Modularity of a Cambrian ptychoparioid trilobite cranidium

The paradox of predictability provides a bridge between micro- and macroevolution

The relationship between the evolutionary dynamics observed in contemporary populations (microevolution) and evolution on timescales of millions of years (macroevolution) has been a topic of considerable debate. Historically, this debate centers on inconsistencies between microevolutionary processes and macroevolutionary patterns. Here, we characterize a striking exception: emerging evidence indicates that standing variation in contemporary populations and macroevolutionary rates of phenotypic divergence is often positively correlated. This apparent consistency between micro- and macroevolution is paradoxical because it contradicts our previous understanding of phenotypic evolution and is so far unexplained. Here, we explore the prospects for bridging evolutionary timescales through an examination of this "paradox of predictability." We begin by explaining why the divergence-variance correlation is a paradox, followed by data analysis to show that the correlation is a general phenomenon across a broad range of temporal scales, from a few generations to tens of millions of years. Then we review complementary approaches from quantitative genetics, comparative morphology, evo-devo, and paleontology to argue that they can help to address the paradox from the shared vantage point of recent work on evolvability. In conclusion, we recommend a methodological orientation that combines different kinds of short-term and long-term data using multiple analytical frameworks in an interdisciplinary research program. Such a program will increase our general understanding of how evolution works within and across timescales.

Distinct causes underlie double-peaked trilobite morphological disparity in cephalic shape

Trilobite cephalic shape disparity varied through geological time and was integral to their ecological niche diversity, and so is widely used for taxonomic assignments. To fully appreciate trilobite cephalic evolution, we must understand how this disparity varies and the factors responsible. We explore trilobite cephalic disparity using a dataset of 983 cephalon outlines of c. 520 species, analysing the associations between cephalic morphometry and taxonomic assignment and geological Period. Elliptical Fourier transformation visualised as a Principal Components Analysis suggests significant differences in morphospace occupation and in disparity measures between the groups. Cephalic shape disparity peaks in the Ordovician and Devonian. The Cambrian-Ordovician expansion of morphospace occupation reflects radiations to new niches, with all trilobite orders established by the late Ordovician. In comparison, the Silurian-Devonian expansion seems solely a result of within-niche diversification. Linear Discriminant Analyses cross-validation, average cephalon shapes, and centroid distances demonstrate that, except for Harpida and the Cambrian and Ordovician Periods, order and geological Period cannot be robustly predicted for an unknown trilobite. Further, k-means clustering analyses suggest the total dataset naturally subdivides into only seven groups that do not correspond with taxonomy, though k-means clusters do decrease in number through the Palaeozoic, aligning with findings of decreasing disparity.

A dynamic and collaborative database for morphogeometric information of trilobites

Modern morphometric-based approaches provide valuable metrics to quantify and understand macroevolutionary and macroecological patterns and processes. Here we describe TriloMorph, an openly accessible database for morpho-geometric information of trilobites, together with a landmark acquisition protocol. In addition to morphological traits, the database contains contextual data on chronostratigraphic age, geographic location, taxonomic information and lithology of landmarked specimens. In this first version, the dataset has broad taxonomic and temporal coverage and comprises more than 55% of all trilobite genera and 85% of families recorded in the Paleobiology Database through the Devonian. We provide a release of geometric morphometric data of 277 specimens linked to published references. Additionally, we established a Github repository for constant input of morphometric data by multiple contributors and present R functions that help with data retrieval and analysis. This is the first attempt of an online, dynamic and collaborative morphometric repository. By bringing this information into a single open database we enhance the possibility of performing global palaeobiological research, providing a major complement to current occurrence-based databases.

Developmental instability in domesticated mammals

Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.

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.

Evolutionary modularity, integration and disparity in an accretionary skeleton: analysis of venerid Bivalvia

Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance-a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family.

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.

Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability

Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis and its temporal dynamics over generations. To address these open questions, we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish (Danio rerio). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed towards a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of 'preset' patterns of modularity that can appear readily and allow for rapid evolution.

A fly in a tube: Macroevolutionary expectations for integrated phenotypes

Phenotypic integration and modularity are ubiquitous features of complex organisms, describing the magnitude and pattern of relationships among biological traits. A key prediction is that these relationships, reflecting genetic, developmental, and functional interactions, shape evolutionary processes by governing evolvability and constraint. Over the last 60 years, a rich literature of research has quantified patterns of integration and modularity across a variety of clades and systems. Only recently has it become possible to contextualize these findings in a phylogenetic framework to understand how trait integration interacts with evolutionary tempo and mode. Here, we review the state of macroevolutionary studies of integration and modularity, synthesizing empirical and theoretical work into a conceptual framework for predicting the effects of integration on evolutionary rate and disparity: a fly in a tube. While magnitude of integration is expected to influence the potential for phenotypic variation to be produced and maintained, thus defining the shape and size of a tube in morphospace, evolutionary rate, or the speed at which a fly moves around the tube, is not necessarily controlled by trait interactions. Finally, we demonstrate this reduced disparity relative to the Brownian expectation for a given rate of evolution with an empirical example: the avian cranium.

Morphological homeostasis in the fossil record

Morphological homeostasis limits the extent to which genetic and/or environmental variation is translated into phenotypic variation, providing generation-to-generation fitness advantage under a stabilizing selection regime. Depending on its lability, morphological homeostasis might also have a longer-term impact on evolution by restricting the variation-and thus the response to directional selection-of a trait. The fossil record offers an inviting opportunity to investigate whether and how morphological homeostasis constrained trait evolution in lineages or clades on long timescales (thousands to millions of years) that are not accessible to neontological studies. Fossils can also reveal insight into the nature of primitive developmental systems that might not be predictable from the study of modern organisms. The ability to study morphological homeostasis in fossils is strongly limited by taphonomic processes that can destroy, blur, or distort the original biological signal: genetic data are unavailable; phenotypic data can be modified by tectonic or compaction-related deformation; time-averaging limits temporal resolution; and environmental variation is hard to study and impossible to control. As a result of these processes, neither allelic sensitivity (and thus genetic canalization) nor macroenvironmental sensitivity (and thus environmental canalization) can be unambiguously assessed in the fossil record. However, homeorhesis-robustness against microenvironmental variation (developmental noise)-can be assessed in ancient developmental systems by measuring the level of fluctuating asymmetry (FA) in a nominally symmetric trait. This requires the analysis of multiple, minimally time-averaged samples of exquisite preservational quality. Studies of FA in fossils stand to make valuable contributions to our understanding of the deep-time significance of homeorhesis. Few empirical studies have been conducted to date, and future paleontological research focusing on how homeorhesis relates to evolutionary rate (including stasis), species survivorship, and purported macroevolutionary trends in evolvability would reap high reward.

EMMLi: A maximum likelihood approach to the analysis of modularity

Identification of phenotypic modules, semiautonomous sets of highly correlated traits, can be accomplished through exploratory (e.g., cluster analysis) or confirmatory approaches (e.g., RV coefficient analysis). Although statistically more robust, confirmatory approaches are generally unable to compare across different model structures. For example, RV coefficient analysis finds support for both two- and six-module models for the therian mammalian skull. Here, we present a maximum likelihood approach that takes into account model parameterization. We compare model log-likelihoods of trait correlation matrices using the finite-sample corrected Akaike Information Criterion, allowing for comparison of hypotheses across different model structures. Simulations varying model complexity and within- and between-module contrast demonstrate that this method correctly identifies model structure and parameters across a wide range of conditions. We further analyzed a dataset of 3-D data, consisting of 61 landmarks from 181 macaque (Macaca fuscata) skulls, distributed among five age categories, testing 31 models, including no modularity among the landmarks and various partitions of two, three, six, and eight modules. Our results clearly support a complex six-module model, with separate within- and intermodule correlations. Furthermore, this model was selected for all five age categories, demonstrating that this complex pattern of integration in the macaque skull appears early and is highly conserved throughout postnatal ontogeny. Subsampling analyses demonstrate that this method is robust to relatively low sample sizes, as is commonly encountered in rare or extinct taxa. This new approach allows for the direct comparison of models with different parameterizations, providing an important tool for the analysis of modularity across diverse systems.

The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics

Variation is the raw material for natural selection, but the factors shaping variation are still poorly understood. Genetic and developmental interactions can direct variation, but there has been little synthesis of these effects with the extrinsic factors that can shape biodiversity over large scales. The study of phenotypic integration and modularity has the capacity to unify these aspects of evolutionary study by estimating genetic and developmental interactions through the quantitative analysis of morphology, allowing for combined assessment of intrinsic and extrinsic effects. Data from the fossil record in particular are central to our understanding of phenotypic integration and modularity because they provide the only information on deep-time developmental and evolutionary dynamics, including trends in trait relationships and their role in shaping organismal diversity. Here, we demonstrate the important perspective on phenotypic integration provided by the fossil record with a study of Smilodon fatalis (saber-toothed cats) and Canis dirus (dire wolves). We quantified temporal trends in size, variance, phenotypic integration, and direct developmental integration (fluctuating asymmetry) through 27,000 y of Late Pleistocene climate change. Both S. fatalis and C. dirus showed a gradual decrease in magnitude of phenotypic integration and an increase in variance and the correlation between fluctuating asymmetry and overall integration through time, suggesting that developmental integration mediated morphological response to environmental change in the later populations of these species. These results are consistent with experimental studies and represent, to our knowledge, the first deep-time validation of the importance of developmental integration in stabilizing morphological evolution through periods of environmental change.

Evolutionary mode routinely varies among morphological traits within fossil species lineages

Recent studies have revitalized interest in methods for detecting evolutionary modes in both fossil sequences and phylogenies. Most of these studies examine single size or shape traits, often implicitly assuming that single phenotypic traits are adequate representations of species-level change. We test the validity of this assumption by tallying the frequency with which traits vary in evolutionary mode within fossil species lineages. After fitting models of directional change, unbiased random walk, and stasis to a dataset of 635 traits across 153 species lineages, we find that within the majority of lineages, evolutionary mode varies across traits and the likelihood of conflicting within-lineage patterns increases with the number of traits analyzed. In addition, single traits may show variation in evolutionary mode even in situations where the overall morphological evolution of the lineage is dominated by one type of mode. These quantified, stratigraphically based findings validate the idea that morphological patterns of mosaic evolution are pervasive across groups of organisms throughout Earth's history.

Functional constraints on tooth morphology in carnivorous mammals

BACKGROUND

The range of potential morphologies resulting from evolution is limited by complex interacting processes, ranging from development to function. Quantifying these interactions is important for understanding adaptation and convergent evolution. Using three-dimensional reconstructions of carnivoran and dasyuromorph tooth rows, we compared statistical models of the relationship between tooth row shape and the opposing tooth row, a static feature, as well as measures of mandibular motion during chewing (occlusion), which are kinetic features. This is a new approach to quantifying functional integration because we use measures of movement and displacement, such as the amount the mandible translates laterally during occlusion, as opposed to conventional morphological measures, such as mandible length and geometric landmarks. By sampling two distantly related groups of ecologically similar mammals, we study carnivorous mammals in general rather than a specific group of mammals.

RESULTS

Statistical model comparisons demonstrate that the best performing models always include some measure of mandibular motion, indicating that functional and statistical models of tooth shape as purely a function of the opposing tooth row are too simple and that increased model complexity provides a better understanding of tooth form. The predictors of the best performing models always included the opposing tooth row shape and a relative linear measure of mandibular motion.

CONCLUSIONS

Our results provide quantitative support of long-standing hypotheses of tooth row shape as being influenced by mandibular motion in addition to the opposing tooth row. Additionally, this study illustrates the utility and necessity of including kinetic features in analyses of morphological integration.

Mosaic heterochrony and evolutionary modularity: the trilobite genus Zacanthopsis as a case study

Logical connections exist between evolutionary modularity and heterochrony, two unifying and structuring themes in the expanding field of evolutionary developmental biology. The former sees complex phenotypes as being made up of semi-independent units of evolutionary transformation; the latter requires such a modular organization of phenotypes to occur in a localized or mosaic fashion. This conceptual relationship is illustrated here by analyzing the evolutionary changes in the cranidial ontogeny of two related species of Cambrian trilobites. With arguments from comparative developmental genetics and functional morphology, we delineate putative evolutionary modules within the cranidium and examine patterns of evolutionary changes in ontogeny at both global and local scales. Results support a case of mosaic heterochrony, that is, a combination of local heterochronies affecting the different parts individuated in the cranidium, leading to the complex pattern of allometric repatterning observed at the global scale. Through this example, we show that recasting morphological analyses of complex phenotypes with a priori knowledge or hypotheses about their organizational and variational properties can significantly improve our interpretation and understanding of evolutionary changes among related taxa, fossil and extant. Such considerations open avenues to investigate the large-scale dynamics of modularity and its role in phenotypic evolution.