Foraging across a variable landscape: behavioral decisions made by woodland caribou at multiple spatial scales

We examined the foraging behavior of woodland caribou (Rangifer tarandus caribou) relative to the spatial and temporal heterogeneity of their environment. We assessed (1) whether caribou altered their behavior over time while making trade-offs between forage abundance and accessibility; and (2) whether foraging decisions were consistent across spatial scales (i.e., as scale increased, similar decision criteria were used at each scale). We discuss whether caribou adjusted their behavior to take advantage of changing forage availability through time and space. At the scale of the feeding site (as revealed by discriminant function analyses), caribou in both forested and alpine (above tree-line) environments selected sites where the biomass of particular lichen species was greatest and snow the least deep. Caribou did not select those species with the highest nutritional value (i.e., digestible protein and energy) in either area. Where snow depth, density, and hardness limited access to terrestrial lichens in the forest, caribou foraged instead at those trees with the greatest amount of arboreal lichen. Selection of lichen species and the influence of snow differed across time, indicating that in this system the abundance or accessibility of forage temporally influenced foraging behavior. A path analysis of forest data and multiple regression analysis of alpine data were used to test the hypothesis that variables important at the scale of the feeding site explained foraging effort at the scale of the patch. For forest patches, our hypothesized model reliably explained foraging effort, but not all variables that were statistically important at the scale of the feeding site were significant predictors at the scale of the patch. For alpine patches, our hypothesized model did not explain a statistically significant portion of the variation in the number of feeding sites within the patch, and none of the individual variables from the feeding site remained statistically significant at the patch scale. The incongruity between those variables important at the scale of the feeding site and those important at the patch showed that spatial scale affects the foraging decisions of woodland caribou. At the scale of the landscape, there was a trade-off between forage abundance and accessibility. Relative to the alpine environment, caribou in the forest foraged at feeding sites and patches with greater amounts of less variably distributed lichen, but deeper less variable snow depths. Considering the behavioral plasticity of woodland caribou, there may be no distinct advantage to foraging in one landscape over the other.     

Universal scaling of species‐abundance distributions across multiple scales

The scale‐dependent species abundance distribution (SAD) is fundamental in ecology, but few spatially explicit models of this pattern have thus far been studied. Here we show spatially explicit neutral model predictions for SADs over a wide range of spatial scales, which appear to match empirical patterns qualitatively. We find that the assumption of a log‐series SAD in the metacommunity made by spatially implicit neutral models can be justified with a spatially explicit model in the large area limit. Furthermore, our model predicts that SADs on multiple scales are characterized by a single, compound parameter that represents the ratio of the survey area to the species’ average biogeographic range (which is in turn set by the speciation rate and the dispersal distance). This intriguing prediction is in line with recent empirical evidence for a universal scaling of the species‐area curve. Hence we hypothesize that empirical SAD patterns will show a similar universal scaling for many different taxa and across multiple spatial scales.     

Strong neutral spatial effects shape tree species distributions across life stages at multiple scales

Traditionally, ecologists use lattice (regional summary) count data to simulate tree species distributions to explore species coexistence. However, no previous study has explicitly compared the difference between using lattice count and basal area data and analyzed species distributions at both individual species and community levels while simultaneously considering the combined scenarios of life stage and scale. In this study, we hypothesized that basal area data are more closely related to environmental variables than are count data because of strong environmental filtering effects. We also address the contribution of niche and the neutral (i.e., solely dependent on distance) factors to species distributions. Specifically, we separately modeled count data and basal area data while considering life stage and scale effects at the two levels with simultaneous autoregressive models and variation partitioning. A principal coordinates of neighbor matrix (PCNM) was used to model neutral spatial effects at the community level. The explained variations of species distribution data did not differ significantly between the two types of data at either the individual species level or the community level, indicating that the two types of data can be used nearly identically to model species distributions. Neutral spatial effects represented by spatial autoregressive parameters and the PCNM eigenfunctions drove species distributions on multiple scales, different life stages and individual species and community levels in this plot. We concluded that strong neutral spatial effects are the principal mechanisms underlying the species distributions and thus shape biodiversity spatial patterns.     

Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines

To understand the structure and function of large molecular machines, accurate knowledge of their stoichiometry is essential. In this study, we developed an integrated targeted proteomics and super‐resolution microscopy approach to determine the absolute stoichiometry of the human nuclear pore complex (NPC), possibly the largest eukaryotic protein complex. We show that the human NPC has a previously unanticipated stoichiometry that varies across cancer cell types, tissues and in disease. Using large‐scale proteomics, we provide evidence that more than one third of the known, well‐defined nuclear protein complexes display a similar cell type‐specific variation of their subunit stoichiometry. Our data point to compositional rearrangement as a widespread mechanism for adapting the functions of molecular machines toward cell type‐specific constraints and context‐dependent needs, and highlight the need of deeper investigation of such structural variants.     

Environmentally co‐occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context‐dependent fitness effects

Plasmids are important mobile elements that can facilitate genetic exchange and local adaptation within microbial communities. We compared the sequences of four co‐occurring pQBR family environmental mercury resistance plasmids and measured their effects on competitive fitness of a Pseudomonas fluorescens SBW25 host, which was isolated at the same field site. Fitness effects of carriage differed between plasmids and were strongly context dependent, varying with medium, plasmid status of competitor and levels of environmental mercury. The plasmids also varied widely in their rates of conjugation and segregational loss. We found that few of the plasmid‐borne accessory genes could be ascribed functions, although we identified a putative chemotaxis operon, a type IV pilus‐encoding cluster and a region encoding putative arylsulfatase enzymes, which were conserved across geographically distant isolates. One plasmid, pQBR55, conferred the ability to catabolize sucrose. Transposons, including the mercury resistance Tn5042, appeared to have been acquired by different pQBR plasmids by recombination, indicating an important role for horizontal gene transfer in the recent evolution of pQBR plasmids. Our findings demonstrate extensive genetic and phenotypic diversity among co‐occurring members of a plasmid community and suggest a role for environmental heterogeneity in the maintenance of plasmid diversity.     

Dissimilarity of stream insect assemblages: effects of multiple scales and spatial distances

In addition to the effects of environmental conditions, biotic assemblages may exhibit spatial structure depending on the scale of study. We tested whether the dissimilarity of stream insect assemblages is related to two types of spatial distances (stream corridor and overland distance), and evaluated the relative importance of diversity components at multiple spatial scales. Field data included assemblages of Ephemeroptera, Plecoptera, and Trichoptera found in 16 streams in four microbasins. We evaluated the relationship of the dissimilarity of assemblages with the distance types, using Mantel tests. In addition, we evaluated the relationships among the diversity components at multiple spatial scales, using additive partitioning analysis. The biological dissimilarities were correlated only with the geographical distances. Additive partitioning showed that the values of richness observed in the β1 (among Surber), β2 (among riffles), β3 (among streams), and β4 (among microbasins) were higher than those expected. The highest variation of the richness was found in β3 (30.6%). We conclude that stream faunas are distributed in patches all over the studied spatial extent, causing a weak relationship of biological dissimilarity with distance but important beta components when compared to a completely homogenous distribution of the fauna.     

Ponds and their catchments: size relationships and influence of land use across multiple spatial scales

The information on both the catchment land use and catchment area has the potential to be adopted into the conservation and management of ponds. There have been, however, few attempts to describe the effects of land use acting at various spatial scales on ponds and the studies were restricted to specific categories of ponds. This paper presents a study on 92 ponds distributed over a broad range of environmental conditions in Central Europe. We combined an extensive field survey and a detailed analysis of sediment and water chemistry with GIS-derived data to estimate the relationship between the area of the ponds and the area of their catchments, and to assess the relationship between pond physico-chemical conditions and land use across multiple spatial scales. Relating the area of ponds to the area of their catchments, we found a significant positive relationship (r = 0.72). Considering land use effects on pond conditions, catchment-scale land use was the only significant spatial extent influencing the physico-chemical conditions. Most notably, the proportion of intensively exploited land (arable land, urban areas) in the catchment scale was positively correlated with the deterioration of pond physico-chemical properties. The results of the study suggest that effective conservation of ponds cannot be achieved merely through the management of narrow buffer zones around them but should involve maintenance of less intensive land use within the whole catchment. Moreover, easily accessible catchment-scale GIS data could serve as a decision-support tool for cost-effective management strategies aimed at improving pond physico-chemical conditions.     

cGAS is activated by DNA in a length‐dependent manner

Cytosolic DNA stimulates innate immune responses, including type I interferons (IFN), which have antiviral and immunomodulatory activities. Cyclic GMP‐AMP synthase (cGAS) recognizes cytoplasmic DNA and signals via STING to induce IFN production. Despite the importance of DNA in innate immunity, the nature of the DNA that stimulates IFN production is not well described. Using low DNA concentrations, we show that dsDNA induces IFN in a length‐dependent manner. This is observed over a wide length‐span of DNA, ranging from the minimal stimulatory length to several kilobases, and is fully dependent on cGAS irrespective of DNA length. Importantly, in vitro studies reveal that long DNA activates recombinant human cGAS more efficiently than short DNA, showing that length‐dependent DNA recognition is an intrinsic property of cGAS independent of accessory proteins. Collectively, this work identifies long DNA as the molecular entity stimulating the cGAS pathway upon cytosolic DNA challenge such as viral infections.     

Variation at range margins across multiple spatial scales: environmental temperature,population genetics and metabolomic phenotype

Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent.     

Force‐ and kinesin‐8‐dependent effects in the spatial regulation of fission yeast microtubule dynamics

Microtubules (MTs) are central to the organisation of the eukaryotic intracellular space and are involved in the control of cell morphology. For these purposes, MT polymerisation dynamics are tightly regulated. Using automated image analysis software, we investigate the spatial dependence of MT dynamics in interphase fission yeast cells with unprecedented statistical accuracy. We find that MT catastrophe frequencies (switches from polymerisation to depolymerisation) strongly depend on intracellular position. We provide evidence that compressive forces generated by MTs growing against the cell pole locally reduce MT growth velocities and enhance catastrophe frequencies. Furthermore, we find evidence for an MT length‐dependent increase in the catastrophe frequency that is mediated by kinesin‐8 proteins (Klp5/6). Given the intrinsic susceptibility of MT dynamics to compressive forces and the widespread importance of kinesin‐8 proteins, we propose that similar spatial regulation of MT dynamics plays a role in other cell types as well. In addition, our systematic and quantitative data should provide valuable input for (mathematical) models of MT organisation in living cells.     

Indicators of biodiversity and ecosystem services: a synthesis across ecosystems and spatial scales

According to the Millennium Ecosystem Assessment, common indicators are needed to monitor the loss of biodiversity and the implications for the sustainable provision of ecosystem services. However, a variety of indicators are already being used resulting in many, mostly incompatible, monitoring systems. In order to synthesise the different indicator approaches and to detect gaps in the development of common indicator systems, we examined 531 indicators that have been reported in 617 peer‐reviewed journal articles between 1997 and 2007. Special emphasis was placed on comparing indicators of biodiversity and ecosystem services across ecosystems (forests, grass‐ and shrublands, wetlands, rivers, lakes, soils and agro‐ecosystems) and spatial scales (from patch to global scale). The application of biological indicators was found most often focused on regional and finer spatial scales with few indicators applied across ecosystem types. Abiotic indicators, such as physico‐chemical parameters and measures of area and fragmentation, are most frequently used at broader (regional to continental) scales. Despite its multiple dimensions, biodiversity is usually equated with species richness only. The functional, structural and genetic components of biodiversity are poorly addressed despite their potential value across habitats and scales. Ecosystem service indicators are mostly used to estimate regulating and supporting services but generally differ between ecosystem types as they reflect ecosystem‐specific services. Despite great effort to develop indicator systems over the past decade, there is still a considerable gap in the widespread use of indicators for many of the multiple components of biodiversity and ecosystem services, and a need to develop common monitoring schemes within and across habitats. Filling these gaps is a prerequisite for linking biodiversity dynamics with ecosystem service delivery and to achieving the goals of global and sub‐global initiatives to halt the loss of biodiversity.     

Body size and spatial scales in avian response to landscapes: a meta‐analysis

Response of species to their environment is dependent on the scales that individuals interact with landscapes. Several life‐history traits have been suggested to influence scales of response to landscapes, but little empirical work has addressed this issue, limiting our ability to predict the relevant scale(s) at which species respond to their environment. Body size is frequently hypothesized to be relevant for predicting the effects of landscape structure on species given correlations between body size and various measures of mobility or perceptual range, yet evidence of this relationship remains equivocal. We conducted a meta‐analysis of 22 studies to address the question of whether body size is related to the characteristic scale at which bird species respond to landscape structure. On the basis of correlation coefficients and linear mixed models, we show that body size is positively related to the characteristic scale of response to landscapes. The strength of this relationship is less than body size – dispersal allometries, suggesting that response to landscapes may be influenced, in part, by factors other than dispersal (e.g. territory size). However, the strength of the observed body size – scale relationship may have been affected by several factors, including limitations in the range of body sizes and landscape extents tested. Our findings suggest that life‐history traits mediate aspects of the scales at which species respond to the landscape and contribute to developing a more predictive framework for investigating scalar relationships in nature.     

Patterns of resource tracking by avian frugivores at multiple spatial scales: two case studies on discordance among scales

Scaling is relevant for the analysis of plant‐frugivore interaction, since the ecological and evolutionary outcomes of seed dispersal depend on the spatial and temporal scale at which frugivory patterns emerge. We analyse the relationship between fruit abundance and frugivore activity at local and landscape spatial scales in two different systems composed, respectively, by the bird‐dispersed woody plants Juniperus communis and Bursera fagaroides, and their frugivore assemblages. We use a hierarchical approach of nested patchiness of fruit‐resource, where patches are defined by individual plants within site, at the local scale, and by sites within region, at the landscape scale. The structure of patches is also described in terms of contrast (differences in fruit availability among patches) and aggregation (spatial distribution of patches). For J. communis, frugivore activity was positively related to fruit availability at the landscape scale, this pattern seldom emerging at the local scale; conversely, B. fagaroides showed a general trend of positive local pattern that disappeared at the landscape scale. These particular trends might be partially explained by differences in contrast and aggregation. The strong contrast among plants within site together with a high aggregation among sites would promote the B. fagaroides pattern to be only local, whereas in J. communis, low aggregation among sites within region would favour a sharp landscape‐scale pattern. Both systems showed discordant patterns of fruit‐resource tracking among consecutive spatial scales, but the sense of discordance differed among systems. These results, and the available multi‐scale frugivory data, suggest that discordance among successive scales allows to link directly frugivory patterns to resource‐tracking mechanisms acting at particular scales, resulting, thus, more informative than concordance observational data, in which landscape patterns might result from accumulated effect of local mechanisms. In this context, we propose new methodological approaches for a better understanding of the hierarchical behavioural mechanisms underpinning the multi‐scale resource tracking by frugivores.     

Gene‐flow across the European crow hybrid zone – a spatial simulation

In hybrid zones populations that are otherwise allopatric meet and produce hybrids. One of the most well‐known hybrid zones occurs throughout much of Europe between the hooded and carrion crows. Even though these species (or subspecies) of crows look very different, genetic differentiation is weak, and introgression seems to be common. In a spatial simulation that was based on empirically estimated values, we investigated how introgressing alleles that would confer some fitness advantage would flow across the zone. The advantage was assumed to be some unknown factor that enhanced survival for carriers relative to non‐carriers. We varied the yearly survival advantage between 0 to 10% and recorded how this would affect zone shape and position. In the simulation we cycled ‘yearly’ events such as reproduction, mortality and juvenile dispersal. We started the simulation by equipping all individuals of one crow type outside the zone with a homozygotic set of the beneficial allele. At all levels of advantage the allele first rapidly became fixed in the donator crow type, then transgressed into the receiving type more slowly and finally became fixed in all individuals. The time until fixation varied from around 176 yr for a 10% advantage to around 20 000 yr for 0% advantage. An exciting discovery was that the position of the zone would move during the introgression but then stop. The reason is that the beneficial allele would be common in the donating type but not in the receiving type during the introgression event. At large the crow hybrid zone appears to have been stable for a long time but there have been small recent northward movements of carrion crows in both Scotland and Denmark. We suggest that introgression by itself is a factor that should be considered as an explanation for why hybrid zones move temporarily.     

Facilitation can maintain clustered spatial pattern of plant populations during density‐dependent mortality: insights from a zone‐of‐influence model

Recent years have seen a growing body of evidence showing that plant competition and facilitation usually operate simultaneously to drive population dynamics, community structure and ecosystem functions. However, the potential role of facilitation in spatial patterning of plant populations has rarely been explicitly examined. We used a ‘zone‐of‐influence’ model to explore how facilitation interacts with competition and abiotic stress to determine the spatial patterning of populations during density‐dependent mortality. Model simulations revealed that started with the same clustered pattern, the final pattern of simulated populations depended strongly on the interaction among facilitation, stress level and size‐symmetry of competition. Asymmetric competition consistently led to immediate and non‐random mortality towards regularity, thus rapidly decayed the initially clustered pattern to final patterns of small‐scale regularity and large‐scale randomness. The role of symmetric competition in decaying the clustered pattern increased with abiotic stress because stress‐induced reductions in plants’ growth rates can make individuals in high‐density clusters more likely to die even from symmetric competition. Facilitation played a clear role in counteracting the effect of stress, thus tended to maintain the degree of clustering of the pattern during density‐dependent mortality. This is because the amelioration of harsh conditions by neighboring plants relieved the reductions in plant growth due to competition, thus slowed down and reduced the mortality inside clusters (relative to that outside clusters). Moreover, the effect of facilitation appeared to increase with abiotic stress. Our results indicate that facilitation among neighboring plants should partially be responsible for clustered population spatial patterns observed in stressful environments, even though its contribution relative to other factors (e.g. local dispersal and environmental heterogeneity) remains to be evaluated. In addition, the potential influence of facilitation on self‐thinning trajectory should be explicitly examined in future modeling and experimental studies considering its effects on density‐dependent mortality.     

From broadscale patterns to fine-scale processes: habitat structure influences genetic differentiation in the pitcher plant midge across multiple spatial scales

The spatial scale at which samples are collected and analysed influences the inferences that can be drawn from landscape genetic studies. We examined genetic structure and its landscape correlates in the pitcher plant midge, Metriocnemus knabi, an inhabitant of the purple pitcher plant, Sarracenia purpurea, across several spatial scales that are naturally delimited by the midge’s habitat (leaf, plant, cluster of plants, bog and system of bogs). We analysed 11 microsatellite loci in 710 M. knabi larvae from two systems of bogs in Algonquin Provincial Park (Canada) and tested the hypotheses that variables related to habitat structure are associated with genetic differentiation in this midge. Up to 54% of variation in individual‐based genetic distances at several scales was explained by broadscale landscape variables of bog size, pitcher plant density within bogs and connectivity of pitcher plant clusters. Our results indicate that oviposition behaviour of females at fine scales, as inferred from the spatial locations of full‐sib larvae, and spatially limited gene flow at broad scales represent the important processes underlying observed genetic patterns in M. knabi. Broadscale landscape features (bog size and plant density) appear to influence oviposition behaviour of midges, which in turn influences the patterns of genetic differentiation observed at both fine and broad scales. Thus, we inferred linkages among genetic patterns, landscape patterns and ecological processes across spatial scales in M. knabi. Our results reinforce the value of exploring such links simultaneously across multiple spatial scales and landscapes when investigating genetic diversity within a species.     

Stage‐dependent physiological responses in a butterfly cause non‐additive effects on phenology

Studies illustrating climate‐induced shifts in phenology typically focus on the timing of a single lifecycle stage. In contrast, species’ responses to climate change are likely to be complex and constrained by interactions and tradeoffs across the lifecycle. We characterized the thermal sensitivity of egg, larval and pupal stages of a native Australian butterfly and then integrated these responses to predict sensitivity of emergence time, survival, and feeding performance on oviposition date and climate. Thermal physiology varied among lifecycle stages and between sexes, with the development rate of eggs, first instar larvae, and pupae being the most sensitive to temperature. As lifecycle stages have different thermal physiologies, the environment experienced by a given stage depends in a complex way on the experience of previous stages. Our simulations indicate that oviposition date strongly influences time spent in each lifecycle‐stage, as well as performance. Under a high emissions climate warming scenario (CSIRO Mk 3.5 climate model, high emissions SRES marker scenario A1F1, and a moderate rate of global warming), we predict development times to decrease by 38 days by 2070. Our analysis illustrates how differences in thermal physiology across the lifecycle may result in non‐additive effects on phenology which, in turn, may constrain species’ responses to global warming. These results highlight the need to view shifts in phenology in the context of an organism's entire lifecycle.