ranges of any solitary terrestrial species. We reveal a trade-off at a population level: hypermetric scaling in male weapons (slope = 1.59) and a closely mirrored reversal in allocation to postcopulatory traits (slope = 0.54). Yet, at the individual level, we find the opposite pattern; males that invest relatively more in weapons for their size class also invest more in postcopulatory traits. Across 36 dung beetle and 41 brentine weevil species, we find the allometric slope explains more trait variation at larger body size ranges; in brentines, population-level scaling patterns become more detectable in species with a larger range in adult body size. Our findings reveal that population-level allometries and individual-level trade-offs can both be important in shaping relative trait allocation; we highlight that the adult body size range is rarely examined but may be integral to gaining a deeper understanding of trade-offs in reproductive allocation.

Anatomy and mobility in the adult cadaveric craniocervical junction

Genetic diseases with craniofacial malformations can be associated with anomalies of the craniocervical joint (CCJ). The functions of the CCJ are thus impaired, as mobility may be either limited by abnormal bone fusion causing headaches, or exaggerated in the case of hypermobility, which may cause irreparable damage to the spinal cord. Restoring the balance between mobility and stability requires surgical correction in children. The anatomy and biomechanics of the CCJ are quite unique, yet have been overlooked in the past decades. Pediatric evidence is so scarce, that investigating the adult CCJ is our best shot to disentangle the form-function relationships of this anatomical region. The motivation of the present study was to understand the morphological and functional basis of motion in the CCJ, in the hope to find morphological features accessible from medical imaging able to predict mobility. To do so, we have quantified the in-vitro kinematics of the CCJ in nine cadaveric asymptomatic adults, and estimated a wide range of mobility variables covering the complexity of spinal motion. We compared these variables with the shape of the occipital, the atlas and the axis, obtained using a dense geometric morphometric approach. Morphological joint congruence was also quantified. Our results suggest a strong relationship between bone shape and motion, with the overall geometry predicting best the primary movements, and the joint facets predicting best the secondary movements. We propose a functional hypothesis stating that the musculoligamental system determines movements of great amplitude, while the shape and congruence of joint facets determine the secondary and coupled movements, especially by varying the geometry of bone stops and the way ligaments are tensioned. We believe this work will provide valuable insights in understanding the biomechanics of the CCJ. Furthermore, it should help surgeons treating CCJ anomalies by enabling them to translate objectives of functional and clinical outcome into clear objectives of morphological outcome.

Small body size is associated with increased evolutionary lability of wing skeleton proportions in birds

Birds are represented by 11,000 species and a great variety of body masses. Modular organisation of trait evolution across birds has facilitated simultaneous adaptation of different body regions to divergent ecological requirements. However, the role modularity has played in avian body size evolution, especially small-bodied, rapidly evolving and diverse avian subclades, such as hummingbirds and songbirds, is unknown. Modularity is influenced by the intersection of biomechanical restrictions, adaptation, and developmental controls, making it difficult to uncover the contributions of single factors such as body mass to skeletal organisation. We develop a novel framework to decompose this complexity, assessing factors underlying the modularity of skeletal proportions in fore-limb propelled birds distributed across a range of body masses. We demonstrate that differences in body size across birds triggers a modular reorganisation of flight apparatus proportions consistent with biomechanical expectations. We suggest weakened integration within the wing facilitates radiation in small birds. Our framework is generalisable to other groups and has the capacity to untangle the multi-layered complexity intrinsic to modular evolution.

Geometric growth of the normal human craniocervical junction from 0 to 18 years old

The craniocervical junction (CCJ) forms the bridge between the skull and the spine, a highly mobile group of joints that allows the mobility of the head in every direction. The CCJ plays a major role in protecting the inferior brainstem (bulb) and spinal cord, therefore also requiring some stability. Children are subjected to multiple constitutive or acquired diseases involving the CCJ: primary bone diseases such as in FGFR-related craniosynostoses or acquired conditions such as congenital torticollis, cervical spine luxation, and neurological disorders. To design efficient treatment plans, it is crucial to understand the relationship between abnormalities of the craniofacial region and abnormalities of the CCJ. This can be approached by the study of control and abnormal growth patterns. Here we report a model of normal skull base growth by compiling a collection of geometric models in control children. Focused analyses highlighted specific developmental patterns for each CCJ bone, emphasizing rapid growth during infancy, followed by varying rates of growth and maturation during childhood and adolescence until reaching stability by 18 years of age. The focus was on the closure patterns of synchondroses and sutures in the occipital bone, revealing distinct closure trajectories for the anterior intra-occipital synchondroses and the occipitomastoid suture. The findings, although based on a limited dataset, showcased specific age-related changes in width and closure percentages, providing valuable insights into growth dynamics within the first 2 years of life. Integration analyses revealed intricate relationships between skull and neck structures, emphasizing coordinated growth at different stages. Specific bone covariation patterns, as found between the first and second cervical vertebrae (C1 and C2), indicated synchronized morphological changes. Our results provide initial data for designing inclusive CCJ geometric models to predict normal and abnormal growth dynamics.

Reassessing the modularity of gene co-expression networks using the Stochastic Block Model

Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is, groups of genes that are more associated with each other than with genes in other groups. While it is reasonable to expect that these modules exist, using methods that assume they exist a priori is risky, as it guarantees that alternative organizations of gene interactions will be ignored. Here, we ask: can we find meaningful communities without imposing a modular organization on gene co-expression networks, and how modular are these communities? For this, we use a recently developed community detection method, the weighted degree corrected stochastic block model (SBM), that does not assume that assortative modules exist. Instead, the SBM attempts to efficiently use all information contained in the co-expression network to separate the genes into hierarchically organized blocks of genes. Using RNA-seq gene expression data measured in two tissues derived from an outbred population of Drosophila melanogaster, we show that (a) the SBM is able to find ten times as many groups as competing methods, that (b) several of those gene groups are not modular, and that (c) the functional enrichment for non-modular groups is as strong as for modular communities. These results show that the transcriptome is structured in more complex ways than traditionally thought and that we should revisit the long-standing assumption that modularity is the main driver of the structuring of gene co-expression networks.

The Role of (Co)variation in Shaping the Response to Selection in New World Leaf-Nosed Bats

AbstractUnderstanding and predicting the evolutionary responses of complex morphological traits to selection remains a major challenge in evolutionary biology. Because traits are genetically correlated, selection on a particular trait produces both direct effects on the distribution of that trait and indirect effects on other traits in the population. The correlations between traits can strongly impact evolutionary responses to selection and may thus impose constraints on adaptation. Here, we used museum specimens and comparative quantitative genetic approaches to investigate whether the covariation among cranial traits facilitated or constrained the response to selection during the major dietary transitions in one of the world's most ecologically diverse mammalian families-the phyllostomid bats. We reconstructed the set of net selection gradients that would have acted on each cranial trait during the major transitions to feeding specializations and decomposed the selection responses into their direct and indirect components. We found that for all transitions, most traits capturing craniofacial length evolved toward adaptive directions owing to direct selection. Additionally, we showed instances of dietary transitions in which the complex interaction between the patterns of covariation among traits and the strength and direction of selection either constrained or facilitated evolution. Our work highlights the importance of considering the within-species covariation estimates to quantify evolvability and to disentangle the relative contribution of variational constraints versus selective causes for observed patterns.

Predator-induced shape plasticity in Daphnia pulex

All animals and plants respond to changes in the environment during their life cycle. This flexibility is known as phenotypic plasticity and allows organisms to cope with variable environments. A common source of environmental variation is predation risk, which describes the likelihood of being attacked and killed by a predator. Some species can respond to the level of predation risk by producing morphological defences against predation. A classic example is the production of so-called 'neckteeth' in the water flea, Daphnia pulex, which defend against predation from Chaoborus midge larvae. Previous studies of this defence have focussed on changes in pedestal size and the number of spikes along a gradient of predation risk. Although these studies have provided a model for continuous phenotypic plasticity, they do not capture the whole-organism shape response to predation risk. In contrast, studies in fish and amphibians focus on shape as a complex, multi-faceted trait made up of different variables. In this study, we analyse how multiple aspects of shape change in D. pulex along a gradient of predation risk from Chaoborus flavicans. These changes are dominated by the neckteeth defence, but there are also changes in the size and shape of the head and the body. We detected change in specific modules of the body plan and a level of integration among modules. These results are indicative of a complex, multi-faceted response to predation and provide insight into how predation risk drives variation in shape and size at the level of the whole organism.

Morphological evolution of bird wings follows a mechanical sensitivity gradient determined by the aerodynamics of flapping flight

The physical principles that govern the function of biological structures also mediate their evolution, but the evolutionary drivers of morphological traits within complex structures can be difficult to predict. Here, we use morphological traits measured from 1096 3-dimensional bird wing scans from 178 species to test the interaction of two frameworks for relating morphology to evolution. We examine whether the evolutionary rate (σ2) and mode is dominated by the modular organization of the wing into handwing and armwing regions, and/or the relationship between trait morphology and functional output (i.e. mechanical sensitivity, driven here by flapping flight aerodynamics). Our results support discretization of the armwing and handwing as morphological modules, but morphological disparity and σ2 varied continuously with the mechanical sensitivity gradient and were not modular. Thus, mechanical sensitivity should be considered an independent and fundamental driver of evolutionary dynamics in biomechanical traits, distinct from morphological modularity.

Plant morpho evo-devo

Evo-devo is often thought of as being the study of which genes underlie which phenotypes. However, evo-devo is much more than this, especially in plant science. In leaf scars along stems, cell changes across wood growth rings, or flowers along inflorescences, plants trace a record of their own development. Plant morpho evo-devo provides data that genes could never furnish on themes such as heterochrony, the evolution of temporal phenotypes, modularity, and phenotype-first evolution. As plant science surges into increasingly -omic realms, it is essential to keep plant morpho evo-devo in full view as an honored member of the evo-devo canon, ensuring that plant scientists can, wherever they are, generate fundamental insights at the appropriate level of biological organization.

Postnatal growth and spatial conformity of the cranium, brain, eyeballs and masseter muscles in the macaque (Macaca mulatta)

Spatial growth constraints in the head region can lead to coordinated patterns of morphological variation that pleiotropically modify genetically defined phenotypes as the tissues compete for space. Here we test for such architectural modifications during rhesus macaque (Macaca mulatta) postnatal ontogeny. We captured cranium and brain shape from 153 MRI datasets spanning 13 to 1090 postnatal days and tested for patterns of covariation with measurements of relative brain, eyeball, and masseter muscle size as well as callosal tract length. We find that the shape of the infant (<365 days) macaque cranium was most closely aligned to masseter muscle and brain size measured relative to face size. Infant brain and juvenile (365-1090 days) cranium shape were more closely linked with brain size relative to basicranium and face size. Meanwhile, the juvenile macaque brain shape was dominated by the size of the brain relative to that of the basicranium. Associations with relative eyeball size and commissural tract lengths were weaker. Our results are consistent with a spatial-packing regime operating during postnatal macaque ontogeny, in which relative growth of the masseter, face and basicranium have a greater influence than brain growth on the overall shape of the cranium and brain.

Regionalization and morphological integration in the vertebral column of Eurasian small-bodied newts (Salamandridae: Lissotriton)

Serially homologous structures may have complex patterns of regionalization and morphological integration, influenced by developmental Hox gene expression and functional constraints. The vertebral column, consisting of a number of repeated, developmentally constrained, and highly integrated units-vertebrae-is such a complex serially homologous structure. Functional diversification increases regionalization and modularity of the vertebral column, particularly in mammals. For salamanders, three concepts of regionalization of the vertebral column have been proposed, recognizing one, two, or three presacral regions. Using three-dimensional geometric morphometrics on vertebra models acquired with microcomputerized tomography scanning, we explored the covariation of vertebrae in four closely related taxa of small-bodied newts in the genus Lissotriton. The data were analyzed by segmented linear regression to explore patterns of vertebral regionalization and by a two-block partial least squares method to test for morphological integration. All taxa show a morphological shift posterior to the fifth trunk vertebra, which corresponds to the two-region concept. However, morphological integration is found to be strongest in the mid-trunk. Taken jointly, these results indicate a highly integrated presacral vertebral column with a subtle two-region differentiation. The results are discussed in relation to specific functional requirements, developmental and phylogenetic constraints, and specific requirements posed by a biphasic life cycle and different locomotor modes (swimming vs. walking). Further research should be conducted on different ontogenetic stages and closely related but ecologically differentiated species.

Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats

AbstractWith diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical function, have been implicated in adaptive diversification. Yet how mechanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adaptations to process them, peak rates of sensory module evolution predate those of some mechanical modules. We propose that the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunities and contributed to the clade's remarkable radiation.

Developmental origin underlies evolutionary rate variation across the placental skull

The placental skull has evolved into myriad forms, from longirostrine whales to globular primates, and with a diverse array of appendages from antlers to tusks. This disparity has recently been studied from the perspective of the whole skull, but the skull is composed of numerous elements that have distinct developmental origins and varied functions. Here, we assess the evolution of the skull's major skeletal elements, decomposed into 17 individual regions. Using a high-dimensional morphometric approach for a dataset of 322 living and extinct eutherians (placental mammals and their stem relatives), we quantify patterns of variation and estimate phylogenetic, allometric and ecological signal across the skull. We further compare rates of evolution across ecological categories and ordinal-level clades and reconstruct rates of evolution along lineages and through time to assess whether developmental origin or function discriminate the evolutionary trajectories of individual cranial elements. Our results demonstrate distinct macroevolutionary patterns across cranial elements that reflect the ecological adaptations of major clades. Elements derived from neural crest show the fastest rates of evolution, but ecological signal is equally pronounced in bones derived from neural crest and paraxial mesoderm, suggesting that developmental origin may influence evolutionary tempo, but not capacity for specialisation. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Speciation and development

Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.

Nothing in evolution makes sense except in the light of code biology

This article highlights the potential contribution of biological codes to the course and dynamics of evolution. The concept of organic codes, developed by Marcello Barbieri, has fundamentally changed our view of how living systems function. The notion that molecular interactions built on adaptors that arbitrarily link molecules from different "worlds" in a conventional, i.e., rule-based way, departs significantly from the law-based constraints imposed on livening things by physical and chemical mechanisms. In other words, living and non-living things behave like rules and laws, respectively, but this important distinction is rarely considered in current evolutionary theory. The many known codes allow quantification of codes that relate to a cell, or comparisons between different biological systems and may pave the way to a quantitative and empirical research agenda in code biology. A starting point for such an endeavour is the introduction of a simple dichotomous classification of structural and regulatory codes. This classification can be used as a tool to analyse and quantify key organising principles of the living world, such as modularity, hierarchy, and robustness, based on organic codes. The implications for evolutionary research are related to the unique dynamics of codes, or ´Eigendynamics´ (self-momentum) and how they determine the behaviour of biological systems from within, whereas physical constraints are imposed mainly from without. A speculation on the drivers of macroevolution in light of codes is followed by the conclusion that a meaningful and comprehensive understanding of evolution depends including codes into the equation of life.

Intravertebral vs. intervertebral integration and modularity in the vertebral column of mammalian carnivorans

The vertebral column is a multicomponent structure whose organization results from developmental and functional demands. According to their distinct somitic origins, individual vertebrae exhibit intravertebral modularity between the centrum and neural spine. However, vertebrae are also organized into larger units called intervertebral modules that result from integration between adjacent vertebrae due to locomotory demands or from common developmental origins due to resegmentation. A previous hypothesis suggested that the boundaries of intervertebral modules coincide with changes in the patterns of intravertebral integration. Here, we explicitly test whether the patterns of modularity and integration between the centrum and neural spine (i.e., intravertebral) in the boundary vertebrae among previously defined intervertebral modules change with respect to those in the vertebrae within intervertebral modules. We quantified intravertebral modularity patterns and quantified the strength of intravertebral integration for each vertebra of the presacral region in 41 species of carnivoran mammals using 3D geometric morphometrics. Our results demonstrate a significant intravertebral modular signal between the centrum and neural spine in all post-cervical vertebrae, including the boundary vertebrae among intervertebral modules. However, the strength of intravertebral integration decreases at the boundary vertebrae. We also found a significant correlation between the degree of intravertebral integration and intervertebral integration. Following our results, we hypothesize that natural selection does not override the integration between the centrum and neural spine at the boundary vertebrae, a pattern that should be influenced by their distinct somitic origins and separate ossification centers during early development. However, natural selection has probably influenced (albeit indirectly) the integration between the centrum and neural spine in the vertebrae that compose the intervertebral modules.

Evolution of median fin patterning and modularity in living and fossil osteichthyans

Morphological and developmental similarities, and interactions among developing structures are interpreted as evidences of modularity. Such similarities exist between the dorsal and anal fins of living actinopterygians, on the anteroposterior axis: (1) both fins differentiate in the same direction [dorsal and anal fin patterning module (DAFPM)], and (2) radials and lepidotrichia differentiate in the same direction [endoskeleton and exoskeleton module (EEM)]. To infer the evolution of these common developmental patternings among osteichthyans, we address (1) the complete description and quantification of the DAFPM and EEM in a living actinopterygian (the rainbow trout Oncorhynchus mykiss) and (2) the presence of these modules in fossil osteichthyans (coelacanths, lungfishes, porolepiforms and 'osteolepiforms'). In Oncorhynchus, sequences of skeletal elements are determined based on (1) apparition (radials and lepidotrichia), (2) chondrification (radials), (3) ossification (radials and lepidotrichia), and (4) segmentation plus bifurcation (lepidotrichia). Correlations are then explored between sequences. In fossil osteichthyans, sequences are determined based on (1) ossification (radials and lepidotrichia), (2) segmentation, and (3) bifurcation of lepidotrichia. Segmentation and bifurcation patterns were found crucial for comparisons between extant and extinct osteichthyan taxa. Our data suggest that the EEM is plesiomorphic at least for actinopterygians, and the DAFPM is plesiomorphic for osteichthyans, with homoplastic dissociation. Finally, recurrent patterns suggest the presence of a Lepidotrichia Patterning Module (LPM).

Whole-body variational modularity in the zebrafish: an inside-out story of a model species

Actinopterygians are the most diversified clade of extant vertebrates. Their impressive morphological disparity bears witness to tremendous ecological diversity. Modularity, the organization of biological systems into quasi-independent anatomical/morphological units, is thought to increase evolvability of organisms and facilitate morphological diversification. Our study aims to quantify patterns of variational modularity in a model actinopterygian, the zebrafish (Danio rerio), using three-dimensional geometric morphometrics on osteological structures isolated from micro-CT scans. A total of 72 landmarks were digitized along cranial and postcranial ossified regions of 30 adult zebrafishes. Two methods were used to test modularity hypotheses, the covariance ratio and the distance matrix approach. We find strong support for two modules, one comprised paired fins and the other comprised median fins, that are best explained by functional properties of subcarangiform swimming. While the skull is tightly integrated with the rest of the body, its intrinsic integration is relatively weak supporting previous findings that the fish skull is a modular structure. Our results provide additional support for the recognition of similar hypotheses of modularity identified based on external morphology in various teleosts, and at least two variational modules are proposed. Thus, our results hint at the possibility that internal and external modularity patterns may be congruent.

A refreshed approach to homology-Prioritizing epistemology over metaphysics

Unease with the inclusion of "sameness" in Owen's definition of homology characterizes a substantial part of the literature on this subject, where this term has acquired an increasingly strict metaphysical flavor. Taken for granted the existence of body features that are "the same," their existence has been explained by appealing to universal laws of form, as the product of common ancestry, or in terms of proximal causes responsible for the emergence of conserved developmental modules. However, a fundamentally different approach is possible, if we shift attention from metaphysics to epistemology. We may reword Owen's statement as follows: organs of different animals, in so far as they can be described as the same despite any difference in form and function, are called homologues. The proposed framework provides an umbrella for both the traditional, all-or-nothing concept of homology, and the less fashionable alternatives of factorial or partial homology, as well as for an extension of homology from form to function. No less attractive is the prospect to handle also ghost homologues, the body parts or organs of which there is non-objective evidence in a given clade, but can nevertheless be represented, in a description that encapsulates some of the traits observable in their extant homologue in the sister clade. Stripped of its different and constraining metaphysical explanations, homology survives as an anchor concept to which different nomadic disciplines and research agendas can be associated.

Flexible conservatism in the skull modularity of convergently evolved myrmecophagous placental mammals

Background

The skull of placental mammals constitutes one of the best studied systems for phenotypic modularity. Several studies have found strong evidence for the conserved presence of two- and six-module architectures, while the strength of trait correlations (integration) has been associated with major developmental processes such as somatic growth, muscle-bone interactions, and tooth eruption. Among placentals, ant- and termite-eating (myrmecophagy) represents an exemplar case of dietary convergence, accompanied by the selection of several cranial morphofunctional traits such as rostrum elongation, tooth loss, and mastication loss. Despite such drastic functional modifications, the covariance patterns of the skull of convergently evolved myrmecophagous placentals are yet to be studied in order to assess the potential consequences of this dietary shift on cranial modularity.

Results

Here, we performed a landmark-based morphometric analysis of cranial covariance patterns in 13 species of myrmecophagous placentals. Our analyses reveal that most myrmecophagous species present skulls divided into six to seven modules (depending on the confirmatory method used), with architectures similar to those of non-myrmecophagous placentals (therian six modules). Within-module integration is also similar to what was previously described for other placentals, suggesting that most covariance-generating processes are conserved across the clade. Nevertheless, we show that extreme rostrum elongation and tooth loss in myrmecophagid anteaters have resulted in a shift in intermodule correlations in the proximal region of the rostrum. Namely, the naso-frontal and maxillo-palatine regions are strongly correlated with the oro-nasal module, suggesting an integrated rostrum conserved from pre-natal developmental processes. In contrast, the similarly toothless pangolins show a weaker correlation between the anterior rostral modules, resembling the pattern of toothed placentals.

Conclusions

These results reveal that despite some integration shifts related to extreme functional and morphological features of myrmecophagous skulls, cranial modular architectures have conserved the typical mammalian scheme.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02030-9.

Exploration of the optimal modularity in assembly line design

It is widely accepted that a proper structural modularity degree of assembly processes in terms of mass customization has a positive effect on their efficiency because it, among other things, increases manufacturing flexibility and productivity. On the other hand, most practical approaches to identify such a degree is rather based on intuition or analytical reasoning than on scientific foundations. However, the first way can be used for simple assembly tasks, but in more complex assembly processes, this method lags behind the second. The purpose was to create a methodology for selection of optimal modular assembly model from among a predefined set of alternatives. The methodology is based on exploration of the relations between modularity measures and complexity issues as well as the relationship between structural modularity and symmetry. Especially, the linkage between modularity and complexity properties has been explored in order to show how modularization can affect distribution of the total structural complexity across the entire assembly line. To solve this selection problem, three different methods are preliminary suggested and compared via a series of numerical tests. The two of them present the novel contribution of this work, while the third method developed earlier for the purpose of finding and evaluating community structure in networks was adapted for a given application domain. Based on obtained results, one of these method is prioritized over another, since it offers more promising results and precision too.

Modularity in the trilobite head consistent with the hypothesized segmental origin of the eyes

The trilobite head served multiple functions and was composed of several fused segments. Yet, the underlying organization of the trilobite head, and whether patterns are conserved across trilobites, remains unclear. Modeling the head as being composed of modules, or subunits that vary and thus have the potential to evolve semi-independently can reveal underlying patterns of organization. Hypotheses of modular organization based on the comparative developmental biology of arthropods were evaluated using geometric morphometrics. Two-dimensional (semi)landmark datasets collected from the cranidia of two Ordovician trilobite species, Calyptaulax annulata (Phacopida) and Cloacaspis senilis (Olenida sensu Adrain, 2011) were analyzed. The degree and pattern of modularity were assessed using the covariance ratio (CR), which compares the covariation within putative modules to the covariation between them, and the fit of different models was compared using an effect size measure derived from the CR. When treating the eyes as a distinct module, the best modular hypothesis identified for C. annulata shows the eyes and anteriormost region of the head integrated as a single module. The best modular hypotheses for C. senilis are more complex but the eyes still covary mostly strongly with the anterior part of the head. The latter is also the case for all other well-supported models for both species. These results can be interpreted as a developmental signal corresponding to the anteriormost ocular segment of early arthropods that is retained throughout development, despite any likely selective pressures related to functional needs.

Evidence for an evo-devo-derived hypothesis on three-dimensional flower shape modularity in a tropical orchid clade

Covarying suites of phenotypic traits, or modules, are increasingly recognized to promote morphological evolution. However, information on how modularity influences flower diversity is rare and lacking for Orchidaceae. Here, we combine high-resolution X-ray computed tomography scanning with three-dimensional geometric morphometrics and phylogenetic comparative methods to test various hypotheses about three-dimensional patterns of flower evolutionary modularity in Malagasy Bulbophyllum orchids and examine rates and modes of module evolution. Based on the four evolutionary modules identified (i.e., sepals, lateral petals, labellum + column-foot, and column-part), our data support the hypothesis that both genetic-developmental and functional adaptive factors shaped evolutionary flower trait covariation in these tropical orchids. In line with "evo-devo" studies, we also find that the labellum evolved independently from the rest of the petal whorl. Finally, we show that modules evolved with different rates, and either in a neutral fashion (only column-part) or under selective constraints, as likely imposed by pollinators. Overall, this study supports current views that modular units can enhance the range and rate of morphological evolution.

An effect size for comparing the strength of morphological integration across studies

Understanding how and why phenotypic traits covary is a major interest in evolutionary biology. Biologists have long sought to characterize the extent of morphological integration in organisms, but comparing levels of integration for a set of traits across taxa has been hampered by the lack of a reliable summary measure and testing procedure. Here, we propose a standardized effect size for this purpose, calculated from the relative eigenvalue variance, V r e l $V_{rel}$ . First, we evaluate several eigenvalue dispersion indices under various conditions, and show that only V r e l $V_{rel}$ remains stable across samples size and the number of variables. We then demonstrate that V r e l $V_{rel}$ accurately characterizes input patterns of covariation, so long as redundant dimensions are excluded from the calculations. However, we also show that the variance of the sampling distribution of V r e l $V_{rel}$ depends on input levels of trait covariation, making V r e l $V_{rel}$ unsuitable for direct comparisons. As a solution, we propose transforming V r e l $V_{rel}$ to a standardized effect size (Z-score) for representing the magnitude of integration for a set of traits. We also propose a two-sample test for comparing the strength of integration between taxa, and show that this test displays appropriate statistical properties. We provide software for implementing the procedure, and an empirical example illustrates its use.

Sexual selection leads to positive allometry but not sexual dimorphism in the expression of horn shape in the blue wildebeest, Connochaetes taurinus

Sexual selection is thought to be an important driver of adaptation, speciation and extinction. Empirically testing these predictions across macroevolutionary timescales first requires an understanding of the morphology of secondary sexual traits in extant taxa. We used three-dimensional geometric morphometrics to analyse a large sample of the skull of the blue wildebeest, Connochaetes taurinus, in which horns are found in both sexes but only used in intrasexual competition in males. We show that the horns fit several predictions of secondary sexual traits; overall skull shape is significantly correlated with size (R² = 0.38, p = 0.001), and the sexually selected horns show drastically higher growth rates and variation than any other skull element, supporting previous findings. We also find that despite showing significant sexual dimorphism in shape and size (R² = 0.21, p = 0.001), allometric growth trajectories of sexes are identical (R² = 0.01, p = 0.635) and dimorphism is not readily detectable without prior knowledge of sex, and is not possible when shape is corrected for size. Our results show that even with strong sexual selection operating in only one sex, the expression of secondary sexual traits may show characteristic and indistinguishable patterns of growth and variance in both sexes.

Heterochronies and allometries in the evolution of the hominid cranium: a morphometric approach using classical anthropometric variables

This article studies the evolutionary change of allometries in the relative size of the two main cranial modules (neurocranium and splanchnocranium) in the five living hominid species and a diverse sample of extinct hominins. We use six standard craniometric variables as proxies for the length, width and height of each cranial module. Factor analysis and two-block partial least squares (2B-PLS) show that the great apes and modern humans share a pervasive negative ontogenetic allometry in the neurocranium and a positive one in the splanchnocranium. This developmental constraint makes it possible to interpret the cranial heterochronies in terms of ontogenetic scaling processes (i.e., extensions or truncations of the ancestral ontogenetic trajectory) and lateral transpositions (i.e., parallel translations of the entire trajectory starting from a different shape for a given cranial size). We hypothesize that ontogenetic scaling is the main evolutionary modality in the australopithecines while in the species of Homo it is also necessary to apply transpositions. Both types of processes are coordinated in Homo, which result in an evolutionary trend toward an increase in brain size and in the degree of paedomorphosis from the earliest habilines.

Breaking constraints: The development and evolution of extreme fin morphology in the Bramidae

The developmental process establishes the foundation upon which natural selection may act. In that same sense, it is inundated with numerous constraints that work to limit the directions in which a phenotype may respond to selective pressures. Extreme phenotypes have been used in the past to identify tradeoffs and constraints and may aid in recognizing how alterations to the Baupläne can influence the trajectories of lineages. The Bramidae, a family of Scombriformes consisting of 20 extant species, are unique in that five species greatly deviate from the stout, ovaloid bodies that typify the bramids. The Ptericlinae, or fanfishes, are instead characterized by relatively elongated body plans and extreme modifications to their medial fins. Here, we explore the development of Bramidae morphologies and examine them through a phylogenetic lens to investigate the concepts of developmental and evolutionary constraints. Contrary to our predictions that the fanfishes had been constrained by inherited properties of an ancestral state, we find that the fanfishes exhibit both increased rates of trait evolution and differ substantially from the other bramids in their developmental trajectories. Conversely, the remaining bramid genera differ little, both among one another and in comparison, to the sister family Caristiidae. In all, our data suggest that the fanfishes have broken constraints, thereby allowing them to mitigate trade‐offs on distinctive aspects of morphology.

The modularity codes

The hypothesis presented here is that codes as described by Marcello Barbieri are the fundamental principle behind biological modularity. Modularity has been studied in different life science disciplines, especially in the fields of evolution and development, as well as in network biology, yet there is still no consensus on how modularity evolved itself. Modularity is basically the functional integrity of multiple molecular players involved in a common process. Codes as defined by Barbieri describe a tripartite relation involving an adapter molecule connecting two other independent types of molecules to each other in an arbitrary, but semantic manner. This form of interaction goes beyond predictable mere physical or chemical one-to-one interactions and always relates three molecules to each other. A code of three topologically related molecules interacting in a defined order may be considered a minimal module on its own, but when one regards a set of multiple, overlapping tripartite, coded interactions, this paves the way towards logically and functionally consistent coherence of multiple participants of a certain, modular process. A theoretical outline of how to identify and describe such modular structures is given.

Consilience of methods for phylogenetic analysis of variance

Simulation-based and permutation-based inferential methods are commonplace in phylogenetic comparative methods, especially as evolutionary data have become more complex and parametric methods more limited for their analysis. Both approaches simulate many random outcomes from a null model to empirically generate sampling distributions of statistics. Although simulation-based and permutation-based methods seem commensurate in purpose, results from analysis of variance (ANOVA) based on the distributions of random F-statistics produced by these methods can be quite different in practice. Differences could be from either the null-model process that generates variation across many simulations or random permutations of the data, or different estimation methods for linear model coefficients and statistics. Unfortunately, because the null-model process and coefficient estimation are intrinsically linked in phylogenetic ANOVA methods, the precise reason for methodological differences has not been fully considered. Here we show that the null-model processes of phylogenetic simulation and randomizing residuals in a permutation procedure are indeed commensurate, and that both also produce results consistent with parametric ANOVA, for cases where parametric ANOVA is possible. We also provide results that caution against using ordinary least-squares estimation along with phylogenetic simulation; a typical phylogenetic ANOVA implementation.

Untangling the relationship between developmental and evolutionary integration

Patterns of integration and modularity among organismal traits are prevalent across the tree of life, and at multiple scales of biological organization. Over the past several decades, researchers have studied these patterns at the developmental, and evolutionary levels. While their work has identified the potential drivers of these patterns at different scales, there appears to be a lack of consensus on the relationship between developmental and evolutionary integration. Here, we review and summarize key studies and build a framework to describe the conceptual relationship between these patterns across organismal scales and illustrate how, and why some of these studies may have yielded seemingly conflicting outcomes. We find that among studies that analyze patterns of integration and modularity using morphological data, the lack of consensus may stem in part from the difficulty of fully disentangling the developmental and functional causes of integration. Nonetheless, in some empirical systems, patterns of evolutionary modularity have been found to coincide with expectations based on developmental processes, suggesting that in some circumstances, developmental modularity may translate to evolutionary modularity. We also advance an extension to Hallgrímsson et al.'s palimpsest model to describe how patterns of trait modularity may shift across different evolutionary scales. Finally, we also propose some directions for future research which will hopefully be useful for investigators interested in these issues.

Complex adaptive landscape for a "Simple" structure: The role of trade-offs in the evolutionary dynamics of mandibular shape in ground squirrels

Trade-offs are inherent features of many biomechanical systems and are often seen as evolutionary constraints. Structural decoupling may provide a way to escape those limits in some systems but not for structures that transmit large forces, such as mammalian mandibles. For such structures to evolve in multiple directions on a complex adaptive landscape, different regions must change shape while maintaining structural integrity. We evaluated the complexity of the adaptive landscape for mandibular shape in Marmotini, a lineage of ground squirrels that varies in the proportions of seeds and foliage in their diets, by comparing the fit of models based on traits that predict changes in mandibular loading. The adaptive landscape was more complex than predicted by a two-peak model with a single dietary shift. The large number of adaptive peaks reflects a high diversity of directions of shape evolution. The number of adaptive peaks also reflects a multiplicity of functional trade-offs posed by the conflicting demands of processing foods with various combinations of material properties. The ability to balance trade-offs for diets with different proportions of the same foods may account for diversification and disparity of lineages in heterogeneous environments. Rather than constraints, trade-offs may be the impetus of evolutionary change.

Drosophila Wing Integration and Modularity: A Multi-Level Approach to Understand the History of Morphological Structures

Simple Summary

The diverse components of any morphological structure are integrated with respect to each other since they have developed, functioned, and evolved together, a phenomenon known as integration. However, this integration is not absolute but organized in units (i.e., modules) that are relatively independent while participating to generate a structure that acts as a functional whole. Even though most of the studies on modularity and integration have focused on variation among individuals within populations, there are more levels of variation that exhibit modularity and integration, deriving from distinct sources such as genetic variation, phenotypic plasticity, fluctuating asymmetry, evolutionary change, among others. Consequently, the present study focused on analysing the integration and modularity of the wing shape of some of the best-known model organisms, i.e., the genus Drosophila, at the static, developmental, and evolutionary levels to acquire a better insight about how modularity and integration act at different analytical levels. The strong integration and overall similarities observed in the variation pattern at multiple levels suggest a shared mechanism underlying the observed variation in Drosophila’s wing shape and added a new piece of evidence of stasis in the evolutionary history of Drosophila wing.

Abstract

Static, developmental, and evolutionary variation are different sources of morphological variation which can be quantified using morphometrics tools. In the present study we have carried out a comparative multiple level study of integration (i.e., static, developmental, and evolutionary) to acquire insight about the relationships that exist between different integration levels, as well as to better understand their involvement in the evolutionary processes related to the diversification of Drosophila’s wing shape. This approach was applied to analyse wing evolution in 59 species across the whole genus in a large dataset (~10,000 wings were studied). Static integration was analysed using principal component analysis, thus providing an integration measurement for overall wing shape. Developmental integration was studied between wing parts by using a partial least squares method between the anterior and posterior compartments of the wing. Evolutionary integration was analysed using independent contrasts. The present results show that all Drosophila species exhibit strong morphological integration at different levels. The strong integration and overall similarities observed at multiple integration levels suggest a shared mechanism underlying this variation, which could result as consequence of genetic drift acting on the wing shape of Drosophila.

Statistics of eigenvalue dispersion indices: Quantifying the magnitude of phenotypic integration

Analysis of trait covariation plays a pivotal role in the study of phenotypic evolution. The magnitude of covariation is often quantified with statistics based on dispersion of eigenvalues of a covariance or correlation matrix-eigenvalue dispersion indices. This study clarifies the statistical justifications of these statistics and elaborates on their sampling properties. The relative eigenvalue variance of a covariance matrix is known in the statistical literature a test statistic for sphericity, and thus is an appropriate measure of eccentricity of variation. The same of a correlation matrix is equal to the average squared correlation, which has a straightforward interpretation as a measure of integration. Here, expressions for the mean and variance of these statistics are analytically derived under multivariate normality, clarifying the effects of sample size N, number of variables p, and parameters on sampling bias and error. Simulations confirm that approximations involved are reasonably accurate with a moderate sample size (N ≥ 16-64). Importantly, sampling properties of these indices are not adversely affected by a high p:N ratio, promising their utility in high-dimensional phenotypic analyses. They can furthermore be applied to shape variables and phylogenetically structured data with appropriate modifications.