Intensive agriculture erodes β-diversity at large scales

Biodiversity is declining from unprecedented land conversions that replace diverse, low-intensity agriculture with vast expanses under homogeneous, intensive production. Despite documented losses of species richness, consequences for β-diversity, changes in community composition between sites, are largely unknown, especially in the tropics. Using a 10-year data set on Costa Rican birds, we find that low-intensity agriculture sustained β-diversity across large scales on a par with forest. In high-intensity agriculture, low local (α) diversity inflated β-diversity as a statistical artefact. Therefore, at small spatial scales, intensive agriculture appeared to retain β-diversity. Unlike in forest or low-intensity systems, however, high-intensity agriculture also homogenised vegetation structure over large distances, thereby decoupling the fundamental ecological pattern of bird communities changing with geographical distance. This ~40% decline in species turnover indicates a significant decline in β-diversity at large spatial scales. These findings point the way towards multi-functional agricultural systems that maintain agricultural productivity while simultaneously conserving biodiversity.     

At what scales does aggregated dispersal lead to coexistence?

Aggregation during dispersal can allow persistence of weak competitors, by creating conditions where stronger competitors are more likely to interact with conspecifics than with heterospecifics. However, aggregation mechanisms operate over a wide range of spatial scales, and species experience space in very different ways. The net effect of dispersal aggregation on coexistence will depend on how these scales interact. We show that it is possible to approximate the effects of aggregated dispersal on coexistence by considering three empirically measurable parameters: the spatial scale of interaction (how strongly competition drops off with distance), the spatial scale of aggregation (how large propagule packets are), and the temporal scale of aggregation (how frequently packets arrive). We use a novel metacommunity moment closure based on this approximation and stochastic simulations to show that aggregated dispersal allows for coexistence only when the stronger competitor is both aggregated and interacts at the same or a smaller spatial scale than the weaker competitor. When species interact and are aggregated at the same scales, coexistence outcomes are only weakly sensitive to the absolute scales of interaction and aggregation, as long as the scale of interaction is smaller than the scale of aggregation. However, coexistence is sensitive to the time‐scale of aggregation: increasing the frequency of packet arrival substantially reduces the region of fitness inequalities where both species persist. Finally, coexistence is less likely and global extinction of both competitors is more frequent when aggregation is fixed (with a constant number of propagules per packet), compared to density‐dependent (number of propagules increases with adult density).     

Plant–microbe interactions at multiple scales across a high-elevation landscape

Here we review the numerous studies of plant–microbe interactions conducted at the Niwot Ridge LTER site in Colorado, USA. By synthesising work at scales ranging from the rhizosphere to the landscape, we offer a mechanistic view of how these interactions are essential to understanding the spatial and temporal structuring of plant and microbial communities across this diverse and changing landscape. These new insights are also important for making predictions about how both plant and microbial communities and populations will respond to future changes in this environment, especially with regard to the potential uphill movement of plants and microbes in response to climate change and nitrogen deposition. We predict that the uphill movement of plants and microbes will be especially apparent, and have the most impact, in areas of the alpine that are now mostly plant free. These areas are currently undergoing a shift from a microbe-dominated ecosystem to one where microbe–plant interactions will play a critical role in reducing nutrient losses to downstream ecosystems.     

Diversity–invasibility relationships across multiple scales in disturbed forest understoreys

Non-native plant species richness may be either negatively or positively correlated with native species due to differences in resource availability, propagule pressure or the scale of vegetation sampling. We investigated the relationships between these factors and both native and non-native plant species at 12 mainland and island forested sites in southeastern Ontario, Canada. In general, the presence of non-native species was limited: <20% of all species at a site were non-native and non-native species cover was <4% m⁻² at 11 of the 12 sites. Non-native species were always positively correlated with native species, regardless of spatial scale and whether islands were sampled. Additionally, islands had a greater abundance of non-native species. Non-native species richness across mainland sites was significantly negatively correlated with mean shape index, a measure of the ratio of forest edge to area, and positively correlated with the mean distance to the nearest forest patch. Other factors associated with disturbance and propagule pressure in northeastern North America forests, including human land use, white-tailed deer populations, understorey light, and soil nitrogen, did not explain non-native richness nor cover better than the null models. Our results suggest that management strategies for controlling non-native plant invasions should aim to reduce the propagule pressure associated with human activities, and maximize the connectivity of forest habitats to benefit more poorly dispersed native species.     

Do evolutionary constraints on thermal performance manifest at different organizational scales?

The two foremost hypotheses on the evolutionary constraints on an organism's thermal sensitivity – the hotter‐is‐better expectation, and the specialist–generalist trade‐off – have received mixed support from empirical studies testing for their existence. Could these conflicting results reflect confusion regarding the organizational level (i.e. species > population > individual) at which these constraints should manifest? We propose that these evolutionary constraints should manifest at different organizational levels because of differences in their underlying causes and requirements. The hotter‐is‐better expectation should only manifest across separate evolutionary units (e.g. species, populations), and not within populations. The specialist–generalist trade‐off, by contrast, should manifest within as well as between separate evolutionary units. We measured the thermal sensitivity of sprint performance for 440 rainforest sun skinks (Lampropholis coggeri) representing 10 populations, and used the resulting performance curves to test for evidence for the hypothesized constraints at two organizational levels: (i) across populations and (ii) within populations. As predicted, the hotter‐is‐better expectation was evident only at the across‐population level, whereas the specialist–generalist trade‐off was evident within, as well as across, populations. Our results suggest that, depending on the processes that drive them, evolutionary constraints can manifest at different organizational levels. Consideration of these underlying processes, and the organizational level at which a constraint should manifest, may help resolve conflicting empirical results.     

How do microbiota associated with an invasive seaweed vary across scales?

Communities are shaped by scale dependent processes. To study the diversity and variation of microbial communities across scales, the invasive and widespread seaweed Agarophyton vermiculophyllum presents a unique opportunity. We characterized pro‐ and eukaryotic communities associated with this holobiont across its known distribution range, which stretches over the northern hemisphere. Our data reveal that community composition and diversity in the holobiont vary at local but also larger geographic scales. While processes acting at the local scale (i.e., within population) are the main structuring drivers of associated microbial communities, changes in community composition also depend on processes acting at larger geographic scales. Interestingly, the largest analysed scale (i.e., native and non‐native ranges) explained variation in the prevalence of predicted functional groups, which could suggest a functional shift in microbiota occurred over the course of the invasion process. While high variability in microbiota at the local scale supports A. vermiculophyllum to be a generalist host, we also identified a number of core taxa. These geographically independent holobiont members imply that cointroduction of specific microbiota may have additionally promoted the invasion process.     

Fish scale development: Hair today, teeth and scales yesterday?

A group of genes in the tumour necrosis factor signalling pathway are mutated in humans and mice with ectodermal dysplasias--a failure of hair and tooth development. A mutation has now been identified in one of these genes, ectodysplasin-A receptor, in the teleost fish Medaka, that results in a failure of scale formation.     

Dispersal scales up the biodiversity–productivity relationship in an experimental source-sink metacommunity

The influence of biodiversity on ecosystem functioning is a major concern of ecological research. However, the biodiversity–ecosystem functioning relationship has very often been studied independently from the mechanisms allowing coexistence. By considering the effects of dispersal and niche partitioning on diversity, the metacommunity perspective predicts a spatial scale-dependence of the shape of the relationship. Here, we present experimental evidence of such scale-dependent patterns. After approximately 500 generations of diversification in a spatially heterogeneous environment, we measured functional diversity (FD) and productivity at both local and regional scales in experimental source-sink metacommunities of the bacterium Pseudomonas fluorescens SBW25. At the regional scale, environmental heterogeneity yielded high levels of FD and we observed a positive correlation between diversity and productivity. At the local scale, intermediate dispersal increased local FD through a mass effect but there was no correlation between diversity and productivity. These experimental results underline the importance of considering the mechanisms maintaining biodiversity and the appropriate spatial scales in understanding its relationship with ecosystem functioning.     

Multi-scale modeling in biology: how to bridge the gaps between scales?

Human physiological functions are regulated across many orders of magnitude in space and time. Integrating the information and dynamics from one scale to another is critical for the understanding of human physiology and the treatment of diseases. Multi-scale modeling, as a computational approach, has been widely adopted by researchers in computational and systems biology. A key unsolved issue is how to represent appropriately the dynamical behaviors of a high-dimensional model of a lower scale by a low-dimensional model of a higher scale, so that it can be used to investigate complex dynamical behaviors at even higher scales of integration. In the article, we first review the widely-used different modeling methodologies and their applications at different scales. We then discuss the gaps between different modeling methodologies and between scales, and discuss potential methods for bridging the gaps between scales.     

Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?

The recognition of transmembrane helices by the translocon is primarily guided by the average hydrophobicity of the potential transmembrane helix. However, the exact hydrophobicity of each amino acid can be identified in several different ways. The free energy of transfer for amino acid analogues between a hydrophobic media, for example, octanol and water can be measured or obtained from simulations, the hydrophobicity can also be estimated by statistical properties from known transmembrane segments and finally the contribution of each amino acid type for the probability of translocon recognition has recently been measured directly. Although these scales correlate quite well, there are clear differences between them and it is not well understood which scale represents neither the biology best nor what the differences are. Here, we try to provide some answers to this by studying the ability of different scales to recognize transmembrane helices and predict the topology of transmembrane proteins. From this analysis it is clear that the biological hydrophobicity scale as well scales created from statistical analysis of membrane helices perform better than earlier experimental scales that are mainly based on measurements of amino acid analogs and not directly on transmembrane helix recognition. Using these results we identified the properties of the scales that perform better than other scales. We find, for instance, that the better performing scales consider proline more hydrophilic. This shows that transmembrane recognition is not only governed by pure hydrophobicity but also by the helix preferences for amino acids, as proline is a strong helix breaker. Proteins 2014; 82:2190–2198. © 2014 Wiley Periodicals, Inc.     

Ecological hierarchies and self-organisation – Pattern analysis,modelling and process integration across scales

A continuing discussion in applied and theoretical ecology focuses on the relationship of different organisational levels and on how ecological systems interact across scales. We address principal approaches to cope with complex across-level issues in ecology by applying elements of hierarchy theory and the theory of complex adaptive systems. A top-down approach, often characterised by the use of statistical techniques, can be applied to analyse large-scale dynamics and identify constraints exerted on lower levels. Current developments are illustrated with examples from the analysis of within-community spatial patterns and large-scale vegetation patterns. A bottom-up approach allows one to elucidate how interactions of individuals shape dynamics at higher levels in a self-organisation process; e.g., population development and community composition. This may be facilitated by various modelling tools, which provide the distinction between focal levels and resulting properties. For instance, resilience in grassland communities has been analysed with a cellular automaton approach, and the driving forces in rodent population oscillations have been identified with an agent-based model. Both modelling tools illustrate the principles of analysing higher level processes by representing the interactions of basic components.The focus of most ecological investigations on either top-down or bottom-up approaches may not be appropriate, if strong cross-scale relationships predominate. Here, we propose an ‘across-scale-approach’, closely interweaving the inherent potentials of both approaches. This combination of analytical and synthesising approaches will enable ecologists to establish a more coherent access to cross-level interactions in ecological systems.     

Individual flowering phenology shapes plant–pollinator interactions across ecological scales affecting plant reproduction

The balance of pollination competition and facilitation among co-flowering plants and abiotic resource availability can modify plant species and individual reproduction. Floral resource succession and spatial heterogeneity modulate plant–pollinator interactions across ecological scales (individual plant, local assemblage, and interaction network of agroecological infrastructure across the farm). Intraspecific variation in flowering phenology can modulate the precise level of spatio-temporal heterogeneity in floral resources, pollen donor density, and pollinator interactions that a plant individual is exposed to, thereby affecting reproduction. We tested how abiotic resources and multi-scale plant–pollinator interactions affected individual plant seed set modulated by intraspecific variation in flowering phenology and spatio-temporal floral heterogeneity arising from agroecological infrastructure. We transplanted two focal insect-pollinated plant species (Cyanus segetum and Centaurea jacea, n = 288) into agroecological infrastructure (10 sown wildflower and six legume–grass strips) across a farm-scale experiment (125 ha). We applied an individual-based phenologically explicit approach to match precisely the flowering period of plant individuals to the concomitant level of spatio-temporal heterogeneity in plant–pollinator interactions, potential pollen donors, floral resources, and abiotic conditions (temperature, water, and nitrogen). Individual plant attractiveness, assemblage floral density, and conspecific pollen donor density (C. jacea) improved seed set. Network linkage density increased focal species seed set and modified the effect of local assemblage richness and abundance on C. segetum. Mutual dependence on pollinators in networks increased C. segetum seed set, while C. jacea seed set was greatest where both specialization on pollinators and mutual dependence was high. Abiotic conditions were of little or no importance to seed set. Intra- and interspecific plant–pollinator interactions respond to spatio-temporal heterogeneity arising from agroecological management affecting wild plant species reproduction. The interplay of pollinator interactions within and between ecological scales affecting seed set implies a co-occurrence of pollinator-mediated facilitative and competitive interactions among plant species and individuals.     

The scales of the zebrafish: host–microbiota interactions from proteins to populations

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Can inverse density dependence at small spatial scales produce dynamic instability in animal populations?

All else being equal, inversely density-dependent (IDD) mortality destabilizes population dynamics. However, stability has not been investigated for cases in which multiple types of density dependence act simultaneously. To determine whether IDD mortality can destabilize populations that are otherwise regulated by directly density-dependent (DDD) mortality, I used scale transition approximations to model populations with IDD mortality at smaller “aggregation” scales and DDD mortality at larger “landscape” scales, a pattern observed in some reef fish and insect populations. I evaluated dynamic stability for a range of demographic parameter values, including the degree of compensation in DDD mortality and the degree of spatial aggregation, which together determine the relative importance of DDD and IDD processes. When aggregation-scale survival was a monotonically increasing function of density (a “dilution” effect), dynamics were stable except for extremely high levels of aggregation combined with either undercompensatory landscape-scale density dependence or certain values of adult fecundity. When aggregation-scale survival was a unimodal function of density (representing both “dilution” and predator “detection” effects), instability occurred with lower levels of aggregation and also depended on the values of fecundity, survivorship, detection effect, and DDD compensation parameters. These results suggest that only in extreme circumstances will IDD mortality destabilize dynamics when DDD mortality is also present, so IDD processes may not affect the stability of many populations in which they are observed. Model results were evaluated in the context of reef fish, but a similar framework may be appropriate for a diverse range of species that experience opposing patterns of density dependence across spatial scales.     

KL₄ peptide induces reversible collapse structures on multiple length scales in model lung surfactant

We investigated the effects of KL₄, a 21-residue amphipathic peptide approximating the overall ratio of positively charged to hydrophobic amino acids in surfactant protein B (SP-B), on the structure and collapse of dipalmitoylphosphatidylcholine and palmitoyl-oleoyl-phosphatidylglycerol monolayers. As reported in prior work on model lung surfactant phospholipid films containing SP-B and SP-B peptides, our experiments show that KL₄ improves surfactant film reversibility during repetitive interfacial cycling in association with the formation of reversible collapse structures on multiple length scales. Emphasis is on exploring a general mechanistic connection between peptide-induced nano- and microscale reversible collapse structures (silos and folds).     

Factors determining plant–neighbour interactions on different spatial scales in young species-rich grassland communities

In naturally colonised species-rich grassland communities, we examined the properties of a plant’s aboveground neighbourhood that affect its performance (aboveground biomass). To this end a range of neighbourhood parameters were measured: number, biomass and species richness of the neighbours, number and biomass of the conspecific neighbours, and light availability at the base of the target plant. We also determined at which neighbourhood size the strongest target plant–neighbour interactions occurred, and whether conspecific neighbours affected competitively stronger or weaker target species differently. Target plant performance varied with target identity, and was significantly affected by light availability and the number of neighbouring plants (neighbourhood density). Depending on the target species, there was also an effect of total neighbour biomass on plant performance. The target plants were most strongly affected by their neighbours within a 3-cm distance, which could account for 78% of the variance in target biomass. Number or biomass of the conspecific neighbours did not contribute to the explanation of target performance in any of the target species. Whereas in an 8-cm neighbourhood the amount of light penetration was the strongest predictor of target performance, the number of neighbours was more important in a 3-cm neighbourhood. These experimental results might be useful to extend existing neighbourhood competition models for one or two species to multi-species competition models.     

Two lowland stream riffles – linkages between physical habitats and macroinvertebrates across multiple spatial scales

The physical structure of two riffles in a lowland Danish stream was studied and its importance for the composition and density of the macroinvertebrate communities was evaluated. The two riffles were visually assessed to be very similar, but measurements revealed that they differed in overall hydraulic conditions, stability, substratum composition and consolidation. Differences affected abundance of both burrowing and surface dwelling macroinvertebrates. The unstable unconsolidated riffle had higher total macroinvertebrate abundance (4137 m⁻² vs. 1698 m⁻²), diptera abundance (2329 m⁻² vs. 386 m⁻²) and total estimated species richness (31.7 vs. 28.8) as well as lower evenness (0.77 vs. 0.83) than the compact riffle. Among samples within the unconsolidated riffle, variations in macroinvertebrate communities were related to differences in mean substratum particle size. Here a linear log–log relationship existed between macroinvertebrate abundance, the abundance of EPT taxa and the median particle size (r ² _total = 0.46, p = 0.002; r ² _EPT = 0.73, p < 0.001). No similar relationships were evident on the consolidated riffle. Moreover, macroinvertebrate communities on the unconsolidated riffle were dominated by species with a high colonising potential. Despite being assessed to the same morphological unit, physical variation between riffles was surprisingly high as the riffles differed substantially with respect to consolidation, substratum heterogeneity and overall hydraulic structure. Macroinvertebrate community structure and composition also differed between riffles despite being drawn from the same species pool. The findings address the question if we use the correct methods and parameters when assessing the macroinvertebrate communities at the scale of the morphological unit.