Pervasive cranial allometry at different anatomical scales and variational levels in extant armadillosAlometría craneal generalizada a diferentes escalas anatómicas y niveles de variación en armadillos actuales.

Allometry, i.e., morphological variation correlated with size, is a major pattern in organismal evolution. Since size varies both within and among species, allometry occurs at different variational levels. However, the variability of allometric patterns across levels is poorly known since its evaluation requires extensive comparative studies. Here, we implemented a 3D geometric morphometric approach to investigate cranial allometry at three main variational levels-static, ontogenetic, and evolutionary-and two anatomical scales-entire cranium and cranial subunits-based on a dense intra- and interspecific sampling of extant armadillo diversity. While allometric trajectories differ among distantly related species, they hardly do so among sister families. This suggests that phylogenetic distance plays an important role in explaining allometric divergences. Beyond trajectories, our analyses revealed pervasive allometric shape changes shared across variational levels and anatomical scales. At the entire cranial scale, craniofacial allometry (relative snout elongation and braincase reduction) is accompanied notably by variations of nuchal crests and postorbital constriction. Among cranial subunits, the distribution of allometry was highly heterogeneous, with the frontal and petrosal bones showing the most pervasive shape changes, some of which were undetected at a more global scale. Evidence of widespread and superimposed allometric variations raises questions on their determinants and anatomical correlates and demonstrates the critical role of allometry in morphological evolution.

A comparison of high-throughput SARS-CoV-2 sequencing methods from nasopharyngeal samples.

The COVID-19 pandemic caused by the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to threaten public health and burden healthcare systems worldwide. Whole SARS-CoV-2 genome sequencing has become essential for epidemiological monitoring and identification of new variants, which could represent a risk of increased transmissibility, virulence, or resistance to vaccines or treatment. Different next-generation sequencing approaches are used in SARS-CoV-2 sequencing, although with different ability to provide whole genome coverage without gaps and to reliably detect new variants. In this study, we compared the performance of three target enrichment methods (two multiplex amplification methods and one hybridization capture) using nasopharyngeal swabs from infected individuals. We applied these target enrichment methods to the same set of nasopharyngeal samples (N = 93) in high-throughput mode. SARS-CoV-2 genome was obtained using short-read next-generation sequencing. We observed that each method has some advantages, such as high mapping rate (CleanPlex and COVIDSeq) or absence of systematic variant calling error (SureSelect) as well as their limitations such as suboptimal uniformity of coverage (CleanPlex), high cost (SureSelect) or supply shortages (COVIDSeq). Nevertheless, each of the three target enrichment kits tested in this study yielded acceptable results of whole SARS-CoV-2 genome sequencing and either of them can therefore be used in prospective programs of genomic surveillance of SARS-CoV-2. Genomic surveillance will be crucial to overcoming the ongoing pandemic of COVID-19, despite its successive waves and continually emerging variants.

Micro- and Macroscale Patterns of Petal Morphogenesis in Nigella damascena (Ranunculaceae) Revealed by Geometric Morphometrics and Cellular Analyses.

Petals, the inner organs in a differentiated perianth, generally play an important role in pollinator attraction. As such they exhibit an extraordinary diversity of shapes, sizes, and colors. Being involved in pollinator attraction and reward, they are privileged targets of evolution. The corolla of the Ranunculaceae species Nigella damascena consists of elaborate nectariferous petals, made of a stalk, upper, and lower lips forming a nectar pouch, shiny pseudonectaries, and pilose ears. While the main events of petal development are properly described, a few is known about the pattern of organ size and shape covariation and the cellular dynamics during development. In this study, we investigated the relationships between morphogenesis and growth of N. damascena petals using geometric morphometrics coupled with the study of cell characteristics. First, we found that petal shape and size dynamics are allometric during development and that their covariation suggests that petal shape change dynamics are exponentially slower than growth. We then found that cell proliferation is the major driver of shape patterning during development, while petal size dynamics are mostly driven by cell expansion. Our analyses provide a quantitative basis to characterize the relationships between shape, size, and cell characteristics during the development of an elaborate floral structure. Such studies lay the ground for future evo-devo investigations of the large morphological diversity observed in nectariferous structures, in Ranunculaceae and beyond.

Disparities in the analysis of morphological disparity.

Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here, we review the most commonly used approaches for characterizing and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no 'one-size-fits-all' approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis.

Geometric morphometrics of nested symmetries unravels hierarchical inter- and intra-individual variation in biological shapes.

Symmetry is a pervasive feature of organismal shape and the focus of a large body of research in Biology. Here, we consider complex patterns of symmetry where a phenotype exhibits a hierarchically structured combination of symmetries. We extend the Procrustes ANOVA for the analysis of nested symmetries and the decomposition of the overall morphological variation into components of symmetry (among-individual variation) and asymmetry (directional and fluctuating asymmetry). We illustrate its use with the Aristotle's lantern, the masticatory apparatus of 'regular' sea urchins, a complex organ displaying bilateral symmetry nested within five-fold rotational symmetry. Our results highlight the importance of characterising the full symmetry of a structure with nested symmetries. Higher order rotational symmetry appears strongly constrained and developmentally stable compared to lower level bilateral symmetry. This contrast between higher and lower levels of asymmetry is discussed in relation to the spatial pattern of the lantern morphogenesis. This extended framework is applicable to any biological object exhibiting nested symmetries, regardless of their type (e.g., bilateral, rotational, translational). Such cases are extremely widespread in animals and plants, from arthropod segmentation to angiosperm inflorescence and corolla shape. The method therefore widens the research scope on developmental instability, canalization, developmental modularity and morphological integration.

Bracketing phenogenotypic limits of mammalian hybridization.

An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey-ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.

How (much) do flowers vary? Unbalanced disparity among flower functional modules and a mosaic pattern of morphospace occupation in the order Ericales.

The staggering diversity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological diversity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and diversity of flowers.

Development and evolution of segmentation assessed by geometric morphometrics: The centipede Strigamia maritima as a case study.

Using the centipede model species Strigamia maritima as a subject of study, we illustrate the potential of geometric morphometrics for investigating the development and evolution of segmentation, with a specific focus on post-embryonic segmental patterning. We show how these techniques can contribute detailed descriptive data for comparative purposes, but also precious information on some features of the developmental system that are considered relevant for the evolvability of a segmented body architecture, such as developmental stability and canalization. Morphometric analyses allow to separately investigate several sources of phenotypic variation along a segmented body axis, like constitutive and random segment heteronomy, both within and among individuals. Specifically, in S. maritima, the segmental pattern of ventral sclerite shapes mirrors that of their bilateral fluctuating asymmetry and among-individual variation in associating the most anterior and most posterior segments in diverging from the central ones. Also, among segments, there seems to be a correlation between fluctuating asymmetry and shape variation among individuals, suggesting that canalization and developmental stability are somehow associated. Overall, these associations might stem from a joint influence of the segmental position on the two processes of developmental buffering.

The geometry of morphospaces: lessons from the classic Raup shell coiling model.

Morphospaces are spatial depictions of morphological variation among biological forms that have become an integral part of the analytical toolkit of evolutionary biologists and palaeobiologists. Nevertheless, the term morphospace brings together a great variety of spaces with different geometries. In particular, many morphospaces lack the metric properties underlying the notions of distance and direction, which are, however, central to the analysis of morphological differences and evolutionary transitions. The problem is illustrated here with the iconic morphospace of coiled shells implemented by Raup 50 years ago. The model, which allows the description of shell coiling geometry of various invertebrate taxa, is a seminal reference in theoretical morphology and morphospace theory, but also a morphometric framework frequently used in empirical studies, particularly of ammonoids. Because of the definition of its underlying parameters, Raup's morphospace does not possess a Euclidean structure and a meaningful interpretation of the spread and spacing of taxa within it is not guaranteed. Focusing on the region of the morphospace occupied by most ammonoids, I detail a landmark-based morphospace circumventing this problem and built from the same input measurements required for the calculation of Raup's parameters. From simulations and a reanalysis of Palaeozoic ammonoid shell disparity, the properties of these morphospaces are compared and their algebraic and geometric relationships highlighted. While Raup's model remains a valuable tool for describing ammonoid shells and relating their shapes to the coiling process, it is demonstrated that quantitative analyses of morphological patterns should be carried out within the landmark-based framework. Beyond this specific case, the increasing use and diversity of morphospaces in evolutionary morphology call for caution when interpreting patterns and comparing results drawn from different types of morphospaces.

Modularity and developmental stability in segmented animals: variation in translational asymmetry in geophilomorph centipedes.

Does a modular body organization present a challenge for developmental control? We investigate the idea of a possible developmental cost of modularity by examining the relationship between modularity and developmental stability in a multi-segmented arthropod taxon: the geophilomorph centipedes. In a sample of eight species, we tested the correlation between developmental stability, estimated from measures of translational fluctuating asymmetry, and the number of trunk segments and some other morphological traits, both at the species and individual levels. We found sizeable differences in size and shape patterns of variation at the level of species. However, we did not find any clear evidence of correlation between fluctuating asymmetry and the number of trunk segments or the other morphological traits considered. Thus, our results provide no support to the idea of a possible trade-off between the cardinality of a modular system and the level of developmental precision in the phenotypic expression of its modules. The results of this exploratory study invite further investigations of patterns of translational fluctuating asymmetry in segmented animals and other modular organisms, as these have the potential to reveal features of developmental stability that cannot be captured by the study of bilateral asymmetry alone.

Why should we investigate the morphological disparity of plant clades?

BACKGROUND: Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. METHODS: Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. KEY RESULTS: Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. CONCLUSIONS: Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and ecological features of plants make them ideally suited to investigating intrinsic and extrinsic constraints on disparity.

What limits the morphological disparity of clades?

The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution.

A superarmored lobopodian from the Cambrian of China and early disparity in the evolution of Onychophora.

We describe Collinsium ciliosum from the early Cambrian Xiaoshiba Lagerstätte in South China, an armored lobopodian with a remarkable degree of limb differentiation including a pair of antenna-like appendages, six pairs of elongate setiferous limbs for suspension feeding, and nine pairs of clawed annulated legs with an anchoring function. Collinsium belongs to a highly derived clade of lobopodians within stem group Onychophora, distinguished by a substantial dorsal armature of supernumerary and biomineralized spines (Family Luolishaniidae). As demonstrated here, luolishaniids display the highest degree of limb specialization among Paleozoic lobopodians, constitute more than one-third of the overall morphological disparity of stem group Onychophora, and are substantially more disparate than crown group representatives. Despite having higher disparity and appendage complexity than other lobopodians and extant velvet worms, the specialized mode of life embodied by luolishaniids became extinct during the Early Paleozoic. Collinsium and other superarmored lobopodians exploited a unique paleoecological niche during the Cambrian explosion.

The floral morphospace--a modern comparative approach to study angiosperm evolution.

Morphospaces are mathematical representations used for studying the evolution of morphological diversity and for the evaluation of evolved shapes among theoretically possible ones. Although widely used in zoology, they--with few exceptions--have been disregarded in plant science and in particular in the study of broad-scale patterns of floral structure and evolution. Here we provide basic information on the morphospace approach; we review earlier morphospace applications in plant science; and as a practical example, we construct and analyze a floral morphospace. Morphospaces are usually visualized with the help of ordination methods such as principal component analysis (PCA) or nonmetric multidimensional scaling (NMDS). The results of these analyses are then coupled with disparity indices that describe the spread of taxa in the space. We discuss these methods and apply modern statistical tools to the first and only angiosperm-wide floral morphospace published by Stebbins in 1951. Despite the incompleteness of Stebbins' original dataset, our analyses highlight major, angiosperm-wide trends in the diversity of flower morphology and thereby demonstrate the power of this previously neglected approach in plant science.

Not all roads can be taken: development induces anisotropic accessibility in morphospace.

Morphospaces are quantitative representations of phenotype space that are widely used in studies of morphological evolution. Do current conceptualizations of morphospaces, however, appropriately reflect the evolutionary dynamics of organisms depicted in these spaces? Most empirical morphospace studies implicitly consider variability of biological forms as isotropic, but such a view appears inadequate when the properties of development mediating phenotypic changes are considered. Here, a trilobite case study is used to visualize the constraints imposed by development on the accessibility structure of morphospace. Variability in the resultant morphospace is strongly anisotropic and reveals discordances between the apparent range of possible phenotypes and their actual accessibility. Homoplasy, directionality, and asymmetry of evolutionary transitions appear as natural consequences of anisotropic variability and point out the limitation of morphological distance for evolutionary inference. Measures of distance in morphospace should be used with considerable caution and must be complemented with developmentally meaningful measures of evolutionary accessibility.

Clades reach highest morphological disparity early in their evolution.

There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the "big five" mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing.

On the relationship between the macroevolutionary trajectories of morphological integration and morphological disparity.

How does the organization of phenotypes relate to their propensity to vary? How do evolutionary changes in this organization affect large-scale phenotypic evolution? Over the last decade, studies of morphological integration and modularity have renewed our understanding of the organizational and variational properties of complex phenotypes. Much effort has been made to unravel the connections among the genetic, developmental, and functional contexts leading to differential integration among morphological traits and individuation of variational modules. Yet, their macroevolutionary consequences on the dynamics of morphological disparity-the large-scale variety of organismal designs-are still largely unknown. Here, I investigate the relationship between morphological integration and morphological disparity throughout the entire evolutionary history of crinoids (echinoderms). Quantitative analyses of interspecific patterns of variation and covariation among characters describing the stem, cup, arm, and tegmen of the crinoid body do not show any significant concordance between the temporal trajectories of disparity and overall integration. Nevertheless, the results reveal marked differences in the patterns of integration for Palaeozoic and post-Palaeozoic crinoids. Post-Palaeozoic crinoids have a higher degree of integration and occupy a different region of the space of integration patterns, corresponding to more heterogeneously structured matrices of correlation among traits. Particularly, increased covariation is observed between subsets of characters from the dorsal cup and from the arms. These analyses show that morphological disparity is not dependent on the overall degree of evolutionary integration but rather on the way integration is distributed among traits. Hence, temporal changes in disparity dynamics are likely constrained by reorganizations of the modularity of the crinoid morphology and not by changes in the variability of individual traits. The differences in integration patterns explain the more stereotyped morphologies of post-Palaeozoic crinoids and, from a broader macroevolutionary perspective, call for a greater attention to the distributional heterogeneities of constraints in morphospace.

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.

Allometric space and allometric disparity: a developmental perspective in the macroevolutionary analysis of morphological disparity.

Here, we advance novel uses of allometric spaces--multidimensional spaces specifically defined by allometric coefficients--with the goal of investigating the focal role of development in shaping the evolution of morphological disparity. From their examination, operational measures of allometric disparity can be derived, complementing standard signals of morphological disparity through an intuitive and process-oriented refinement of established analytical protocols used in disparity studies. Allometric spaces thereby become a promising context to reveal different patterns of evolutionary developmental changes and to assess their relative prevalence and importance. Such spaces offer a novel domain of investigation of phenotypic variation and should help in detecting large-scale trends, thus placing various macroevolutionary phenomena in an explicitly developmental context. Ammonoidea (Cephalopoda) at the Lower-Middle Jurassic transition were chosen as a case study to illustrate this methodological approach. We constructed two phenotypic spaces: a static, adult one (adult morphospace) and a dynamic, developmental one (allometric space). Comparative disparity analyses show a strikingly stable occupation in both spaces, despite extensive change in taxonomic composition. In contrast, disparity analyses of subclades reveal clearly distinct morphological and allometric disparity dynamics. Allometric approaches allow developmental insights into morphological diversification otherwise intractable from the analysis of adult morphospace alone.

Combining ontogenetic and evolutionary scales of morphological disparity: a study of early Jurassic ammonites.

Two major research themes in Evolutionary Developmental Biology and in Paleobiology, respectively, have each become central for the analysis and interpretation of morphological changes in evolution: the study of ontogeny/phylogeny connections, mainly within the widespread and controversial framework of heterochrony; and the study of morphological disparity, the morphological signal of biodiversity, describing secular changes in morphospace occupation during the history of any given clade. Although enriching in their respective fields, these two themes have remained rather isolated to date, despite the potential value of integrating them as some recent studies begin to suggest. Here, we explore the recent notion of developmental morphospace-morphospace carrying ontogenetic information-as a potential tool for bridging the gap between disparity dynamics and developmental dynamics. We elaborate this approach with a case study of Early Jurassic ammonite family Hildoceratidae (Mollusca, Cephalopoda). Morphometric analyses of the shell shape of 20 species spanning the morphological spectrum of the family are used to quantify and contrast juvenile and adult disparity levels. Adult disparity is significantly greater than juvenile disparity at the family level; yet, some subclades also display different patterns. In addition, comparisons of ontogenetic trajectories underline the prevalence of heterochrony-based evolutionary modifications within subfamilies (via ontogenetic scaling); they also point to the probable existence of pervasive developmental constraints structuring inhomogeneous morphospace occupation.