The Natural Historian's Guide to the CT Galaxy: Step-by-Step Instructions for Preparing and Analyzing Computed Tomographic (CT) Data Using Cross-Platform, Open Access Software

BFEX: A Toolbox for Finite Element Analysis With Fossils and Blender

(1) Finite Element Analysis (FEA) has become a common method when studying fossils. As computer systems and tools advance, new software like Fossils is developed to make FE analyses more efficient. (2) However, the preparation of input data for analysis remains time-consuming. In particular, surface mesh cleaning and the selection of groups of nodes for the boundary conditions (muscle forces and prescribed displacements) usually require graphical programs that are either not well adapted to this task or require an expensive license. (3) To address this, we introduce BFEX (Blender Finite Element eXporter), a Blender add-on that simplifies model creation for FEA with Fossils. (4) This approach helps streamline the entire process, making it more user-friendly.

Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes

Colonization of a novel habitat is often followed by phenotypic diversification in the wake of ecological opportunity. However, some habitats should be inherently more constraining than others if the challenges of that environment offer few evolutionary solutions. We examined this push-and-pull on macroevolutionary diversification following habitat transitions in the anglerfishes (Lophiiformes). We constructed a phylogeny with extensive sampling (1,092 loci and ~38% of species), combined with three-dimensional phenotypic data from museum specimens. We used these datasets to examine the tempo and mode of phenotypic diversification. The deep-sea pelagic anglerfishes originated from a benthic ancestor and shortly after experienced rapid lineage diversification rates. This transition incurred shifts towards larger jaws, smaller eyes and a more laterally compressed body plan. Despite these directional trends, this lineage still evolved high phenotypic disparity in body, skull and jaw shapes. In particular, bathypelagic anglerfishes show high variability in body elongation, while benthic anglerfishes are constrained around optimal shapes. Within this radiation, phenotypic evolution was concentrated among recently diverged lineages, notably those that deviated from the archetypical globose body plan. Taken together, these results demonstrate that spectacular evolutionary radiations can unfold even within environments with few ecological resources and demanding physiological challenges.

Phenotypic Convergence Is Stronger and More Frequent in Herbivorous Fishes

Constraints on phenotypic evolution can lead to patterns of convergent evolution, by limiting the "pool" of potential phenotypes in the face of endogenous (functional, developmental) or exogenous (competition, predation) selective pressures. Evaluation of convergence depends on integrating ecological and morphological data within a robust, comparative phylogenetic context. The staggering diversity of teleost fishes offers a multitude of lineages adapted for similar ecological roles and, therefore, offers numerous replicated evolutionary experiments for exploring phenotypic convergence. However, our understanding of fish feeding systems has been primarily shaped by marine species, with the monolithic exception of freshwater cichlids. Here we use piranhas and pacus (Serrasalmidae) to explore the evolution of different feeding ecologies and their morphological proxies in Neotropical freshwater environments. Specifically, we explore whether convergence is more widespread among plant-eating fishes, arising from strong constraints on phenotypic evolution in herbivores. Using osteological micro-computed tomographic imaging (μCT), we describe the major axes of morphological variation in pacus and piranhas, regarding their diet and feeding behaviors. Next, we evaluated whether herbivorous niches are less labile than other dietary guilds and whether herbivorous species' phenotypes evolve at a slower evolutionary rate than other taxa. We then assess how convergent herbivorous taxa are, using three different suites of morphological characters (dental, jaw, and abdominal morphometrics). Ecologically, herbivory is not a dead end, exhibiting similar observed transition rates as those between carnivores and omnivores. However, we documented widespread convergence in herbivores and that herbivores have slower rates of phenotypic evolution than carnivores. Most instances of convergence are found in herbivorous taxa, specifically in frugivores and folivores. Moreover, instances of "complete" convergence, indicated by positive convergence metrics observed in more than one morphometric dataset, were only found in herbivores. Herbivores do appear to evolve under constrained circumstances, but this has not limited their ecological ability.

JA, Martins EP. Evolutionary Links Between Skull Shape and Body Size Suggest Allometric Forces and Selection at Work in a Generalist Group of Lizards

The vertebrate skull is a complex structure, and studies of skull shape have yielded considerable insight into the evolutionary forces shaping specialized phenotypes in organisms as diverse as bats, frogs, and fossorial animals. Here, we used phylogenetic comparative analyses of CT scans of male skulls from 57 species of Sceloporus lizards to explore patterns of skull evolution in a group of generalist taxa. We found that most interspecific variation is in terms of skull elongation such that some species have long, narrow skulls, whereas others exhibit more compact and robust skulls. We also found strong links to overall body size, with evolutionary shifts to larger bodies being associated with more compact skulls and slower evolutionary rates. This is the opposite of the pattern in most mammals in which larger bodied species have longer snouts, and more like the pattern in frogs in which function has played a more important evolutionary role. Also, unlike other vertebrates, the jaw, anterior, and posterior parts of the Sceloporus skull are largely integrated, having evolved independently of each other only to a limited, albeit significant, degree. Our results emphasize the importance of body size in the evolutionary shaping of the skull and suggest that additional studies of behavioral function in a generalist group are warranted.

Freshwater Habitats Promote Rapid Rates of Phenotypic Evolution in Sculpin Fishes (Perciformes: Cottoidea)

AbstractInvasions of freshwater habitats by marine fishes provide exceptional cases of habitat-driven biological diversification. Freshwater habitats make up less than 1% of aquatic habitats but contain ∼50% of fish species. However, while the dominant group of freshwater fishes (Otophysi) is older than that of most marine fishes (Percomorphaceae), it is less morphologically diverse. Classically, scientists have invoked differences in the tempo and/or mode of evolution to explain such cases of unequal morphological diversification. We tested for evidence of these phenomena in the superfamily Cottoidea (sculpins), which contains substantial radiations of marine and freshwater fishes. We find that the morphology of freshwater sculpins evolves faster but under higher constraint than that of marine sculpins, causing widespread convergence in freshwater sculpins and more morphological disparity in marine sculpins. The endemic freshwater sculpins of Lake Baikal, Siberia, are exceptions that demonstrate elevated novelty akin to that of marine sculpins. Several tantalizing factors may explain these findings, such as differences in habitat stability and/or habitat connectivity between marine and freshwater systems.

Comparative osteology of the skull of cowbirds (Icteridae: Molothrus)

Detailed osteological descriptions of the craniomandibular complex of passerine birds are lacking for most species, limiting our understanding of their diversity and evolution. Cowbirds (genus Molothrus) are a small but widespread group of New World nine-primaried songbirds, well-known for their unique brooding parasitic behavior. However, detailed osteological data for cowbirds and other Icteridae are currently scarce and several features of their skulls remain undescribed or poorly known. To address this issue, a detailed comparative osteology of cowbird skulls is presented here for the first time based on data from x-ray microcomputed tomography, dry skeletal data, and multivariate analyses of linear morphometric data. Cowbird skulls offer some functional insights, with many finch-like features probably related to a seed-rich diet that distinguishes them from most other icterids. In addition, features previously overlooked in earlier studies might provide valuable phylogenetic information at different levels of passerine phylogeny (Passerida, Emberizoidea, Icteridae, and Agelaiinae), including some of the otic region and nasal septum. Comparisons among cowbirds show that there is substantial cranial variation within the genus, with M. oryzivorus being the most divergent cowbird species. Within the genus, distantly related species share similar overall skull morphology and proportions, but detailed osteological data allow species identification even in cases of strong convergence. Further efforts are warranted to furnish baseline data for future studies of this iconic group of Neotropical birds and to fully integrate it into phylogenetic comparative frameworks.

Dental Dynamics: A Fast New Tool for Quantifying Tooth and Jaw Biomechanics in 3D Slicer

Teeth reveal how organisms interact with their environment. Biologists have long looked at the diverse form and function of teeth to study the evolution of feeding, fighting, and development. The exponential rise in the quantity and accessibility of computed tomography (CT) data has enabled morphologists to study teeth at finer resolutions and larger macroevolutionary scales. Measuring tooth function is no easy task, in fact, much of our mechanical understanding is derived from dental shape. Categorical descriptors of tooth shape such as morphological homodonty and heterodonty, overlook nuances in function by reducing tooth diversity for comparative analysis. The functional homodonty method quantitatively assesses the functional diversity of whole dentitions from tooth shape. This method uses tooth surface area and position to calculate the transmission of stress and estimates a threshold for functionally homodont teeth through bootstrapping and clustering techniques. However, some vertebrates have hundreds or thousands of teeth and measuring the shape and function of every individual tooth can be a painstaking task. Here, we present Dental Dynamics, a module for 3D Slicer that allows for the fast and precise quantification of dentitions and jaws. The tool automates the calculation of several tooth traits classically used to describe form and function (i.e., aspect ratio, mechanical advantage, force, etc.). To demonstrate the usefulness of our module we used Dental Dynamics to quantify 780 teeth across 20 salamanders that exhibit diverse ecologies. We coupled these data with the functional homodonty method to investigate the hypothesis that arboreal Aneides salamanders have novel tooth functions. Dental Dynamics provides a new and fast way to measure teeth and increases the accessibility of the functional homodonty method. We hope Dental Dynamics will encourage further theoretical and methodological development for quantifying and studying teeth.

Interactive three-dimensional atlas of the mineralized skeleton of the sand tiger shark Carcharias taurus

Non-invasive computed tomography (CT) of an adult sand tiger shark Carcharias taurus Rafinesque, 1810 is used to provide an interactive three-dimensional 'general' shark (Selachimorpha) anatomy atlas. Given its post-cranial body morphology, the sand tiger shark appeared to be a well-chosen candidate and through comparison of the sand tiger shark with several other representatives of all eight established orders of sharks, we confirm that the relatively large degree of mineralization of the endoskeleton, along with the overall size, makes the sand tiger shark an ideal candidate for skeletal segmentation and construction of a skeletal atlas using conventional CT. This atlas both increases accessibility to the internal morphological features of the sand tiger shark and provides a more generalized overview of the skeletal anatomy of sharks and can aid as a supplement to destructive fresh dissection of specimens in the future and the construction of future skeletal atlases of other less mineralized sharks.

The first full body diffusible iodine-based contrast-enhanced computed tomography dataset and teaching materials for a member of the Testudines

Diffusible iodine-based contrast-enhanced Computed Tomography (diceCT) is now a widely used technique for imaging metazoan soft anatomy. Turtles present a particular challenge for anatomists; gross dissection is inherently destructive and irreversible, whereas their near complete shell of bony plates, covered with keratinous scutes, presents a barrier for iodine diffusion and significantly increases contrast-enhanced CT preparation time. Consequently, a complete dataset visualizing the internal soft anatomy of turtles at high resolution and in three dimensions has not yet been successfully achieved. Here we outline a novel method that augments traditional diceCT preparation with an iodine injection technique to acquire the first full body contrast-enhanced dataset for the Testudines. We show this approach to be an effective method of staining the soft tissues inside the shell. The resulting datasets were processed to produce anatomical 3D models that can be used in teaching and research. As diceCT becomes a widely employed method for nondestructively documenting the internal soft anatomy of alcohol preserved museum specimens, we hope that methods applicable to the more challenging of these, such as turtles, will contribute toward the growing stock of digital anatomy in online repositories.

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.

Simulated biomechanical performance of morphologically disparate ant mandibles under bite loading

Insects evolved various modifications to their mouthparts, allowing for a broad exploration of feeding modes. In ants, workers perform non-reproductive tasks like excavation, food processing, and juvenile care, relying heavily on their mandibles. Given the importance of biting for ant workers and the significant mandible morphological diversity across species, it is essential to understand how mandible shape influences its mechanical responses to bite loading. We employed Finite Element Analysis to simulate biting scenarios on mandible volumetric models from 25 ant species classified in different feeding habits. We hypothesize that mandibles of predatory ants, especially trap-jaw ants, would perform better than mandibles of omnivorous species due to their necessity to subdue living prey. We defined simulations to allow only variation in mandible morphology between specimens. Our results demonstrated interspecific differences in mandible mechanical responses to biting loading. However, we found no evident differences in biting performance between the predatory and the remaining ants, and trap-jaw mandibles did not show lower stress levels than other mandibles under bite loading. These results suggest that ant feeding habit is not a robust predictor of mandible biting performance, a possible consequence of mandibles being employed as versatile tools to perform several tasks.

Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation

Almost nothing is known about the diets of bathypelagic fishes, but functional morphology can provide useful tools to infer ecology. Here we quantify variation in jaw and tooth morphologies across anglerfishes (Lophiiformes), a clade spanning shallow and deep-sea habitats. Deep-sea ceratioid anglerfishes are considered dietary generalists due to the necessity of opportunistic feeding in the food-limited bathypelagic zone. We found unexpected diversity in the trophic morphologies of ceratioid anglerfishes. Ceratioid jaws span a functional continuum ranging from species with numerous stout teeth, a relatively slow but forceful bite, and high jaw protrusibility at one end (characteristics shared with benthic anglerfishes) to species with long fang-like teeth, a fast but weak bite and low jaw protrusibility at the other end (including a unique 'wolftrap' phenotype). Our finding of high morphological diversity seems to be at odds with ecological generality, reminiscent of Liem's paradox (morphological specialization allowing organisms to have broader niches). Another possible explanation is that diverse ceratioid functional morphologies may yield similar trophic success (many-to-one mapping of morphology to diet), allowing diversity to arise through neutral evolutionary processes. Our results highlight that there are many ways to be a successful predator in the deep sea.

Sex estimation from virtual models: exploring the potential of stereolithic 3D crania models for morphoscopic trait scoring

Modern computed tomography (CT) databases are becoming an accepted resource for the practice and development of identification methods in forensic anthropology. However, the utility of 3D models created using free and open-source visualization software such as 3D Slicer has not yet been thoroughly assessed for morphoscopic biological profiling methods where virtual methods of analysis are becoming more common. This paper presents a study that builds on the initial findings from Robles et al. (2020) to determine the feasibility of estimating sex on stereolithic (STL) 3D cranial models produced from CT scans from a modern, living UK population (n = 80) using equation 2 from the Walker's (2008) morphoscopic method. Kendall's coefficients of concordance (KCC) indicated substantial agreement using cranial features scores in an inter-observer test and a video-inter-observer test. Fleiss' Kappa scores showed moderate agreement (0.50) overall between inter-observer sex estimations, and for observer sex estimations in comparison to recorded sexes (0.56). It was found that novice users could virtually employ morphoscopic sex estimation methods effectively on STL 3D cranial models from modern individuals. This study also highlights the potential that digital databases of modern living populations can offer forensic anthropology.

Key points

First example of Walker's (2008) method applied to a living UK population.Open-source software is a valuable resource for crime reconstruction approaches.Male scoring bias was observed in method application.Forensic anthropologists would benefit from virtual anthropology training to use and interpret 3D models.Digital databases offer more ethical, diverse, modern populations for future research.

DiceCT for fishes: recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes

Computed tomography (CT) scanning and other high-throughput three-dimensional (3D) visualization tools are transforming the ways we study morphology, ecology and evolutionary biology research beyond generating vast digital repositories of anatomical data. Contrast-enhanced chemical staining methods, which render soft tissues radio-opaque when coupled with CT scanning, encompass several approaches that are growing in popularity and versatility. Of these, the various diceCT techniques that use an iodine-based solution like Lugol's have provided access to an array of morphological data sets spanning extant vertebrate lineages. This contribution outlines straightforward means for applying diceCT techniques to preserved museum specimens of cartilaginous and bony fishes, collectively representing half of vertebrate species diversity. This study contrasts the benefits of using either aqueous or ethylic Lugol's solutions and reports few differences between these methods with respect to the time required to achieve optimal tissue contrast. It also explores differences in minimum stain duration required for different body sizes and shapes and provides recommendations for staining specimens individually or in small batches. As reported by earlier studies, the authors note a decrease in pH during staining with either aqueous or ethylic Lugol's. Nonetheless, they could not replicate the drastic declines in pH reported elsewhere. They provide recommendations for researchers and collections staff on how to incorporate diceCT into existing curatorial practices, while offsetting risk to specimens. Finally, they outline how diceCT with Lugol's can aid ichthyologists of all kinds in visualizing anatomical structures of interest: from brains and gizzards to gas bladders and pharyngeal jaw muscles.

Measuring compound eye optics with microscope and microCT images

With a great variety of shapes and sizes, compound eye morphologies give insight into visual ecology, development, and evolution, and inspire novel engineering. In contrast to our own camera-type eyes, compound eyes reveal their resolution, sensitivity, and field of view externally, provided they have spherical curvature and orthogonal ommatidia. Non-spherical compound eyes with skewed ommatidia require measuring internal structures, such as with MicroCT (µCT). Thus far, there is no efficient tool to characterize compound eye optics, from either 2D or 3D data, automatically. Here we present two open-source programs: (1) the ommatidia detecting algorithm (ODA), which measures ommatidia count and diameter in 2D images, and (2) a µCT pipeline (ODA-3D), which calculates anatomical acuity, sensitivity, and field of view across the eye by applying the ODA to 3D data. We validate these algorithms on images, images of replicas, and µCT eye scans from ants, fruit flies, moths, and a bee.

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.

The Core Concepts, Competencies, and Grand Challenges of Comparative Vertebrate Anatomy and Morphology

Core concepts offer coherence to the discourse of a scientific discipline and facilitate teaching by identifying large unifying themes that can be tailored to the level of the class and expertise of the instructor. This approach to teaching has been shown to encourage deeper learning that can be integrated across subdisciplines of biology and has been adopted by several other biology subdisciplines. However, Comparative Vertebrate Anatomy, although one of the oldest biological areas of study, has not had its core concepts identified. Here, we present five core concepts and seven competencies (skills) for Comparative Vertebrate Anatomy that came out of an iterative process of engagement with the broader community of vertebrate morphologists over a 3-year period. The core concepts are (A) evolution, (B) structure and function, (C) morphological development, (D) integration, and (E) human anatomy is the result of vertebrate evolution. The core competencies students should gain from the study of comparative vertebrate anatomy are (F) tree thinking, (G) observation, (H) dissection of specimens, (I) depiction of anatomy, (J) appreciation of the importance of natural history collections, (K) science communication, and (L) data integration. We offer a succinct description of each core concept and competency, examples of learning outcomes that could be used to assess teaching effectiveness, and examples of relevant resources for both instructors and students. Additionally, we pose a grand challenge to the community, arguing that the field of Comparative Vertebrate Anatomy needs to acknowledge racism, androcentrism, homophobia, genocide, slavery, and other influences in its history and address their lingering effects in order to move forward as a thriving discipline that is inclusive of all students and scientists and continues to generate unbiased knowledge for the betterment of humanity. Despite the rigorous process used to compile these core concepts and competencies, we anticipate that they will serve as a framework for an ongoing conversation that ensures Comparative Vertebrate Anatomy remains a relevant field in discovery, innovation, and training of future generations of scientists.

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.

A Roadmap to Reconstructing Muscle Architecture from CT Data

Skeletal muscle is responsible for voluntary force generation across animals, and muscle architecture largely determines the parameters of mechanical output. The ability to analyze muscle performance through muscle architecture is thus a key step towards better understanding the ecology and evolution of movements and morphologies. In pennate skeletal muscle, volume, fiber lengths, and attachment angles to force transmitting structures comprise the most relevant parameters of muscle architecture. Measuring these features through tomographic techniques offers an alternative to tedious and destructive dissections, particularly as the availability of tomographic data is rapidly increasing. However, there is a need for streamlined computational methods to access this information efficiently. Here, we establish and compare workflows using partially automated image analysis for fast and accurate estimation of animal muscle architecture. After isolating a target muscle through segmentation, we evaluate freely available and proprietary fiber tracing algorithms to reconstruct muscle fibers. We then present a script using the Blender Python API to estimate attachment angles, fiber lengths, muscle volume, and physiological cross-sectional area. We apply these methods to insect and vertebrate muscle and provide guided workflows. Results from fiber tracing are consistent compared to manual measurements but much less time-consuming. Lastly, we emphasize the capabilities of the open-source three-dimensional software Blender as both a tool for visualization and a scriptable analytic tool to process digitized anatomical data. Across organisms, it is feasible to extract, analyze, and visualize muscle architecture from tomography data by exploiting the spatial features of scans and the geometric properties of muscle fibers. As digital libraries of anatomies continue to grow, the workflows and approach presented here can be part of the open-source future of digital comparative analysis.

Redescription of Conniella apterygia Allen and its reassignment in the genus Cirrhilabrus Temminck and Schlegel (Teleostei: Labridae), with comments on cirrhilabrin pelvic morphology

Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six additional specimens. The genus is closely allied to Cirrhilabrus, sharing similarities in general morphological and meristic details, but is separated from Cirrhilabrus and most other labrid fishes in lacking pelvic fins and a pelvic girdle. Recent molecular phylogenetic studies have provided strong evidence for the deep nesting of Conniella within Cirrhilabrus, contradicting its generic validity and suggesting that the loss of pelvic elements is autapomorphic. Consequently, the species is redescribed and assigned to the genus Cirrhilabrus, as Cirrhilabrus apterygia new combination. The pelvic morphologies of related cirrhilabrin labrids are discussed, and a new synapomorphy is identified for Paracheilinus.

Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia)

Insights into the generation of diversity in both plants and animals have relied heavily on studying speciation in adaptive radiations. Russia's Lake Baikal has facilitated a putative adaptive radiation of cottid fishes (sculpins), some of which are highly specialized to inhabit novel niches created by the lake's unique geology and ecology. Here, we test evolutionary relationships and novel morphological adaptation in a piece of this radiation: the Baikal cottid genus, Cottocomephorus, a morphologically derived benthopelagic genus of three described species. We used a combination of mitochondrial DNA and restriction site associated DNA sequencing from all Cottocomephorus species. Analysis of mitochondrial cytochrome b haplotypes was only able to two resolve two lineages: C. grewingkii and C. comephoroides/inermis. Phylogenetic inference, principal component analysis, and faststructure of genome-wide SNPs uncovered three lineages within Cottocomephorus: C. comephoroides, C. inermis and C. grewingkii. We found recent divergence and admixture between C. comephoroides and C. inermis and deep divergence between these two species and C. grewingkii. Contrasting other fish radiations, we found no evidence of ancient hybridization among Cottocomephorus species. Digital morphology revealed highly derived pelagic phenotypes that reflect divergence by specialization to the benthopelagic niche in Cottocomephorus. Among Cottocomephorus species, we found evidence of ongoing adaptation to the pelagic zone. This pattern highlights the importance of speciation along a benthic-pelagic gradient seen in Cottocomephorus and across other adaptive fish radiations.

Implementing Fabrication as a Pedagogical Tool in Vertebrate Anatomy Courses: Motivation, Inclusion, and Lessons

Increasing course structure by incorporating active learning and multimodal pedagogical strategies benefits all learners. Students of vertebrate anatomy can especially benefit from practicing fabrication, or "making", incorporating skills such as 3D digital modeling, 3D printing, and using familiar low-tech materials to construct informed replicas of animal anatomy. Student perceptions of active learning projects are shaped by motivation theories such as the expectancy-value theory and self-directed learning, both of which are briefly reviewed here. This paper offers inspiration and resources to instructors for establishing a makerspace in an anatomy lab and leveraging community partners to stimulate students to construct their own versions of nature's designs. Learning science in informal environments and specifically in makerspaces has been shown to promote equity and increase motivation to study science. Examples here emphasize accessibility for diverse learners, including strategies for instructors to ensure ease of student access to 3D technology. Scaffolding formative assessments builds student confidence and expertise, further closing opportunity gaps. Two specific cases are detailed where fabrication and the use of 3D digital models are used to augment student learning of vertebrate anatomy at a small liberal arts college. In a semester-long research project in an introductory biomechanics course, students investigate, write about, and build models of animal anatomy of their choice. They use simple materials, crafting supplies, household tools, and/or 3D printing to demonstrate structures of interest, enhancing understanding of the physical principles of animal form and function. Given increased availability of CT data online, students can download, analyze, and 3D print skeletal models of both common and endangered animals. Comparative anatomy students reported that they had increased motivation to study intricate skeletal anatomy simply by manipulating bones in a 3D software assignment. Students in both classes reported enjoying the use of fabrication in learning vertebrate anatomy and this may establish a pattern of lifelong learning.

Future Tail Tales: A Forward-Looking, Integrative Perspective on Tail Research

Synopsis Tails are a defining characteristic of chordates and show enormous diversity in function and shape. Although chordate tails share a common evolutionary and genetic-developmental origin, tails are extremely versatile in morphology and function. For example, tails can be short or long, thin or thick, and feathered or spiked, and they can be used for propulsion, communication, or balancing, and they mediate in predator-prey outcomes. Depending on the species of animal the tail is attached to, it can have extraordinarily multi-functional purposes. Despite its morphological diversity and broad functional roles, tails have not received similar scientific attention as, for example, the paired appendages such as legs or fins. This forward-looking review article is a first step toward interdisciplinary scientific synthesis in tail research. We discuss the importance of tail research in relation to five topics: (1) evolution and development, (2) regeneration, (3) functional morphology, (4) sensorimotor control, and (5) computational and physical models. Within each of these areas, we highlight areas of research and combinations of long-standing and new experimental approaches to move the field of tail research forward. To best advance a holistic understanding of tail evolution and function, it is imperative to embrace an interdisciplinary approach, re-integrating traditionally siloed fields around discussions on tail-related research.

Modernizing Medical Museums Through the 3D Digitization of Pathological Specimens

The anatomical collections at the National Museum of Health and Medicine (NMHM) contain skeletal specimens that highlight the history of military and civilian medicine dating from the American Civil War and the founding of the museum as the Army Medical Museum in 1862. Today, NMHM curates over 6400 gross skeletal specimens consisting primarily of pathological or anomalous single bone elements that display a variety of pathological conditions, including congenital anomalies, neoplasms, healed and unhealed trauma and infectious diseases, and surgical interventions such as amputations and excisions. In an effort to increase accessibility to these pathological specimens, NMHM is collaborating with Virginia Commonwealth University (VCU) and the Laboratory Division of the Federal Bureau of Investigation (FBI) to digitize and disseminate high-quality 3D models via online portals, enabling scholars and educators to manipulate, analyze, and 3D print the models from anywhere in the world. Many institutions with courses in paleopathology and forensic anthropology do not have reference collections or access to museum collections for hands-on teaching. Therefore a digital repository of osteological specimens can provide an unprecedented and unique resource of exemplars for scholars and educators. The sharing of these military medical assets improves historical knowledge and diagnostic capabilities in the fields of medicine and anthropology. This chapter outlines the digitization processes that are being utilized to increase access to these pathological skeletal specimens through multimodal 3D capture.

A guide for optimal iodine staining and high-throughput diceCT scanning in snakes

Diffusible iodine-based contrast-enhanced computed tomography (diceCT) visualizes soft tissue from micro-CT (µCT) scans of specimens to uncover internal features and natural history information without incurring physical damage via dissection. Unlike hard-tissue imaging, taxonomic sampling within diceCT datasets is currently limited. To initiate best practices for diceCT in a nonmodel group, we outline a guide for staining and high-throughput µCT scanning in snakes. We scanned the entire body and one region of interest (i.e., head) for 23 specimens representing 23 species from the clades Aniliidae, Dipsadinae, Colubrinae, Elapidae, Lamprophiidae, and Viperidae. We generated 82 scans that include 1.25% Lugol's iodine stained (soft tissue) and unstained (skeletal) data for each specimen. We found that duration of optimal staining time increased linearly with body size; head radius was the best indicator. Postreconstruction of scans, optimal staining was evident by evenly distributed grayscale values and clear differentiation among soft-tissue anatomy. Under and over stained specimens produced poor contrast among soft tissues, which was often exacerbated by user bias during "digital dissections" (i.e., segmentation). Regardless, all scans produced usable data from which we assessed a range of downstream analytical applications within ecology and evolution (e.g., predator-prey interactions, life history, and morphological evolution). Ethanol destaining reversed the known effects of iodine on the exterior appearance of physical specimens, but required substantially more time than reported for other destaining methods. We discuss the feasibility of implementing diceCT techniques for a new user, including approximate financial and temporal commitments, required facilities, and potential effects of staining on specimens. We present the first high-throughput workflow for full-body skeletal and diceCT scanning in snakes, which can be generalized to any elongate vertebrates, and increases publicly available diceCT scans for reptiles by an order of magnitude.

Patterns of Body Shape Diversity and Evolution in Intertidal and Subtidal Lineages of Combtooth Blennies (Blenniidae)

Marine intertidal zones can be harsher and more dynamic than bordering subtidal zones, with extreme and temporally variable turbulence, water velocity, salinity, temperature, and dissolved oxygen levels. Contrasting environmental conditions and ecological opportunities in subtidal versus intertidal habitats may generate differing patterns of morphological diversity. In this study we used phylogenetic comparative methods, measurements of body length, and two-dimensional landmarks to characterize body shape and size diversity in combtooth blennies (Ovalentaria: Blenniidae) and test for differences in morphological diversity between intertidal, subtidal, and supralittoral zones. We found that subtidal combtooth blennies have significantly higher body shape disparity and occupy a region of morphospace three times larger than intertidal lineages. The intertidal morphospace was almost entirely contained within the subtidal morphospace, showing that intertidal combtooth blennies did not evolve unique body shapes. We found no significant differences in body size disparity between tidal zones, no correlations between body shape and tidal zone or body size and tidal zone, and no body shape convergence associated with tidal zone. Our findings suggest that a subset of combtooth blenny body shapes are suitable for life in both subtidal and intertidal habitats. Many species in regions of morphospace unique to subtidal combtooth blennies exhibit distinct microhabitat use, which suggests subtidal environments promoted morphological diversification via evolutionary microhabitat transitions. In contrast, limited intertidal body shape diversity may be due to strong selective pressures that constrained body shape evolution and environmental filtering that prevented colonization of intertidal zones by certain subtidal body shapes.

Three-dimensional segmentation of computed tomography data using Drishti Paint: new tools and developments

Computed tomography (CT) has become very widely used in scientific and medical research and industry for its non-destructive and high-resolution means of detecting internal structure. Three-dimensional segmentation of computed tomography data sheds light on internal features of target objects. Three-dimensional segmentation of CT data is supported by various well-established software programs, but the powerful functionalities and capabilities of open-source software have not been fully revealed. Here, we present a new release of the open-source volume exploration, rendering and three-dimensional segmentation software, Drishti v. 2.7. We introduce a new tool for thresholding volume data (i.e. gradient thresholding) and a protocol for performing three-dimensional segmentation using the 3D Freeform Painter tool. These new tools and workflow enable more accurate and precise digital reconstruction, three-dimensional modelling and three-dimensional printing results. We use scan data of a fossil fish as a case study, but our procedure is widely applicable in biological, medical and industrial research.