Comparative functional morphology indicates niche partitioning among sympatric marine reptiles.

Mesozoic marine ecosystems were dominated by diverse lineages of aquatic tetrapods. For over 50 Ma in the Jurassic until the Early Cretaceous, plesiosaurians, ichthyosaurians and thalattosuchian crocodylomorphs coexisted at the top levels of trophic food webs. We created a functional dataset of continuous craniomandibular and dental characters known from neontological studies to be functionally significant in modern aquatic tetrapods. We analysed this dataset with multivariate ordination and inferential statistics to assess functional similarities and differences in the marine reptile faunas of two well-sampled Jurassic ecosystems deposited in the same seaway: the Oxford Clay Formation (OCF, Callovian-early Oxfordian, Middle-Late Jurassic) and the Kimmeridge Clay Formation (KCF, Kimmeridgian-Tithonian, Late Jurassic) of the UK. Lower jaw-based macroevolutionary trends are similar to those of tooth-based diversity studies. Closely related species cluster together, with minimal overlaps in the morphospace. Marine reptile lineages were characterized by the distinctive combinations of features, but we reveal multiple instances of morphofunctional convergence among different groups. We quantitatively corroborate previous observations that the ecosystems in the OCF and KCF were markedly distinct in faunal composition and structure. Morphofunctional differentiation may have enabled specialization and was an important factor facilitating the coexistence of diverse marine reptile assemblages in deep time.

A Cybertaxonomic Revision of the "Crocidura pergrisea" Species Complex with a Special Focus on Endemic Rocky Shrews: Crocidura armenica and Crocidura arispa (Soricidae).

The extraction of museum DNA from a unique collection of samples of the "Crocidura pergrisea" species complex, which comprises local endemics of Central and West Asia, allowed us to determine their inter- and intragroup relationships. The first step of this study was the re-evaluation of heavily damaged type specimens of C. armenica via a microcomputed-tomography-based cybertaxonomic approach (CTtax), which enabled a precise description of the species' morphology; three-dimensional models of the cybertypes were made available through the MorphoBank Repository. We developed the "AProMaDesU" pipeline on the basis of five requirements for micro-CT-based cyber-datasets in relation to mammalian collections. Our second step was a combination of several meticulous approaches to morphological investigation against a background of a cytb-based phylogeny, which helped us to make a taxonomic decision about the status of species of the "pergrisea" group, e.g., C. arispa, C. armenica, and C. serezkyensis, when the morphological results were partly incongruent with the molecular phylogeny. Nevertheless, under two assumptions, our findings preserved a separate species-level status of C. serezkyensis and C. arispa. In addition, we restored the species-level status of C. armenica. This taxonomic decision is based on our morphospace analysis, which revealed unique craniomandibular shape transformations within the rocky shrews that helped them with the transition to a new area of morphospace/trophic niches and consequently separated them from the other analyzed Crocidura groups.

The global pattern of epiphytic liverwort disparity: insights from Frullania.

The geographical and ecological patterns of morphological disparity are crucial to understand how species are assembled within communities in the context of the evolutionary history, morphological evolution and ecological interactions. However, with limited exceptions, rather few studies have been conducted on the global pattern of disparity, particularly in early land plants. Here we explored the spatial accumulation of disparity in a morphologically variable and species rich liverwort genus Frullania in order to test the hypothesis of latitude disparity gradient. We compiled a morphological data set consisting of eight continuous traits for 244 currently accepted species, and scored the species distribution into 19 floristic regions worldwide. By reconstructing the morphospace of all defined regions and comparisons, we identified a general Gondwana-Laurasia pattern of disparity in Frullania. This likely results from an increase of ecological opportunities and / or relaxed constraints towards low latitudes. The lowest disparity occurred in arid tropical regions, largely due to a high extinction rate as a consequence of paleoaridification. There was weak correlation between species diversity and disparity at different spatial scales. Furthermore, long-distance dispersal may have partially shaped the present-day distribution of Frullania disparity, given its frequency and the great contribution of widely distributed species to local morphospace. This study not only highlighted the crucial roles of paleoenvironmental changes, ecological opportunities, and efficient dispersal on the global pattern of plant disparity, but also implied its dependence on the ecological and physiological function of traits.

High floral disparity without pollinator shifts in buzz-bee-pollinated Melastomataceae.

Shifts among functional pollinator groups are commonly regarded as sources of floral morphological diversity (disparity) through the formation of distinct pollination syndromes. While pollination syndromes may be used for predicting pollinators, their predictive accuracy remains debated, and they are rarely used to test whether floral disparity is indeed associated with pollinator shifts. We apply classification models trained and validated on 44 functional floral traits across 252 species with empirical pollinator observations and then use the validated models to predict pollinators for 159 species lacking observations. In addition, we employ multivariate statistics and phylogenetic comparative analyses to test whether pollinator shifts are the main source of floral disparity in Melastomataceae. We find strong support for four well-differentiated pollination syndromes ('buzz-bee', 'nectar-foraging vertebrate', 'food-body-foraging vertebrate', 'generalist'). While pollinator shifts add significantly to floral disparity, we find that the most species-rich 'buzz-bee' pollination syndrome is most disparate, indicating that high floral disparity may evolve without pollinator shifts. Also, relatively species-poor clades and geographic areas contributed substantially to total disparity. Finally, our results show that machine-learning approaches are a powerful tool for evaluating the predictive accuracy of the pollination syndrome concept as well as for predicting pollinators where observations are missing.

Twenty years on from Developmental Plasticity and Evolution: middle-range theories and how to test them.

In Developmental Plasticity and Evolution, Mary-Jane West-Eberhard argued that the developmental mechanisms that enable organisms to respond to their environment are fundamental causes of adaptation and diversification. Twenty years after publication of this book, this once so highly controversial claim appears to have been assimilated by a wealth of studies on 'plasticity-led' evolution. However, we suggest that the role of development in explanations for adaptive evolution remains underappreciated in this body of work. By combining concepts of evolvability from evolutionary developmental biology and quantitative genetics, we outline a framework that is more appropriate to identify developmental causes of adaptive evolution. This framework demonstrates how experimental and comparative developmental biology and physiology can be leveraged to put the role of plasticity in evolution to the test.

The interaction between heterochrony and mechanical forces as main driver of floral evolution.

Heterochrony acts as a fundamental process affecting the early development of organisms in creating a subtle shift in the timing of initiation or the duration of a developmental process. In flowers this process is linked with mechanical forces that cause changes in the interaction of neighbouring floral organs by altering the timing and rate of initiation of organs. Heterochrony leads to a delay or acceleration of the development of neighbouring primordia, inducing a change in the morphospace of the flowers. As changes in the timing of development may affect organs differently at different stages of development, these shifts eventually lead to major morphological changes such as altered organ positions, fusions, or organ reductions with profound consequences for floral evolution and the diversification of flowers. By concentrating on early developmental stages in flowers it is possible to understand how heterochrony is responsible for shifts in organ position and the establishment of a novel floral Bauplan. However, it remains difficult to separate heterochrony as a process from pattern, as both are intimately linked. Therefore it is essential to connect different patterns in flowers through the process of developmental change.Examples illustrating the importance of heterochronic shifts affecting different organs of the flower are presented and discussed. These cover the transition from inflorescence to flower through the interaction of bracts and bracteoles, the pressure exercised by the perianth on the androecium and gynoecium, the inversed influence of stamens on petals, and the centrifugal influence of carpels on the androecium. Different processes are explored, including the occurrence of obdiplostemony, the onset of common primordia, variable carpel positions, and organ reduction and loss.

Modelling evolutionary tempo and mode using formal morphological spaces and Markov chain principles.

Evolutionary tempo and mode summarize ancient and controversial subjects of theoretical biology such as gradualism, convergence, contingence, trends, and entrenchment. We employed an integrative methodological approach to explore the evolutionary tempo and mode of Lepidosaurian phalangeal formulae (PFs). This approach involves quantifying the frequencies of morphological changes along an evolutionary trajectory. The five meristic characters encoded by PFs are particularly valuable in revealing evolutionary patterns, owing to their discrete nature and extensive documentation in the literature. Based on a pre-existing dataset of PFs from 649 taxa (35 Lepidosauria families, including fossils), from which there exists a unique repertoire of 53 formulations, our approach simultaneously considers phenetic and phylogenetic data. This culminates in a diagram accounting for the phylogenetic dynamic of evolution traversing across different regions of morphospace. The method involves enumerating phenotypical options, reconstructing phenotypes across the phylogeny, projecting phenotypes onto a morphospace, and constructing a flow network from the frequency of evolutionary transitions between unique phenotypic conditions. This approach links Markovian chains and evolutionary trajectories to formally define parameters that describe the underlying transitions of morphological change. Among other results, we found that (a) PF evolution exhibits a clear trend towards reduction in the phalangeal count and that (b) evolutionary change tends to occur significantly between morphologically similar PFs. Notwithstanding, although minor but not trivial, transitions between distant formulas -jumps- occur. Our results support a pluralistic view including stasis, gradualism, and saltationism discriminating their prevalence in a target character evolution.

Evolution of Plumage Patterns in a Pattern Morphospace: A Phylogenetic Analysis of Melanerpine Woodpeckers.

AbstractPlumage patterns of melanerpine (Melanerpes-Sphyrapicus) woodpeckers are strikingly diverse. Understanding the evolution and function of this diversity is challenging because of the difficulty of quantifying plumage patterns. We use a three-dimensional space to characterize the evolution of melanerpine achromatic plumage patterns. The axes of the space are three pattern features (spatial frequency, orientation, and contrast) quantified using two-dimensional fast Fourier transformation of museum specimen images. Mapping plumage in pattern space reveals differences in how species and subclades occupy the space. To quantify these differences, we derive two new measures of pattern: pattern diversity (diversity across plumage patches within a species) and pattern uniqueness (divergence of patterns from those of other species). We estimate that the melanerpine ancestor had mottled plumage and find that pattern traits across patches and subclades evolve at different rates. We also find that smaller species are more likely to display horizontal face patterning. We promote pattern spaces as powerful tools for investigating animal pattern evolution.

Angiosperm flowers reached their highest morphological diversity early in their evolutionary history.

Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation and diversification. Accordingly, the quantification of floral morphological diversity (disparity) among angiosperm subgroups and through time may give important insights into the evolutionary history of angiosperms as a whole. Based on a comprehensive dataset focusing on 30 characters describing floral structure across angiosperms, we used 1201 extant and 121 fossil flowers to measure floral disparity and explore patterns of floral evolution through time and across lineages. We found that angiosperms reached their highest floral disparity in the Early Cretaceous. However, decreasing disparity toward the present likely has not precluded the innovation of other complex traits at other morphological levels, which likely played a key role in the outstanding angiosperm species richness. Angiosperms occupy specific regions of the theoretical morphospace, indicating that only a portion of the possible floral trait combinations is observed in nature. The ANA grade, the magnoliids, and the early-eudicot grade occupy large areas of the morphospace (higher disparity), whereas nested groups occupy narrower regions (lower disparity).

The ontogeny of disparity in Cupressaceae seed cones.

Ontogenetic shape change has long been recognized to be important in generating patterns of morphological diversity and may be especially important in plant reproductive structures. We explore how seed cone disparity in Cupressaceae changes over ontogeny by comparing pollination-stage and mature cones. We sampled cones at pollen and seed release and measured cone scales using basic morphometric shape variables. We used multivariate statistical methods, particularly hypervolume overlap calculations, to measure morphospace occupation and disparity. Cone scales at both pollination and maturity exhibit substantial variability, although the disparity is greater at maturity. Mature cone scales are also more clustered in trait space, showing less overlap with other taxa than at pollination. These patterns reflect two growth strategies that generate closed cones over maturation, either through thin laminar scales or relatively thick, peltate scales, resulting in two distinct regions of morphospace occupation. Disparity patterns in Cupressaceae seed cones change over ontogeny, reflecting shifting functional demands that require specific patterns of cone scale growth. The evolution of Cupressaceae reproductive disparity therefore represents selection for trajectories of ontogenetic shape change, a phenomenon that should be widespread across seed plants.

Intrinsic and extrinsic drivers of shape variation in the albatross compound bill.

Albatross are the largest seabirds on Earth and have a suite of adaptations for their pelagic lifestyle. Rather than having a bill made of a single piece of keratin, Procellariiformes have a compound rhamphotheca, made of several joined plates. Drivers of the shape of the albatross bill have not been explored. Here we use three-dimensional scans of 61 upper bills from 12 species of albatross to understand whether intrinsic (species assignment & size) or extrinsic (diet) factors predict bill shape. Diet is a significant predictor of bill shape with coarse dietary categories providing higher R2 values than dietary proportion data. We also find that of the intrinsic factors, species assignment accounts for ten times more of the variation than size (72% versus 6.8%) and that there is a common allometric vector of shape change between all species. When considering species averages in a phylogenetic framework, there are significant Blomberg's K results for both shape and size (K = 0.29 & 1.10) with the first axis of variation having a much higher K value (K = 1.9), reflecting the split in shape at the root of the tree. The influence of size on bill shape is limited, with species assignment and diet predicting far more of the variation. The results show that both intrinsic and extrinsic factors are needed to understand morphological evolution.

Isotopic niches do not follow the expectations of niche conservatism in the bird genus Cinclodes.

Phenotypic traits are expected to be more similar among closely related species than among species that diverged long ago (all else being equal). This pattern, known as phylogenetic niche conservatism, also applies to traits that are important to determine the niche of species. To test this hypothesis on ecological niches, we analysed isotopic data from 254 museum study skins from 12 of the 16 species of the bird genus Cinclodes and measured stable isotope ratios for four different elements: carbon, nitrogen, hydrogen and oxygen. We find that all traits, measured individually, or as a composite measurement, lack any phylogenetic signal, which in turn suggests a high level of lability in ecological niches. We compared these metrics to the measurements of morphological traits in the same genus and found that isotopic niches are uniquely evolutionarily labile compared to other traits. Our results suggest that, in Cinclodes, the realized niche evolves much faster than expected by the constraints of phylogenetic history and poses the question of whether this is a general pattern across the tree of life.

A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions.

Developmental complexity stemming from the dynamic interplay between genetic and biomechanic factors canalizes the ways genotypes and phenotypes can change in evolution. As a paradigmatic system, we explore how changes in developmental factors generate typical tooth shape transitions. Since tooth development has mainly been researched in mammals, we contribute to a more general understanding by studying the development of tooth diversity in sharks. To this end, we build a general, but realistic, mathematical model of odontogenesis. We show that it reproduces key shark-specific features of tooth development as well as real tooth shape variation in small-spotted catsharks Scyliorhinus canicula. We validate our model by comparison with experiments in vivo. Strikingly, we observe that developmental transitions between tooth shapes tend to be highly degenerate, even for complex phenotypes. We also discover that the sets of developmental parameters involved in tooth shape transitions tend to depend asymmetrically on the direction of that transition. Together, our findings provide a valuable base for furthering our understanding of how developmental changes can lead to both adaptive phenotypic change and trait convergence in complex, phenotypically highly diverse, structures.

An oncospace for human cancers.

Human cancers comprise an heterogeneous array of diseases with different progression patterns and responses to therapy. However, they all develop within a host context that constrains their natural history. Since it occurs across the diversity of organisms, one can conjecture that there is order in the cancer multiverse. Is there a way to capture the broad range of tumor types within a space of the possible? Here we define the oncospace, a coordinate system that integrates the ecological, evolutionary and developmental components of cancer complexity. The spatial position of a tumor results from its departure from the healthy tissue along these three axes, and progression trajectories inform about the components driving malignancy across cancer subtypes. We postulate that the oncospace topology encodes new information regarding tumorigenic pathways, subtype prognosis, and therapeutic opportunities: treatment design could benefit from considering how to nudge tumors toward empty evolutionary dead ends in the oncospace.

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.

Behavioural function and development of body-to-limb proportions and active movement ranges in three stick insect species.

Overall body proportions and relative limb length are highly characteristic for most insect taxa. In case of the legs, limb length has mostly been discussed with regard to parameters of locomotor performance and, in particular cases, as an adaptation to environmental factors or to the mating system. Here, we compare three species of stick and leaf insects (Phasmatodea) that differ strongly in the length ratio between antennae and walking legs, with the antennae of Medauroidea extradentata being much shorter than its legs, nearly equal length of antennae and legs in Carausius morosus, and considerably longer antennae than front legs in Aretaon asperrimus. We show that that relative limb length is directly related to the near-range exploration effort, with complementary function of the antennae and front legs irrespective of their length ratio. Assuming that these inter-species differences hold for both sexes and all developmental stages, we further explore how relative limb length differs between sexes and how it changes throughout postembryonic development. We show that the pattern of limb-to-body proportions is species-characteristic despite sexual dimorphism, and find that the change in sexual dimorphism is strongest during the last two moults. Finally, we show that antennal growth rate is consistently higher than that of front legs, but differs categorically between the species investigated. Whereas antennal growth rate is constant in Carausius, the antennae grow exponentially in Medauroidea and with a sudden boost during the last moult in Aretaon.

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 new Meckel's cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace.

Fossil chondrichthyan remains are mostly known from their teeth, scales or fin spines only, whereas their cartilaginous endoskeletons require exceptional preservational conditions to become fossilized. While most cartilaginous remains of Famennian (Late Devonian) chondrichthyans were found in older layers of the eastern Anti-Atlas, such fossils were unknown from the Hangenberg black shale (HBS) and only a few chondrichthyan teeth had been found therein previously. Here, we describe a Meckel's cartilage from the Hangenberg black shale in Morocco, which is the first fossil cartilage from these strata. Since no teeth or other skeletal elements have been found in articulation, we used elliptical Fourier (EFA), principal component (PCA), and hierarchical cluster (HCA) analyses to morphologically compare it with 41 chondrichthyan taxa of different size and age and to evaluate its possible systematic affiliation. PCA and HCA position the new specimen closest to some acanthodian and elasmobranch jaws. Accordingly, a holocephalan origin was excluded. The jaw shape as well as the presence of a polygonal pattern, typical for tessellated calcified cartilage, suggest a ctenacanth origin and we assigned the new HBS Meckel's cartilage to the order Ctenacanthiformes with reservations.

Periodic Environmental Disturbance Drives Repeated Ecomorphological Diversification in an Adaptive Radiation of Antarctic Fishes.

AbstractThe ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early-burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In systems with periodic disturbances, species-rich clades can contain nested adaptive radiations of subclades with their own distinct diversification histories, and how adaptive radiation theory applies in these cases is less clear. Here, we investigated patterns of ecological and phenotypic diversification within two iterative adaptive radiations of cryonotothenioid fishes in Antarctica's Southern Ocean: crocodile icefishes and notoperches. For both clades, we observe evidence of repeated diversification into disparate regions of trait space between closely related taxa and into overlapping regions of trait space between distantly related taxa. We additionally find little evidence that patterns of ecological divergence are correlated with evolution of morphological disparity, suggesting that these axes of divergence may not be tightly linked. Finally, we reveal evidence of repeated convergence in sympatry that suggests niche complementarity. These findings reflect the dynamic history of Antarctic marine habitats and may guide hypotheses of diversification dynamics in environments characterized by periodic disturbance.