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Synopsis 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. 

Abstract ObjectivesIncreased use of three‐dimensional (3D) imaging data has led to a need for methods capable of capturing rich shape descriptions. Semi‐landmarks have been demonstrated to increase shape information but placement in 3D can be time consuming, computationally expensive, or may introduce artifacts. This study implements and compares three strategies to more densely sample a 3D image surface. Materials and methodsThree dense sampling strategies: patch, patch‐thin‐plate spline (TPS), and pseudo‐landmark sampling, are implemented to analyze skulls from three species of great apes. To evaluate the shape information added by each strategy, the semi or pseudo‐landmarks are used to estimate a transform between an individual and the population average template. The average mean root squared error between the transformed mesh and the template is used to quantify the success of the transform. ResultsThe landmark sets generated by each method result in estimates of the template that on average were comparable or exceeded the accuracy of using manual landmarks alone. The patch method demonstrates the most sensitivity to noise and missing data, resulting in outliers with large deviations in the mean shape estimates. Patch‐TPS and pseudo‐landmarking provide more robust performance in the presence of noise and variability in the dataset. ConclusionsEach landmarking strategy was capable of producing shape estimations of the population average templates that were generally comparable to manual landmarks alone while greatly increasing the density of the shape information. This study highlights the potential trade‐offs between correspondence of the semi‐landmark points, consistent point spacing, sample coverage, repeatability, and computational time. 

Abstract 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. 

Synopsis 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. 

Abstract Large‐scale digitization projects such as#ScanAllFishesandoVertare generating high‐resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyse them.Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, and acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research.We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python‐scriptable open‐source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open‐access 3D models or import users own 3D volumes, to annotate 3D curve and patch‐based landmarks, generate landmark templates, conduct geometric morphometric analyses of 3D organismal form using both landmark‐driven and landmark‐free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology.Our goal is to establish a community of organismal biologists centred around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort. 

Abstract Many vertebrates are armored over all or part of their body. The armor may serve several functional roles including defense, offense, visual display, and signal of experience/capability. Different roles imply different tradeoffs; for example, defensive armor usually trades resistance to attack for maneuverability. The poachers (Agonidae), 47 species of scorpaeniform fishes, are a useful system for understanding the evolution and function of armor due to their variety and extent of armoring. Using publically available CT‐scan data from 27 species in 16 of 21 genera of poachers we compared the armor to axial skeletal in the mid body region. The ratio of average armor density to average skeleton density ranged from 0.77 to 1.17. From a defensive point of view, the total investment in mineralization (volume * average density) is more interesting. There was 10 times the material invested in the armor as in the endoskeleton in some small, smooth plated species, likeAspidophoroides olrikii. At the low end, some visually arresting species likePercis japonica, had ratios as low as 2:1. We categorized the extent and type (impact vs. abrasion) in 34Agonopsis vulsaacross all 35+ plates in the eight rows along the body. The ventral rows show abrasive damage along the entire length of the fish that gets worse with age. Impact damage to head and tail plates gets more severe and occurs at higher rates with age. The observed damage rates and the large investment in mineralization of the armor suggest that it is not just for show, but is a functional defensive structure. We cannot say what the armor is defense against, but the abrasive damage on the ventrum implies their benthic lifestyle involves rubbing on the substrate. The impact damage could result from predatory attacks or from intraspecific combat. 

Abstract Durophagous predators consume hard‐shelled prey such as bivalves, gastropods, and large crustaceans, typically by crushing the mineralized exoskeleton. This is costly from the point of view of the bite forces involved, handling times, and the stresses inflicted on the predator's skeleton. It is not uncommon for durophagous taxa to display an ontogenetic shift from softer to harder prey items, implying that it is relatively difficult for smaller animals to consume shelled prey. Batoid fishes (rays, skates, sawfishes, and guitarfishes) have independently evolved durophagy multiple times, despite the challenges associated with crushing prey harder than their own cartilaginous skeleton.Potamotrygon leopoldiis a durophagous freshwater ray endemic to the Xingu River in Brazil, with a jaw morphology superficially similar to its distant durophagous marine relatives, eagle rays (e.g.,Aetomylaeus, Aetobatus). We used second moment of area as a proxy for the ability to resist bending and analyzed the arrangement of the mineralized skeleton of the jaw ofP. leopoldiover ontogeny using data from computed tomography (CT) scans. The jaws ofP. leopoldido not resist bending nearly as well as other durophagous elasmobranchs, and the jaws are stiffest nearest the joints rather than beneath the dentition. While second moment has similar material distribution over ontogeny, mineralization of the jaws under the teeth increases with age. Neonate rays have low jaw stiffness and poor mineralization, suggesting thatP. leopoldimay not feed on hard‐shelled prey early in life. These differences in the shape, stiffness and mineralization of the jaws ofP. leopoldicompared to its durophagous relatives show there are several solutions to the problem of crushing shelled prey with a compliant skeleton. 

ABSTRACT 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.