Four-bar linkage modelling in teleost pharyngeal jaws : computer simulations of bite kinetics

Author Posting. © The Author(s), 2006. This is the author's version of the work. It is posted here by permission of Anatomical Society of Great Britain and Ireland for personal use, not for redistribution. The definitive version was published in Journal of Anatomy 209 (2006): 79-92, doi:10.1111/j.1469-7580.2006.00551.x.The pharyngeal arches of the red drum (Sciaenops ocellatus) possess large toothplates and a complex musculoskeletal design for biting and crushing hard prey. The morphology of pharyngeal apparatus is described from dissections of six specimens, with a focus on the geometric conformation of contractile and rotational elements. Four major muscles operate the rotational 4th epibranchial (EB4) and 3rd pharyngobranchial (PB3) elements to create pharyngeal bite force, including the levator posterior (LP), levator externus 3/4 (LE), obliquus posterior (OP), and 3rd obliquus dorsalis (OD). A biomechanical model of upper pharyngeal jaw biting is developed using lever mechanics and four-bar linkage theory from mechanical engineering. A pharyngeal four-bar linkage is proposed that involves the posterior skull as the fixed link, the LP muscle as input link, the epibranchial bone as coupler link, and the toothed pharyngobranchial as output link. We used a computer model to simulate contraction of the four major muscles, with the LP as the dominant muscle whose length determined the position of the linkage. When modeling lever mechanics, we found that the effective mechanical advantages of the pharyngeal elements were low, resulting in little resultant bite force. In contrast, the force advantage of the four-bar linkage was relatively high, transmitting approximately 50% of the total muscle force to the bite between the toothplates. Pharyngeal linkage modeling enables quantitative functional morphometry of a key component of the fish feeding system, and the model is now available for ontogenetic and comparative analyses of fishes with pharyngeal linkage mechanisms.This research was funded by NSF grant DEB 0235307 to M. Westneat

Form and function of damselfish skulls: rapid and repeated evolution into a limited number of trophic niches

BACKGROUND: Damselfishes (Perciformes, Pomacentridae) are a major component of coral reef communities, and the functional diversity of their trophic anatomy is an important constituent of the ecological morphology of these systems. Using shape analyses, biomechanical modelling, and phylogenetically based comparative methods, we examined the anatomy of damselfish feeding among all genera and trophic groups. Coordinate based shape analyses of anatomical landmarks were used to describe patterns of morphological diversity and determine positions of functional groups in a skull morphospace. These landmarks define the lever and linkage structures of the damselfish feeding system, and biomechanical analyses of this data were performed using the software program JawsModel4 in order to calculate the simple mechanical advantage (MA) employed by different skull elements during feeding, and to compute kinematic transmission coefficients (KT) that describe the efficiency with which angular motion is transferred through the complex linkages of damselfish skulls. RESULTS: Our results indicate that pomacentrid planktivores are significantly different from other damselfishes, that biting MA values and protrusion KT ratios are correlated with pomacentrid trophic groups more tightly than KT scores associated with maxillary rotation and gape angle, and that the MAs employed by their three biting muscles have evolved independently. Most of the biomechanical parameters examined have experienced low levels of phylogenetic constraint, which suggests that they have evolved quickly. CONCLUSION: Joint morphological and biomechanical analyses of the same anatomical data provided two reciprocally illuminating arrays of information. Both analyses showed that the evolution of planktivory has involved important changes in pomacentrid functional morphology, and that the mechanics of upper jaw kinesis have been of great importance to the evolution of damselfish feeding. Our data support a tight and biomechanically defined link between structure and the functional ecology of fish skulls, and indicate that certain mechanisms for transmitting motion through their jaw linkages may require particular anatomical configurations, a conclusion that contravenes the concept of "many-to-one mapping" for fish jaw mechanics. Damselfish trophic evolution is characterized by rapid and repeated shifts between a small number of eco-morphological states, an evolutionary pattern that we describe as reticulate adaptive radiation

Performance Limits of Labriform Propulsion and Correlates with Fin Shape and Motion

Labriform locomotion, which is powered by oscillating the paired pectoral fins, varies along a continuum from rowing the fins back and forth to flapping the fins up and down. It has generally been assumed (i) that flapping is more mechanically efficient than rowing, a hypothesis confirmed by a recent simulation experiment, and (ii) that flapping should be associated with wing-shaped fins while rowing should be associated with paddle-shaped fins, To determine whether these hypotheses and the results of the simulation experiment are consistent with natural variation, we compared the steady swimming performance (critical swimming speed) of four species of labrid fish (Cirrhilabrus rubripinnis, Pseudocheilinus octolaenia, Gomphosus varius and Halichoeres bivittatus) selected to form two pairs of closely related species that vary in fin shape and in the direction of fin motion. The results were consistent with expectations. Within each pair, the species with the best swimming performance also had (i) a fin shape characterized by a higher aspect ratio, a longer leading edge relative to the trailing edge fin rays and the center of fin area located closer to: the fin base, and (ii) a steeper (more dorsoventral) stroke, plane

Comparative kinematics of the forelimb during swimming in red-eared slider (Trachemys scripta) and spiny softshell (Apalone spinifera) turtles

Softshell turtles (Family Trionychidae) possess extensive webbing between the digits of the manus, suggesting that the forelimb may serve as an effective thrust generator during aquatic locomotion. However, the hindlimb has previously been viewed as the dominant propulsive organ in swimming freshwater turtles. To evaluate the potential role of the forelimb in thrust production during swimming in freshwater turtles, we compared the forelimb morphology and three-dimensional forelimb kinematics of a highly aquatic trionychid turtle, the spiny softshell Apalone spinifera, and a morphologically generalized emydid turtle, the red-eared slider Trachemys scripta. Spiny softshells possess nearly twice as much forelimb surface area as sliders for generating drag-based thrust. In addition, although both species use drag-based propulsion, several aspects of forelimb kinematics differ significantly between these species. During the thrust phase of the forelimb cycle, spiny softshells hold the elbow and wrist joints significantly straighter than sliders, thereby further increasing the surface area of the limb that can move water posteriorly and increasing the velocity of the distal portion of the forelimb. These aspects of swimming kinematics in softshells should increase forelimb thrust production and suggest that the forelimbs make more substantial contributions to forward thrust in softshell turtles than in sliders. Spiny softshells also restrict forelimb movements to a much narrower dorsoventral and anteroposterior range than sliders throughout the stroke, thereby helping to minimize limb movements potentially extraneous to forward thrust production. These comparisons demonstrate considerable diversity in the forelimb kinematics of turtles that swim using rowing motions of the limbs and suggest that the evolution of turtle forelimb mechanics produced a variety of contrasting solutions for aquatic specialization

Quantitative color profiling of digital images with earth mover’s distance using the R package colordistance

Biological color may be adaptive or incidental, seasonal or permanent, species- or population-specific, or modified for breeding, defense or camouflage. Although color is a hugely informative aspect of biology, quantitative color comparisons are notoriously difficult. Color comparison is limited by categorization methods, with available tools requiring either subjective classifications, or expensive equipment, software, and expertise. We present an R package for processing images of organisms (or other objects) in order to quantify color profiles, gather color trait data, and compare color palettes on the basis of color similarity and amount. The package treats image pixels as 3D coordinates in a “color space,” producing a multidimensional color histogram for each image. Pairwise distances between histograms are computed using earth mover’s distance, a technique borrowed from computer vision, that compares histograms using transportation costs. Users choose a color space, parameters for generating color histograms, and a pairwise comparison method to produce a color distance matrix for a set of images. The package is intended as a more rigorous alternative to subjective, manual digital image analyses, not as a replacement for more advanced techniques that rely on detailed spectrophotometry methods unavailable to many users. Here, we outline the basic functions of colordistance, provide guidelines for the available color spaces and quantification methods, and compare this toolkit with other available methods. The tools presented for quantitative color analysis may be applied to a broad range of questions in biology and other disciplines

Fluid Dynamics of Flapping Aquatic Flight in the Bird Wrasse: Three-dimensional unsteady computations with fin deformation

Many fishes that swim with the paired pectoral fins use fin-stroke parameters that produce thrust force from lift in a mechanism of underwater flight. These locomotor mechanisms are of interest to behavioral biologists, biomechanics researchers and engineers. In the. present study, we performed the first three-dimensional unsteady computations of fish swimming with oscillating and deforming fins. The objective of these computations was to investigate the fluid dynamics of force production associated with the flapping aquatic flight of the bird wrasse Gomphosus varius. For this computational work, we used the geometry of the wrasse and its pectoral fin, and previously measured fin kinematics, as the starting points for computational investigation of three-dimensional (3-D) unsteady fluid dynamics. We performed a 3-D steady computation and a complete set of 3-D quasi-steady computations for a range of pectoral fin positions and surface velocities. An unstructured, grid-based, unsteady Navier-Stokes solver with automatic adaptive remeshing was then used to compute the unsteady How about the wrasse through several complete cycles of pectoral fin oscillation. The shape deformation of the pectoral fin throughout the oscillation was taken from the experimental kinematics. The pressure distribution on the body of the bird wrasse and its pectoral fins was computed and integrated to give body and fin forces which were decomposed into lift and thrust. The velocity field variation on the surface of the wrasse body, on the pectoral fins and in the near-wake was computed throughout the swimming cycle. We compared our computational results for the steady, quasi-steady and unsteady cases with the experimental data on axial and vertical acceleration obtained from the pectoral fin kinematics experiments. These comparisons show that steady state computations are incapable of describing the fluid dynamics of flapping fins. Quasi-steady state computations, with correct incorporation of the experimental kinematics, are useful when determining trends in force production, but do not provide accurate estimates of the magnitudes of the forces produced. By contrast, unsteady computations about the deforming pectoral fins using experimentally measured fin kinematics were found to give excellent agreement, both in the time history of force production throughout the flapping strokes and in the magnitudes of the generated forces

Fluid Dynamics of Flapping Aquatic Flight in the Bird Wrasse: Three-Dimensional Unsteady Computations With Fin Deformation

Many fishes that swim with the paired pectoral fins use fin-stroke parameters that produce thrust force from lift in a mechanism of underwater flight. These locomotor mechanisms are of interest to behavioral biologists, biomechanics researchers and engineers. In the present study, we performed the first three-dimensional unsteady computations of fish swimming with oscillating and deforming fins. The objective of these computations was to investigate the fluid dynamics of force production associated with the flapping aquatic flight of the bird wrasse Gomphosus varius. For this computational work, we used the geometry of the wrasse and its pectoral fin, and previously measured fin kinematics, as the starting points for computational investigation of three-dimensional (3-D) unsteady fluid dynamics. We performed a 3-D steady computation and a complete set of 3-D quasisteady computations for a range of pectoral fin positions and surface velocities. An unstructured, grid-based, unsteady Navier-Stokes solver with automatic adaptive remeshing was then used to compute the unsteady flow about the wrasse through several complete cycles of pectoral fin oscillation. The shape deformation of the pectoral fin throughout the oscillation was taken from the experimental kinematics. The pressure distribution on the body of the bird wrasse and its pectoral fins was computed and integrated to give body and fin forces which were decomposed into lift and thrust. The velocity field variation on the surface of the wrasse body, on the pectoral fins and in the near-wake was computed throughout the swimming cycle. We compared our computational results for the steady, quasi-steady and unsteady cases with the experimental data on axial and vertical acceleration obtained from the pectoral fin kinematics experiments. These comparisons show that steady state computations are incapable of describing the fluid dynamics of flapping fins. Quasi-steady state computations, with correct incorporation of the experimental kinematics, are useful when determining trends in force production, but do not provide accurate estimates of the magnitudes of the forces produced. By contrast, unsteady computations about the deforming pectoral fins using experimentally measured fin kinematics were found to give excellent agreement, both in the time history of force production throughout the flapping strokes and in the magnitudes of the generated forces

Physiological integration of coral colonies is correlated with bleaching resistance

Inter-module physiological integration of colonial organisms can facilitate colony-wide coordinated responses to stimuli that strengthen colony fitness and stress resistance. In scleractinian corals, whose colonial integration ranges from isolated polyps to a seamless continuum of polyp structures and functions, this coordination improves responses to injury, predation, disease, and stress and may be one of the indications of an evolutionary origin of Symbiodinium symbiosis. However, observations of species-specific coral bleaching patterns suggest that highly integrated coral colonies may be more susceptible to thermal stress, and support the hypothesis that communication pathways between highly integrated polyps facilitate the dissemination of toxic byproducts created during the bleaching response. Here we reassess this hypothesis by parameterizing an integration index using 7 skeletal features that have been historically employed to infer physiological integration. We examine the relationship between this index and bleaching response across a phylogeny of 88 diverse coral species. Correcting for phylogenetic relationships among species in the analyses reveals significant patterns among species characters that could otherwise be obscured in simple cross-species comparisons using standard statistics, whose assumptions of independence are violated by the shared evolutionary history among species. Similar to the observed benefits of in creased coloniality for other types of stressors, the results indicate a significantly reduced bleaching response among coral species with highly integrated colonies

Pengembangan Media Pembelajaran Matematika Berbantu Wondershare dengan Pendekatan Rme pada Materi SMP

Pemilihan media pembelajaran yang kurang tepat dapat membuat siswa kurang antusias terhadap mata pelajaran matematika. Sehingga banyak siswa yang mendapat nilai dibawah KKM. Solusinya dibutuhkan media pembelajaran yang menarik serta dapat menumbuhkan antusias siswa dalam belajar.Penelitian ini bertujuan untuk mengembangkan media pembelajaran berbantu wondershare dengan pendekatan RME sehingga menghasilkan media yang layak dan efektif digunakan selama pembelajaran. Jenis penelitian ini adalah penelitian Research and Development dengan menggunakan model pengembangan ADDIE, terdiri dari 5 tahapan yaitu analisis, design, developmen, implementasi, evaluasi.Sebelum diimplementasikan, media pembelajaran terlebih dahulu dilakukan uji validasi oleh ahli media, ahli materi serta angket tanggapan siswa. Hasil validasi ahli tersebut berkriteria sangat baik sehingga media pembelajaran layak untuk digunakan.Pembelajaran dengan media pembelajaran berbantu wondershare dengan pendekatan RME efektif digunakan oleh peserta didik. Hal ini di buktikan dari rata rata kelas eksperimen dan kontrol yaitu 82,03 dan 60,54. Ketuntasan belajar individu kelas ekperimen terdapat 31 siswa tuntas dari 36 siswa, dan kelas kontrol terdapat 8 siswa tuntas dari 27 siswa. Dilihat dari ketuntasan belajar klasikal siswa untuk kelas kontrol dan eksperimen sebesar 22,86% dan 86,11%. Dengan analisis menggunakan uji t pihak kanan diperoleh nilaiyaitu 9,607>1,667 maka H0 ditolak, jadi pembelajaran dengan menggunakan media pembelajaran berbantuan wondershare dengan pendekatan RME lebih baik dibandingkan dengan pembelajaran konvensional pada materi SMP

Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science