Pollen and spores: Microscopic keys to understanding the earth's biodiversity

The most distinctive feature of planet Earth is that, unlike any other world in this solar system, it is rich in biodiversity. Our own species, which evolved as part of the biosphere that sustains us, has the intelligence and curiosity to explore the world around us and to understand its complexity. Given the environmental challenges that lie ahead we have much to learn by exploring all aspects of biodiversity. One astonishingly informative field of investigation is palynology, the study of the pollen grains and spores of plants. These microscopic, self-contained biological units are surrounded by chemically resistant cell walls with distinctive structures and symmetry. They can provide insights into such fundamental questions as how and when plants first colonised the land or how the earth's vegetation has developed through geological time and on finer time scales. They provide phylogenetic evidence important in plant systematics and model systems for understanding plant development at the cellular level. This short voyage through the microscopic world of pollen grains and spores is a personal account of the interest and importance of these microscopic keys to understanding the earth's biodiversity.     

Spatial hierarchical approach in community ecology: a way beyond high context-dependency and low predictability in local phenomena

Patterns and functioning of communities, which are determined by a set of processes operating at a large variety of spatial and temporal scales, exhibit quite high context-dependency and low predictability at the fine spatial scales at which recent studies have concentrated. More attention to broader scale and across-scale phenomena may be useful to search for general patterns and rules in communities. In this context, it is effective to incorporate hierarchical spatial scale explicitly into the experimental and sampling design of field studies, an approach referred to here as the spatial hierarchical approach, focusing on a particular assemblage in which biological interaction and species life history are well known. The spatial hierarchical approach can provide insight into the effects of scale in operating processes and answers to a number of important questions in community ecology such as: (1) detection of patterns and processes in spatiotemporal variability in communities, including how to explain the partitioning of pattern information of species diversity at a broad scale into finer scales, and the pattern of spatial variability of community properties at the finest spatial scale; (2) evaluation of changes in patterns observed in macroecology at finer scales; (3) testing of models explaining the coexistence of competing species; and (4) detection of latitudinal patterns in spatiotemporal variability in communities and their causal processes.     

SCALE AND HIERARCHY IN MACROEVOLUTION

Abstract: Scale and hierarchy must be incorporated into any conceptual framework for the study of macroevolution, i.e. evolution above the species level. Expansion of temporal and spatial scales reveals evolutionary patterns and processes that are virtually inaccessible to, and unpredictable from, short‐term, localized observations. These larger‐scale phenomena range from evolutionary stasis at the species level and the mosaic assembly of complex morphologies in ancestral forms to the non‐random distribution in time and space of the origin of major evolutionary novelties, as exemplified by the Cambrian explosion and post‐extinction recoveries of metazoans, and the preferential origin of major marine groups in onshore environments and tropical waters. Virtually all of these phenomena probably involve both ecological and developmental factors, but the integration of these components with macroevolutionary theory has only just begun. Differential survival and reproduction of units can occur at several levels within a biological hierarchy that includes DNA sequences, organisms, species and clades. Evolution by natural selection can occur at any level where there is heritable variation that affects birth and death of units by virtue of interaction with the environment. This dynamic can occur when selfish DNA sequences replicate disproportionately within genomes, when organisms enjoy fitness advantages within populations (classical Darwinian selection), when differential speciation or extinction occurs within clades owing to organismic properties (effect macroevolution), and when differential speciation or extinction occurs within clades owing to emergent, species‐level properties (in the strict sense species selection). Operationally, emergent species‐level properties such as geographical range can be recognized by testing whether their macroevolutionary effects are similar regardless of the different lower‐level factors that produce them. Large‐scale evolutionary trends can be driven by transformation of species, preferential production of species in a given direction, differential origination or extinction, or any combination of these; the potential for organismic traits to hitch‐hike on other factors that promote speciation or damp extinction is high. Additional key attributes of macroevolutionary dynamics within biological hierarchies are that (1) hierarchical levels are linked by upward and downward causation, so that emergent properties at a focal level do not impart complete independence; (2) hierarchical effects are asymmetrical, so that dynamics at a given focal level need not propagate upwards, but will always cascade downwards; and (3) rates are generally, although not always, faster at lower hierarchical levels. Temporal and spatial patterns in the origin of major novelties and higher taxa are significantly discordant from those at the species and genus levels, suggesting complex hierarchical effects that remain poorly understood. Not only are many of the features promoting survivorship during background times ineffective during mass extinctions, but also they are replaced in at least some cases by higher‐level, irreducible attributes such as clade‐level geographical range. The incorporation of processes that operate across hierarchical levels and a range of temporal and spatial scales has expanded and enriched our understanding of evolution.     

A comprehensive view of polyamine and histamine metabolism to the light of new technologies

Polyamines and histamine are biogenic amines with multiple biological roles. In spite of the evidence for the involvement of both polyamines and histamine metabolism impairment in several highly prevalent pathological conditions, multiple questions concerning the molecular processes behind these effects remain to be elucidated. More comprehensive and systemic studies integrating molecular biology, biophysical and bioinformatics tools could contribute to accelerate the advances in this research area. This review is designed to underscore the main questions to be answered in polyamine and histamine research and how these new systemic approaches could help to find these answers.     

A hierarchical multi‐scale analysis of the spatial relationship between parasitism and host density in urban habitats

Studies on spatial density dependence in parasitism have paid scarce attention to how changes in host density at different hierarchical scales could influence parasitism in an herbivore at a particular scale. Here, we evaluated if rates of parasitism per leaf (by the whole parasitic complex and by dominant species) of the specialist leaf miner Liriomyza commelinae (Diptera: Agromyzidae) respond to variations in host density at the leaf, plant patch and site levels in an urban setting. We used multi‐level Bayesian models that incorporate the spatial hierarchy occurring in this system, as well as habitat factors previously found to have an effect on the L. commelinae parasitoid community in an urban context (patch size, patch isolation and urbanization level). According to the fitted model, overall parasitism rates decreased with increasing number of mines per leaf, being independent of host‐density variations at patch and site level. Patch structure was found to have a strong effect on parasitism rates per leaf. The analysis of parasitism by parasitoid species separately showed consistent results with the response at community level. These results suggest that parasitism of the parasitoid community here studied would be sensitive to hierarchical cues related to the host at the leaf level and to the host habitat at the patch level.     

Combining field experiments and individual-based modeling to identify the dynamically relevant organizational scale in a field system

Community ecologists continually strive to build analytical models that realistically describe long‐term dynamics of the systems they study. A key step in this process is identifying which details are relevant for predicting dynamics. Currently, this remains a limiting step in development of analytical theory because experimental field ecology, which provides the key empirical insight, and theoretical ecology, which translates empirical knowledge into analytical theory, remain weakly linked. I illustrate how an individual‐based computational model of species interactions is a useful way to bridge the gulf between empirical research and theory development. I built a computational model that reproduced key natural history and biological detail of an old‐field interaction web composed of a predator species, a herbivore species and two plant groups that had been the subject of extensive previous field research. I examined, using simulation experiments, how individual behavior of herbivores in response to changing resource and predator abundance scaled to long‐term population‐level and community‐level dynamics. The simulation experiments revealed that the long‐term community dynamics could be highly predictable because of two counterintuitive reasons. First, seasonality was a strong forcing variable on the system that removed the possibility of serial dependence in population abundance over time. Second, because of seasonality, short‐term behavioral responses of herbivores played a much stronger role in shaping community structure than longer‐term processes such as density responses. So, simply knowing the short‐term responses of herbivores at the evolutionary ecological level was sufficient to forecast the long‐term outcome of experimental manipulations. This study shows that an individual‐based model, once it is calibrated to the real‐world field system, can provide key insight into the biological detail that analytical models should include to predict long‐term dynamics.     

Numerical modeling of bone tissue adaptation—A hierarchical approach for bone apparent density and trabecular structure

In this work, a three-dimensional model for bone remodeling is presented, taking into account the hierarchical structure of bone. The process of bone tissue adaptation is mathematically described with respect to functional demands, both mechanical and biological, to obtain the bone apparent density distribution (at the macroscale) and the trabecular structure (at the microscale). At global scale bone is assumed as a continuum material characterized by equivalent (homogenized) mechanical properties. At local scale a periodic cellular material model approaches bone trabecular anisotropy as well as bone surface area density. For each scale there is a material distribution problem governed by density-based design variables which at the global level can be identified with bone relative density. In order to show the potential of the model, a three-dimensional example of the proximal femur illustrates the distribution of bone apparent density as well as microstructural designs characterizing both anisotropy and bone surface area density. The bone apparent density numerical results show a good agreement with Dual-energy X-ray Absorptiometry (DXA) exams. The material symmetry distributions obtained are comparable to real bone microstructures depending on the local stress field. Furthermore, the compact bone porosity is modeled giving a transversal isotropic behavior close to the experimental data. Since, some computed microstructures have no permeability one concludes that bone tissue arrangement is not a simple stiffness maximization issue but biological factors also play an important role.     

Decomposing the heterogeneity of species distributions into multiple scales: a hierarchical framework for large‐scale count surveys

We introduce a novel spatially explicit framework for decomposing species distributions into multiple scales from count data. These kinds of data are usually positively skewed, have non‐normal distributions and are spatially autocorrelated. To analyse such data, we propose a hierarchical model that takes into account the observation process and explicitly deals with spatial autocorrelation. The latent variable is the product of a positive trend representing the non‐constant mean of the species distribution and of a stationary positive spatial field representing the variance of the spatial density of the species distribution. Then, the different scales of emergent structures of the distribution of the population in space are modelled from the latent density of the species distribution using multi‐scale variogram models. Multi‐scale kriging is used to map the spatial patterns previously identified by the multi‐scale models. We show how our framework yields robust and precise estimates of the relevant scales both for spatial count data simulated from well‐defined models, and in a real case‐study based on seabird count data (the common guillemot Uria aalge) provided by large‐scale aerial surveys of the Bay of Biscay (France) performed over a winter. Our stochastic simulation study provides guidelines on the expected uncertainties of the scales estimates. Our results indicate that the spatial structure of the common guillemot can be modelled as a three‐level hierarchical system composed of a very broad‐scale pattern (～ 200 km) with a stable location over time that might be environmentally controlled, a broad‐scale pattern (～ 50 km) with a variable shape and location, that might be related to shifts in prey distribution, and a fine‐scale pattern (～ 10 km) with a rather stable shape and location, that might be controlled by behavioural processes. Our framework enables the development of robust, scale‐dependent hypotheses regarding the potential ecological processes that control species distributions.     

Hierarchical Dragonfly Wing: Microstructure-Biomechanical Behavior Relations

The dragonfly wing,which consists of veins and membrane,is of biological hierarchical material.We observed the cross-sections of longitudinal veins and membrane using Environmental Scanning Electron Microscopy (ESEM).Based on the experiments and previous studies,we described the longitudinal vein and the membrane in terms of two hierarchical levels of organization of composite materials at the micro- and nano-scales.The longitudinal vein of dragonfly wing has a complex sandwich structure with two chitinous shells and a protein layer,and it is considered as the first hierarchical level of the vein.Moreover,the chitinous shells are concentric multilayered structures.Clusters of nano-fibrils grow along the circumferential orientation embedded into the protein layer.It is considered as the second level of the hierarchy.Similarly,the upper and lower epidermises of membrane constitute the first hierarchical level of organization in micro scale.Similar to the vein shell,the membrane epidermises were found to be a paralleled multilayered structure,defined as the second hierarchical level of the membrane.Combining with the mechanical behavior analysis of the dragonfly wing,we concluded that the growth orientation of the hierarchical structure of the longitudinal vein and membrane is relevant to its biomechanical behavior.     

Controlling composition of coexisting phases via molecular transitions

Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely unexplored how the behavior of phase-separating systems with molecular transitions differs between thermodynamic equilibrium and cases in which the detailed balance of the molecular transition rates is broken because of the presence of fuel. Here, we present a model of a phase-separating ternary mixture in which two components can convert into each other. At thermodynamic equilibrium, we find that molecular transitions can give rise to a lower dissolution temperature and thus reentrant phase behavior. Moreover, we find a discontinuous thermodynamic phase transition in the composition of the droplet phase if both converting molecules attract themselves with similar interaction strength. Breaking the detailed balance of the molecular transition leads to quasi-discontinuous changes in droplet composition by varying the fuel amount for a larger range of intermolecular interactions. Our findings showcase that phase separation with molecular transitions provides a versatile mechanism to control properties of intracellular and synthetic condensates via discontinuous switches in droplet composition.     

Linking the concept of scale to studies of biological diversity: evolving approaches and tools

Although the concepts of scale and biological diversity independently have received rapidly increasing attention in the scientific literature since the 1980s, the rate at which the two concepts have been investigated jointly has grown much more slowly. We find that scale considerations have been incorporated explicitly into six broad areas of investigation related to biological diversity: (1) heterogeneity within and among ecosystems, (2) disturbance ecology, (3) conservation and restoration, (4) invasion biology, (5) importance of temporal scale for understanding processes, and (6) species responses to environmental heterogeneity. In addition to placing the papers of this Special Feature within the context of brief summaries of the expanding literature on these six topics, we provide an overview of tools useful for integrating scale considerations into studies of biological diversity. Such tools include hierarchical and structural-equation modelling, kriging, variable-width buffers, k -fold cross-validation, and cascading graph diagrams, among others. Finally, we address some of the major challenges and research frontiers that remain, and conclude with a look to the future.     

Chromatin assembly: a basic recipe with various flavours

Packaging of eukaryotic genomes into chromatin is a hierarchical mechanism, starting with histone deposition onto DNA to produce nucleosome arrays, which then further fold and ultimately form functional domains. Recent studies provide interesting insight into how nucleosome assembly is coordinated with histone and DNA metabolism and underline the combined contribution of histone chaperones and chromatin remodelers. How these factors operate at a molecular level is a matter of current investigation. New data highlight the importance of histone dimers as deposition entities for de novo nucleosome assembly and identify dedicated machineries involved in histone variant deposition.     

Uncovering the different scales in deer–forest interactions

Deer are regarded to be a keystone species as they play a crucial role in the way an ecosystem functions. Most deer–forest interaction studies apply a single scale — process of analyzing ecological interactions by only taking into account one dependent variable — to understand how deer browsing behavior shapes different forest components, but they overlook the fact that forests respond to multiple scales simultaneously. This research evaluates the effect of browsing by wild deer on temperate and boreal forests at different scales by synthesizing seminal papers, specifically (a) what are the effects of deer population density in forest regeneration? (b) What are the effects of deer when forests present diverging spatial characteristics? (c) What are the effects on vegetation at different temporal scales? and (d) What are the hierarchical effects of deer when considering other trophic levels? Additionally, a framework based on modern technology is proposed to answer the multiscale research questions previously identified. When analyzing deer–forest interactions at different scales, the strongest relationships occur at the extremes. For example: when deer assemblage occurs in low or high density and is composed of a mix of small and large species. As forests on poor soils remain restrained in size, isolated and chronically browsed. When forests harbor incomplete trophic levels, the effects spill over to lower trophic levels. To better understand the complexities in deer–forest interactions, researchers should combine technology‐based instruments like fixed sensors and drones with field‐tested methods such observational studies and experiments to tackle multiscale research questions.     

Biological hierarchies and the nature of extinction

Hierarchy theory recognises that ecological and evolutionary units occur in a nested and interconnected hierarchical system, with cascading effects occurring between hierarchical levels. Different biological disciplines have routinely come into conflict over the primacy of different forcing mechanisms behind evolutionary and ecological change. These disconnects arise partly from differences in perspective (with some researchers favouring ecological forcing mechanisms while others favour developmental/historical mechanisms), as well as differences in the temporal framework in which workers operate. In particular, long‐term palaeontological data often show that large‐scale (macro) patterns of evolution are predominantly dictated by shifts in the abiotic environment, while short‐term (micro) modern biological studies stress the importance of biotic interactions. We propose that thinking about ecological and evolutionary interactions in a hierarchical framework is a fruitful way to resolve these conflicts. Hierarchy theory suggests that changes occurring at lower hierarchical levels can have unexpected, complex effects at higher scales due to emergent interactions between simple systems. In this way, patterns occurring on short‐ and long‐term time scales are equally valid, as changes that are driven from lower levels will manifest in different forms at higher levels. We propose that the dual hierarchy framework fits well with our current understanding of evolutionary and ecological theory. Furthermore, we describe how this framework can be used to understand major extinction events better. Multi‐generational attritional loss of reproductive fitness (MALF) has recently been proposed as the primary mechanism behind extinction events, whereby extinction is explainable solely through processes that result in extirpation of populations through a shutdown of reproduction. While not necessarily explicit, the push to explain extinction through solely population‐level dynamics could be used to suggest that environmentally mediated patterns of extinction or slowed speciation across geological time are largely artefacts of poor preservation or a coarse temporal scale. We demonstrate how MALF fits into a hierarchical framework, showing that MALF can be a primary forcing mechanism at lower scales that still results in differential survivorship patterns at the species and clade level which vary depending upon the initial environmental forcing mechanism. Thus, even if MALF is the primary mechanism of extinction across all mass extinction events, the primary environmental cause of these events will still affect the system and result in differential responses. Therefore, patterns at both temporal scales are relevant.     

Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: linking theory to data

Understanding stability across ecological hierarchies is critical for landscape management in a changing world. Recent studies showed that synchrony among lower‐level components is key to scaling temporal stability across two hierarchical levels, whether spatial or organizational. But an extended framework that integrates both spatial scale and organizational level simultaneously is required to clarify the sources of ecosystem stability at large scales. However, such an extension is far from trivial when taking into account the spatial heterogeneities in real‐world ecosystems. In this paper, we develop a partitioning framework that bridges variability and synchrony measures across spatial scales and organizational levels in heterogeneous metacommunities. In this framework, metacommunity variability is expressed as the product of local‐scale population variability and two synchrony indices that capture the temporal coherence across species and space, respectively. We develop an R function ‘var.partition’ and apply it to five types of desert plant communities to illustrate our framework and test how diversity shapes synchrony and variability at different hierarchical levels. As the observation scale increased from local populations to metacommunities, the temporal variability of plant productivity was reduced mainly by factors that decreased species synchrony. Species synchrony decreased from local to regional scales, and spatial synchrony decreased from species to community levels. Local and regional species diversity were key factors that reduced species synchrony at the two scales. Moreover, beta diversity contributed to decreasing spatial synchrony among communities. We conclude that our new framework offers a valuable toolbox for future empirical studies to disentangle the mechanisms and pathways by which ecological factors influence stability at large scales.     

The carrying capacity of ecosystems

We analyse the concept of carrying capacity (CC), from populations to the biosphere, and offer a definition suitable for any level. For communities and ecosystems, the CC evokes density‐dependence assumptions analogous to those of population dynamics. At the biosphere level, human CC is uncertain and dynamic, leading to apprehensive rather than practical conclusions. The term CC is widely used among ecological disciplines but remains vague and elusive. We propose the following definition: the CC is ‘the limit of growth or development of each and all hierarchical levels of biological integration, beginning with the population, and shaped by processes and interdependent relationships between finite resources and the consumers of those resources’. The restrictions of the concept relate to the hierarchical approach. Emergent properties arise at each level, and environmental heterogeneity restrains the measurement and application of the CC. Because the CC entails a myriad of interrelated, ever‐changing biotic and abiotic factors, it must not be assumed constant, if we are to derive more effective and realistic management schemes. At the ecosystem level, stability and resilience are dynamic components of the CC. Historical processes that help shape global biodiversity (e.g. continental drift, glaciations) are likely drivers of large‐scale changes in the earth's CC. Finally, world population growth and consumption of resources by humanity will necessitate modifications to the paradigm of sustainable development, and demand a clear and fundamental understanding of how CC operates across all biological levels.     

丹顶鹤多尺度生境选择机制——以黄河三角洲自然保护区为例

生境在鸟类生活史中发挥着重要的作用,关系到鸟类的生存和繁衍。由于鸟类对环境变化的响应发生在等级序列空间尺度上,基于多尺度的研究更能深入刻画鸟类-环境之间关系。以丹顶鹤(Grus japonensis)为研究对象,以其迁徙和越冬的重要地区-黄河三角洲自然保护区为研究区域,应用等级方差分解法和等级划分法,分析丹顶鹤与微生境、斑块、景观尺度因子之间的关系,探求丹顶鹤生境选择的主要影响因素和尺度。等级方差分解结果表明,在第1等级水平,景观尺度因子与微生境、斑块尺度因子之间的联合效应大于独立效应,景观尺度因子的独立效应大于微生境和斑块尺度因子;在第2等级水平,景观尺度上的景观组成因子重要性大于景观结构因子,微生境尺度上的植被和水分因子为重要影响因素。等级划分结果表明,景观尺度上,翅碱蓬滩涂、水体面积大小是主要影响因素;微生境尺度上,植被盖度和水深为主要限制因子;在斑块尺度上,斑块类型对丹顶鹤生境选择最为重要。研究认为,在黄河三角洲自然保护区,景观尺度是影响丹顶鹤生境选择的主要尺度,景观尺度因子通过与微生境和斑块尺度因子的独立和联合作用制约着丹顶鹤在保护区的生境选择和空间分布格局。建议加强对翅碱蓬滩涂、芦苇沼泽、水体等湿地生境的保护和管理,规范和控制保护区内人类活动强度。     

Multi-scale lung modeling

Multi-scale modeling of biological systems has recently become fashionable due to the growing power of digital computers as well as to the growing realization that integrative systems behavior is as important to life as is the genome. While it is true that the behavior of a living organism must ultimately be traceable to all its components and their myriad interactions, attempting to codify this in its entirety in a model misses the insights gained from understanding how collections of system components at one level of scale conspire to produce qualitatively different behavior at higher levels. The essence of multi-scale modeling thus lies not in the inclusion of every conceivable biological detail, but rather in the judicious selection of emergent phenomena appropriate to the level of scale being modeled. These principles are exemplified in recent computational models of the lung. Airways responsiveness, for example, is an organ-level manifestation of events that begin at the molecular level within airway smooth muscle cells, yet it is not necessary to invoke all these molecular events to accurately describe the contraction dynamics of a cell, nor is it necessary to invoke all phenomena observable at the level of the cell to account for the changes in overall lung function that occur following methacholine challenge. Similarly, the regulation of pulmonary vascular tone has complex origins within the individual smooth muscle cells that line the blood vessels but, again, many of the fine details of cell behavior average out at the level of the organ to produce an effect on pulmonary vascular pressure that can be described in much simpler terms. The art of multi-scale lung modeling thus reduces not to being limitlessly inclusive, but rather to knowing what biological details to leave out.