The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.     

Morphological evolution of the lizard skull: a geometric morphometrics survey

Patterns of diversity among lizard skulls were studied from a morphological, phylogenetic, and functional perspective. A sample of 1,030 lizard skulls from 441 species in 17 families was used to create a lizard skull morphospace. This morphospace was combined with a phylogeny of lizard families to summarize general trends in the evolution of the lizard skull. A basal morphological split between the Iguania and Scleroglossa was observed. Iguanians are characterized by a short, high skull, with large areas of attachment for the external adductor musculature, relative to their sister group. The families of the Iguania appear to possess more intrafamilial morphological diversity than families of the Scleroglossa, but rarefaction of the data reveals this to be an artifact caused by the greater number of species represented in Iguanian families. Iguanian families also appear more dissimilar to one another than families of the Scleroglossa. Permutation tests indicate that this pattern is real and not due to the smaller number of families in the Iguanidae. Parallel and convergent evolution is observed among lizards with similar diets: ant and termite specialists, carnivores, and herbivores. However, these patterns are superimposed over the more general phylogenetic pattern of lizard skull diversity. This study has three central conclusions. Different clades of lizards show different patterns of disparity and divergence in patterns of morphospace occupation. Phylogeny imposes a primary signal upon which a secondary ecological signal is imprinted. Evolutionary patterns in skull metrics, taken with functional landmarks, allow testing of trends and the development of new hypotheses concerning both shape and biomechanics.     

Testing different 3D techniques using geometric morphometrics: Implications for cranial fluctuating asymmetry in humans

This study aimed to test the performance of 3D digitizer, CT scanner, and surface scanner in detecting cranial fluctuating asymmetry. Sets of 32 landmarks (6 in the midline and 13 bilateral) were acquired from 14 archeological crania using a 3D digitizer, and from 3D models generated from a CT scanner and surface scanner using Viewbox 4. Levels of shape variation were analyzed in MorphoJ using Procrustes analysis of variance and Principal component analysis. Intra-observer error accounted for 1.7%, 1.8%, and 4.5% of total shape variation for 3D digitizer, CT scanner, and surface scanner respectively. Fluctuating asymmetry accounted for 15%–16% of total shape variation. Variation between techniques accounted for 18% of total shape variation. We found a higher level of missing landmarks in our surface scan data than for both 3D digitizer and CT scanner data, and both 3D model-based techniques sometimes obscured taphonomic damage. All three 3D techniques are appropriate for measuring cranial fluctuating asymmetry. We advise against combining data collected with different techniques.     

Geometric morphometrics: recent applications to the study of evolution and development

The field of morphometrics is developing quickly and recent advances allow for geometric techniques to be applied easily to many zoological problems. This paper briefly introduces geometric morphometric techniques and then reviews selected areas where those techniques have been applied to questions of general interest. This paper is relevant to non-specialists looking for an entry into geometric morphometric methods and for ideas of how to incorporate them into the study of variation within and between species, the measurement of developmental stability, the role of development in shaping evolution and the special problem of measuring the shape of fossil specimens that are deformed from their original shape.     

3D reconstruction of the pelvis from bi-planar radiography

3D personalized models are more and more requested for clinical and biomechanical studies. Techniques based on bi-planar X-rays present the advantage of a low radiation dose for the patient. However, up to now, such techniques have shown limited accuracy in the case of pelvis reconstruction. This study proposes and validates a method providing accurate 3D personalized model of the pelvis from bi-planar X-rays. The algorithm is based on the fast computation of an initial solution followed by local deformations based on 2D anatomical points and contours that are digitized in both radiographs. Results were close to CT-scan reconstructions (mean difference 1.6 mm and differences under 4.3 mm for 95% of the points). Moreover, 3D morphometry of the pelvis could be obtained with an accuracy of 5%. This technique provides 3D patient specific model with a low radiation dose.     

Pure moment testing for spinal biomechanics applications: fixed versus 3D floating ring cable-driven test designs

Pure moment testing has become a standard protocol for in vitro assessment of the effect of surgical techniques or devices on the bending rigidity of the spine. Of the methods used for pure moment testing, cable-driven set-ups are popular due to their low requirements and simple design. Fixed loading rings are traditionally used in conjunction with these cable-driven systems. However, the accuracy and validity of the loading conditions applied with fixed ring designs have raised some concern, and discrepancies have been found between intended and prescribed loading conditions for flexion-extension. This study extends this prior work to include lateral bending and axial torsion, and compares this fixed ring design with a novel "3D floating ring" design. A complete battery of multi-axial bending tests was conducted with both rings in multiple different configurations using an artificial lumbar spine. Applied moments were monitored and recorded by a multi-axial load cell at the base of the specimen. Results indicate that the fixed ring design deviates as much as 77% from intended moments and induces non-trivial shear forces (up to 18 N) when loaded to a non-destructive maximum of 4.5 Nm. The novel 3D floating ring design largely corrects the inherent errors in the fixed ring design by allowing additional directions of unconstrained motion and producing uniform loading conditions along the length of the specimen. In light of the results, it is suggested that the 3D floating ring set-up be used for future pure moment spine biomechanics applications using a cable-driven apparatus.     

Geometric morphometrics of the skull of various murid rodents (Mammalia, Rodentia): relation of the skull shape to the trophic specialization

Presented is a brief overview of basic principles and notions of geometric morphometrics, a new approach to quantitative analysis of shape variations. This approach is applied to analysis of variation of the skull shape in the sample of 18 muroid genera belonging to the families Cricetidae, Arvicolidae and Gerbillidae. The skull shape is described by landmarks, and skulls are compared by resistant fit and superimposition methods. Under consideration is relation of skull shape to the trophic specialization, to family belonging, and to body size. Axial skull reveals more conspicuous relation to each of the factor analyzed as compared to mandible. Zygomatic region and tooth raw are most differentiable, while change of auditory bulla is of secondary effect. Transition from omnivorous through granivorous to grass-eating specialization involves the same trend in each of the family studied in the case of axial skull but not of mandible. Most dependent of trophic specialization appeared to be shape of axial skull rather then of mandible. Arvicolines are most specific in respect to the skull shape. Shape to size relation, although rather slight, also involves the same zygomatic-dental region. The results obtained indicate probably that geometric morphometrics does reveal variations in the skull shape that are free of the size effect.     

Creating physical 3D stereolithograph models of brain and skull

The human brain and skull are three dimensional (3D) anatomical structures with complex surfaces. However, medical images are often two dimensional (2D) and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR) and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50) used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine.     

The skull of Monolophosaurus jiangi (Dinosauria: Theropoda) and its implications for early theropod phylogeny and evolution

The Middle Jurassic was a critical time in the evolution of theropod dinosaurs, highlighted by the origination and initial radiation of the large‐bodied and morphologically diverse Tetanurae. Middle Jurassic tetanurans are rare, but have been described from Europe, South America and China. In particular, China has yielded a number of potential basal tetanurans, but these have received little detailed treatment in the literature. Chief among these is Monolophosaurus jiangi, known from a single skeleton that includes a nearly complete and well‐preserved skull characterized by a bizarre cranial crest. Here, we redescribe the skull of Monolophosaurus, which is one of the most complete basal tetanuran skulls known and the only quality source of cranial data for Middle Jurassic Chinese theropods. The cranial crest is atomized into a number of autapomorphic features and several characters confirm the tetanuran affinities of Monolophosaurus. However, several features suggest a basal position within Tetanurae, which contrasts with most published cladistic analyses, which place Monolophosaurus within the more derived Allosauroidea. Cranial characters previously used to diagnose Allosauroidea are reviewed and most are found to have a much wider distribution among Theropoda, eroding an allosauroid position for Monolophosaurus and questioning allosauroid monophyly. The use of phylogenetic characters relating to theropod cranial crests is discussed and a protocol for future use is given. The systematic position of Guanlong wucaii is reviewed, and a basal tyrannosauroid affinity is upheld contrary to one suggestion of a close relationship between this taxon and Monolophosaurus. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 573–607.     

Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.     

三维几何形态学概述及其在昆虫学中的应用

长期以来二维（two-dimensional, 2D）数据是几何形态学（geometric morphometrics）分析的最主要的数据类型,在推动几何形态学的发展过程中起到了奠基性的作用,并也解决了很多重大的科学问题,展示了几何形态学强大的科学计算能力与问题解决能力。但有些特殊的科学问题或者特殊的形态结构,无法通过二维数据完美解决,亟需大规模、大尺度三维（three-dimensional, 3D）数据的支持,这对几何形态学的三维化发展提出需求。更重要的是,随着三维数据获取成本的日渐降低,大量三维数据涌现出来。因此,三维几何形态学应运而生。本文对三维几何形态学的原理及其应用进行了概述,重点探讨了三维几何形态学与二维几何形态学的异同点,并对前者的两个发展阶段（少量样本的形态模拟与准定量比较及大量样本的定量比较）进行了概述,评价了四维数据和有限元等方法的应用,指出了该方法在昆虫学领域的发展潜力,最后对该方法在样本量增加、硬件提升、数据分辨率提高、新算法的开发、分析结果的呈现及3D打印等方面的发展趋势进行了展望。     

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes. Presented at the joint biannual meeting of the SFB-GEIMM-GRIP, Anglet France, 14–19 October, 2006.     

The shrew tamed by Wolff's law: Do functional constraints shape the skull through muscle and bone covariation?

Bone is a highly plastic tissue that reflects the many potential sources of variation in shape. Here, we focus on the functional aspects of bone remodeling. We choose the skull for our analyses because it is a highly integrated system that plays a fundamental role in feeding and is thus, likely under strong natural selection. Its principal mechanical components are the bones and muscles that jointly produce bite force and jaw motion. Understanding the covariations among these three components is of interest to understand the processes driving the evolution of the feeding apparatus. In this study, we quantitatively and qualitatively compare interactions between these three components in shrews from populations known to differ in shape and bite force. Bite force was measured in the field using a force transducer and skull shape was quantified using surface geometric morphometric approaches based on µCT‐scans of the skulls of same individuals. The masseter, temporalis, pterygoideus, and digastricus muscles of these individuals were dissected and their cross sectional areas determined. Our results show strong correlations between bite force and muscle cross sectional areas as well as between bite force and skull shape. Moreover, bite force explains an important amount of skull shape variation. We conclude that interactions between bone shape and muscle characteristics can produce different morpho‐functional patterns that may differ between populations and may provide a suitable target for selection to act upon. J. Morphol. 276:301–309, 2015. © 2014 Wiley Periodicals, Inc.     

ROC analysis: applications to the classification of biological sequences and 3D structures

ROC ('receiver operator characteristics') analysis is a visual as well as numerical method used for assessing the performance of classification algorithms, such as those used for predicting structures and functions from sequence data. This review summarizes the fundamental concepts of ROC analysis and the interpretation of results using examples of sequence and structure comparison. We overview the available programs and provide evaluation guidelines for genomic/proteomic data, with particular regard to applications to large and heterogeneous databases used in bioinformatics.     

3D bioprinting and the current applications in tissue engineering

Bioprinting as an enabling technology for tissue engineering possesses the promises to fabricate highly mimicked tissue or organs with digital control. As one of the biofabrication approaches, bioprinting has the advantages of high throughput and precise control of both scaffold and cells. Therefore, this technology is not only ideal for translational medicine but also for basic research applications. Bioprinting has already been widely applied to construct functional tissues such as vasculature, muscle, cartilage, and bone. In this review, the authors introduce the most popular techniques currently applied in bioprinting, as well as the various bioprinting processes. In addition, the composition of bioink including scaffolds and cells are described. Furthermore, the most current applications in organ and tissue bioprinting are introduced. The authors also discuss the challenges we are currently facing and the great potential of bioprinting. This technology has the capacity not only in complex tissue structure fabrication based on the converted medical images, but also as an efficient tool for drug discovery and preclinical testing. One of the most promising future advances of bioprinting is to develop a standard medical device with the capacity of treating patients directly on the repairing site, which requires the development of automation and robotic technology, as well as our further understanding of biomaterials and stem cell biology to integrate various printing mechanisms for multi‐phasic tissue engineering.     

Ontogenetic development and sexual dimorphism of franciscana dolphin skull: A 3D geometric morphometric approach

The aim of this work was to study the postnatal ontogenetic development of Pontoporia blainvillei skull, identifying major changes on shape, and relating them to relevant factors in the life history of the species. We analyzed a complete ontogenetic series (73♂, 83♀) with three‐dimensional geometric morphometric techniques. Immature dolphins showed a very well‐developed braincase and a poorly developed rostrum, and the principal postnatal changes affected the rostrum and the temporal fossa, both structures implied functionally to the feeding apparatus, thus suggesting a specialized mode for catch fast prey in P. blainvillei. Osseous elements associated with sound production were already well developed on immature dolphins, suggesting the importance of this apparatus since the beginning of postnatal life. Sexual dimorphism was detected on both shape and size variables. Females were bigger than males, in accordance with previous studies. Shape differences between sexes were found on the posterior part of premaxillaries and external bony nares (P < 0.01), suggesting that this sexual dimorphism is related to differences on vocalization capabilities. J. Morphol. 275:1366–1375, 2014. © 2014 Wiley Periodicals, Inc.     

重庆晚侏罗世两处兽脚类足迹组合与四川盆地侏罗纪地层(英文)

重庆市已报道了4处侏罗纪的恐龙足迹点,包括下侏罗统珍珠冲组的大足化石点,该地点发现了中国迄今最古老的蜥脚类行迹;另外两处化石点(南岸和金鸡)的层位曾被视为中或上侏罗统,这里首次将其确认为上侏罗统上沙溪庙组;第4处化石点(成渝), 本文全部作者目前都未曾观察,这里不做描述。南岸化石点是南岸重庆足迹(Chongqingpus nananensis)模式标本的所在地,位于重庆市中心,曾发现过大量兽脚类足迹,如今已消逝在城市化进程中。幸运的是,这批标本被保存于重庆自然博物馆,本文作者曾前后两次对其进行研究,并得出文中的结论。南岸重庆足迹为中型足迹(平均长约29 cm), 最可能被卡岩塔足迹(Kayentapus)所囊括,这批标本中有一些保存着边界不清的拇趾迹。该化石点的其他足迹被归于似异样龙足迹(cf. Anomoepus)。其他较小的、来自重庆市周边中侏罗统中部的足迹此前已被归于跷脚龙足迹(Grallator)。金鸡化石点保存了一条孤立的兽脚类行迹,因其粗壮的特征而被暂时归于似窄足龙足迹(cf. Therangospodus)。金鸡点的行迹也保存了非连续出现的拇趾迹。虽然重庆市和四川盆地及其周边更广泛地区之侏罗纪地层发现的兽脚类足迹日渐增多,但要明确其确切地质年龄及有效的足迹分类依然需要进一步工作。这是因为侏罗纪的恐龙足迹尽管丰富,但显示出连续变化的形态学特征,而保存状况的变化更使其难以在时间与空间上做出定义与鉴别。     

Directional asymmetry in the limbs,skull and pelvis of the silver fox (V. vulpes)

Directional asymmetry (DA) is a characteristic of most vertebrates, most strikingly exhibited by the placement of various organs (heart, lungs, liver, etc.) but also noted in small differences in the metrics of skeletal structures such as the pelvis of certain fish or sauropsids. We have analyzed DA in the skeleton of the fox (V. vulpes), using ～1,000 radiographs of foxes from populations used in the genetic analysis of behavior and morphology. Careful measurements from this robust data base demonstrate that: 1) DA occurs in the limb bones, the ileum, and ischium and in the mandible; 2) regardless of the direction of the length asymmetry vector of a particular skeletal unit, the vectorial direction of length is always opposite to that of width; 3) with the exception of the humerus and radius, there is no correlation or inverse correlation between vectorial amplitudes or magnitudes of bone asymmetries. 4) Postnatal measurements on foxes demonstrate that the asymmetry increases after birth and continues to change (increasing or decreasing) during postnatal growth. 5) A behavior test for preferential use of a specific forelimb exhibited fluctuating asymmetry but not DA. None of the skeletal asymmetries were significantly correlated with a preferential use of a specific forelimb. We suggest that for the majority of fox skeletal parameters, growth on the right and left side of the fox are differentially biased resulting in fixed differences between the two sides in either the rate of growth or the length of the period during which growth occurs. Random effects around these fixed differences perturb the magnitude of the effects such that the magnitudes of length and width asymmetries are not inversely correlated at the level of individual animals. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.     

3D生物打印技术在微生物修复中的应用

排放到环境中的各种农药、多环芳烃、卤代芳烃等有机污染物以及阻燃剂等新兴污染物,对环境污染、农产品质量和环境安全造成了沉重负担。因此,有效去除环境中的有机污染物已成为迫在眉睫的挑战。3D生物打印技术已经在医学材料、制药等行业中发挥着重要作用。现在,越来越多的微生物被确定适合通过3D生物打印生产具有复杂结构和功能的生物材料。微生物的3D生物打印越来越受到环境微生物学家和生物技术专家的关注。本文综述了用于污染物微生物去除的不同3D生物打印技术的原理和优缺点,及用于微生物生物修复技术的可行性,并指出了可能遇到的限制和挑战。