Morphospace

Herbarium specimens reveal links between leaf shape of Capsella bursa-pastoris and climate

PREMISE

Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf shapes, quantifying variation in leaf shape and the effects of environmental factors on leaf shape has proven challenging.

METHODS

To investigate leaf shape variation in a species with inconsistently shaped leaves, we used geometric morphometric modeling and deterministic techniques to analyze approximately 500 digitized specimens of Capsella bursa-pastoris collected throughout the continental United States over 100 years. We generated a morphospace of the leaf shapes and modeled leaf shape as a function of environment and time.

RESULTS

Leaf shape variation of C. bursa-pastoris was strongly associated with temperature over its growing season, with lobing decreasing as temperature increased. While we expected to see changes in variation over time, our results show that the level of leaf shape variation was consistent over the 100 years.

CONCLUSIONS

Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.

The distribution of seaweed forms and foundational assumptions in seaweed biology

Seaweeds are the most phylogenetically diverse group of multicellular organisms and rank foremost among marine keystone species. Due to their taxonomic diversity and functional importance, previous studies have classified seaweeds into functional groups based on qualitative or semi-quantitative traits, such as seaweed form, anatomy, and thickness. Despite the widespread use of seaweed functional groups from basic marine ecology to coastal monitoring, it is not known how accurate such morphology-based proposals are in grouping seaweeds by their form. To address this uncertainty at the foundations of seaweed biology, we surveyed and gathered all available data on seaweed forms using PRISMA protocols. We used the surface area to volume ratio (SA:V), a quantitative and universal measure of seaweed form, to assess the distribution and diversity of seaweed morphology across 99 species from three phyla. We show that seaweed surface area to volume ratio values span 3.64 orders of magnitude and follow a continuous and exponential distribution, without any significant gaps or clusters. We also tested current functional group schemes based on morphology and anatomy and showed that only 30% to 38% of their groups showed any significant pairwise differences in morphology. Our results challenge the basis of the current functional group approach in seaweed biology and suggest that a trait-based framework based on quantitative and continuous measures of seaweed form could provide a simpler and more accurate alternative to functionally assess seaweed ecology and physiology, as well as its implications for coastal ecosystem management.

An explainable map of human gastruloid morphospace reveals gastrulation failure modes and predicts teratogens

Human gastrulation is a critical stage of development where many pregnancies fail due to poorly understood mechanisms. Using the 2D gastruloid, a stem cell model of human gastrulation, we combined high-throughput drug perturbations and mathematical modelling to create an explainable map of gastruloid morphospace. This map outlines patterning outcomes in response to diverse perturbations and identifies variations in canonical patterning and failure modes. We modeled morphogen dynamics to embed simulated gastruloids into experimentally-determined morphospace to explain how developmental parameters drive patterning. Our model predicted and validated the two greatest sources of patterning variance: cell density-based modulations in Wnt signaling and SOX2 stability. Assigning these parameters as axes of morphospace imparted interpretability. To demonstrate its utility, we predicted novel teratogens that we validated in zebrafish. Overall, we show how stem cell models of development can be used to build a comprehensive and interpretable understanding of the set of developmental outcomes.

Chemical composition from photos: Dried solution drops reveal a morphogenetic tree

Under nonequilibrium conditions, inorganic systems can produce a wealth of life-like shapes and patterns which, compared to well-formed crystalline materials, remain widely unexplored. A seemingly simple example is the formation of salt deposits during the evaporation of sessile droplets. These evaporites show great variations in their specific patterns including single rings, creep, small crystals, fractals, and featureless disks. We have explored the patterns of 42 different salts at otherwise constant conditions. Based on 7,500 images, we show that distinct pattern families can be identified and that some salts (e.g., Na2SO4 and NH4NO3) are bifurcated creating two distinct motifs. Family affiliations cannot be predicted a priori from composition alone but rather emerge from the complex interplay of evaporation, crystallization, thermodynamics, capillarity, and fluid flow. Nonetheless, chemical composition can be predicted from the deposit pattern with surprisingly high accuracy even if the set of reference images is small. These findings suggest possible applications including smartphone-based analyses and lightweight tools for space missions.

Male and female contributions to diversity among birdwing butterfly images

Machine learning (ML) newly enables tests for higher inter-species diversity in visible phenotype (disparity) among males versus females, predictions made from Darwinian sexual selection versus Wallacean natural selection, respectively. Here, we use ML to quantify variation across a sample of > 16,000 dorsal and ventral photographs of the sexually dimorphic birdwing butterflies (Lepidoptera: Papilionidae). Validation of image embedding distances, learnt by a triplet-trained, deep convolutional neural network, shows ML can be used for automated reconstruction of phenotypic evolution achieving measures of phylogenetic congruence to genetic species trees within a range sampled among genetic trees themselves. Quantification of sexual disparity difference (male versus female embedding distance), shows sexually and phylogenetically variable inter-species disparity. Ornithoptera exemplify high embedded male image disparity, diversification of selective optima in fitted multi-peak OU models and accelerated divergence, with cases of extreme divergence in allopatry and sympatry. However, genus Troides shows inverted patterns, including comparatively static male embedded phenotype, and higher female than male disparity - though within an inferred selective regime common to these females. Birdwing shapes and colour patterns that are most phenotypically distinctive in ML similarity are generally those of males. However, either sex can contribute majoritively to observed phenotypic diversity among species.

Herbarium specimens reveal links between Capsella bursa-pastoris leaf shape and climate

Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf margin features, quantifying leaf shape variation and the effects of environmental factors on leaf shape has proven challenging. To investigate leaf shape variation in species with inconsistent shapes, we analyzed approximately 500 digitized Capsella bursa-pastoris specimens collected throughout the continental U.S. over a 100-year period with geometric morphometric modeling and deterministic techniques. We generated a morphospace of C. bursa-pastoris leaf shapes and modeled leaf shape as a function of environment and time. Our results suggest C. bursa-pastoris leaf shape variation is strongly associated with temperature over the C. bursa-pastoris growing season, with lobing decreasing as temperature increases. While we expected to see changes in variation over time, our results show that level of leaf shape variation is consistent over the 100-year period. Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.

Mesozoic evolution of cicadas and their origins of vocalization and root feeding

Extant cicada (Hemiptera: Cicadoidea) includes widely distributed Cicadidae and relictual Tettigarctidae, with fossils ascribed to these two groups based on several distinct, minimally varying morphological differences that define their extant counterparts. However, directly assigning Mesozoic fossils to modern taxa may overlook the role of unique and transitional features provided by fossils in tracking their early evolutionary paths. Here, based on adult and nymphal fossils from mid-Cretaceous Kachin amber of Myanmar, we explore the phylogenetic relationships and morphological disparities of fossil and extant cicadoids. Our results suggest that Cicadidae and Tettigarctidae might have diverged at or by the Middle Jurassic, with morphological evolution possibly shaped by host plant changes. The discovery of tymbal structures and anatomical analysis of adult fossils indicate that mid-Cretaceous cicadas were silent as modern Tettigarctidae or could have produced faint tymbal-related sounds. The discovery of final-instar nymphal and exuviae cicadoid fossils with fossorial forelegs and piercing-sucking mouthparts indicates that they had most likely adopted a subterranean lifestyle by the mid-Cretaceous, occupying the ecological niche of underground feeding on root. Our study traces the morphological, behavioral, and ecological evolution of Cicadoidea from the Mesozoic, emphasizing their adaptive traits and interactions with their living environments.

Evo-Devo Mechanobiology: The Missing Link

While the modern framework of evolutionary development (evo-devo) has been decidedly genetic, historic analyses have also considered the importance of mechanics in the evolution of form. With the aid of recent technological advancements in both quantifying and perturbing changes in the molecular and mechanical effectors of organismal shape, how molecular and genetic cues regulate the biophysical aspects of morphogenesis is becoming increasingly well studied. As a result, this is an opportune time to consider how the tissue-scale mechanics that underlie morphogenesis are acted upon through evolution to establish morphological diversity. Such a focus will enable a field of evo-devo mechanobiology that will serve to better elucidate the opaque relations between genes and forms by articulating intermediary physical mechanisms. Here, we review how the evolution of shape is measured and related to genetics, how recent strides have been made in the dissection of developmental tissue mechanics, and how we expect these areas to coalesce in evo-devo studies in the future.

Mapping and exploring the organoid state space using synthetic biology

The functional relevance of an organoid is dependent on the differentiation, morphology, cell arrangement and biophysical properties, which collectively define the state of an organoid. For an organoid culture, an individual organoid or the cells that compose it, these state variables can be characterised, most easily by transcriptomics and by high-content image analysis. Their states can be compared to their in vivo counterparts. Current evidence suggests that organoids explore a wider state space than organs in vivo due to the lack of niche signalling and the variability of boundary conditions in vitro. Using data-driven state inference and in silico modelling, phase diagrams can be constructed to systematically sort organoids along biochemical or biophysical axes. These phase diagrams allow us to identify control strategies to modulate organoid state. To do so, the biochemical and biophysical environment, as well as the cells that seed organoids, can be manipulated.

A Mathematical Model for Mollusc Shells Based on Parametric Surfaces and the Construction of Theoretical Morphospaces

In this study, we propose a mathematical model based on parametric surfaces for the shell morphology of the phylum Mollusca. Since David Raup’s pioneering works, many mathematical models have been proposed for different contexts to describe general shell morphology; however, there has been a gap in the practicality of models that allow the estimation of their parameter values in real specimens. Our model collects ideas from previous pioneering studies; it rests on the equation of the logarithmic spiral, uses a fixed coordinate system (coiling axis), and defines the position of the generating curve with a local moving system using the Frenet frame. However, it improves upon previous models by applying apex formation, rotations, and substantially different parameter definitions. Furthermore, the most conspicuous improvement is the development of a simple and standardized methodology to obtain the six theoretical parameters from shell images from different mollusc classes and to generate useful theoretical morphospaces. The model was applied to reproduce the shape of real mollusc-shell specimens from Gasteropoda, Cephaloda and Bivalvia, which represent important classes in geological time. We propose a specific methodology to obtain the parameters in four morphological groups: helicoidal, planispiral, conic, and valve-like shells, thereby demonstrating that the model offers an adequate representation of real shells. Finally, possible improvements to the model are discussed along with further work. Based on the above considerations, the capacity of the model to allow the construction of theoretical morphospaces, the methodology to estimate parameters and from the comparison between several existing models for shells, we believe that our model can contribute to future research on the development, diversity and evolutionary processes that generated the diversity in mollusc shells.

Evolutionary contingency in lingulid brachiopods across mass extinctions

Morphology usually serves as an effective proxy for functional ecology,^1,2,3,4,5 and evaluating morphological, anatomical, and ecological changes permits a deeper understanding of the nature of diversification and macroevolution.^{5,6,7,8,9,10,11,12} Lingulid (order Lingulida) brachiopods are both diverse and abundant during the early Palaeozoic but decrease in diversity over time, with only a few genera of linguloids and discinoids present in modern marine ecosystems, resulting in them frequently being referred to as "living fossils."^13,14,15 The dynamics that drove this decline remain uncertain, and it has not been determined if there is an associated decline in morphological and ecological diversity. Here, we apply geometric morphometrics to reconstruct global morphospace occupation for lingulid brachiopods through the Phanerozoic, with results showing that maximum morphospace occupation was reached by the Early Ordovician. At this time of peak diversity, linguloids with a sub-rectangular shell shape already possessed several evolutionary features, such as the rearrangement of mantle canals and reduction of the pseudointerarea, common to all modern infaunal forms. The end Ordovician mass extinction has a differential effect on linguloids, disproportionally wiping out those forms with a rounded shell shape, while forms with sub-rectangular shells survived both the end Ordovician and the Permian-Triassic mass extinctions, leaving a fauna predominantly composed of infaunal forms. For discinoids, both morphospace occupation and epibenthic life strategies remain consistent through the Phanerozoic. Morphospace occupation over time, when considered using anatomical and ecological analyses, suggests that the limited morphological and ecological diversity of modern lingulid brachiopods reflects evolutionary contingency rather than deterministic processes.