Multibody dynamics analysis (MDA) as a numerical modelling tool to reconstruct the function and palaeobiology of extinct organisms

Recent advances in computer technology have substantially changed the field of palaeontology in the last two decades. Palaeontologists now have a whole new arsenal of powerful digital techniques available to study fossil organisms in unprecedented detail and to test hypotheses regarding function and behaviour. Multibody dynamics analysis (MDA) is one of these techniques and although it originated as a tool used in the engineering and automotive industry, it holds great potential to address palaeontological questions as well. MDA allows the simulation of dynamic movements in complex objects consisting of multiple linked components. As such, this technique is ideally suited to model biological structures and to obtain quantifiable results that can be used to test the function of musculoskeletal systems rigorously. However, despite these advantages, MDA has seen a slow uptake by the palaeontological community. The most likely reason for this lies in the steep learning curve and complexity of the method. This paper provides an overview of the underlying principles of MDA and outlines the main steps involved in conducting analyses. A number of recent studies using MDA to reconstruct the palaeobiology of fossil organisms are presented and the potential for future studies is discussed. Similar to other computational techniques, including finite element analysis and computational fluid dynamics, the non-invasive and exploratory power of MDA makes it ideally suited to study the form and function in vertebrates for which no modern analogues exist.     

Electron backscatter diffraction (EBSD) analysis of maniraptoran eggshells with important implications for microstructural and taphonomic interpretations

Electron backscatter diffraction (EBSD) is a useful tool for gathering crystallographic information from carbonate biominerals because it maps out the orientation of crystal grains very precisely. EBSD has become popular in invertebrate palaeontology but its application in vertebrate palaeontology remains limited. However, the study of fossil eggshells is a field where EBSD has wide potential applicability and provides a quantitative approach to fossil eggshell research as well as new qualitative data. Here we analyse fossil and extant maniraptoran dinosaur eggshells using EBSD analysis emphasizing four different aspects. The mapping imaging clarifies previously ambiguous characters such as squamatic ultrastructure and allows a more objective evaluation of avian and non‐avian maniraptoran eggshell. In particular, our results imply that the presence of an external zone in the manirpatoran eggshell is not diagnostic of avian eggshell. EBSD analysis can be also used for differentiating true pore canals from cracks in the eggshell radial section, thereby determining the biological genuineness or otherwise of a pore‐like structure. Finally, the misorientation angle distribution of the material shows a clear dichotomy that may reflect reproductive brooding strategy, although further studies on contact incubation of palaeognaths and neognaths are needed to confirm this.     

A novel solution for fluid flow problems based on the lattice Boltzmann method

Recently, phase separation and fluid flow problems have represented an important development in fluid dynamics, which has many important industrial applications. Lattice Boltzmann method (LBM) is the numerical method that explains the behaviour of fluid dynamics in mesoscopic scale single-component single-phase and multi-component multiphase flows. In this paper, we study the lattice Boltzmann models (LBMs) in two dimensions (2D) with nine directions (Q9), that is the D2Q9 model was used to study the phase separation and observe that the phenomenon of fluid flow in a cylinder has obstacle and square cavity. The simulation results show that fluid flows in the square cavity and in the cylinder, present phase separation of single-component multiphase fluid flow.     

Fossils of parasites: what can the fossil record tell us about the evolution of parasitism?

Parasites are common in many ecosystems, yet because of their nature, they do not fossilise readily and are very rare in the geological record. This makes it challenging to study the evolutionary transition that led to the evolution of parasitism in different taxa. Most studies on the evolution of parasites are based on phylogenies of extant species that were constructed based on morphological and molecular data, but they give us an incomplete picture and offer little information on many important details of parasite–host interactions. The lack of fossil parasites also means we know very little about the roles that parasites played in ecosystems of the past even though it is known that parasites have significant influences on many ecosystems. The goal of this review is to bring attention to known fossils of parasites and parasitism, and provide a conceptual framework for how research on fossil parasites can develop in the future. Despite their rarity, there are some fossil parasites which have been described from different geological eras. These fossils include the free‐living stage of parasites, parasites which became fossilised with their hosts, parasite eggs and propagules in coprolites, and traces of pathology inflicted by parasites on the host's body. Judging from the fossil record, while there were some parasite–host relationships which no longer exist in the present day, many parasite taxa which are known from the fossil record seem to have remained relatively unchanged in their general morphology and their patterns of host association over tens or even hundreds of millions of years. It also appears that major evolutionary and ecological transitions throughout the history of life on Earth coincided with the appearance of certain parasite taxa, as the appearance of new host groups also provided new niches for potential parasites. As such, fossil parasites can provide additional data regarding the ecology of their extinct hosts, since many parasites have specific life cycles and transmission modes which reflect certain aspects of the host's ecology. The study of fossil parasites can be conducted using existing techniques in palaeontology and palaeoecology, and microscopic examination of potential material such as coprolites may uncover more fossil evidence of parasitism. However, I also urge caution when interpreting fossils as examples of parasites or parasitism‐induced traces. I point out a number of cases where parasitism has been spuriously attributed to some fossil specimens which, upon re‐examination, display traits which are just as (if not more) likely to be found in free‐living taxa. The study of parasite fossils can provide a more complete picture of the ecosystems and evolution of life throughout Earth's history.     

Breaking down shell strength: inferences from experimental compression and future directions enabled by 3D printing

Mollusc and brachiopod shells have served as biological armour for hundreds of millions of years. Studying shell strength in compression experiments can provide insights into macroevolution, predator–prey dynamics, and anthropogenic impacts on aquatic ecosystems. These studies have been conducted across fields including palaeontology, ecology, conservation biology and engineering using a range of techniques for a variety of purposes. Using this approach, studies have demonstrated that predators can cause changes in prey shell morphology in the laboratory over both short timescales and over longer evolutionary timescales. Similarly, environmental factors such as nutrient concentration and ocean acidification have been shown to influence shell strength. Experimental compression tests have been used to study the functional morphology of shell-crushing predators and to test how the taphonomic state of shells (e.g. presence of drill holes, degree of shell degradation) may influence their likelihood of being preserved in the fossil record. This review covers the basic principles and experimental design of compression tests used to infer shell strength. Although many investigations have used this methodology, few provide a detailed explanation of how meaningfully to interpret data generated using compression experiments for those unfamiliar with this method. Furthermore, this review provides a compilation of the findings of studies that have employed these experimental methods to address specific themes: taphonomy, morphology, predation, environmental variables, and climate change. Many authors have used experimental compression tests, however, disparities among methodologies (e.g. in experimental design, taxa, specimen preservation, etc.) limit the applicability of findings from taxon-specific studies to broader eco-evolutionary questions. The review highlights confounding factors, such as shell thickness, size, damage, microstructure, and taphonomic state, and address how they can be mitigated using three-dimensional (3D)-printed model shells. 3D prints have been demonstrated as valuable proxies for understanding aspects of shell morphology that cannot otherwise be experimentally isolated. Using 3D printed models allows simplification of complex biological systems for idealized experimental studies. Such studies can isolate specific aspects of shell morphology to establish fundamental relationships between form and function. Establishing standardized methods of testing shell strength in this way will not only permit comparison across studies but also will enable investigators systematically to add complexity to their models.     

History matters: ecometrics and integrative climate change biology

Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time-an approach we call 'ecometrics'. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.     

Preface: Ostracoda and the four pillars of evolutionary wisdom

Morphology, palaeontology, genetics and ecology are the main scientific domains contributing theories, concepts and new data to evolutionary biology. Ostracods are potentially very good model organisms for evolutionary studies because they combine an excellent fossil record with a wide extant distribution and, therefore, allow studies on both patterns and processes leading to extant diversity. This preface provides an overview of the 15 contributions to the present volume and concludes that this set of papers supports the claim that ostracod studies are situated in all main evolutionary domains.     

Palaeontology and Evolutionary Developmental Biology: A Science of the Nineteenth and Twenty–first Centuries

A wind of change has swept through palaeontology in the past few decades. Contrast Sir Peter Medawar’s dismissive: ‘palaeontology is a particularly undemanding branch of science’ (as recalled by John Maynard Smith in Sabbagh 1999, p. 158) with ‘Palaeontology: grasping the opportunities in the science of the twenty–first century’, the title of a contribution to a special issue of Geobios by the Cambridge palaeontologist, Simon Conway Morris (1998a). The winds of change have come partly from palaeontologists seeking to broaden the impact of their studies and partly from biologists (neontologists) realizing the contributions that palaeontology can make to their disciplines. Consequently, impressions of past life preserved in stone are coming alive. Fossils are being described and analyzed using new tools and languages as the static fossil record becomes a record of transitions in patterns that can be explained and related to biological, ecological, climatic and tectonic changes. The latest addition is evolutionary developmental biology, or ‘evo–devo’, whose language provides a new basis upon which to interpret anatomical change, both materially and mechanistically. In this review I examine the major contributions made by palaeontology, how palaeontology has been linked to evolution and to embryology in the past, and how links with evo–devo have enlivened and will continue to enliven both palaeontology and evo–devo. Closer links between the two fields should illuminate important unresolved issues related to the origin of the metazoans (e.g. Why is there a conflict between molecular clocks and the fossil record in timing the metazoan radiation; were Precambrian metazoan ancestors similar to extant larvae or to miniature adults?) and to diversification of the metazoans (e.g. How do developmental constraints bias the direction of evolution; how do microevolutionary developmental processes relate to macroevolutionary changes?).     

Darwin and palaeontology: a re-evaluation of his interpretation of the fossil record

Charles Darwin's empirical research in palaeontology, especially on fossil invertebrates, has been relatively neglected as a source of insight into his thinking, other than to note that he viewed the fossil record as very incomplete. During the Beagle voyage, Darwin gained extensive experience with a wide diversity of fossil taxa, and he thought deeply about the nature of the fossil record. That record was, for him, a major source of evidence for large-scale transmutation, but much less so for natural selection or single lineages. Darwin's interpretation of the fossil record has been criticised for its focus on incompleteness, but the record as he knew it was extremely incomplete. He was compelled to address this in arguing for descent with modification, which was likely his primary goal. Darwin's gradualism has been both misrepresented and exaggerated, and has distracted us from the importance of the fossil record in his thinking, which should be viewed in the context of the multiple, sometimes competing demands of the multifaceted argument he presented in the Origin of Species.     

An optical-manipulation technique for cells in physiological flows

We have developed a technique to manipulate human red blood cells (RBCs) in hydrodynamic flows. This method applies optical tweezers to trap and move microbead-attached RBCs in a liquid medium at various speeds, while it significantly minimizes laser heating and photon-induced stress for normal operation with laser-trapped cells. Computational fluid dynamics is applied to simulate flow-induced shear stress over the cell membrane and to correlate quantitatively the forces with the cell deformations. RBCs can be manipulated under physiological conditions by this approach, which may open an avenue to design principles for the next generation of cell sorting and delivery.     

Breaking symmetry in non-planar bifurcations: distribution of flow and wall shear stress

Non-planarity in blood vessels is known to influence arterial flows and wall shear stress. To gain insight, computational fluid dynamics (CFD) has been used to investigate effects of curvature and out-of-plane geometry on the distribution of fluid flows and wall shear stresses in a hypothetical non-planar bifurcation. Three-dimensional Navier-Stokes equations for a steady state Newtonian fluid were solved numerically using a finite element method. Non-planarity in one of the two daughter vessels is found to deflect flow from the inner wall of the vessel to the outer wall and to cause changes in the distribution of wall shear stresses. Results from this study agree to experimental observations and CFD simulations in the literature, and support the view that non-planarity in blood vessels is a factor with important haemodynamic significance and may play a key role in vascular biology and pathophysiology.     

计算流体力学在古生物学中的应用——以寒武纪始海百合在COMSOL软件中的模拟为例

提要关于古生物生态位和功能形态学方面的研究通常是推测性的,而定量分析工作较少。此外由于缺少现生生物做对比等诸多因素,使得有些假说存在争议。计算流体力学CFD (computational fluid dynamics)在验证这些推测性假说上具有极大的潜力,并为了解古生物的生活环境以及解释生物在进化过程中的形态变化提供了新的契机。COMSOL Multiphysics作为一款多物理场仿真软件,适用于对古生物的CFD模拟,本文以凯里组始海百合Globoeocrinus模型在COMSOL中的流体实验为案例,来论证关于Globoeocrinus螺旋的腕会使附近的水体形成湍性流动进而帮助滤食这一假说的可能性。流体模拟结果表明在水流流速0.01–0.5 m/s的范围内,Globoeocrinus腕周围并没有出现湍性流动的涡,而是形成了低流速域。低流速域的形成有利于增加始海百合滤取食物的概率。同时文章详细介绍了在COMSOL中进行案例研究的操作步骤,以期望帮助更多的古生物研究者理解和应用CFD技术。     

Functional adaptation of spiriferide brachiopod morphology

It has been suggested that spiriferide morphologies have evolved to adapt to a variety of environmental conditions. Through a computational fluid dynamics approach, we examined how the spiriferide original form was optimized for a lotic condition, specifically addressing the functionalization of the Devonian spiriferide brachiopod Paraspirifer bownockeri to generate passive feeding flows. The results using four models, each of which differed in the development of the spiriferide shell depression, i.e. sulcus, showed that a deeper sulcus functions to create strong spiral flows so as to align on the feeding organ inside the shell. Among the sulcus‐developed models, only the mimic of the natural form could generate comparative slow flows with a stable inflow area. The fossil record of spiriferides shows a morphological trade‐off between the development of the sulcus and wing form. We concluded that spiriferide shells with such a morphological combination evolved to produce various feeding strategies, resulting in diversification.     

Les gisements fossilifères

The papers published in the Annales de Paléontologie over the past hundred years, illustrate the evolving views relevant to the interpretation and excavation of fossil sites. Because of the abundance and quality of their fossil record, the “Fossillagerstätte” has certainly contributed to a boom in palaeontology. These localities have enriched our knowledge about the biodiversity of animals and plants from the different geological periods. At the same time, they have played an important role in reconstructions on ancient environments. The prerequisite for palaeoecological synthesis requires a critical investigation of the geological conditions of the selected localities. Thus, is the goal of taphonomic analysis which has led to the development of the excavation sites. Over time, the palaeontological data has been complemented by observations from the ichnological, sedimentological and geochemical record. Recently, more sophisticated techniques related, for example, to palaeochemistry or to geomicrobiology, have strengthed the message delivered by the fossiliferous localities. One problem, however, is that the growing success of palaeontology with general public, has gained the attention of illicit fossil collectors and the covetousness of traders, resulting in detrimental pillage of the palaeontological sites.     

Rates of speciation in the fossil record

Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.     

Fossil avian eggshell preserves ancient DNA

Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.     

寒武纪大爆发——来自贵州的化石证据*

寒武纪展示了生物演化和生态创新最为关键的一段历史, 在此期间发生了后生动物快速的辐射性演化事件, 被称为“寒武纪大爆发”。近四十年来, 基于寒武纪特异埋藏生物群的大量研究为解密寒武纪大爆发具体过程、主要动物类群起源与生态演化作出了重要贡献。贵州素有古生物王国之称, 在寒武系地层中不仅保存了大量解剖学细节精美的化石资源, 也在多个地区产出时间连续的生物组合演化序列, 在探讨动物起源与演化、全球地层对比及群落古生态学等方面具有极其重要的科研价值。近年来, 以小壳动物群、牛蹄塘生物群、杷榔生物群、剑河生物群、凯里生物群等多个生物群在贵州的发现提供了早期后生生物的新信息, 加密了中国乃至全球早期后生生物特异埋藏化石群的演化链, 为全面揭示寒武纪生物群落面貌、早期多门类后生动物的辐射演化和海洋生物群落演替提供了独特的意义, 最终为深入解读寒武纪大爆发的过程与发生机制提供重要实证。本文简要总结了贵州地区在该领域的主要学术贡献, 结合全球研究进展, 对目前存在的问题和未来研究方向提出展望。     

Large Eddy Simulation and Reynolds-Averaged Navier-Stokes modeling of flow in a realistic pharyngeal airway model: an investigation of obstructive sleep apnea

Computational fluid dynamics techniques employing primarily steady Reynolds-Averaged Navier-Stokes (RANS) methodology have been recently used to characterize the transitional/turbulent flow field in human airways. The use of RANS implies that flow phenomena are averaged over time, the flow dynamics not being captured. Further, RANS uses two-equation turbulence models that are not adequate for predicting anisotropic flows, flows with high streamline curvature, or flows where separation occurs. A more accurate approach for such flow situations that occur in the human airway is Large Eddy Simulation (LES). The paper considers flow modeling in a pharyngeal airway model reconstructed from cross-sectional magnetic resonance scans of a patient with obstructive sleep apnea. The airway model is characterized by a maximum narrowing at the site of retropalatal pharynx. Two flow-modeling strategies are employed: steady RANS and the LES approach. In the RANS modeling framework both k-epsilon and k-omega turbulence models are used. The paper discusses the differences between the airflow characteristics obtained from the RANS and LES calculations. The largest discrepancies were found in the axial velocity distributions downstream of the minimum cross-sectional area. This region is characterized by flow separation and large radial velocity gradients across the developed shear layers. The largest difference in static pressure distributions on the airway walls was found between the LES and the k-epsilon data at the site of maximum narrowing in the retropalatal pharynx.     

Computational fluid dynamics simulations on a Devonian spiriferid Paraspirifer bownockeri (Brachiopoda): Generating mechanism of passive feeding flows

A mechanism of generating passive feeding flow for the Devonian spiriferide brachiopod Paraspirifer bownockeri was theoretically elucidated through fluid dynamics simulations for flow around rigid shells. The RANS equations were used as a turbulence model, and the unsteady incompressible flow was solved using the finite volume method. Two directions of ventral and dorsal flows were investigated as typical cases where little exchange flow occurs inside the shells. The digital model of the shell was constructed using image processing of X-ray CT images of a shell replica made by molding a polycarbonate plate to a well-preserved fossil specimen of Paraspirifer. To examine the effect of flow velocity, three conditions of ambient flow velocity were adopted for both the ventral and dorsal flows. The pressure distribution along the gape showed that a relatively high pressure occurred around the sulcus in all simulated cases. This high pressure generated inflow from the sulcus and subsequent spiral internal flow, especially in fast ambient flows. This means that the sulcus generated the considerable pressure gradient around the gape passively and generated the stable intake of seawater and a spiral flow of water inside the shell for feeding. We conclude that the shell form of certain spiriferides could generate spiral flows so as to promote passive feeding, and the sulcus is interpreted as an important form for the passive intake of water.