Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network.

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

It Pays to Be Bumpy: Drag Reducing Armor in the Pacific Spiny Lumpsucker, Eumicrotremus orbis.

Armor is a multipurpose set of structures that has evolved independently at least 30 times in fishes. In addition to providing protection, armor can manipulate flow, increase camouflage, and be sexually dimorphic. There are potential tradeoffs in armor function: increased impact resistance may come at the cost of maneuvering ability; and ornate armor may offer visual or protective advantages, but could incur excess drag. Pacific spiny lumpsuckers (Eumicrotremus orbis) are covered in rows of odontic, cone-shaped armor whorls, protecting the fish from wave driven impacts and the threat of predation. We are interested in measuring the effects of lumpsucker armor on the hydrodynamic forces on the fish. Bigger lumpsuckers have larger and more complex armor, which may incur a greater hydrodynamic cost. In addition to their protective armor, lumpsuckers have evolved a ventral adhesive disc, allowing them to remain stationary in their environment. We hypothesize a tradeoff between the armor and adhesion: little fish prioritize suction, while big fish prioritize protection. Using micro-CT, we compared armor volume to disc area over lumpsucker development and built 3D models to measure changes in drag over ontogeny. We found that drag and drag coefficients decrease with greater armor coverage and vary consistently with orientation. Adhesive disc area is isometric but safety factor increases with size, allowing larger fish to remain attached in higher flows than smaller fish.

Formation of a fringe: A look inside baleen morphology using a multimodal visual approach.

Filter-feeding has been present for hundreds of millions of years, independently evolving in aquatic vertebrates' numerous times. Mysticete whales are a group of gigantic, marine filter-feeders that are defined by their fringed baleen and are divided into two groups: balaenids and rorquals. Recent studies have shown that balaenids likely feed using a self-cleaning, cross-flow filtration mechanism where food particles are collected and then swept to the esophagus for swallowing. However, it is unclear how filtering is achieved in the rorquals (Balaenopteridae). Lunging rorqual whales engulf enormous masses of both prey and water; the prey is then separated from the water through baleen plates lining the length of their upper jaw and positioned perpendicular to flow. Rorqual baleen is composed of both major (larger) and minor (smaller) keratin plates containing embedded fringe that extends into the whale's mouth, forming a filtering fringe. We used a multimodal approach, including microcomputed tomography (µCT) and scanning electron microscopy (SEM), to visualize and describe the variability in baleen anatomy across five species of rorqual whales, spanning two orders of magnitude in body length. For most morphological measurements, larger whales exhibited hypoallometry relative to body length. µCT and SEM revealed that the major and minor plates break away from the mineralized fringes at variable distances from the gums. We proposed a model for estimating the effective pore size to determine whether flow scales with body length or prey size across species. We found that pore size is likely not a proxy for prey size but instead, may reflect changes in resistance through the filter that affect fluid flow.

Lip service: Histological phenotypes correlate with diet and feeding ecology in herbivorous pacus.

Complex prey processing requires the repositioning of food between the teeth, as modulated by a soft tissue appendage like a tongue or lips. In this study, we trace the evolution of lips and ligaments, which are used during prey capture and prey processing in an herbivorous group of fishes. Pacus (Serrasalmidae) are Neotropical freshwater fishes that feed on leaves, fruits, and seeds. These prey are hard or tough, require high forces to fracture, contain abrasive or caustic elements, or deform considerably before failure. Pacus are gape-limited and do not have the pharyngeal jaws many bony fishes use to dismantle and/or transport prey. Despite their gape limitation, pacus feed on prey larger than their mouths, relying on robust teeth and a hypertrophied lower lip for manipulation and breakdown of food. We used histology to compare the lip morphology across 14 species of pacus and piranhas to better understand this soft tissue. We found that frugivorous pacus have larger, more complex lips which are innervated and folded at their surface, while grazing species have callused, mucus-covered lips. Unlike mammalian lips or tongues, pacu lips lack any intrinsic skeletal or smooth muscle. This implies that pacu lips lack dexterity; however, we found a novel connection to the primordial ligament which suggests that the lips are actuated by the jaw adductors. We propose that pacus combine hydraulic repositioning of prey inside the buccal cavity with direct oral manipulation, the latter using a combination of a morphologically heterodont dentition and compliant lips for reorienting food.

Sticky, stickier and stickiest - a comparison of adhesive performance in clingfish, lumpsuckers and snailfish.

The coastal waters of the North Pacific are home to the northern clingfish (Gobiesox maeandricus), Pacific spiny lumpsucker (Eumicrotremus orbis) and marbled snailfish (Liparis dennyi) - three fishes that have evolved ventral adhesive discs. Clingfish adhesive performance has been studied extensively, but relatively little is known about the performance of other sticky fishes. Here, we compared the peak adhesive forces and work to detachment of clingfish, lumpsuckers and snailfish on surfaces of varying roughness and over ontogeny. We also investigated the morphology of their adhesive discs through micro-computed tomography scanning and scanning electron microscopy. We found evidence that adhesive performance is tied to the intensity and variability of flow regimes in the fishes' habitats. The northern clingfish generates the highest adhesive forces and lives in the rocky intertidal zone where it must resist exposure to crashing waves. Lumpsuckers and snailfish both generate only a fraction of the clingfish's adhesive force, but live more subtidal where currents are slower and less variable. However, lumpsuckers generate more adhesive force relative to their body weight than snailfish, which we attribute to their higher-drag body shape and frequent bouts into the intertidal zone. Even so, the performance and morphology data suggest that snailfish adhesive discs are stiffer and built more efficiently than lumpsucker discs. Future studies should focus on sampling additional diversity and designing more ecologically relevant experiments when investigating differences in adhesive performance.

Bone Density Variation in Rattails (Macrouridae, Gadiformes): Buoyancy, Depth, Body Size, and Feeding.

Extreme abiotic factors in deep-sea environments, such as near-freezing temperatures, low light, and high hydrostatic pressure, drive the evolution of adaptations that allow organisms to survive under these conditions. Pelagic and benthopelagic fishes that have invaded the deep sea face physiological challenges from increased compression of gasses at depth, which limits the use of gas cavities as a buoyancy aid. One adaptation observed in deep-sea fishes to increase buoyancy is a decrease of high-density tissues. In this study, we analyze mineralization of high-density skeletal tissue in rattails (family Macrouridae), a group of widespread benthopelagic fishes that occur from surface waters to greater than 7000 m depth. We test the hypothesis that rattail species decrease bone density with increasing habitat depth as an adaptation to maintaining buoyancy while living under high hydrostatic pressures. We performed micro-computed tomography (micro-CT) scans on 15 species and 20 specimens of rattails and included two standards of known hydroxyapatite concentration (phantoms) to approximate voxel brightness to bone density. Bone density was compared across four bones (eleventh vertebra, lower jaw, pelvic girdle, and first dorsal-fin pterygiophore). On average, the lower jaw was significantly denser than the other bones. We found no correlation between bone density and depth or between bone density and phylogenetic relationships. Instead, we observed that bone density increases with increasing specimen length within and between species. This study adds to the growing body of work that suggests bone density can increase with growth in fishes, and that bone density does not vary in a straightforward way with depth.

Biomechanics of the jaws of spotted ratfish.

Elasmobranch fishes (sharks, skates and rays) consume prey of a variety of sizes and properties, and the feeding mechanism typically reflects diet. Spotted ratfish, Hydrolagus colliei (Holocephali, sister group of elasmobranchs), consume both hard and soft prey; however, the morphology of the jaws does not reflect the characteristics typical of durophagous elasmobranchs. This study investigated the mechanical properties and morphological characteristics of the jaws of spotted ratfish over ontogeny, including strain, stiffness and second moment of area, to evaluate the biomechanical function of the feeding structures. Compressive stiffness of the jaws (E=13.51-21.48 MPa) is similar to that of silicone rubber, a very flexible material. In Holocephali, the upper jaw is fused to the cranium; we show that this fusion reduces deformation experienced by the upper jaw during feeding. The lower jaw resists bending primarily in the posterior half of the jaw, which occludes with the region of the upper jaw that is wider and flatter, thus potentially providing an ideal location for the lower jaw to crush or crack prey. The mechanical properties and morphology of the feeding apparatus of spotted ratfish suggest that while the low compressive stiffness is a material limit of the jaw cartilage, spotted ratfish, and perhaps all holocephalans, evolved structural solutions (i.e. fused upper jaw, shape variation along lower jaw) to meet the demands of a durophagous diet.

Interspecific differences in the flow regimes and drag of North Pacific skate egg cases.

Skates are a diverse group of dorso-ventrally compressed cartilaginous fishes found primarily in high-latitude seas. These slow-growing oviparous fishes deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1-4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or "break-away velocity," each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programming software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.

Dual spring force couples yield multifunctionality and ultrafast, precision rotation in tiny biomechanical systems.

Small organisms use propulsive springs rather than muscles to repeatedly actuate high acceleration movements, even when constrained to tiny displacements and limited by inertial forces. Through integration of a large kinematic dataset, measurements of elastic recoil, energetic math modeling and dynamic math modeling, we tested how trap-jaw ants (Odontomachus brunneus) utilize multiple elastic structures to develop ultrafast and precise mandible rotations at small scales. We found that O. brunneus develops torque on each mandible using an intriguing configuration of two springs: their elastic head capsule recoils to push and the recoiling muscle-apodeme unit tugs on each mandible. Mandibles achieved precise, planar, circular trajectories up to 49,100 rad s-1 (470,000 rpm) when powered by spring propulsion. Once spring propulsion ended, the mandibles moved with unconstrained and oscillatory rotation. We term this mechanism a 'dual spring force couple', meaning that two springs deliver energy at two locations to develop torque. Dynamic modeling revealed that dual spring force couples reduce the need for joint constraints and thereby reduce dissipative joint losses, which is essential to the repeated use of ultrafast, small systems. Dual spring force couples enable multifunctionality: trap-jaw ants use the same mechanical system to produce ultrafast, planar strikes driven by propulsive springs and for generating slow, multi-degrees of freedom mandible manipulations using muscles, rather than springs, to directly actuate the movement. Dual spring force couples are found in other systems and are likely widespread in biology. These principles can be incorporated into microrobotics to improve multifunctionality, precision and longevity of ultrafast systems.

The effects of soft and rough substrates on suction-based adhesion.

The northern clingfish (Gobiesox maeandricus) has a suction-based adhesive disc that can stick to incredibly rough surfaces, a challenge for stiff commercial suction cups. Both clingfish discs and bioinspired suction cups have stiff cores but flexible edges that can deform to overcome surface irregularities. Compliant surfaces are common in nature and technical settings, but performance data for fish and commercial cups are gathered from stiff surfaces. We quantified the interaction between substrate compliance, surface roughness and suction performance for the northern clingfish, commercial suction cups and three biomimetic suction cups with disc rims of varying compliance. We found that all cups stick better on stiffer substrates and worse on more compliant ones, as indicated by peak stress values. On compliant substrates, surface roughness had little effect on adhesion, even for commercial cups that normally fail on hard, rough surfaces. We propose that suction performance on compliant substrates can be explained in part by effective elastic modulus, the combined elastic modulus from a cup-substrate interaction. Of all the tested cups, the biomimetic cups performed the best on compliant surfaces, highlighting their potential to be used in medical and marine geotechnical fields. Lastly, we discuss the overmolding technique used to generate the bioinspired cups and how it is an important tool for studying biology.

SegmentGeometry: A Tool for Measuring Second Moment of Area in 3D Slicer.

Second moment of area is a measure of how well the cross-section of a beam will resist bending because of its shape. Many have used second moment of area to investigate the mechanical adaptations of biological structures from stingray jaws to animal limb bones. In this context it is important to acknowledge the assumptions of beam theory, in which second moment of area plays a key role, if reasonable results are desired. For example, to minimize shear the structure should be at least 10 times longer than it is wide and deflection should be minimal. Analyzing the internal geometry of biological structures has never been easier or more accessible given the wide, and growing availability of micro-CT scans. Here, we offer a guide on the care that needs to be taken when interpreting second moment of area, and present open-access, open-source software that can process hundreds if not thousands of structures in a short time frame. SegmentGeometry, an extension for the open-source imaging platform 3D Slicer, iterates slice-by-slice through 3D structures to calculate second moment of area and other cross-sectional properties. We analyzed 2 case studies to demonstrate the power of this tool and to highlight interpretations that can be gleaned from second moment of area. Second moment of area is just one part of the Euler-Bernoulli beam theory and considering the full equation would greatly increase the number and diversity of questions that can be answered.

Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges.

Actin is a fundamental member of an ancient superfamily of structural intracellular proteins and plays a crucial role in cytoskeleton dynamics, ciliogenesis, phagocytosis, and force generation in both prokaryotes and eukaryotes. It is shown that actin has another function in metazoans: patterning biosilica deposition, a role that has spanned over 500 million years. Species of glass sponges (Hexactinellida) and demosponges (Demospongiae), representatives of the first metazoans, with a broad diversity of skeletal structures with hierarchical architecture unchanged since the late Precambrian, are studied. By etching their skeletons, organic templates dominated by individual F-actin filaments, including branched fibers and the longest, thickest actin fiber bundles ever reported, are isolated. It is proposed that these actin-rich filaments are not the primary site of biosilicification, but this highly sophisticated and multi-scale form of biomineralization in metazoans is ptterned.

"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19.

The COVID-19 pandemic shut down undergraduate research programs across the United States. A group of 23 colleges, universities, and research institutes hosted remote undergraduate research programs in the life sciences during Summer 2020. Given the unprecedented offering of remote programs, we carried out a study to describe and evaluate them. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from students' perspectives. Strengths included the quality of mentorship, opportunities for learning and professional development, and a feeling of connection with a larger community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote Research Experiences for Undergraduates (REUs) that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

Examining Cultural Structures and Functions in Biology.

Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.

Pacific Spiny Lumpsucker armor-Development, damage, and defense in the intertidal.

Predation, combat, and the slings and arrows of an abrasive and high impact environment, represent just some of the biotic and abiotic stressors that fishes are armored against. The Pacific Spiny Lumpsucker (Eumicrotremus orbis) found in the subtidal of the Northern Pacific Ocean is a rotund fish covered with epidermal, cone-shaped, enamel odontodes. The Lumpsucker is a poor swimmer in the wave swept rocky intertidal, and this armor may be a lightweight solution to the problem of collisions with abiotic obstacles. We use micro-CT and scanning electron microscopy to reveal the morphology and ontogeny of the armor, and to quantify the amount of mineralization relative to the endoskeleton. The non-overlapping odontodes are organized into eight rows-six rows on the body, one row surrounding the eye, and one row underneath the chin. Odontodes start as a single, hooked cone; and they grow by the addition of cusps that accrete into a spiral. The mineral investment in armor compared to skeleton increases over ontogeny. Damage to the armor occurs both through passive abrasion and breakage from impact; and there is no evidence of replacement, or repair of damaged odontodes.

Shark spiral intestines may operate as Tesla valves.

Looking to nature for inspiration has led to many diverse technological advances. The spiral valve intestine of sharks has provided the opportunity to observe the efficiency of different valve systems. It is supposed that the spiral intestine present in sharks, skates and rays slows the transit rate of digesta through the gut and provides increased surface area for the absorption of nutrients. In this investigation, we use a novel technique-creating three-dimensional reconstructions from CT scans of spiral intestines-to describe the morphology of the spiral intestine of at least one species from 22 different shark families. We discuss the morphological data in an evolutionary, dietary and functional context. The evolutionary analyses suggest that the columnar morphology is the ancestral form of the spiral intestine. Dietary analyses reveal no correlation between diet type and spiral intestine morphology. Flow rate was slowed significantly more when the two funnel-shaped spiral intestines were subjected to flow in the posterior to anterior direction, indicating their success at producing unidirectional flow, similar to a Tesla valve. These data are available to generate additional three-dimensional morphometrics, create computational models of the intestine, as well as to further explore the function of the gastrointestinal tract of sharks in structural and physiological contexts.

Foretelling the Flex-Vertebral Shape Predicts Behavior and Ecology of Fishes.

We modeled swimming kinematics and body mechanics of several fish species of varying habitat and body shape based on measurements of internal vertebral morphology. SYNOPSIS: One key evolutionary innovation that separates vertebrates from invertebrates is the notochord, a central element that provides the stiffness needed for powerful movements. Later, the notochord was further stiffened by the vertebrae, cartilaginous, and bony elements, surrounding the notochord. The ancestral notochord is retained in modern vertebrates as intervertebral material, but we know little about its mechanical interactions with surrounding vertebrae. In this study, the internal shape of the vertebrae-where this material is found-was quantified in 16 species of fishes with various body shapes, swimming modes, and habitats. We used micro-computed tomography to measure the internal shape. We then created and mechanically tested physical models of intervertebral joints. We also mechanically tested actual vertebrae of five species. Material testing shows that internal morphology of the centrum significantly affects bending and torsional stiffness. Finally, we performed swimming trials to gather kinematic data. Combining these data, we created a model that uses internal vertebral morphology to make predictions about swimming kinematics and mechanics. We used linear discriminant analysis (LDA) to assess the relationship between vertebral shape and our categorical traits. The analysis revealed that internal vertebral morphology is sufficient to predict habitat, body shape, and swimming mode in our fishes. This model can also be used to make predictions about swimming in fishes not easily studied in the laboratory, such as deep sea and extinct species, allowing the development of hypotheses about their natural behavior.

Scale performance and composition in a small Amazonian armored catfish, Corydoras trilineatus.

The cory catfishes (Callichthyidae) are small, South American armored catfishes with a series of dermal scutes that run the length of the fish from posterior to the parieto-supraoccipital down to the caudal peduncle. In this study, we explore the anatomy and functional performance of the armored scutes in the three-striped cory catfish, Corydoras trilineatus. The lateral surface has a dorsal and a ventral row of scutes that interact at the horizontal septum. The scutes have little overlap with sequential posterior scutes (~33% overlap) and a deep ridge in the internal surface that connects to the underlying soft tissue. The internal surface of C. trilineatus scutes is stiffer than the external surface, contrary to the findings in a related species of cory catfish, C. aeneus, which documented a hypermineralized, enamel-like, non-collagenous, hyaloine layer along the external surface of the scute. Clearing and staining of C. trilineatus scutes revealed that the scutes have highly mineralized (~50% mineralization) regions embedded in between areas of low mineralization along the posterior margin. Puncture tests showed that posterior scutes were weaker than both anterior and middle scutes, and scutes attached to the body required 50% more energy to puncture than isolated scutes. Corydoras trilineatus has the strongest armor in areas critical for protecting vital organs and the external armored scute receives synergistic benefits from interactions to the soft underlying tissue, which combine to provide a tough protective armor that still allows for flexible mobility.

Acanthemblemaria aceroi, a new species of tube blenny from the Caribbean coast of South America with notes on Acanthemblemaria johnsoni (Teleostei: Chaenopsidae).

Acanthemblemaria aceroi new species is described from the upwelling region of the Caribbean coasts of Venezuela and Colombia. It differs from its closest relative, Acanthemblemaria rivasi Stephens, 1970, known from Panama and Costa Rica, in the posterior extent of the infraorbitals, details of head spination, and unique COI sequences. The description of Acanthemblemaria johnsonsi Almany Baldwin, 1996, heretofore known only from Tobago, is expanded based on specimens from islands offshore of eastern Venezuela.

The Evolutionary Continuum of Functional Homodonty to Heterodonty in the Dentition of Halichoeres Wrasses.

Vertebrate dentitions are often collapsed into a few discrete categories, obscuring both potentially important functional differences between them and insight into their evolution. The terms homodonty and heterodonty typically conflate tooth morphology with tooth function, and require context-dependent subcategories to take on any specific meaning. Qualifiers like incipient, transient, or phylogenetic homodonty attempt to provide a more rigorous definition but instead highlight the difficulties in categorizing dentitions. To address these issues, we recently proposed a method for quantifying the function of dental batteries based on the estimated stress of each tooth (inferred using surface area) standardized for jaw out-lever (inferred using tooth position). This method reveals a homodonty-heterodonty functional continuum where small and large teeth work together to transmit forces to a prey item. Morphological homodonty or heterodonty refers to morphology, whereas functional homodonty or heterodonty refers to transmission of stress. In this study, we use Halichoeres wrasses to explore how functional continuum can be used in phylogenetic analyses by generating two continuous metrics from the functional homodonty-heterodonty continuum. Here we show that functionally heterodont teeth have evolved at least three times in Halichoeres wrasses. There are more functionally heterodont teeth on upper jaws than on lower jaws, but functionally heterodont teeth on the lower jaws bear significantly more stress. These nuances, which have functional consequences, would be missed by binning entire dentitions into discrete categories. This analysis points out areas worth taking a closer look at from a mechanical and developmental point of view with respect to the distribution and type of heterodonty seen in different jaws and different areas of jaws. These data, on a small group of wrasses, suggest continuous dental variables can be a rich source of insight into the evolution of fish feeding mechanisms across a wider variety of species.