High-Density Geometric Morphometric Analysis of Intraspecific Cranial Integration in the Barred Grass Snake (Natrix helvetica) and Green Anole (Anolis carolinensis)

How do phenotypic associations intrinsic to an organism, such as developmental and mechanical processes, direct morphological evolution? Comparisons of intraspecific and clade-wide patterns of phenotypic covariation could inform how population-level trends ultimately dictate macroevolutionary changes. However, most studies have focused on analyzing integration and modularity either at macroevolutionary or intraspecific levels, without a shared analytical framework unifying these temporal scales. In this study, we investigate the intraspecific patterns of cranial integration in two squamate species: Natrix helvetica and Anolis carolinensis. We analyze their cranial integration patterns using the same high-density three-dimensional geometric morphometric approach used in a prior squamate-wide evolutionary study. Our results indicate that Natrix and Anolis exhibit shared intraspecific cranial integration patterns, with some differences, including a more integrated rostrum in the latter. Notably, these differences in intraspecific patterns correspond to their respective interspecific patterns in snakes and lizards, with few exceptions. These results suggest that interspecific patterns of cranial integration reflect intraspecific patterns. Hence, our study suggests that the phenotypic associations that direct morphological variation within species extend across micro- and macroevolutionary levels, bridging these two scales.

A Comparison of Semilandmarking Approaches in the Analysis of Size and Shape

Often, few landmarks can be reliably identified in analyses of form variation and covariation. Thus, ‘semilandmarking’ algorithms have increasingly been applied to surfaces and curves. However, the locations of semilandmarks depend on the investigator’s choice of algorithm and their density. In consequence, to the extent that different semilandmarking approaches and densities result in different locations of semilandmarks, they can be expected to yield different results concerning patterns of variation and co-variation. The extent of such differences due to methodology is, as yet, unclear and often ignored. In this study, the performance of three landmark-driven semilandmarking approaches is assessed, using two different surface mesh datasets (ape crania and human heads) with different degrees of variation and complexity, by comparing the results of morphometric analyses. These approaches produce different semilandmark locations, which, in turn, lead to differences in statistical results, although the non-rigid semilandmarking approaches are consistent. Morphometric analyses using semilandmarks must be interpreted with due caution, recognising that error is inevitable and that results are approximations. Further work is needed to investigate the effects of using different landmark and semilandmark templates and to understand the limitations and advantages of different semilandmarking approaches.

Evolutionary integration and modularity in the diversity of the suckermouth armoured catfishes

The evolution of morphological diversity has held a long-standing fascination among scientists. In particular, do bodies evolve as single, integrated units or do different body parts evolve semi-independently (modules)? Suckermouth armoured catfishes (Loricariidae) have a morphology that lends nicely to evolutionary modularity and integration studies. In addition to a ventrally facing oral jaw that directly contacts surfaces, the neurocranium and pectoral girdle are fused, which limits movement of the anterior part of the body. Functional constraints suggest it is likely the head and post-cranial body act as separate modules that can evolve independently. If true, one would expect to see a two- or three-module system where the head and post-cranial body are morphologically distinct. To test this hypothesis, we quantified shape using geometric morphometric analysis and assessed the degree of modularity across functionally important regions. We found the armoured catfish body is highly modularized, with varying degrees of integration between each module. Within subfamilies, there are different patterns of evolutionary modularity and integration, suggesting that the various patterns may have driven diversification along a single trajectory in each subfamily. This study suggests the evolution of armoured catfish diversification is complex, with morphological evolution influenced by interactions within and between modules.

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.

On Information Rank Deficiency in Phenotypic Covariance Matrices

This paper investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory, then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in a model system. Lastly, we propose methods to treat for this information rank deficiency. Our first goal is to establish how the rank of a typical geometric morphometric covariance matrix relates to the information entropy of its eigenvalue spectrum. This requires clear definitions of matrix rank, of which we define three: the full matrix rank (equal to the number of input variables), the mathematical rank (the number of non-zero eigenvalues), and the information rank or 'effective rank' (equal to the number of non-redundant eigenvalues). We demonstrate that effective rank deficiency arises from a combination of methodological factors - Generalized Procrustes analysis, use of the correlation matrix, and insufficient sample size - as well as phenotypic covariance. Secondly, we use dire wolf jaws to document how differences in effective rank deficiency bias two metrics used to measure phenotypic integration. The eigenvalue variance characterizes the integration change incorrectly, and the standardized generalized variance lacks the sensitivity needed to detect subtle changes in integration. Both metrics are impacted by the inclusion of many small, but non-zero, eigenvalues arising from a lack of information in the covariance matrix, a problem that usually becomes more pronounced as the number of landmarks increases. We propose a new metric for phenotypic integration that combines the standardized generalized variance with information entropy. This metric is equivalent to the standardized generalized variance, but calculated only from those eigenvalues that carry non-redundant information. It is the standardized generalized variance scaled to the effective rank of the eigenvalue spectrum. We demonstrate that this metric successfully detects the shift of integration in our dire wolf sample. Our third goal is to generalize the new metric to compare data sets with different sample sizes and numbers of variables. We develop a standardization for matrix information based on data permutation, then demonstrate that Smilodon jaws are more integrated than dire wolf jaws. Finally, we describe how our information entropy-based measure allows phenotypic integration to be compared in dense semilandmark data sets without bias, allowing characterization of the information content of any given shape, a quantity we term 'latent dispersion'.

Cranial shape diversification in horses: variation and covariation patterns under the impact of artificial selection

The potential of artificial selection to dramatically impact phenotypic diversity is well known. Large-scale morphological changes in domestic species, emerging over short timescales, offer an accelerated perspective on evolutionary processes. The domestic horse (Equus caballus) provides a striking example of rapid evolution, with major changes in morphology and size likely stemming from artificial selection. However, the microevolutionary mechanisms allowing to generate this variation in a short time interval remain little known. Here, we use 3D geometric morphometrics to quantify skull morphological diversity in the horse, and investigate modularity and integration patterns to understand how morphological associations contribute to cranial evolvability in this taxon. We find that changes in the magnitude of cranial integration contribute to the diversification of the skull morphology in horse breeds. Our results demonstrate that a conserved pattern of modularity does not constrain large-scale morphological variations in horses and that artificial selection has impacted mechanisms underlying phenotypic diversity to facilitate rapid shape changes. More broadly, this study demonstrates that studying microevolutionary processes in domestic species produces important insights into extant phenotypic diversity.

Under pressure: the relationship between cranial shape and burrowing force in caecilians (Gymnophiona)

Caecilians are elongate, limbless and annulated amphibians that, with the exception of one aquatic family, all have an at least partly fossorial lifestyle. It has been suggested that caecilian evolution resulted in sturdy and compact skulls with fused bones and tight sutures, as an adaptation to their head-first burrowing habits. However, although their cranial osteology is well described, relationships between form and function remain poorly understood. In the present study, we explored the relationship between cranial shape and in vivo burrowing forces. Using micro-computed tomography (µCT) data, we performed 3D geometric morphometrics to explore whether cranial and mandibular shapes reflected patterns that might be associated with maximal push forces. The results highlight important differences in maximal push forces, with the aquatic Typhlonectes producing a lower force for a given size compared with other species. Despite substantial differences in head morphology across species, no relationship between overall skull shape and push force could be detected. Although a strong phylogenetic signal may partly obscure the results, our conclusions confirm previous studies using biomechanical models and suggest that differences in the degree of fossoriality do not appear to be driving the evolution of head shape.

What does modularity mean?

Modularity is now generally recognized as a fundamental feature of organisms, one that may have profound consequences for evolution. Modularity has recently become a major focus of research in organismal biology across multiple disciplines including genetics, developmental biology, functional morphology, population and evolutionary biology. While the wealth of new data, and also new theory, has provided exciting and novel insights, the concept of modularity has become increasingly ambiguous. That ambiguity is underlain by diverse intuitions about what modularity means, and the ambiguity is not merely about the meaning of the word-the metrics of modularity are measuring different properties and the methods for delimiting modules delimit them by different, sometimes conflicting criteria. The many definitions, metrics and methods can lead to substantial confusion not just about what modularity means as a word but also about what it means for evolution. Here we review various concepts, using graphical depictions of modules. We then review some of the metrics and methods for analyzing modularity at different levels. To place these in theoretical context, we briefly review theories about the origins and evolutionary consequences of modularity. Finally, we show how mismatches between concepts, metrics and methods can produce theoretical confusion, and how potentially illogical interpretations can be made sensible by a better match between definitions, metrics, and methods.

Size, microhabitat, and loss of larval feeding drive cranial diversification in frogs

Habitat is one of the most important factors shaping organismal morphology, but it may vary across life history stages. Ontogenetic shifts in ecology may introduce antagonistic selection that constrains adult phenotype, particularly with ecologically distinct developmental phases such as the free-living, feeding larval stage of many frogs (Lissamphibia: Anura). We test the relative influences of developmental and ecological factors on the diversification of adult skull morphology with a detailed analysis of 15 individual cranial regions across 173 anuran species, representing every extant family. Skull size, adult microhabitat, larval feeding, and ossification timing are all significant factors shaping aspects of cranial evolution in frogs, with late-ossifying elements showing the greatest disparity and fastest evolutionary rates. Size and microhabitat show the strongest effects on cranial shape, and we identify a "large size-wide skull" pattern of anuran, and possibly amphibian, evolutionary allometry. Fossorial and aquatic microhabitats occupy distinct regions of morphospace and display fast evolution and high disparity. Taxa with and without feeding larvae do not notably differ in cranial morphology. However, loss of an actively feeding larval stage is associated with higher evolutionary rates and disparity, suggesting that functional pressures experienced earlier in ontogeny significantly impact adult morphological evolution.

Cranial integration in the ring-necked parakeet, Psittacula krameri (Psittaciformes: Psittaculidae)

The study of integration and modularity aims to describe the organization of components that make up organisms, and the evolutionary, developmental and functional relationships among them. Both have been studied at the interspecific (evolutionary) and intraspecific (phenotypic and ontogenetic) levels to different degrees across various clades. Although evolutionary modularity and integration are well-characterized across birds, knowledge of intraspecific patterns is lacking. Here, we use a high-density, three-dimensional geometric morphometric approach to investigate patterns of integration and modularity in Psittacula krameri, a highly successful invasive parrot species that exhibits the derived vertical palate and cranio-facial hinge of the Psittaciformes. Showing a pattern of nine distinct cranial modules, our results support findings from recent research that uses similar methods to investigate interspecific integration in birds. Allometry is not a significant influence on cranial shape variation within this species; however, within-module integration is significantly negatively correlated with disparity, with high variation concentrated in the weakly integrated rostrum, palate and vault modules. As previous studies have demonstrated differences in beak shape between invasive and native populations, variation in the weakly integrated palate and rostrum may have facilitated evolutionary change in these parts of the skull, contributing to the ring-necked parakeet’s success as an invasive species.

Brain Reconstruction Across the Fish-Tetrapod Transition; Insights From Modern Amphibians

The fish-tetrapod transition (which incorporates the related fin-limb and water-land transitions) is celebrated as one of the most important junctions in vertebrate evolution. Sarcopterygian fishes (the “lobe-fins”) are today represented by lungfishes and coelacanths, but during the Paleozoic they were much more diverse. It was some of these sarcopterygians, a lineage of the tetrapodomorph fishes, that gave rise to tetrapods (terrestrial vertebrates with limbs bearing digits). This spectacular leap took place during the Devonian Period. Due to the nature of preservation, it is the hard parts of an animal’s body that are most likely to fossilize, while soft tissues such as muscular and brain tissues, typically fail to do so. Thus, our understanding of the adaptations of the hard skeletal structures of vertebrates is considerably greater than that of the soft tissue systems. Fortunately, the braincases of early vertebrates are often ossified and thereby have the potential to provide detailed morphological information. However, the correspondence between brain and endocast (an internal mold of the cavity) has historically been considered poor in most “lower” vertebrates and consequently neglected in such studies of brain evolution. Despite this, recent work documenting the spatial relationship in extant basal sarcopterygians (coelacanth, lungfish, axolotl, and salamander) has highlighted that this is not uniformly the case. Herein, we quantify and illustrate the brain-endocast relationship in four additional extant basal tetrapod exemplars: neobatrachian anurans (frogs) Breviceps poweri and Ceratophrys ornata; and gymnophionans (caecilians) Gegeneophis ramaswamii and Rhinatrema bivittatum. We show that anurans and caecilians appear to have brains that fill their endocasts to a similar degree to that of lungfishes and salamanders, but not coelacanth. Ceratophrys has considerably lower correspondence between the brain and endocast in the olfactory tract and mesencephalic regions, while Breviceps has low correspondence along its ventral endocranial margin. The brains of caecilians reflect their endocasts most closely (vol. ∼70%). The telencephalon is tightly fitted within the endocast in all four taxa. Our findings highlight the need to adequately assess the brain-endocast relationship in a broad range of vertebrates, in order to inform neural reconstructions of fossil taxa using the Extant Phylogenetic Bracket approach and future studies of brain evolution.

Ontogenetic origins of cranial convergence between the extinct marsupial thylacine and placental gray wolf

Phenotypic convergence, describing the independent evolution of similar characteristics, offers unique insights into how natural selection influences developmental and molecular processes to generate shared adaptations. The extinct marsupial thylacine and placental gray wolf represent one of the most extraordinary cases of convergent evolution in mammals, sharing striking cranial similarities despite 160 million years of independent evolution. We digitally reconstructed their cranial ontogeny from birth to adulthood to examine how and when convergence arises through patterns of allometry, mosaicism, modularity, and integration. We find the thylacine and wolf crania develop along nearly parallel growth trajectories, despite lineage-specific constraints and heterochrony in timing of ossification. These constraints were found to enforce distinct cranial modularity and integration patterns during development, which were unable to explain their adult convergence. Instead, we identify a developmental origin for their convergent cranial morphologies through patterns of mosaic evolution, occurring within bone groups sharing conserved embryonic tissue origins. Interestingly, these patterns are accompanied by homoplasy in gene regulatory networks associated with neural crest cells, critical for skull patterning. Together, our findings establish empirical links between adaptive phenotypic and genotypic convergence and provides a digital resource for further investigations into the developmental basis of mammalian evolution.

Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence

An integrative definition of sesamoid bones has been recently proposed, highlighting their relationship with tendons and ligaments, their genetic origin, the influence of epigenetic stimuli on their development, and their variable tissue composition. Sesamoid bones occur mainly associated with a large number of mobile joints in vertebrates, most commonly in the postcranium. Here, we present a survey of the distribution pattern of sesamoids in 256 taxa of Caudata and Gymnophiona and 24 taxa of temnospondyls and lepospondyls, based on dissections, high-resolution X-ray computed tomography from digital databases and literature data. These groups have a pivotal role in the interpretation of the evolution of sesamoids in Lissamphibia and tetrapods in general. Our main goals were: (1) to contribute to the knowledge of the comparative anatomy of sesamoids in Lissamphibia; (2) to assess the evolutionary history of selected sesamoids. We formally studied the evolution of the observed sesamoids by optimizing them in the most accepted phylogeny of the group. We identified only three bony or cartilaginous sesamoids in Caudata: the mandibular sesamoid, which is adjacent to the jaw articulation; one located on the mandibular symphysis; and one located in the posterior end of the maxilla. We did not observe any cartilaginous or osseous sesamoid in Gymnophiona. Mapping analyses of the sesamoid dataset of urodeles onto the phylogeny revealed that the very conspicuous sesamoid in the mandibular symphysis of Necturus beyeri and Amphiuma tridactylum is an independent acquisition of these taxa. On the contrary, the sesamoid located between the maxilla and the lower jaw is a new synapomorphy that supports the node of Hydromantes platycephalus and Karsenia coreana. The absence of a mandibular sesamoid is plesiomorphic to Caudata, whereas it is convergent in seven different families. The absence of postcranial sesamoids in salamanders might reveal a paedomorphic pattern that would be visible in their limb joints.

Morphological integration and modularity in the hyperkinetic feeding system of aquatic-foraging snakes

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of eight bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 μCT-scanned skulls and high-density geometric morphometric methods to address the origin and patterns of variation and integration in the feeding bones of aquatic-foraging snakes. By comparing alternate superimposition protocols allowing us to analyze the entire kinetic feeding system simultaneously, we find that the feeding bones are highly integrated, driven predominantly by functional selective pressures. The most supported pattern of modularity contains four modules, each associated with distinct functional roles: the mandible, the palatopterygoid arch, the maxilla, and the suspensorium. Further, the morphological disparity of each bone is not linked to its magnitude of integration, indicating that integration within the feeding system does not strongly constrain morphological evolution, and that adequate biomechanical solutions to a wide range of feeding ecologies and behaviors are readily evolvable within the constraint due to integration in the snake feeding system.

Synchrotron microtomography applied to the volumetric analysis of internal structures of Thoropa miliaris tadpoles

Amphibians are models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change due to their sensitivity and vulnerability to changes in the environment. Developmental series of amphibians are informative about their biology, and X-ray based 3D reconstruction holds promise for quantifying morphological changes during growth—some with a direct impact on the possibility of an experimental investigation on several of the ecological topics listed above. However, 3D resolution and discrimination of their soft tissues have been difficult with traditional X-ray computed tomography, without time-consuming contrast staining. Tomographic data were initially performed (pre-processing and reconstruction) using the open-source software tool SYRMEP Tomo Project. Data processing and analysis of the reconstructed tomography volumes were conducted using the segmentation semi-automatic settings of the software Avizo Fire 8, which provide information about each investigated tissues, organs or bone elements. Hence, volumetric analyses were carried out to quantify the development of structures in different tadpole developmental stages. Our work shows that synchrotron X-ray microtomography using phase-contrast mode resolves the edges of the internal tissues (as well as overall tadpole morphology), facilitating the segmentation of the investigated tissues. Reconstruction algorithms and segmentation software played an important role in the qualitative and quantitative analysis of each target structure of the Thoropa miliaris tadpole at different stages of development, providing information on volume, shape and length. The use of the synchrotron X-ray microtomography setup of the SYRMEP beamline of Elettra Synchrotron, in phase-contrast mode, allows access to volumetric data for bone formation, eye development, nervous system and notochordal changes during the development (ontogeny) of tadpoles of a cycloramphid frog Thoropa miliaris. As key elements in the normal development of these and any other frog tadpole, the application of such a comparative ontogenetic study, may hold interest to researchers in experimental and environmental disciplines.

Hymenophore configuration of the oak mazegill (Daedalea quercina)

The complex hymenophore configuration of the oak mazegill (Daedalea quercina, Polyporales) is rarely quantified, although quantifications are important analytical tools to assess form and growth. We quantified the hymenophore configuration of the oak mazegill by manual counting of tubes and tubular branches and ends. Complementary measurements were made with the software AngioTool. We found that the number of tubular branches and ends varied substantially between specimens, with a positive correlation with hymenophore area (5-51 cm²). We then measured complexity as tubular branches and ends per area, and complexity was not correlated with the size of the basidiocarps. Basidiocarps from two locations were compared (Hald ege, N = 11; Hvidding krat, N = 7), and the prevalence of branches and that of ends were greater in the Hvidding krat hymenophores (P < 0.001 and P = 0.029, respectively). Additionally, lacunarity, a measure of complexity ("gappiness"), gave a higher score for the Hald ege hymenophores (P = 0.002). Lacunarity analysis of multiple species of Polyporales showed that the oak mazegill hymenophore is comparatively complex. Concerning factors that affect hymenophore complexity of the oak mazegill, we observed that greater hymenophore complexity was associated with abrupt boundaries between growth zones on the pileus surface. Several years of monitoring documented that basidiocarps can remodel to gravitational changes and heal from damage. In conclusion, intra- and interspecies differences of hymenophore configuration can be quantified. In oak mazegill, hymenophore complexity is not dependent on size per se, although abrupt borders between growth zones are associated with increased complexity. Some of the variation between basidiocarps may reflect aspects of the ecology of the individual fungus.

Metamorphosis shapes cranial diversity and rate of evolution in salamanders

Metamorphosis is widespread across the animal kingdom and induces fundamental changes in the morphology, habitat and resources used by an organism during its lifetime. Metamorphic species are likely to experience more dynamic selective pressures through ontogeny compared with species with single-phase life cycles, which may drive divergent evolutionary dynamics. Here, we reconstruct the cranial evolution of the salamander using geometric morphometric data from 148 species spanning the order's full phylogenetic, developmental and ecological diversity. We demonstrate that life cycle influences cranial shape diversity and rate of evolution. Shifts in the rate of cranial evolution are consistently associated with transitions from biphasic to either direct-developing or paedomorphic life cycle strategies. Direct-developers exhibit the slowest rates of evolution and the lowest disparity, and paedomorphic species the highest. Species undergoing complete metamorphosis (biphasic and direct-developing) exhibit greater cranial modularity (evolutionary independence among regions) than do paedomorphic species, which undergo differential metamorphosis. Biphasic and direct-developing species also display elevated disparity relative to the evolutionary rate for bones associated with feeding, whereas this is not the case for paedomorphic species. Metamorphosis has profoundly influenced salamander cranial evolution, requiring greater autonomy of cranial elements and facilitating the rapid evolution of regions that are remodelled through ontogeny. Rather than compounding functional constraints on variation, metamorphosis seems to have promoted the morphological evolution of salamanders over 180 million years, which may explain the ubiquity of this complex life cycle strategy across disparate organisms.

Cranial integration in the fire salamander, Salamandra salamandra (Caudata: Salamandridae)

Phenotypic integration and modularity are concepts that represent the pattern of connectivity of morphological structures within an organism. Integration describes the coordinated variation of traits, and analyses of these relationships among traits often reveals the presence of modules, sets of traits that are highly integrated but relatively independent of other traits. Phenotypic integration and modularity have been studied at both the evolutionary and static level across a variety of clades, although most studies thus far are focused on amniotes, and especially mammals. Using a high-dimensional geometric morphometric approach, we investigated the pattern of cranial integration and modularity of the Italian fire salamander (Salamandra salamandra giglioli). We recovered a highly modular pattern, but this pattern did not support either entirely developmental or functional hypotheses of cranial organisation, possibly reflecting complex interactions amongst multiple influencing factors. We found that size had no significant effect on cranial shape, and that morphological variance of individual modules had no significant relationship with degree of within-module integration. The pattern of cranial integration in the fire salamander is similar to that previously recovered for caecilians, with highly integrated jaw suspensorium and occipital regions, suggesting possible conservation of patterns across lissamphibians.

Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data

The study of modularity is paramount for understanding trends of phenotypic evolution, and for determining the extent to which covariation patterns are conserved across taxa and levels of biological organization. However, biologists currently lack quantitative methods for statistically comparing the strength of modular signal across datasets, and a robust approach for evaluating alternative modular hypotheses for the same dataset. As a solution to these challenges, we propose an effect size measure ( Z CR ) derived from the covariance ratio, and develop hypothesis-testing procedures for their comparison. Computer simulations demonstrate that Z CR displays appropriate statistical properties and low levels of mis-specification, implying that it correctly identifies modular signal, when present. By contrast, alternative methods based on likelihood (EMMLi) and goodness of fit (MINT) suffer from high false positive rates and high model mis-specification rates. An empirical example in sigmodontine rodent mandibles is provided to illustrate the utility of Z CR for comparing modular hypotheses. Overall, we find that covariance ratio effect sizes are useful for comparing patterns of modular signal across datasets or for evaluating alternative modular hypotheses for the same dataset. Finally, the statistical philosophy for pairwise model comparisons using effect sizes should accommodate any future analytical developments for characterizing modular signal.

High-Density Morphometric Analysis of Shape and Integration: The Good, the Bad, and the Not-Really-a-Problem

The field of comparative morphology has entered a new phase with the rapid generation of high-resolution three-dimensional (3D) data. With freely available 3D data of thousands of species, methods for quantifying morphology that harness this rich phenotypic information are quickly emerging. Among these techniques, high-density geometric morphometric approaches provide a powerful and versatile framework to robustly characterize shape and phenotypic integration, the covariances among morphological traits. These methods are particularly useful for analyses of complex structures and across disparate taxa, which may share few landmarks of unambiguous homology. However, high-density geometric morphometrics also brings challenges, for example, with statistical, but not biological, covariances imposed by placement and sliding of semilandmarks and registration methods such as Procrustes superimposition. Here, we present simulations and case studies of high-density datasets for squamates, birds, and caecilians that exemplify the promise and challenges of high-dimensional analyses of phenotypic integration and modularity. We assess: (1) the relative merits of "big" high-density geometric morphometrics data over traditional shape data; (2) the impact of Procrustes superimposition on analyses of integration and modularity; and (3) differences in patterns of integration between analyses using high-density geometric morphometrics and those using discrete landmarks. We demonstrate that for many skull regions, 20-30 landmarks and/or semilandmarks are needed to accurately characterize their shape variation, and landmark-only analyses do a particularly poor job of capturing shape variation in vault and rostrum bones. Procrustes superimposition can mask modularity, especially when landmarks covary in parallel directions, but this effect decreases with more biologically complex covariance patterns. The directional effect of landmark variation on the position of the centroid affects recovery of covariance patterns more than landmark number does. Landmark-only and landmark-plus-sliding-semilandmark analyses of integration are generally congruent in overall pattern of integration, but landmark-only analyses tend to show higher integration between adjacent bones, especially when landmarks placed on the sutures between bones introduces a boundary bias. Allometry may be a stronger influence on patterns of integration in landmark-only analyses, which show stronger integration prior to removal of allometric effects compared to analyses including semilandmarks. High-density geometric morphometrics has its challenges and drawbacks, but our analyses of simulated and empirical datasets demonstrate that these potential issues are unlikely to obscure genuine biological signal. Rather, high-density geometric morphometric data exceed traditional landmark-based methods in characterization of morphology and allow more nuanced comparisons across disparate taxa. Combined with the rapid increases in 3D data availability, high-density morphometric approaches have immense potential to propel a new class of studies of comparative morphology and phenotypic integration.

A Practical Guide to Sliding and Surface Semilandmarks in Morphometric Analyses

Advances in imaging technologies, such as computed tomography (CT) and surface scanning, have facilitated the rapid generation of large datasets of high-resolution three-dimensional (3D) specimen reconstructions in recent years. The wealth of phenotypic information available from these datasets has the potential to inform our understanding of morphological variation and evolution. However, the ever-increasing ease of compiling 3D datasets has created an urgent need for sophisticated methods of capturing high-density shape data that reflect the biological complexity in form. Landmarks often do not take full advantage of the rich shape information available from high-resolution 3D specimen reconstructions, as they are typically restricted to sutures or processes that can be reliably identified across specimens and exclude most of the surface morphology. The development of sliding and surface semilandmark techniques has greatly enhanced the quantification of shape, but their application to diverse datasets can be challenging, especially when dealing with the variable absence of some regions within a structure. Using comprehensive 3D datasets of crania that span the entire clades of birds, squamates and caecilians, we demonstrate methods for capturing morphology across incredibly diverse shapes. We detail many of the difficulties associated with applying semilandmarks to comparable regions across highly disparate structures, and provide solutions to some of these challenges, while considering the consequences of decisions one makes in applying these approaches. Finally, we analyze the benefits of high-density sliding semilandmark approaches over landmark-only studies for capturing shape across diverse organisms and discuss the promise of these approaches for the study of organismal form.

Shifts in cranial integration associated with ecological specialization in pinnipeds (Mammalia, Carnivora)

Patterns of trait integration reflect the underlying genetic and developmental architecture of morphology and significantly influence the direction of evolution. Nevertheless, the relationship between integration and disparity is complex and unlikely to be uniform across large phylogenetic and ecological scales. To date, there are little data comparing patterns of integration across major ecological transitions, limiting understanding of the processes driving changes in trait integration and their consequences. Here, we investigated patterns of cranial integration and disparity across pinnipeds, three closely related carnivoran families that have undergone a secondary adaptation to the aquatic niche with varying levels of ecological differentiation. With a three-dimensional geometric morphometric dataset of 677 specimens spanning 15 species, we compared five models of trait integration, and examined the effects of sexual dimorphism and allometry on model support. Pinnipeds varied greatly in patterns of cranial integration compared to terrestrial carnivorans. Interestingly, this variation is concentrated in phocids, which may reflect the broader range of ecological and life-history specializations across phocid species, and greater independence from the terrestrial habitat observed in that group, relative to otariids. Overall, these results indicate that major ecological transitions, and presumably large changes in selection pressures, may drive changes in phenotypic trait integration.