Find research datasets worth reusing

Data from: Spatial variation of soil respiration in a cropland under winter wheat and summer maize rotation in the North China Plain

Spatial variation of soil respiration (Rs) in cropland ecosystems must be assessed to evaluate the global terrestrial carbon budget. This study aims to explore the spatial characteristics and controlling factors of Rs in a cropland under winter wheat and summer maize rotation in the North China Plain. We collected Rs data from 23 sample plots in the cropland. At the late jointing stage, the daily mean Rs of summer maize (4.74 μmol CO2 m-2 s-1) was significantly higher than that of winter wheat (3.77μmol CO2 m-2 s-1). However, the spatial variation of Rs in summer maize (coefficient of variation, CV = 12.2%) was lower than that in winter wheat (CV = 18.5%). A similar trend in CV was also observed for environmental factors but not for biotic factors, such as leaf area index, aboveground biomass, and canopy chlorophyll content. Pearson's correlation analyses based on the sampling data revealed that the spatial variation of Rs was poorly explained by the spatial variations of biotic factors, environmental factors, or soil properties alone for winter wheat and summer maize. The similarly non-significant relationship was observed between Rs and the enhanced vegetation index (EVI), which was used as surrogate for plant photosynthesis. EVI was better correlated with field-measured leaf area index than the normalized difference vegetation index and red edge chlorophyll index. All the data from the 23 sample plots were categorized into three clusters based on the cluster analysis of soil carbon/nitrogen and soil organic carbon content. An apparent improvement was observed in the relationship between Rs and EVI in each cluster for both winter wheat and summer maize. The spatial variation of Rs in the cropland under winter wheat and summer maize rotation could be attributed to the differences in spatial variations of soil properties and biotic factors. The results indicate that applying cluster analysis to minimize differences in soil properties among different clusters can improve the role of remote sensing data as a proxy of plant photosynthesis in semi-empirical Rs models and benefit the acquisition of Rs in cropland ecosystems at large scales.

opencc-zeroDec 2017View details →

Data from: Assessing impact of exogenous features on biotic phenomena in the presence of strong spatial dependence: a lake sturgeon case study in natural stream settings

Modeling spatially explicit data provides a powerful approach to identify the effects of exogenous features associated with biological processes, including recruitment of stream fishes. However, the complex spatial and temporal dynamics of the stream and the species' reproductive and early life stage behaviors present challenges to drawing valid inference using traditional regression models. In these settings it is often difficult to ensure the spatial independence among model residuals---a key assumption that must be met to ensure valid inference. We present statistical models capable of capturing complex residual anisotropic patterns through the addition of spatial random effects within an inferential framework that acknowledges uncertainty in the data and parameters. Proposed models are used to explore the impact of environmental variables on Lake sturgeon (Acipenser fulvescens) reproduction, particularly questions about patterns in egg deposition. Our results demonstrate the need to apply valid statistical methods to identify relationships between response variables, e.g., egg counts, across locations, and environmental covariates in the presence of strong and anisotropic autocorrelation in stream systems. The models may be applied to other settings where gamete distribution or, more generally, other biotic phenomena may be associated with spatially dynamic and anisotropic processes.

Data from: Spatial patterning of prey at reproduction to reduce predation risk: what drives dispersion from groups?

Group-living is a widespread behaviour thought to be an evolutionary adaptation for reducing predation risk. Many group-living species, however, spend a portion of their life cycle as dispersed individuals, suggesting that the costs and benefits of these opposing behaviours vary temporally. Here, we evaluated mechanistic hypotheses for explaining individual dispersion as a tactic for reducing predation risk at reproduction (i.e. birthing) in an otherwise group-living animal. Using simulation analyses parameterized by empirical data, we assessed whether dispersion increases reproductive success by: (i) increasing predator search time, (ii) reducing predator encounter rates because individuals are inconspicuous relative to groups, or (iii) eliminating the risk of multiple kills per encounter. Simulations indicate that dispersion only becomes favourable when detectability increases with group size and there is risk of multiple kills per encounter. This latter effect, however, is likely the primary mechanism driving females to disperse at reproduction because group detectability effects are presumably constant year round. We suggest that the risk of multiple kills imposed by highly vulnerable offspring may be an important factor influencing dispersive behaviour in many species and conservation strategies for such species will require protecting sufficient space to allow dispersion to effectively reduce predation risk.

opencc-zeroDec 2011View details →

Data from: Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best-fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best-fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers, in contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features as well as more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.

Data from: Spatial separation without territoriality in shark communities

Spatial separation within predator communities can arise via territoriality but also from competitive interactions between and within species. However, linking competitive interactions to predator distribution patterns is difficult and theoretical models predict different habitat selection patterns dependent on habitat quality and how competition manifests itself. While models generally consider competitors to be either equal in ability, or for one phenotype to have a fixed advantage over the other, few studies consider that an animal may only have a competitive advantage in specific habitats. We used > 10 years of telemetry data, habitat surveys and behavioral experiments, to show spatial partitioning between and within two species of reef shark (grey reef, Carcharhinus amblyrhinchos, and blacktip reef sharks, C. melanopterus) at an unfished Pacific atoll. Within a species, sharks remained within small 'sub-habitats' with very few movements of individuals between sub-habitats, which previous models have suggested could be caused by intra-specific competition. Blacktip reef sharks were more broadly distributed across habitat types but a greater proportion used lagoon and backreef habitats, while grey reef sharks preferred forereef habitats. Grey reef sharks at a nearby atoll where blacktip reef sharks are absent, were distributed more broadly between habitat types than when both species were present. A series of individual-based models predict that habitat separation would only arise if there are competitive interactions between species that are habitat-specific, with grey reefs having a competitive advantage on the forereefs and blacktips in the lagoons and backreef. We provide compelling evidence that competition drives distribution patterns and spatial separation of a marine predator community, and highlight that competitive advantages may not be constant but rather dependent on habitats.

Data from: Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study

Landscape features notoriously affect spatial patterns of biodiversity. For instance, in dendritic ecological networks (such as river basins), dendritic connectivity has been proposed to create unique spatial patterns of biodiversity. Here, we compared genetic datasets simulated under a lattice-like, a dendritic and a circular landscape to test the influence of dendritic connectivity on neutral genetic diversity. The circular landscape had a level of connectivity similar to that of the dendritic landscape, so as to isolate the influence of dendricity on genetic diversity. We found that genetic diversity and differentiation varied strikingly among the three landscapes. For instance, the dendritic landscape generated higher total number of alleles and higher global Fst than the lattice-like landscape, and these indices also varied between the dendritic and the circular landscape, suggesting an effect of dendricity. Furthermore, in the dendritic landscape, allelic richness was higher in highly connected demes (e.g. confluences in rivers) than in low connected demes (e.g. upstream and downstream populations), which was not the case in the circular landscape, hence confirming the major role of dendricity. This led to bell-shaped distributions of allelic richness along an upstream-downstream gradient. Conversely, genetic differentiation (Fst) was lower in highly than in low connected demes (which was not observed in circular landscape), and significant patterns of isolation-by-distance (IBD) were also observed in the dendritic landscape. We conclude that in dendritic networks, the combined influence of dendricity and connectivity generates unique spatial patterns of neutral genetic diversity, which has implications for population geneticists and conservationists.

Data from: Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning

1.Plant-soil feedback (PSF) has been identified as a key driver of local plant diversity and evenness in competitive communities. However, while it has been shown that spatial PSF heterogeneity can alter plant performance and competitive interactions, there is no proof of principle that spatial PSF heterogeneity enhances community diversity. 2.Using a grassland model system we separated two aspects of spatial heterogeneity: the number of species conditioning the soil and spatial distribution of the PSFs. 3.Our data show that PSFs promoted a higher plant evenness when the soil was conditioned by multiple species (mixed-conditioned), then when the soil was conditioned by a single species (mono-conditioned). On mono-conditioned soils, heterospecifics typically outperformed the focal species. In addition, there was a trend for increasing community evenness from uniform, via fine-grained to coarse-grained mixed-conditioned soils, but this was not significant. 4.On mixed-conditioned soils, performance of all competing species was intermediate to the best and the worst mono-conditioned soils, leading to higher community evenness. 5.Our data demonstrate that PSFs play a role in promoting plant evenness. Across mono-conditioned soils, PSF led to altered competitive hierarchies. However, on soils conditioned by multiple species, competitive ability among species was more similar and this led to higher plant evenness. The spatial distribution of the heterogeneity, on the other hand, did not significantly affect plant evenness. Our data therefore show that community evenness was more strongly related to the number of plant species that conditioned the soil than the spatial distribution of the PSF heterogeneity. Future studies need to investigate the importance of PSFs in the field across plant life-stages and multiple generations.

Data from: Shape up or ship out: migratory behaviour predicts morphology across spatial scale in a freshwater fish

1. Migration is a widespread phenomenon, with powerful ecological and evolutionary consequences. Morphological adaptations to reduce the energetic costs associated with migratory transport are commonly documented for migratory species. However, few studies have investigated whether variation in body morphology can be explained by variation in migratory strategy within a species. 2. We address this question in roach Rutilus rutilus, a partially migratory freshwater fish that migrates from lakes into streams during winter. We both compare body shape between populations that differ in migratory opportunity (open vs. closed lakes), and between individuals from a single population that vary in migratory propensity (migrants and residents from a partially migratory population). Following hydrodynamic theory, we posit that migrants should have a more shallow body depth, to reduce the costs associated with migrating into streams with higher flow conditions than the lakes the residents occupy all year round. 3. We find evidence both across and within populations to support our prediction, with individuals from open lakes and migrants from the partially migratory population having a more slender, shallow-bodied morphology than fish from closed lakes and all-year residents. 4. Our data suggest that a shallow body morphology is beneficial to migratory individuals and our study is one of the first to link migratory strategy and intraspecific variation in body shape.

opencc-zeroDec 2017View details →

Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification, and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analyzed genetic origin of 6483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically divergent Atlantic cod ecotypes throughout the study area and study period. A 'fjord' ecotype dominated in numbers deep inside fjords while a 'North Sea' ecotype was the only type found in offshore North Sea. Both ecotypes coexisted in similar proportions throughout coastal habitats at all spatial scales. The size-at-age of the North Sea ecotype on average exceeded that of the fjord ecotype by 20% in length and 80% in weight across all habitats. Different growth and size among individuals of the two types might be one of several ecologically significant variables that allow for stable coexistence of closely related populations within the same habitat. Management plans, biodiversity initiatives, and other mitigation strategies that do not account for the mixture of species ecotypes are unlikely to meet objectives related to the sustainability of fish and fisheries.

Data from: Sociodemographic factors modulate the spatial response of brown bears to vacancies created by hunting

1.There is a growing recognition of the importance of indirect effects from hunting on wildlife populations, e.g., social and behavioral changes due to harvest, which occur after the initial offtake. Nonetheless, little is known about how the removal of members of a population influences the spatial configuration of the survivors. 2.We studied how surviving brown bears (Ursus arctos) used former home ranges that had belonged to casualties of the annual bear hunting season in southcentral Sweden (2007-2015). We used resource selection functions to explore the effects of the casualty's and survivor's sex, age, and their pairwise genetic relatedness, population density, and hunting intensity on survivors' spatial responses to vacated home ranges. 3.We tested the competitive release hypothesis, whereby survivors that increase their use of a killed bear's home range are presumed to have been released from intraspecific competition. We found strong support for this hypothesis, as survivors of the same sex as the casualty consistently increased their use of its vacant home range. Patterns were less pronounced or absent when the survivor and casualty were of opposite sex. 4.Genetic relatedness between the survivor and the casualty emerged as the most important factor explaining increased use of vacated male home ranges by males, with a stronger response from survivors of lower relatedness. Relatedness was also important for females, but it did not influence use following removal; female survivors used home ranges of higher related female casualties more, both before and after death. Spatial responses by survivors were further influenced by bear age, population density, and hunting intensity. 5.We have showed that survivors exhibit a spatial response to vacated home ranges caused by hunting casualties, even in non-territorial species such as the brown bear. This spatial reorganization can have unintended consequences for population dynamics and interfere with management goals. Altogether, our results underscore the need to better understand the short- and long-term indirect effects of hunting on animal social structure and their resulting distribution in space.

Data from: Large-scale functional networks identified from resting-state EEG using spatial ICA

Several methods have been applied to EEG or MEG signals to detect functional networks. In recent works using MEG/EEG and fMRI data, temporal ICA analysis has been used to extract spatial maps of resting-state networks with or without an atlas-based parcellation of the cortex. Since the links between the fMRI signal and the electromagnetic signals are not fully established, and to avoid any bias, we examined whether EEG alone was able to derive the spatial distribution and temporal characteristics of functional networks. To do so, we propose a two-step original method: 1) An individual multi-frequency data analysis including EEG-based source localisation and spatial independent component analysis, which allowed us to characterize the resting-state networks. 2) A group-level analysis involving a hierarchical clustering procedure to identify reproducible large-scale networks across the population. Compared with large-scale resting-state networks obtained with fMRI, the proposed EEG-based analysis revealed smaller independent networks thanks to the high temporal resolution of EEG, hence hierarchical organization of networks. The comparison showed a substantial overlap between EEG and fMRI networks in motor, premotor, sensory, frontal, and parietal areas. However, there were mismatches between EEG-based and fMRI-based networks in temporal areas, presumably resulting from a poor sensitivity of fMRI in these regions or artefacts in the EEG signals. The proposed method opens the way for studying the high temporal dynamics of networks at the source level thanks to the high temporal resolution of EEG. It would then become possible to study detailed measures of the dynamics of connectivity.

opencc-zeroDec 2012View details →

Data from: Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe

The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well-characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on multilocus sequence typing and the Wolbachia surface protein wsp showed that all R. cingulata individuals are infected with wCin2 identical to wCer2 in R. cerasi. In contrast, wCin1, a strain identical to wCer1 in R. cerasi, was present in several European populations of R. cingulata, but not in any individual from the United States. Surveys of R. cingulata from Germany and Hungary indicated that the frequency of wCin1 infection increased dramatically in just a few years with at least two independent horizontal transmission events in Germany and Hungary. This is further corroborated by the analysis of the mitochondrial cytochrome oxidase II gene that showed linkage of wCin1 with two distinct haplotypes in Germany, one of which is also infected with wCin1 in Hungary. In summary, our study provides strong evidence for a very recent interspecific Wolbachia transmission with a subsequent spatial spread in field populations.

opencc-zeroDec 2012View details →

Data from: Tracking individuals shows spatial fidelity is a key regulator of ant social organization

Ants live in organized societies with a marked division of labor among workers, but little is known about how this is generated. We use a tracking system to continuously monitor individually-tagged workers in six colonies of the ant Camponotus fellah over 41 days. Network analyses of over 9 million interactions revealed three distinct groups that differ in behavioral repertoires. Each group represents a functional behavioral unit with workers moving from one group to the next as they age. The rate of interactions was much higher within- than between groups. The precise information on spatial and temporal distribution of all individuals permitted calculation of the expected rates of within- and between-group interactions. These values suggest that the network of interaction within colonies is primarily mediated by age-induced changes in the spatial location of workers.

Data from: Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability

The kidney podocyte's function depends on finger-like projections (foot processes) that interdigitate with those from neighboring cells to form the glomerular filtration barrier. The integrity of the barrier depends on spatial control of dynamics of actin cytoskeleton in the foot processes. We determined how imbalances in regulation of actin cytoskeletal dynamics can result in pathological morphology. We obtained 3-D electron microscopy images of podocytes and used quantitative features to build dynamical models to investigate how regulation of actin dynamics within foot processes controls local morphology. We find that imbalances in regulation of actin bundling, lead to chaotic spatial patterns that could impair the foot process morphology. Simulation results are consistent with experimental observations for cytoskeletal reconfiguration by dysregulated RhoA or Rac1, and they predict compensatory mechanisms for biochemical stability. We conclude that podocyte morphology, optimized for filtration, is intrinsically fragile, whereby local transient biochemical imbalances may lead to permanent morphological changes associated with pathophysiology.

opencc-zeroAug 2019View details →

Data from: Interacting maternal and spatial cues influence natal dispersal out of social groups

Proximate cues for animal dispersal are complex and varied. Multiple cues may provide information about different aspects of habitat quality, and these aspects may interact with each other, as well as with population density in different ways. We examined how individuals incorporate multiple cues in their decisions to emigrate and immigrate in the colonial orb-weaving spider, Cyrtophora citricola. We manipulated maternal feeding as a cue for prey abundance and measured the size of the maternal web, which provides a limited space for philopatric offspring and a second potential dispersal cue. In addition, we recorded all immigration events to determine dispersal distances and the cues juveniles may use in settlement. Dispersal increased when mothers were poorly fed, web sizes were small, and clutch sizes were large. In addition to these overall effects, maternal feeding also interacted with web size, indicating that offspring from well-fed mothers were more tolerant of high sibling densities. We also detected a threshold for the effect of clutch size on dispersal for the first egg sac: below 20 offspring, there was no effect of clutch size, but dispersal increased with clutch size for larger clutches. Dispersal distances were often short, and immigrants preferred sheltered trees and those occupied by adult females. Dispersal not only depended on multiple cues, but these cues interacted, and the importance of web size suggested that saturation of the natal web might force dispersal, at least for spiders with poorly-fed mothers. How one aspect of habitat quality influences dispersal can therefore depend on the state of other aspects of habitat quality. In particular, some natal resources, such as a nest or territory, may become saturated and limit group size, but this limit will also depend on other factors, such as prey availability.

opencc-zeroDec 2018View details →

Data from: Stiffness gradients facilitate ovipositor bending and spatial probing control in a parasitic wasp

Many parasitic wasps use slender and steerable ovipositors to lay eggs in hosts hidden in substrates, but it is currently unknown how steering is achieved. The ovipositors generally consist of three longitudinally connected elements, one dorsal and two ventral valves that can slide along each other. For the parasitic wasp Diachasmimorpha longicaudata, it has been shown that protraction of the ventral valves causes incurving of the ventral valves towards the dorsal one, which results in a change in probing direction. We hypothesize that this shape change is due to differences in bending stiffness along the ovipositor. Alignment of the stiff tip of the dorsal valve with a more flexible ventral S-shaped region situated just behind the tip straightens this S-bend and results in upwards rotation of the ventral tip. We show that the S-shaped region of the ventral valves has a low bending stiffness because it contains soft materials such as resilin. In contrast, the large cross-sectional area of the dorsal valve tip area probably results in a high bending stiffness. Elsewhere, the dorsal valve is less stiff than the ventral valves. Our results support the hypothesis that the interaction between the stiff dorsal valve portion and the more flexible S-shaped region co-determines the configurational tip changes required for steering the ovipositor in any desired direction along curved paths in the substrate. This provides novel insights in the understanding of steering mechanisms of the hymenopteran ovipositor, and for application in man-made probes.

opencc-zeroDec 2017View details →

Data from: Cascading spatial and trophic impacts of oak decline on the soil food web

1. Tree defoliation and mortality have considerably increased worldwide during the last decades due to global change drivers such as increasing drought or invasive pests and pathogens. However, the effects of this tree decline on soil food webs are poorly understood. 2. In this study we evaluated the impacts of Quercus suber decline on soil food webs of Mediterranean mixed forests invaded by the exotic oomycete pathogen Phytophthora cinnamomi, using soil nematodes as bioindicator taxa. We used a spatially-explicit neighborhood approach to predict the characteristics of the nematode community (diversity, trophic structure, and several indices indicative of soil food web conditions) as a function of the characteristics of the tree and shrub community (species composition, size and health status). 3. Our results indicate that the process of defoliation and mortality of Q. suber caused significant alterations in the nematode trophic structure increasing the abundance of lower trophic levels (bacterivores, fungivores and herbivores) and decreasing the abundance of higher levels (predators and omnivores). Furthermore, Q. suber decline altered the functional composition of soil communities, producing a setback of the ecological succession in the soil food web to an earlier stage (decrease in the maturity index and increase in the plant-parasitic index), simplified soil food webs (decrease in the structure index), and shifts in the predominant decomposition channel (increase in the fungivores/bacterivores ratio). 4. We also detected contrasting characteristics of the nematode community in neighborhoods dominated by coexistent woody species, which suggests potential for long-term indirect effects on soil food webs due to the substitution of Q. suber by non-declining species. 5. Synthesis: Our study provides novel results that show the major impacts that ongoing health deterioration of dominant tree species can have on the structure and composition of soil food webs in forest systems invaded by exotic pathogens, with cascading consequences for soil biogeochemical processes in both the short- and long-term.

Data from: The spatial distribution of foragers and food patches can influence antipredator vigilance

Antipredator vigilance is a major component of defenses against predators for many prey species. For group foragers, such vigilance is predicted by models to decrease with group size reflecting better predator detection ability and risk dilution in larger groups. Influential vigilance models for group foragers have made simplifying and often quite restrictive assumptions. Prey species, for instance, are expected to search for resources in groups of fixed sizes although frequent changes in group sizes often occur while foraging. Groups of prey in the same area are also assumed to be attacked independently, but predators could sequentially target several local groups after a failed attempt. I propose a framework in which prey animals can form groups by joining feeding neighbors and also adjust their vigilance in these groups of varying sizes. Predators can attack one of the many groups that occur in the same area and can also target groups of specific sizes. I used a genetic algorithm approach to simultaneously tackle joining and vigilance choices by prey individuals. I show that joining tendencies and the effect of group size on vigilance can vary with forager population size, the spatial distribution of resources, and predator attack tactics. The modeling framework adopted here generates several novel predictions about vigilance and joining tendencies for group foragers, and highlights the importance of considering the availability and vulnerability of prey groups in the same habitat when predicting antipredator vigilance.

Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts

The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference of nuclear compartments, for which we have developed statistical tools to quantitatively study and explore nuclear organization. These tools combine replicate images to generate 'aggregate maps' which represent the spatial preferences of nuclear compartments. We present two examples of different compartments in mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of spatial preference within the cell nucleus. Specifically, the spatial preference of RNA polymerase II is preserved across normal and immortalized cells, whereas PML nuclear bodies exhibit a change in spatial preference from avoiding the centre in normal cells to exhibiting a preference for the centre in immortalized cells. In addition, we show that SC35 splicing speckles are excluded from the nuclear boundary and localize throughout the nucleoplasm and in the interchromatin space in non-transformed WI-38 cells. This new methodology is thus able to reveal the effect of large-scale perturbation on spatial architecture and preferences that would not be obvious from single cell imaging.

Data from: Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third-order stream at Konza Prairie over a 2- to 64-day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta-, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early-stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.