Multiple scales and the relationship between density and spatial aggregation in littoral zone communities

Understanding the constraints on community composition at multiple spatial scales is an immense challenge to community and ecosystem ecologists. As community composition is basically the composite result of species’ spatial patterning, studying this spatial patterning across scales may yield clues as to which scales of environmental heterogeneity influence communities. The now widely documented positive interspecific relationship between ‘regional’ range and mean ‘local’ abundance has become a generalisation describing the spatial patterning of species at coarse scales. We address some of the shortcomings of this generalisation, as well as examine the cross‐scale spatial patterning (aggregation and density levels) of littoral‐benthic invertebrates in very large lakes. Specifically, we (a) determine whether the positive range‐abundance relationship can be reinterpreted in terms of the actual spatial structure of species distributions, (b) examine the relationship between aggregation and density across different spatial scales, and (c) determine whether the spatial patterning of species (e.g. low density/aggregated distribution) is constant across scales, that is, whether our interpretation of a species spatial pattern is dependent on the scale at which we choose to observe the system. Spatial aggregation of littoral invertebrates was generally a negative function of mean density across all spatial scales and seasons (autumn and spring). This relationship may underlie positive range‐abundance relationships. Species that were uncommon and highly aggregated at coarse spatial scales can be abundant and approach random distributions at finer spatial scales. Also, the change in spatial aggregation of closely related taxa across spatial scales was idiosyncratic. The idiosyncratic cross‐scale spatial patterning of species implies that multiple scales of environmental heterogeneity may influence the assembly of littoral communities. Due to the multi‐scale, species‐specific spatial patterning of invertebrates, littoral zone communities form a complex spatial mosaic, and a ‘spatially explicit’ approach will be required by limnologists in order to link littoral‐benthic community patterns with ecosystem processes in large oligotrophic lakes.     

The herd,a source of flexibility for livestock farming systems faced with uncertainties?

'Adapt to endure' has become a necessity in agriculture, but the means to do so remain largely undefined. The aim of this literature review is to analyse how the herd contributes to a livestock farming system's capacity to adapt to a changing world and evolve when the future is uncertain. We identify six categories of elements linked to the herd, called 'sources of flexibility', that are used to manage perturbation. The first three are: using the animal's adaptive capacities, using the diversity of species and breeds and combining the diversity of animal products. The last three are: organising the mobility of animals and livestock farmers, juggling the herd numbers and mastering the balance between productivity and herd survival. These sources of flexibility are described in the literature by studying the different ways in which they are used. For example, the 'juggle herd numbers' source is described by volume, categories of animals, type of transfer, such as births, purchases or gifts, and timing of use, especially linked to the timing of the perturbation. Identified studies also compare or rank sources and analyse the connections between them. The flexibility framework (management science) is used for this analysis according to the levels of organisation of a livestock farming system: a strategic level referring to long-term options and to the capacity to modify the system structure, and an operational level referring to adjustment decisions during the productive cycle, the presence or absence of intervention by the livestock farmer, and the time scales involved. We conclude that the decision to use one or another source (in terms of modalities, alternatives, scheduling and combinations) is made according to the production objectives, the structural means, the type/frequency/intensity of perturbations and the context/environment. Consequently, the flexibility of a livestock farming system cannot be assessed in absolute terms. Enhancing flexibility needs management of all elements and scales involved (and not only the herd), and requires diversity to be organised at different scales.     

Single-cell patterning and axis characterization in the murine and human definitive endoderm

Defining the precise regionalization of specified definitive endoderm progenitors is critical for understanding the mechanisms underlying the generation and regeneration of respiratory and digestive organs, yet the patterning of endoderm progenitors remains unresolved, particularly in humans. We performed single-cell RNA sequencing on endoderm cells during the early somitogenesis stages in mice and humans. We developed molecular criteria to define four major endoderm regions (foregut, lip of anterior intestinal portal, midgut, and hindgut) and their developmental pathways. We identified the cell subpopulations in each region and their spatial distributions and characterized key molecular features along the body axes. Dorsal and ventral pancreatic progenitors appear to originate from the midgut population and follow distinct pathways to develop into an identical cell type. Finally, we described the generally conserved endoderm patterning in humans and clear differences in dorsal cell distribution between species. Our study comprehensively defines single-cell endoderm patterning and provides novel insights into the spatiotemporal process that drives establishment of early endoderm domains.Subject terms: Developmental biology, Stem cells     

Mobility at the scale of meters

When archeologists discuss mobility, we are most often referring to a phenomenon that operates on the scale of kilometers, 1 - 4 but much of human mobility, at least if measured in terms of frequency of movement, occurs at much smaller scales, ranging from centimeters to tens of meters. Here we refer to the movements we make within the confines of our homes or places of employment. With respect to nomadic peoples, movements at this scale would include movements within campsites. Understanding mobility at small scales is important to archeology because small‐scale mobility decisions are a critical factor affecting spatial patterning observed in archeological sites. In this paper, we examine the factors affecting small‐scale mobility decisions in a Mongolian reindeer herder summer camp and the implications of those decisions with regard to archeological spatial patterning.     

紫花野菊叶上毛状体的发育形态学研究

利用光镜和扫描电镜研究了紫花野菊叶表面毛状体结构和发育。较详细地描述和讨论了这两种毛的个体发育过程。     

Interactions between Shh, Sostdc1 and Wnt signaling and a new feedback loop for spatial patterning of the teeth

Each vertebrate species displays specific tooth patterns in each quadrant of the jaw: the mouse has one incisor and three molars, which develop at precise locations and at different times. The reason why multiple teeth form in the jaw of vertebrates and the way in which they develop separately from each other have been extensively studied, but the genetic mechanism governing the spatial patterning of teeth still remains to be elucidated. Sonic hedgehog (Shh) is one of the key signaling molecules involved in the spatial patterning of teeth and other ectodermal organs such as hair, vibrissae and feathers. Sostdc1, a secreted inhibitor of the Wnt and Bmp pathways, also regulates the spatial patterning of teeth and hair. Here, by utilizing maternal transfer of 5E1 (an anti-Shh antibody) to mouse embryos through the placenta, we show that Sostdc1 is downstream of Shh signaling and suggest a Wnt-Shh-Sostdc1 negative feedback loop as a pivotal mechanism controlling the spatial patterning of teeth. Furthermore, we propose a new reaction-diffusion model in which Wnt, Shh and Sostdc1 act as the activator, mediator and inhibitor, respectively, and confirm that such interactions can generate the tooth pattern of a wild-type mouse and can explain the various tooth patterns produced experimentally.     

Spatial patterns of weeds along a gradient of landscape complexity

Processes that drive spatial patterning among plant species are of ongoing interest, mostly because these patterns have implications for the structure and function of plant communities. We investigated the spatial strategies of weeds focusing on how spatial patterns of weeds are mediated by agricultural landscape complexity and species life-history attributes. We quantified the spatial distribution of 110 weed species using data collected in ten landscapes in central western France along a gradient of landscape complexity, from structurally complex (numerous small fields) to structurally simple (few large fields). We then related differences observed in species’ distribution patterns to ecological attributes of species for resource exploitation and dispersion. Our study reveals that weeds were spatially aggregated at the landscape scale. Their spatial patterns are related to the frequency of occurrence of weeds but surprisingly not directly to the seed dispersal type, nor to the degree of habitat specialization. We show that landscape complexity had no direct effect on the spatial patterning of weeds but through interactions with species attributes. Our results point to the importance of interactions between landscape complexity and species attributes in the spatial patterning of weed species even in intensively managed fields. These patterns appear to be a consequence of the spatial arrangement of landscape elements as well as the result of landscape filtering on species attributes.     

A two-step patterning process increases the robustness of periodic patterning in the fly eye

Complex periodic patterns can self-organize through dynamic interactions between diffusible activators and inhibitors. In the biological context, self-organized patterning is challenged by spatial heterogeneities (‘noise’) inherent to biological systems. How spatial variability impacts the periodic patterning mechanism and how it can be buffered to ensure precise patterning is not well understood. We examine the effect of spatial heterogeneity on the periodic patterning of the fruit fly eye, an organ composed of ～800 miniature eye units (ommatidia) whose periodic arrangement along a hexagonal lattice self-organizes during early stages of fly development. The patterning follows a two-step process, with an initial formation of evenly spaced clusters of ～10 cells followed by a subsequent refinement of each cluster into a single selected cell. Using a probabilistic approach, we calculate the rate of patterning errors resulting from spatial heterogeneities in cell size, position and biosynthetic capacity. Notably, error rates were largely independent of the desired cluster size but followed the distributions of signaling speeds. Pre-formation of large clusters therefore greatly increases the reproducibility of the overall periodic arrangement, suggesting that the two-stage patterning process functions to guard the pattern against errors caused by spatial heterogeneities. Our results emphasize the constraints imposed on self-organized patterning mechanisms by the need to buffer stochastic effects. Author summary Complex periodic patterns are common in nature and are observed in physical, chemical and biological systems. Understanding how these patterns are generated in a precise manner is a key challenge. Biological patterns are especially intriguing, as they are generated in a noisy environment; cell position and cell size, for example, are subject to stochastic variations, as are the strengths of the chemical signals mediating cell-to-cell communication. The need to generate a precise and robust pattern in this ‘noisy’ environment restricts the space of patterning mechanisms that can function in the biological setting. Mathematical modeling is useful in comparing the sensitivity of different mechanisms to such variations, thereby highlighting key aspects of their design.We use mathematical modeling to study the periodic patterning of the fruit fly eye. In this system, a highly ordered lattice of differentiated cells is generated in a two-dimensional cell epithelium. The pattern is first observed by the appearance of evenly spaced clusters of ～10 cells that express specific genes. Each cluster is subsequently refined into a single cell, which initiates the formation and differentiation of a miniature eye unit, the ommatidium. We formulate a mathematical model based on the known molecular properties of the patterning mechanism, and use a probabilistic approach to calculate the errors in cluster formation and refinement resulting from stochastic cell-to-cell variations (‘noise’) in different quantitative parameters. This enables us to define the parameters most influencing noise sensitivity. Notably, we find that this error is roughly independent of the desired cluster size, suggesting that large clusters are beneficial for ensuring the overall reproducibility of the periodic cluster arrangement. For the stage of cluster refinement, we find that rapid communication between cells is critical for reducing error. Our work provides new insights into the constraints imposed on mechanisms generating periodic patterning in a realistic, noisy environment, and in particular, discusses the different considerations in achieving optimal design of the patterning network.     

四川省缙云山栲树种群结构和动态的初步研究

 栲树(Castanopsis fargesii)是亚热带常绿阔叶林的建群种和优势种之一。本文应用相邻格子样方法和每木调查法进行野外抽样,对缙云山栲树种群的立木级结构和分布格局及其动态特点进行了分析,并探讨了研究长生命期常绿阔叶树种种群的方法问题。结果表明,应用立木级结构代替年龄结构研究栲树种群的结构和动态特征是适用的。立木级结构和存活曲线分析表明栲树种群具有增长型的动态特征。同时应用一次性的调查资料研究了栲树种群的分布格局及其动态特征,显示出栲树种群在其发育过程中,分布格局由集群分布向随机分布变化,而且这种变化是和种群的数量的动态变化有关。引起分布格局发生变化的主要原因是种内及种间竞争所导致的自疏和它疏。     

Chinmo and neuroblast temporal identity

Although spatial patterning during embryonic development is well characterized, a corresponding framework for temporal patterning has not been established. In this issue, Zhu et al. (2006) identify the Chinmo protein as conferring temporal identity on the neural progeny of Drosophila neuroblasts, revealing appealing parallels with spatial patterning.     

Topographical and physicochemical modification of material surface to enable patterning of living cells.

Precise control of the architecture of multiple cells in culture and in vivo via precise engineering of the material surface properties is described as cell patterning. Substrate patterning by control of the surface physicochemical and topographic features enables selective localization and phenotypic and genotypic control of living cells. In culture, control over spatial and temporal dynamics of cells and heterotypic interactions draws inspiration from in vivo embryogenesis and haptotaxis. Patterned arrays of single or multiple cell types in culture serve as model systems for exploration of cell-cell and cell-matrix interactions. More recently, the patterned arrays and assemblies of tissues have found practical applications in the fields of Biosensors and cell-based assays for Drug Discovery. Although the field of cell patterning has its origins early in this century, an improved understanding of cell-substrate interactions and the use of microfabrication techniques borrowed from the microelectronics industry have enabled significant recent progress. This review presents the important early discoveries and emphasizes results of recent state-of-the-art cell patterning methods. The review concludes by illustrating the growing impact of cell patterning in the areas of bioelectronic devices and cell-based assays for drug discovery.     

Continued range expansion of introduced reindeer on South Georgia

Reindeer were introduced 70 years ago to the Stromness Bay area on the subantarctic island of South Georgia, and the herd is still surviving. Two glaciers confine the herd, and movements are restricted even within the area due to a rugged topography. The Husvik herd has recently expanded its range within this area, and today approximately 88% of the vegetated area is affected by grazing. The grazing effects are described, and the value of the introduction as a natural experiment is discussed.     

Why did the buffalo cross the park? Resource shortages,but not infections,drive dispersal in female African buffalo (Syncerus caffer)

Dispersal facilitates population health and maintains resilience in species via gene flow. Adult dispersal occurs in some species, is often facultative, and is poorly understood, but has important management implications, particularly with respect to disease spread. Although the role of adult dispersal in spreading disease has been documented, the potential influence of disease on dispersal has received little attention. African buffalo (Syncerus caffer) are wide‐ranging and harbor many pathogens that can affect nearby livestock. Dispersal of adult buffalo has been described, but ecological and social drivers of buffalo dispersal are poorly understood. We investigated drivers of adult buffalo dispersal during a 4‐year longitudinal study at Kruger National Park, South Africa. We monitored the spatial movement of 304 female buffalo in two focal areas using satellite and radio collars, capturing each buffalo every 6 months to assess animal traits and disease status. We used generalized linear mixed models to determine whether likelihood of dispersal for individual female buffalo was influenced by animal traits, herd identity, environmental variables, gastrointestinal parasites, or microparasite infections. The likelihood and drivers of buffalo dispersal varied by herd, area, and year. In the Lower Sabie herd, where resources were abundant, younger individuals were more likely to disperse, with most dispersal occurring in the early wet season and during an unusually dry year, 2009. In the resource‐poor Crocodile Bridge area, buffalo in poor condition were most likely to disperse. Our findings suggest that dispersal of female buffalo is driven by either seasonal (Lower Sabie) or perhaps social (Crocodile Bridge) resource restriction, indicating resource limitation and dispersal decisions are tightly linked for this social ungulate. We found no direct effects of infections on buffalo dispersal, assuaging fears that highly infectious individuals might be more prone to dispersing, which could accelerate the spatial spread of infectious diseases.     

Herbivores as architects of savannas: inducing and modifying spatial vegetation patterning

In this paper, we address the question whether and through which mechanisms herbivores can induce spatial patterning in savanna vegetation, and how the role of herbivory as a determinant of vegetation patterning changes with herbivore density and the pre-existing pattern of vegetation. We thereto developed a spatially explicit simulation model, including growth of grasses and trees, vertical zonation of browseable biomass, and spatially explicit foraging by grazers and browsers. We show that herbivores can induce vegetation patterning when two key assumptions are fulfilled. First, herbivores have to increase the attractiveness of a site while foraging so that they will revisit this site, e.g. through an increased availability or quality of forage. Second, foraging should be spatially explicit, e.g. when foraging at a site influences vegetation at larger spatial scales or when vegetation at larger spatial scales influences the selection and utilisation of a site. The interaction between these two assumptions proved to be crucial for herbivores to produce spatial vegetation patterns, but then only at low to intermediate herbivore densities. High herbivore densities result in homogenisation of vegetation. Furthermore, our model shows that the pre-existing spatial pattern in vegetation influences the process of vegetation patterning through herbivory. However, this influence decreases when the heterogeneity and dominant scale of the initial vegetation decreases. Hence, the level of adherence of the herbivores to forage in pre-existing patches increases when these pre-existing patches increase in size and when the level of vegetation heterogeneity increases. The findings presented in this paper, and critical experimentation of their ecological validity, will increase our understanding of vegetation patterning in savanna ecosystems, and the role of plant–herbivore interactions therein.     

Topographical and Physicochemical Modification of Material Surface to Enable Patterning of Living Cells

ABSTRACT:?

Precise control of the architecture of multiple cells in culture and in vivo via precise engineering of the material surface properties is described as cell patterning. Substrate patterning by control of the surface physicochemical and topographic features enables selective localization and phenotypic and genotypic control of living cells. In culture, control over spatial and temporal dynamics of cells and heterotypic interactions draws inspiration from in vivo embryogenesis and haptotaxis. Patterned arrays of single or multiple cell types in culture serve as model systems for exploration of cell-cell and cell-matrix interactions. More recently, the patterned arrays and assemblies of tissues have found practical applications in the fields of Biosensors and cell-based assays for Drug Discovery. Although the field of cell patterning has its origins early in this century, an improved understanding of cell-substrate interactions and the use of microfabrication techniques borrowed from the microelectronics industry have enabled significant recent progress. This review presents the important early discoveries and emphasizes results of recent state-of-the-art cell patterning methods. The review concludes by illustrating the growing impact of cell patterning in the areas of bioelectronic devices and cell-based assays for drug discovery.     

Contribution of rarity and commonness to patterns of species richness

There is little understanding in ecology as to how biodiversity patterns emerge from the distribution patterns of individual species. Here we consider the question of the contributions of rare (restricted range) and common (widespread) species to richness patterns. Considering a species richness pattern, is most of the spatial structure, in terms of where the peaks and troughs of diversity lie, caused by the common species or the rare species (or neither)? Using southern African and British bird richness patterns, we show here that commoner species are most responsible for richness patterns. While rare and common species show markedly different species richness patterns, most spatial patterning in richness is caused by relatively few, more common, species. The level of redundancy we found suggests that a broad understanding of what determines the majority of spatial variation in biodiversity may be had by considering only a minority of species.     

Scale-dependent inhibition drives regular tussock spacing in a freshwater marsh

Regular spatial patterning is common in nature, and various mechanisms of self-organization have been proposed to explain regular patterning. We report on regular spatial patterning in Carex stricta in a freshwater wetland and investigate the applicability of theoretical models that explain regular patterning based on inhibition, facilitation, or interaction between the two. Spectral analysis of aerial photographs revealed that tussocks were regularly spaced at an average distance of 60 cm. Photosynthetically active radiation varied significantly with distance from the tussock and was lowest at intermediate distance from the tussock center (15-40 cm). Using transplants to assay growth conditions, we found that C. stricta grew well in all distance classes with and without natural C. stricta biomass, except at intermediate distances when buried in C. stricta wrack. Our experimental results reveal that C. stricta inhibits its growth in a scale-dependent manner: inhibition was found to peak at intermediate distance from the tussock. We compared three alternative models to examine potential mechanisms driving regularity and found that, similar to our experimental results, scale-dependent inhibition provides the best explanation for the observed regular tussock spacing. Our study underlines the importance of scale-dependent feedback in the formation of regular spatial patterning in ecosystems.     

Modelling both dominance and species distribution provides a more complete picture of changes to mangrove ecosystems under climate change

Dominant species influence the composition and abundance of other species present in ecosystems. However, forecasts of distributional change under future climates have predominantly focused on changes in species distribution and ignored possible changes in spatial and temporal patterns of dominance. We develop forecasts of spatial changes for the distribution of species dominance, defined in terms of basal area, and for species occurrence, in response to sea level rise for three tree taxa within an extensive mangrove ecosystem in northern Australia. Three new metrics are provided, indicating the area expected to be suitable under future conditions (E_occupied), the instability of suitable area (E_instability) and the overlap between the current and future spatial distribution (E_overlap). The current dominance and occurrence were modelled in relation to a set of environmental variables using boosted regression tree (BRT) models, under two scenarios of seedling establishment: unrestricted and highly restricted. While forecasts of spatial change were qualitatively similar for species occurrence and dominance, the models of species dominance exhibited higher metrics of model fit and predictive performance, and the spatial pattern of future dominance was less similar to the current pattern than was the case for the distributions of species occurrence. This highlights the possibility of greater changes in the spatial patterning of mangrove tree species dominance under future sea level rise. Under the restricted seedling establishment scenario, the area occupied by or dominated by a species declined between 42.1% and 93.8%, while for unrestricted seedling establishment, the area suitable for dominance or occurrence of each species varied from a decline of 68.4% to an expansion of 99.5%. As changes in the spatial patterning of dominance are likely to cause a cascade of effects throughout the ecosystem, forecasting spatial changes in dominance provides new and complementary information in addition to that provided by forecasts of species occurrence.     

The importance of water regimes operating at small spatial scales for the diversity and structure of wetland vegetation

1. In most cases, the most important determinant of wetland vegetation is the water regime. Although water regime is usually described and managed at the scale of whole wetlands, the patterning of vegetation is likely to be determined by water regimes that are experienced at much finer spatial scales. In this study, we assess the significance of internal heterogeneity in water regimes and the role that this heterogeneity plays in vegetation patterning. 2. The effects of water regime on wetland plant species richness and vegetation structure were studied at Dowd Morass, a 1500 ha, Ramsar‐listed wetland in south‐eastern Australia that is topographically heterogeneous. Data on plant variables and water depth were collected along 45 (50 m) transects throughout the wetland and related to water regimes assigned individually for each transect. Wetland plants were assigned to plant functional groups (PFG) that describe the response of plants to the presence or absence of water at different life stages. 3. The classification of water depth data indicated four distinct water regimes in the wetland that were differentiated primarily by the duration of the dry period. Representatives of all PFGs co‐existed over small spatial scales where topographical variation was present, and the richness and cover of understorey species declined as transects became more deeply and permanently flooded. Some PFGs (e.g. amphibious fluctuation tolerator‐low growing and amphibious fluctuation responder‐morphologically plastic) were eliminated by extended periods of flooding, which increased the cover but not richness of submerged plants. Species richness and foliage projective cover declined as water regimes shifted from shallow and frequently exposed conditions to regimes typified by deeper and longer inundation. Cover of the structurally dominant woody species was compromised by deeply flooded conditions but vegetative regeneration occurred despite high water levels. 4. Internal topographical variation generates mosaics of water regimes at fine spatial scales that allow plant species with different water regime requirements to co‐exist over small distances. Deep water and an absence of dry periods result in decreased cover of plants and an overall loss of species richness in the understorey. Water regimes are described that promote regeneration and cover of structurally dominant taxa and increased species richness in the understorey. The study demonstrates a strong association between vegetation and the diverse water regimes that exist within a single wetland, a pattern that will be useful for modelling the effects of modified water regimes on wetland vegetation.     

Modulation of the extracellular matrix patterning of thrombospondins by actin dynamics and thrombospondin oligomer state

Thrombospondins (TSPs) are evolutionarily-conserved, secreted glycoproteins that interact with cell surfaces and extracellular matrix (ECM) and have complex roles in cell interactions. Unlike the structural components of the ECM that form networks or fibrils, TSPs are deposited into ECM as arrays of nanoscale puncta. The cellular and molecular mechanisms for the patterning of TSPs in ECM are poorly understood. In the present study, we investigated whether the mechanisms of TSP patterning in cell-derived ECM involves actin cytoskeletal pathways or TSP oligomer state. From tests of a suite of pharmacological inhibitors of small GTPases, actomyosin-based contractility, or actin microfilament integrity and dynamics, cytochalasin D and jasplakinolide treatment of cells were identified to result in altered ECM patterning of a model TSP1 trimer. The strong effect of cytochalasin D indicated that mechanisms controlling puncta patterning depend on global F-actin dynamics. Similar spatial changes were obtained with endogenous TSPs after cytochalasin D treatment, implicating physiological relevance. Under matched experimental conditions with ectopically-expressed TSPs, the magnitude of the effect was markedly lower for pentameric TSP5 and Drosophila TSP, than for trimeric TSP1 or dimeric Ciona TSPA. To distinguish between the variables of protein sequence or oligomer state, we generated novel, chimeric pentamers of TSP1. These proteins accumulated within ECM at higher levels than TSP1 trimers, yet the effect of cytochalasin D on the spatial distribution of puncta was reduced. These findings introduce a novel concept that F-actin dynamics modulate the patterning of TSPs in ECM and that TSP oligomer state is a key determinant of this process.