Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes

Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

A comprehensive STPA-PSO framework for quantifying smart glasses risks in manufacturing

The integration of cutting-edge technologies, such as wearables, in complex systems is crucial for enhancing collaboration between humans and machines in the era of Industry 5.0. However, this increased interaction also introduces new challenges and risks, including the potential for human errors. A thorough analysis of the literature reveals an absence of studies that have quantified these risks, underscoring the utmost importance of this research. To address the above gap, the present study introduces the STPA-PSO methodology, which aims to quantify the risks associated with the use of smart glasses in complex systems, with a specific focus on human error risks. The proposed methodology leverages the Systems-Theoretic Process Analysis (STPA) approach to proactively identify hazards, while harnessing the power of the Particle Swarm Optimization (PSO) algorithm to accurately calculate and optimize risks, including those related to human errors. To validate the effectiveness of the methodology, a case study involving the assembly of a refrigerator was conducted, encompassing various critical aspects, such as the Industrial, Financial, and Occupational Health and Safety (OHS) aspects. The results provide evidence of the efficacy of the STPA-PSO approach in assessing, quantifying, and managing risks during the design stage. By proposing a robust and comprehensive risk quantification framework, this study makes a significant contribution to the advancement of system safety analysis in complex environments, providing invaluable insights for the seamless integration of wearables and ensuring safer interactions between humans and machines.

Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.

Linking morphology, performance, and habitat utilization: adaptation across biologically relevant 'levels' in tamarins

BACKGROUND

Biological adaptation manifests itself at the interface of different biologically relevant 'levels', such as ecology, performance, and morphology. Integrated studies at this interface are scarce due to practical difficulties in study design. We present a multilevel analysis, in which we combine evidence from habitat utilization, leaping performance and limb bone morphology of four species of tamarins to elucidate correlations between these 'levels'.

RESULTS

We conducted studies of leaping behavior in the field and in a naturalistic park and found significant differences in support use and leaping performance. Leontocebus nigrifrons leaps primarily on vertical, inflexible supports, with vertical body postures, and covers greater leaping distances on average. In contrast, Saguinus midas and S. imperator use vertical and horizontal supports for leaping with a relatively similar frequency. S. mystax is similar to S. midas and S. imperator in the use of supports, but covers greater leaping distances on average, which are nevertheless shorter than those of L. nigrifrons. We assumed these differences to be reflected in the locomotor morphology, too, and compared various morphological features of the long bones of the limbs. According to our performance and habitat utilization data, we expected the long bone morphology of L. nigrifrons to reflect the largest potential for joint torque generation and stress resistance, because we assume longer leaps on vertical supports to exert larger forces on the bones. For S. mystax, based on our performance data, we expected the potential for torque generation to be intermediate between L. nigrifrons and the other two Saguinus species. Surprisingly, we found S. midas and S. imperator having relatively more robust morphological structures as well as relatively larger muscle in-levers, and thus appearing better adapted to the stresses involved in leaping than the other two.

CONCLUSION

This study demonstrates the complex ways in which behavioral and morphological 'levels' map onto each other, cautioning against oversimplification of ecological profiles when using large interspecific eco-morphological studies to make adaptive evolutionary inferences.

Stable decoding of working memory load through frequency bands

Numerous studies have shown that working memory modulates every frequency band's power in the human brain. Yet, the question of how the highly distributed working memory adapts to external demands remains unresolved. Here, we explored frequency band modulations underlying working memory load, taking executive control under account. We hypothesized that synchronizations underlying various cognitive functions may be sequenced in time to avoid interference and that transient modulation of decoding accuracy of task difficulty would vary with increasing difficulty. We recorded whole scalp EEG data from 12 healthy participants, while they performed a visuo-spatial n-back task with three conditions of increasing difficulty, after an initial learning phase. We analyzed evoked spectral perturbations and time-resolved decoding of individual synchronization. Surprisingly, our results provide evidence for persistent decoding above the level-of-chance (83.17% AUC) for combined frequency bands. In fact, the decoding accuracy was higher for the combined than for isolated frequency bands (AUC from 65.93% to 74.30%). However, in line with our hypothesis, frequency band clusters transiently emerged in parieto-occipital regions within two separate time windows for alpha-/beta-band (relative synchronization from approximately 200 to 600 ms) and for the delta-/theta-band (relative desynchronization from approximately 600 to 1000 ms). Overall, these findings highlight concurrent sustained and transient measurable features of working memory load. This could reflect the emergence of stability within and between functional networks of the complex working memory system. In turn, this process allows energy savings to cope with external demands.

Trapped in the morphospace: The relationship between morphological integration and functional performance

The evolution of complex morphological structures can be characterized by the interplay between different anatomical regions evolving under functional integration in response to shared selective pressures. Using the highly derived humeral morphology of talpid moles as a model, here we test whether functional performance is linked to increased levels of evolutionary integration between humerus subunits and, if so, what the strength is of the relationship. Combining two-dimensional geometric morphometrics, phylogenetic comparative methods, and functional landscape modeling, we demonstrate that the high biomechanical performance of subterranean moles' humeri is coupled with elevated levels of integration, whereas taxa with low-performance values show intermediate or low integration. Theoretical morphs occurring in high-performance areas of the functional landscape are not occupied by any species, and show a marked drop in covariation levels, suggesting the existence of a strong relationship between integration and performance in the evolution of talpid moles' humeri. We argue that the relative temporal invariance of the subterranean environment may have contributed to stabilize humeral morphology, trapping subterranean moles in a narrow region of the landscape and impeding any attempt to reposition on a new ascending slope.

Omics technologies in poultry health and productivity - part 1: current use in poultry research

In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.

Interactions among multiple selective pressures on the form–function relationship in insular stream fishes

Relationships between body shape and escape performance are well established for many species. However, organisms can face multiple selection pressures that might impose competing demands. Many fishes use fast starts for escaping predator attacks, whereas some species of gobiid fishes have evolved the ability to climb waterfalls out of predator-dense habitats. The ancestral ‘powerburst’ climbing mechanism uses lateral body undulations to move up waterfalls, whereas a derived ‘inching’ mechanism uses rectilinear locomotion. We examined whether fast-start performance is impacted by selection imposed from the new functional demands of climbing. We predicted that non-climbing species would show morphology and fast-start performance that facilitate predator evasion, because these fish live consistently with predators and are not constrained by the demands of climbing. We also predicted that, by using lateral undulations, powerburst climbers would show escape performance superior to that of inchers. We compared fast starts and body shape across six goby species. As predicted, non-climbing fish exhibited distinct morphology and responded more frequently to an attack stimulus than climbing species. Contrary to our predictions, we found no differences in escape performance among climbing styles. These results indicate that selection for a competing pressure need not limit the ability of prey to escape predator attacks.

Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids

The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

The Complexity and Fractal Geometry of Nuclear Medicine Images

Irregularity in shape and behavior is the main feature of every anatomical system, including human organs, tissues, cells, and sub-cellular entities. It has been shown that this property cannot be quantified by means of the classical Euclidean geometry, which is only able to describe regular geometrical objects. In contrast, fractal geometry has been widely applied in several scientific fields. This rapid growth has also produced substantial insights in the biomedical imaging. Consequently, particular attention has been given to the identification of pathognomonic patterns of "shape" in anatomical entities and their changes from natural to pathological states. Despite the advantages of fractal mathematics and several studies demonstrating its applicability to oncological research, many researchers and clinicians remain unaware of its potential. Therefore, this review aims to summarize the complexity and fractal geometry of nuclear medicine images.

Kinematic integration during prey capture varies among individuals but not ecological contexts in bluegill sunfish, Lepomis macrochirus (Perciformes: Centrarchidae)

The general ability of components of an organism to work together to achieve a common goal has been termed integration and is often studied empirically by deconstructing organisms into component parts and quantifying covariation between them. Kinematic traits describing movement are useful for allowing organisms to respond to ecological contexts that vary over short time spans (milliseconds, minutes, etc.). Integration of these traits can contribute to the maintenance of the function of the whole organism, but it is unclear how modulation of component kinematic traits affects their integration. We examined the integration of swimming and feeding during capture of alternative prey types in bluegill sunfish (Lepomis macrochirus). Despite the expected modulation of kinematics, integration within individuals was inflexible across prey types, suggesting functional redundancy for solving a broad constraint. However, integration was variable among individuals, suggesting that individuals vary in their solutions for achieving whole-organism function and that this solution acts as a ‘top-down’ regulator of component traits, which provides insight into why kinematic variation is observed. Additionally, variation in kinematic integration among individuals could serve as an understudied target of environmental selection on prey capture, which is a necessary first step towards the observed divergence in integration among populations and species.

Multifunctional Structures and Multistructural Functions: Integration in the Evolution of Biomechanical Systems

Integration is an essential feature of complex biomechanical systems, with coordination and covariation occurring among and within structural components at time scales that vary from microseconds to deep evolutionary time. Integration has been suggested to both promote and constrain morphological evolution, and the effects of integration on the evolution of structure likely vary by system, clade, historical contingency, and time scale. In this introduction to the 2019 symposium "Multifunctional Structures and Multistructural Functions," we discuss the role of integration among structures in the context of functional integration and multifunctionality. We highlight articles from this issue of Integrative and Comparative Biology that explore integration within and among kinematics, sensory and motor systems, physiological systems, developmental processes, morphometric dimensions, and biomechanical functions. From these myriad examples it is clear that integration can exist at multiple levels of organization that can interact with adjacent levels to result in complex patterns of structural and functional phenotypes. We conclude with a synthesis of major themes and potential future directions, particularly with respect to using multifunctionality, itself, as a trait in evolutionary analyses.

Impact of transition to a subterranean lifestyle on morphological disparity and integration in talpid moles (Mammalia, Talpidae)

BACKGROUND

Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures.

RESULTS

Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration.

CONCLUSIONS

Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes in the pattern of traits covariation between the humerus and the mandible, suggesting the presence of strong phylogenetic conservatism within this pattern.

Investigating the evolution and development of biological complexity under the framework of epigenetics

Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore the link between complexity and adaptation. Although recently developed metrics allow for a unified framework, they omit developmental mechanisms. We argue that a better approach to the empirical study of complexity and its evolution includes developmental mechanisms. We then consider epigenetic mechanisms and their role in shaping developmental and evolutionary trajectories, as well as the development and organization of complexity. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Finally, we explore hybridization complexes and hybrid organisms as potential models for studying the association between epigenetics and complexity. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution.

This manuscript argues that biological complexity is better understood under the framework of epigenetics and that the epigenetic interactions emerge from the self‐regulation of complex systems. Hybrids are offered as models to study these properties.

Beyond Suction-Feeding Fishes: Identifying New Approaches to Performance Integration During Prey Capture in Aquatic Vertebrates

Organisms are composed of hierarchically arranged component parts that must work together to successfully achieve whole organism functions. In addition to integration among individual parts, some ecological demands require functional systems to work together in a type of inter-system performance integration. While performance can be measured by the ability to successfully accomplish ecologically relevant tasks, integration across performance traits can provide a deeper understanding of how these traits allow an organism to survive. The ability to move and the ability to consume food are essential to life, but during prey capture these two functions are typically integrated. Suction-feeding fishes have been used as a model of these interactions, but it is unclear how other ecologically relevant scenarios might reduce or change integration. To stimulate further research into these ideas, we highlight three contexts with the potential to result in changes in integration and underlying performance traits: (1) behavioral flexibility in aquatic feeding modes for capturing alternative prey types, (2) changes in the physical demands imposed by prey capture across environments, and (3) secondary adaptation for suction prey capture behaviors. These examples provide a broad scope of potential drivers of integration that are relevant to selection pressures experienced across vertebrate evolution. To demonstrate how these ideas can be applied and stimulate hypotheses, we provide observations from preliminary analyses of locally adapted populations of Trinidadian guppies (Poecilia reticulata) capturing prey using suction and biting feeding strategies and an Atlantic mudskipper (Periophthalmus barbarus) capturing prey above and below water. We also include a re-analysis of published data from two species of secondarily aquatic cetaceans, beluga whales (Delphinapterus leucas) and Pacific white-sided dolphins (Lagenorhynchus obliquidens), to examine the potential for secondary adaptation to affect integration in suction prey capture behaviors. Each of these examples support the broad importance of integration between locomotor and feeding performance but outline new ways that these relationships can be important when suction demands are reduced or altered. Future work in these areas will yield promising insights into vertebrate evolution and we hope to encourage further discussion on possible avenues of research on functional integration during prey capture.

A Hierarchical View of Gecko Locomotion: Photic Environment, Physiological Optics, and Locomotor Performance

Terrestrial animals move in complex habitats that vary over space and time. The characteristics of these habitats are not only defined by the physical environment, but also by the photic environment, even though the latter has largely been overlooked. For example, numerous studies of have examined the role of habitat structure, such as incline, perch diameter, and compliance, on running performance. However, running performance likely depends heavily on light level. Geckos are an exceptional group for analyzing the role of the photic environment on locomotion as they exhibit several independent shifts to diurnality from a nocturnal ancestor, they are visually-guided predators, and they are extremely diverse. Our initial goal is to discuss the range of photic environments that can be encountered in terrestrial habitats, such as day versus night, canopy cover in a forest, fog, and clouds. We then review the physiological optics of gecko vision with some new information about retina structures, the role of vision in motor-driven behaviors, and what is known about gecko locomotion under different light conditions, before demonstrating the effect of light levels on gecko locomotor performance. Overall, we highlight the importance of integrating sensory and motor information and establish a conceptual framework as guide for future research. Several future directions, such as understanding the role of pupil dynamics, are dependent on an integrative framework. This general framework can be extended to any motor system that relies on sensory information, and can be used to explore the impact of performance features on diversification and evolution.

Functional coupling in the evolution of suction feeding and gill ventilation of sculpins (Perciformes: Cottoidei)

Suction feeding and gill ventilation in teleosts are functionally coupled, meaning that there is an overlap in the structures involved with both functions. Functional coupling is one type of morphological integration, a term that broadly refers to any covariation, correlation, or coordination among structures. Suction feeding and gill ventilation exhibit other types of morphological integration, including functional coordination (a tendency of structures to work together to perform a function) and evolutionary integration (a tendency of structures to covary in size or shape across evolutionary history). Functional coupling, functional coordination, and evolutionary integration have each been proposed to limit morphological diversification to some extent. Yet teleosts show extraordinary cranial diversity, suggesting that there are mechanisms within some teleost clades that promote morphological diversification, even within the highly integrated suction feeding and gill ventilatory systems. To investigate this, we quantified evolutionary integration among four mechanical units associated with suction feeding and gill ventilation in a diverse clade of benthic, primarily suction-feeding fishes (Cottoidei; sculpins and relatives). We reconstructed cottoid phylogeny using molecular data from 108 species, and obtained 24 linear measurements of four mechanical units (jaws, hyoid, opercular bones, and branchiostegal rays) from micro-CT reconstructions of 44 cottoids and 1 outgroup taxon. We tested for evolutionary correlation and covariation among the four mechanical units using phylogenetically corrected principal component analysis to reduce the dimensionality of measurements for each unit, followed by correlating phylogenetically independent contrasts and computing phylogenetic generalized least squares models from the first principle component axis of each of the four mechanical units. The jaws, opercular bones, and branchiostegal rays show evolutionary integration, but the hyoid is not positively integrated with these units. To examine these results in an ecomorphological context, we used published ecological data in phylogenetic ANOVA models to demonstrate that the jaw is larger in fishes that eat elusive or grasping prey (e.g., prey that can easily escape or cling to the substrate) and that the hyoid is smaller in intertidal and hypoxia-tolerant sculpins. Within Cottoidei, the relatively independent evolution of the hyoid likely has reduced limitations on morphological evolution within the highly morphologically integrated suction feeding and gill ventilatory systems.

Rapid Divergence of Predator Functional Traits Affects Prey Composition in Aquatic Communities

Identifying traits that underlie variation in individual performance of consumers (i.e., trait utility) can help reveal the ecological causes of population divergence and the subsequent consequences for species interactions and community structure. Here, we document a case of rapid divergence (over the past 100 generations, or ∼150 years) in foraging traits and feeding efficiency between a lake and stream population pair of threespine stickleback. Building on predictions from functional trait models of fish feeding, we analyzed foraging experiments with a Bayesian path analysis and elucidated the traits explaining variation in foraging performance and the species composition of ingested prey. Despite extensive previous research on the divergence of foraging traits among populations and ecotypes of stickleback, our results provide novel experimental evidence of trait utility for jaw protrusion, gill raker length, and gill raker spacing when foraging on a natural zooplankton assemblage. Furthermore, we discuss how these traits might contribute to the differential effects of lake and stream stickleback on their prey communities, observed in both laboratory and mesocosm conditions. More generally, our results illustrate how the rapid divergence of functional foraging traits of consumers can impact the biomass, species composition, and trophic structure of prey communities.

Integration between swim speed and mouth size evolves repeatedly in Trinidadian guppies and aligns with suction-feeding fishes

Well-supported correlations between swim speed and mouth size during prey capture suggest the broad existence of an integrated relationship between locomotion and feeding in suction-feeding fishes. However, the influence of specialization on this relationship is unclear. We used divergent populations of Trinidadian guppies (Poecilia reticulata) to test whether integration during suction is generalizable to a non-suction specialist and whether intraspecific specialization of component systems affects their integration. Guppies from replicate high- and low-predation streams were recorded capturing wild-type zooplankton using suction. Alternative general linear models supported a positive correlation between swim speed and mouth size in derived low-predation populations, suggesting that the relationship can be extended in some cases. High-predation populations lack this integration, which may be the result of direct selection or constraints imposed by selection on locomotion. As guppies invade new habitats they may be evolving a new, integrated performance phenotype from a non-integrated ancestor.

Angling-induced injuries have a negative impact on suction feeding performance and hydrodynamics in marine shiner perch, Cymatogaster aggregata

Fishing is a popular and lucrative sport around the world and, in some cases, may contribute to declining fish stocks. To mediate this problem and maintain fish biomass in aquatic ecosystems, catch-and-release fishing, whereby a fish is caught and immediately released, has been implemented in many countries. It is unclear whether the injuries to the mouth that are caused by the hook have an impact on feeding performance of fishes. Using high-speed video and computational fluid dynamics (CFD), we asked whether injuries around the mouth caused by fishing hooks have a negative impact on suction feeding performance (measured as maximum prey velocity) of the commonly angled marine shiner perch (Cymatogaster aggregata). We hypothesized that fish with mouth injuries would exhibit decreased feeding performance compared with controls. Ten shiner perch were caught using scientific angling and 10 were caught using a seine net. Feeding events were then recorded at 500 frames per second using a high-speed camera. Compared with the control group, maximum prey velocity was significantly lower in the injured group (P<0.01). Maximum gape, time to peak gape, maximum jaw protrusion and predator-prey distance were comparable between the control and injured groups, leading us to conclude that the injury-induced hole in the buccal cavity wall reduced the pressure gradient during mouth expansion, thereby reducing the velocity of water entering the fish's mouth. This was confirmed with our CFD modelling. Fishing injuries in nature are likely to depress feeding performance of fish after they have been released, although it is currently unclear whether this has a significant impact on survival.

The ontogenetic scaling of form and function in the spotted ratfish, Hydrolagus colliei (Chondrichthyes: Chimaeriformes): Fins, muscles, and locomotion

The alteration of form and function through the life of a fish can have profound impacts on the ability to move through water. Although several studies have examined morphology and function in relation to body size, there is a paucity of data for chondrichthyans, an ancient group of fishes. Ratfishes are interesting in that they utilize flapping pectoral fins to drive movement, and they diverged from elasmobranchs early in the gnathostome phylogeny. Using the spotted ratfish, Hydrolagus colliei, we quantified the scaling of traits relevant for locomotion, including median and paired fin external anatomy, the musculature of the pectoral and pelvic fins, and the kinematics of the pectoral fins. Whereas pelvic fins scaled with either positive allometry (fin span and area) or isometry (fin chord length at the base of the fin), pectoral fin measurements either scaled with negative allometry (fin span and aspect ratio) or isometry (fin area and chord length). Correspondingly, all pelvic fin muscles exhibited positive allometry, whereas pectoral muscles exhibited a mix of isometric and positively allometric growth. Caudal fin area and body frontal area both scaled with positive allometry, whereas dorsal fin area and span scale with isometry. Pectoral fin amplitude during swimming exhibited isometry, and fin beat frequency decreased with body size. Our results highlight the complex changes in form and function throughout ontogeny. Finally, we highlight that hierarchical differentiation in morphology can occur during growth, potentially leading to complex changes in performance of a functional system.

Evolution of skeletal and muscular morphology within the functionally integrated lower jaw adduction system of sculpins and relatives (Cottoidei)

Vertebrate lever mechanics are defined by the morphology of skeletal elements and the properties of their muscular actuators; these metrics characterize functional diversity. The components of lever systems work in coordination ("functional integration") and may show strong covariation across evolutionary history ("evolutionary integration"), both of which have been hypothesized to constrain phenotypic diversity. We quantified evolutionary integration in a functionally integrated system - the lower jaw of sculpins and relatives (Actinopterygii: Cottoidei). Sculpins primarily rely on suction feeding for prey capture, but there is considerable variation in evasiveness of their prey, resulting in variation in anatomy of the lower jaw-closing mechanism. We used functionally-relevant linear measurements to characterize skeletal and muscular components of this system among 25 cottoid species and two outgroup Hexagrammoidei (greenling) species. We quantified evolutionary covariation and correlation of jaw-closing mechanical advantage (i.e., skeletal leverage) and muscle architecture (i.e., gearing) by correlating phylogenetically independent contrasts and fitting phylogenetically corrected generalized least squares models. We found no evidence of evolutionary covariation in muscle architecture and skeletal leverage. While we found a positive evolutionary correlation between out-lever length and adductor muscle fiber length, there was no significant evolutionary correlation between in-lever length and adductor muscle fiber length. We also found a positive evolutionary correlation between in- and out-lever lengths. These results suggest that skeletal morphology and muscle morphology contribute independently to biomechanical diversity among closely related species, indicating the importance of considering both skeletal and muscular variation in studies of ecomorphological diversification.

Genetic analyses in Lake Malawi cichlids identify new roles for Fgf signaling in scale shape variation

Elasmoid scales are the most common epithelial appendage among vertebrates, however an understanding of the genetic mechanisms that underlie variation in scale shape is lacking. Using an F2 mapping cross between morphologically distinct cichlid species, we identified >40 QTL for scale shape at different body positions. We show that while certain regions of the genome regulate variation in multiple scales, most are specific to scales at distinct positions. This suggests a degree of regional modularity in scale development. We also identified a single QTL for variation in scale shape disparity across the body. Finally, we screened a QTL hotspot for candidate loci, and identified the Fgf receptor fgfr1b as a prime target. Quantitative rtPCR and small molecule manipulation support a role for Fgf signaling in shaping cichlid scales. While Fgfs have previously been implicated in scale loss, these data reveal new roles for the pathway in scale shape variation.

Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation

Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator-prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process.

Individuals of the common Namib Day Gecko vary in how adaptive simplification alters sprint biomechanics

Locomotion inextricably links biomechanics to ecology as animals maneuver through mechanically challenging environments. Faster individuals are more likely to escape predators, surviving to produce more offspring. Fast sprint speed evolved several times in lizards, including geckos. However, the underlying mechanisms determining performance await discovery in many clades. Novel morphological structures influence these mechanisms by adding complexity to the government of locomotion. Gecko adhesion coevolves with modified muscles, tendons, and reflexes. We explored how the Namib Day Gecko, Rhoptropus afer, sprints on ecologically relevant substrates. Locomotion requires that many moving parts of the animal work together; we found knee and ankle extension are the principal drivers of speed on a level surface while contributions to sprinting uphill are more evenly distributed among motions of the femur, knee, and ankle. Although geckos are thought to propel themselves with specialized, proximally located muscles that retract and rotate the femur, we show with path analysis that locomotion is altered in this secondarily terrestrial gecko. We present evidence of intraspecific variation in the use of adhesive toe pads and suggest that the subdigital adhesive toe pad may increase sprint speed in this species. We argue kinematics coevolve with the secondarily terrestrial lifestyle of this species.

Comparative Analyses of Phenotypic Trait Covariation within and among Populations

Many morphological, behavioral, physiological, and life-history traits covary across the biological scales of individuals, populations, and species. However, the processes that cause traits to covary also change over these scales, challenging our ability to use patterns of trait covariance to infer process. Trait relationships are also widely assumed to have generic functional relationships with similar evolutionary potentials, and even though many different trait relationships are now identified, there is little appreciation that these may influence trait covariation and evolution in unique ways. We use a trait-performance-fitness framework to classify and organize trait relationships into three general classes, address which ones more likely generate trait covariation among individuals in a population, and review how selection shapes phenotypic covariation. We generate predictions about how trait covariance changes within and among populations as a result of trait relationships and in response to selection and consider how these can be tested with comparative data. Careful comparisons of covariation patterns can narrow the set of hypothesized processes that cause trait covariation when the form of the trait relationship and how it responds to selection yield clear predictions about patterns of trait covariation. We discuss the opportunities and limitations of comparative approaches to evaluate hypotheses about the evolutionary causes and consequences of trait covariation and highlight the importance of evaluating patterns within populations replicated in the same and in different selective environments. Explicit hypotheses about trait relationships are key to generating effective predictions about phenotype and its evolution using covariance data.

Effect of craniofacial genotype on the relationship between morphology and feeding performance in cichlid fishes

The relationship between morphology and performance is complex, but important for understanding the adaptive nature of morphological variation. Recent studies have sought to better understand this system by illuminating the interconnectedness of different functional systems; however, the role of genetics is often overlooked. In this study, we attempt to gain insights into this relationship by examining the effect of genotypic variation at putative craniofacial loci on the relationship between morphology and feeding performance in cichlids. We studied two morphologically disparate species, as well as a morphologically intermediate hybrid population. We assessed feeding performance, jaw protrusion, and general facial morphology for each fish. We also genotyped hybrid animals at six previously identified craniofacial loci. Cichlid species were found to differ in facial geometry, kinematic morphology, and performance. Significant correlations were also noted between these variables; however, the explanatory power of facial geometry in predicting performance was relatively poor. Notably, when hybrids were grouped by genotype, the relationship between shape and performance improved. This relationship was especially robust in animals with the specialist allele at sox9b, a well-characterized regulator of craniofacial development. These data suggest a novel role for genotype in influencing complex relationships between form and function.

Morphological modularity in the vertebral column of Felidae (Mammalia, Carnivora)

BACKGROUND

Previous studies have demonstrated that the clear morphological differences among vertebrae across the presacral column are accompanied by heterogeneous functional signals in vertebral shape. Further, several lines of evidence suggest that the mammalian axial skeleton is a highly modular structure. These include its composition of serial units, a trade-off between high shape variance and strong conservation of vertebral count, and direct association of regions with anterior expression sites of Hox genes. Here we investigate the modular organisation of the presacral vertebral column of modern cats (Felidae, Carnivora, Mammalia) with pairwise comparisons of vertebral shape covariation (i.e. integration) and evaluate our results against hypotheses of developmental and functional modularity. We used three-dimensional geometric morphometrics to quantify vertebral shape and then assessed integration between pairs of vertebrae with phylogenetic two-block partial least square analysis (PLS).

RESULTS

Six modules were identified in the pairwise analyses (vertebrae included are designated as 'C' for cervical, 'T' for thoracic, and 'L' for lumbar): an anterior module (C1 to T1); a transitional module situated between the last cervicals and first thoracics (C6 to T2); an anterior to middle thoracic set (T4 to T8); an anticlinal module (T10 and T11); a posterior set composed of the last two thoracics and lumbars (T12 to L7); and a module showing covariation between the cervicals and the posterior set (T12 to L7). These modules reflect shared developmental pathways, ossification timing, and observed ecological shape diversification in living species of felids.

CONCLUSIONS

We show here that patterns of shape integration reflect modular organisation of the vertebral column of felids. Whereas this pattern corresponds with hypotheses of developmental and functional regionalisation in the axial skeleton, it does not simply reflect major vertebral regions. This modularity may also have permitted vertebral partitions, specifically in the posterior vertebral column, to be more responsive to selection and achieve higher morphological disparity than other vertebral regions.

Asymmetry and integration of cellular morphology in Micrasterias compereana

Background

Unicellular green algae of the genus Micrasterias (Desmidiales) have complex cells with multiple lobes and indentations, and therefore, they are considered model organisms for research on plant cell morphogenesis and variation. Micrasterias cells have a typical biradial symmetric arrangement and multiple terminal lobules. They are composed of two semicells that can be further differentiated into three structural components: the polar lobe and two lateral lobes. Experimental studies suggested that these cellular parts have specific evolutionary patterns and develop independently. In this study, different geometric morphometric methods were used to address whether the semicells of Micrasterias compereana are truly not integrated with regard to the covariation of their shape data. In addition, morphological integration within the semicells was studied to ascertain whether individual lobes constitute distinct units that may be considered as separate modules. In parallel, I sought to determine whether the main components of morphological asymmetry could highlight underlying cytomorphogenetic processes that could indicate preferred directions of variation, canalizing evolutionary changes in cellular morphology.

Results

Differentiation between opposite semicells constituted the most prominent subset of cellular asymmetry. The second important asymmetric pattern, recovered by the Procrustes ANOVA models, described differentiation between the adjacent lobules within the quadrants. Other asymmetric components proved to be relatively unimportant. Opposite semicells were shown to be completely independent of each other on the basis of the partial least squares analysis analyses. In addition, polar lobes were weakly integrated with adjacent lateral lobes. Conversely, higher covariance levels between the two lateral lobes of the same semicell indicated mutual interconnection and significant integration between these parts.

Conclusions

Micrasterias cells are composed of several successively disintegrated parts. These integration patterns concurred with presumed scenarios of morphological evolution within the lineage. In addition, asymmetric differentiation in the shape of the lobules involves two major patterns: asymmetry across the isthmus axis and among the adjacent lobules. Notably, asymmetry among the adjacent lobules may be related to evolutionary differentiation among species, but it may also point out developmental instability related to environmental factors.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0855-1) contains supplementary material, which is available to authorized users.

Integration of swimming kinematics and ram suspension feeding in a model American paddlefish, Polyodon spathula

Ram suspension-feeding fishes swim with an open mouth to force water through the oral cavity and extract prey items that are too small to be pursued individually. Recent research has indicated that, rather than using a dead-end mechanical sieve, American paddlefish (Polyodon spathula Walbaum) employ vortical cross-step filtration. In this filtration mechanism, vortical flow that is generated posterior to the branchial arches organizes crossflow filtration processes into a spatial structure across the gill rakers. Despite the known impact of locomotor kinematics on fluid flow around the bodies of swimming fish, the effects of locomotor kinematics on filtration mechanisms in ram suspension feeders are unknown. Potential temporal organization of filtration mechanisms in ram suspension-feeding fish has not been studied previously. We investigated the effects of locomotor kinematics associated with undulatory swimming on intra-oral flow patterns and food particle transport. A mechanized model of the oral cavity was used to simulate the swimming kinematics of suspension-feeding paddlefish. We recorded fluctuations of flow speed and pressure within the model, which occurred at a frequency that corresponded with the frequency of the model's strides. Using the mechanized model in a flow tank seeded with Artemia cysts, we also showed that swimming kinematics aided the transport of this simulated food to the posterior margins of the gill slots, although the time scale of this transport is expected to vary with prey parameters such as size and concentration. Dye stream experiments revealed that, while stable vortical flow formed due to flow separation downstream of backward-facing steps in control trials, vortical flow structures in mechanized trials repeatedly formed and shed. These findings suggest strong integration between locomotor and feeding systems in ram suspension-feeding fishes.

Swimming performance of Bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems

Many bacterial species use flagella for self-propulsion in aqueous media. In the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. Therefore, the motility of soil bacteria might have special requirements. An important soil bacterial genus is Bradyrhizobium, with species that possess one flagellar system and others with two different flagellar systems. Among the latter is B. diazoefficiens, which may express its subpolar and lateral flagella simultaneously in liquid medium, although its swimming behaviour was not described yet. These two flagellar systems were observed here as functionally integrated in a swimming performance that emerged as an epistatic interaction between those appendages. In addition, each flagellum seemed engaged in a particular task that might be required for swimming oriented toward chemoattractants near the soil inner surfaces at viscosities that may occur after the loss of soil gravitational water. Because the possession of two flagellar systems is not general in Bradyrhizobium or in related genera that coexist in the same environment, there may be an adaptive tradeoff between energetic costs and ecological benefits among these different species.

Patterns of variation in feeding strike kinematics of juvenile ghost praying mantis (Phyllocrania paradoxa): are components of the strike stereotypic?

Functional systems, such as feeding mechanics, often involve the evolution of several components of the musculoskeletal system that are moved in coordination to capture prey. Because these systems often involve the quick movement of several structures, some feeding systems have been hypothesized to be stereotypic. While the motor activity patterns are often stereotyped, the subsequent kinematics can be variable, many times in response to variation in prey stimulus (e.g., prey position). Patterns of feeding kinematics have been well studied among vertebrates, with less attention on invertebrate systems. The goal of this study was to examine the amount of stereotypy in the feeding strike kinematics of praying mantises. We filmed 8 juvenile ghost praying mantises (Phyllocrania paradox) at 1000 Hz, across several days within instar 7. We digitized several points that represent the movement of the coxa, trochanter-femur and tibia of the raptorial foreleg to obtain a set of kinematics including angles and angular velocities of the joint, as well as body lunge. Using the coefficient of variation, we found less stereotypy in the approach stage of the strike compared to the sweep. Using Bonferroni corrected Pearson's correlations of kinematics with prey position we found few traits related to prey position with the exception of some kinematics of the coxa joint and the amount of lunge used during the strike. Our results suggest that several components of the praying mantis strike are stereotypic, while others exhibit flexibility to ensure successful capture of the prey.

Body ram, not suction, is the primary axis of suction feeding diversity in spiny-rayed fishes

Suction feeding fishes exhibit diverse prey capture strategies that vary in their relative use of suction and predator approach (ram), which is often referred to as the ram-suction continuum. Previous research has found that ram varies more than suction distances among species, such that ram accounts for most differences in prey capture behaviors. To determine whether these findings hold at broad evolutionary scales, we collected high-speed videos of 40 species of spiny-rayed fishes (Acanthomorpha) feeding on live prey. For each strike, we calculated the contributions of suction, body ram (swimming), and jaw ram (mouth movement relative to the body) to closing the distance between predator and prey. We confirm that the contribution of suction distance is limited even in this phylogenetically and ecologically broad sample of species, with the extreme suction area of prey capture space conspicuously unoccupied. Instead of a continuum from suction to ram, we find that variation in body ram is the major factor underlying the diversity of prey-capture strategies among suction-feeding fishes. Independent measurement of the contribution of jaw ram revealed that it is an important component of diversity among spiny-rayed fishes, with a number of ecomorphologies relying heavily on jaw ram, including pivot feeding in syngnathiforms, extreme jaw protruders, and benthic sit-and-wait ambush predators. A combination of morphological and behavioral innovations have allowed fish to invade the extreme jaw ram area of prey capture space. We caution that while two-species comparisons may support a ram-suction trade-off, these patterns do not speak to broader patterns across spiny-rayed fishes