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11,506 results for “Dynamics”
Data from: Linking dynamical complexities from activation signals to transcription responses
The transcription of inducible genes involves signaling pathways that induce DNA binding of the downstream transcription factors to form functional promoter states. How the transcription dynamics is linked to the temporal variations of activation signals is far to be fully understood. In this work, we develop a mathematical model with multiple promoter states to address this question. Each promoter state has its own activation and inactivation rates, and is selected randomly with a probability that may change in time. Under the activation of constant signals, our analysis shows that if only the activation rates differ among the promoter states, then the mean transcription level $m(t)$ displays only a monotone or monophasic growth pattern. In a sharp contrast, if the inactivation rates change with the promoter states, then $m(t)$ may display multiphasic growth patterns. Upon the activation of signals that oscillate periodically, $m(t)$ also oscillates later, almost periodically in the same frequency, but the magnitude decreases in the frequency and is almost completely attenuated at large frequencies. This gives a surprising indication that multiple promoter states could filter out the signal oscillation and the noise in the random promoter state selection, as observed in the transcription of a gene activated by p53 in breast carcinoma cells. Our approach may help develop a theoretical framework to integrate coherently the genetic circuit with the promoter states to elucidate the linkage from the activation signal to the temporal profile of transcription outputs.
Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli
Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.
Data from: Disentangling demographic co-effects of predation and pollution on population dynamics
In nature species react to a variety of endogenous and exogenous ecological factors. Understanding the mechanisms by which these factors interact and drive population dynamics is a need for understanding and managing ecosystems. In this study we assess, using laboratory experiments, the effects that the combinations of two exogenous factors exert on the endogenous structure of the population dynamics of a size-structured population of Daphnia. One exogenous factor was size-selective predation, which was applied on experimental populations through simulating: (a) selective predation on small prey, (b) selective predation on large prey and (c) non-selective predation. The second exogenous factor was pesticide exposure, applied experimentally in a quasi-continuous regime. Our analysis combined theoretical models and statistical testing of experimental data for analyzing how the density dependence structure of the population dynamics was shifted by the different exogenous factors. Our results showed that pesticide exposure interacted with the mode of predation in determining the endogenous dynamics. Populations exposed to the pesticide and to either selective predation on newborns or selective predation on adults exhibited marked nonlinear effects of pesticide exposure. However, the specific mechanisms behind such nonlinear effects were dependent on the mode of size-selectivity. In populations under non-selective predation the pesticide exposure exerted a weak lateral effect. The ways in which endogenous process and exogenous factors may interact determine population dynamics. Increases in equilibrium density results in higher variance of population fluctuations but do not modify the stability properties of the system, while changes in the maximum growth rate induce changes in the dynamic regimes and stability properties of the population. Future consideration for research includes the consequences of the seasonal variation in the composition and activity of the predator assembly in interaction with the seasonal variation in exposure to agrochemicals on freshwater population dynamics.
Data from: Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.
Data from: A shift from exploitation to interference competition with increasing density affects population and community dynamics
Intraspecific competition influences population and community dynamics and occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. We grew experimental microcosms of protozoa and bacteria under different combinations of protozoan density and basal resource availability. We then solved a dynamic predator–prey model for parameters of the functional response using population growth rates measured in our experiment. As population density increased, competition shifted from exploitation to interference, and competition was less dependent on resource levels. Surprisingly, the effect of resources was weakest when competition was the most intense. We found that at low population densities, competition was largely exploitative and resource availability had a large effect on population growth rates, but the effect of resources was much weaker at high densities. This shift in competitive mechanism could have implications for interspecific competition, trophic interactions, community diversity, and natural selection. We also tested whether this shift in the mechanism of competition with protozoa density affected the structure of the bacterial prey community. We found that both resources and protozoa density affected the structure of the bacterial prey community, suggesting that competitive mechanism may also affect trophic interactions.
Data from: Assessment of dynamic material properties of intact rocks using seismic wave attenuation: an experimental study
The mechanical properties of any substance are essential facts to understand its behaviour and make the maximum use of the particular substance. Rocks are indeed an important substance, as they are of significant use in the energy industry, specifically for fossil fuels and geothermal energy. Attenuation of seismic waves is a non-destructive technique to investigate mechanical properties of reservoir rocks under different conditions. The attenuation characteristics of five different rock types, siltstone, shale, Australian sandstone, Indian sandstone and granite, were investigated in the laboratory using ultrasonic and acoustic emission instruments in a frequency range of 0.1–1 MHz. The pulse transmission technique and spectral ratios were used to calculate the attenuation coefficient (α) and quality factor (Q) values for the five selected rock types for both primary (P) and secondary (S) waves, relative to the reference steel sample. For all the rock types, the attenuation coefficient was linearly proportional to the frequency of both the P and S waves. Interestingly, the attenuation coefficient of granite is more than 22% higher than that of siltstone, sandstone and shale for both P and S waves. The P and S wave velocities were calculated based on their recorded travel time, and these velocities were then used to calculate the dynamic mechanical properties including elastic modulus (E), bulk modulus (K), shear modulus (µ) and Poisson's ratio (ν). The P and S wave velocities for the selected rock types varied in the ranges of 2.43–4.61 km s−1 and 1.43–2.41 km h−1, respectively. Furthermore, it was observed that the P wave velocity was always greater than the S wave velocity, and this confirmed the first arrival of P waves to the sensor. According to the experimental results, the dynamic E value is generally higher than the static E value obtained by unconfined compressive strength tests.
Data from: Cyclic population dynamics and density-dependent intransitivity as pathways to coexistence between co-occurring annual plants
1. Recent studies have brought renewed attention to the importance of complex species interactions - notably intransitive interactions - to patterns of plant community diversity. One underappreciated avenue through which intransitivity can occur is through cyclic population dynamics. Though such cyclic intransitive relationships have been extensively studied in predator-prey systems, evidence of their importance in competitive communities, notably plant communities, is more limited. Most studies of coexistence in plant communities assume fixed-point coexistence even while utilizing models that allow for cyclic population dynamics. 2. In this paper, we explore the potential for density-dependent, cyclic population dynamics and intransitivity in a model for annual plants. We then examine how these density-dependent cycles impact mutual invasibility and ultimately stable coexistence between plant species pairs. We do this using data collected from four co-occurring annual plant species living in natural wildflower communities in SW Western Australia. To maximize the number of biologically plausible pathways by which coexistence mediated by density-dependent cyclic intransitivity can occur, we use an annual plant model that allows for competitive direct interactions, facilitative direct interactions, and higher-order interactions between species. 3. Results from our empirically-parameterized model suggest that monocultures of all four focal species can have cyclic solutions with periodicity greater than 1 under sunny ("open") or shaded field conditions. Cyclic patterns drive variation in annual abundance patterns, with stable solutions for persistent monocultures and invasibility potential (the capacity of one population to invade another) common. Mutual invasibility in the face of cyclic population dynamics was found for just one of six species pairs, only under open environmental conditions. Our results illustrate the potential for cyclic intransitivity to both drive and prevent stable coexistence in environmentally heterogeneous biological communities. 4. Synthesis. We provide analytical and empirical evidence that coexistence in competitive communities (annual plants) can be achieved under non-equilibrium circumstances, through density-dependent cyclic intransitivity. Our results suggest that cyclic population dynamics may be common and important for coexistence dynamics in some types of communities. In such communities, the exploration of stable coexistence should therefore include consideration of cyclic as well as fixed-point equilibria for maximal accuracy.
Data from: Threshold dynamics in plant succession after tree planting in agricultural riparian zones
Trajectories of plant communities can be described by different models of plant succession. While a Clementsian (gradual continuum model) or Gleasonian approach (relay floristics model) has traditionally been used to inform restoration outcomes, alternative succession models developed recently may better represent restoration trajectories. The threshold dynamics succession model, which predicts an abrupt species turnover after an environmental threshold is crossed, has never been used in a restoration context. This model might, however, better describe shifts in plant competitive ranking and facilitation interactions during species turnover. Fifty-three riparian zones, planted with trees 3–17 years prior to sampling, and 14 natural riparian forests were studied in two agricultural watersheds of south-eastern Québec (Canada). The cover of vegetation strata was assessed at the site scale, and the cover of plant species was estimated in a total of 784 1-m2 plots. Canopy cover was measured stereoscopically for each plot. As revealed by Principal Response Curves and broken stick models, herbaceous species composition was stable during the first 12–13 years after tree planting, but then abruptly shifted. This two-step pattern in species turnover followed the increase in canopy cover after tree planting. Once canopy cover passed a threshold of ca 40%, plant succession started and led to the re-establishment of forest communities 17 years after planting. Following herbaceous species turnover, the cover of ecological groups changed significantly towards covers of natural riparian forests: shade-tolerant species generally increased, while light-demanding and non-native species decreased. Vegetation structure was also significantly affected by tree planting: tree and shrub cover increased, while monocot cover decreased. Synthesis and applications. Tree planting efficiently restored herbaceous forest communities in riparian zones by inducing a species turnover mediated by light availability corresponding to the threshold dynamics model in plant succession. Fostering and monitoring canopy closure in tree-planted riparian zones should improve restoration success and the design of alternative strategies. The innovative statistical approach of this study aiming to identify succession patterns and their associated theoretical models can guide future restoration in any type of ecosystem around the world to bridge the gap between science and management.
Data from: Ecological speciation in dynamic landscapes
Although verbal theories of speciation consider landscape changes, ecological speciation is usually modeled in a fixed geographical arrangement. Yet landscape changes occur, at different spatio-temporal scales, due to geological, climatic or ecological processes, and these changes result in repeated divisions and reconnections of populations. We examine the effect of such landscape dynamics on speciation. We use a stochastic, sexual population model with polygenic inheritance, embedded in a landscape dynamics model (allopatry-sympatry oscillations). We show that, under stabilizing selection, allopatry easily generates diversity, but species coexistence is evolutionarily unsustainable. Allopatry produces refuges whose persistence depends on the characteristic time scales of the landscape dynamics. Under disruptive selection, assuming that sympatric speciation is impossible due to Mendelian inheritance, allopatry is necessary for ecological differentiation. The completion of reproductive isolation, by reinforcement, then requires several sympatric phases. These results demonstrate that the succession of past, current and future geographical arrangements considerably influence the speciation process.
Data from: Metaecosystem dynamics of marine phytoplankton alters resource use efficiency along stoichiometric gradients
Metaecosystem theory addresses the link between local (within habitats) and regional (between habitats) dynamics by simultaneously analyzing spatial community ecology and abiotic matter flow. Here, we experimentally address how spatial resource gradients and connectivity affect resource use efficiency (RUE) and stoichiometry in marine phytoplankton at local and regional scales. We created gradostat metaecosystems consisting of five linearly interconnected patches, which either were arranged in countercurrent gradients of nitrogen (N) and phosphorus (P) supply or with a uniform spatial distribution of nutrients, and which had either low or high connectivity. Gradient metaecosystems were characterized by higher remaining N and P concentrations (and N:P ratios) than uniform ones, a difference reduced by higher connectivity. The position of the patch in the gradient strongly constrained elemental stoichiometry, local biovolume production and RUE. Expectedly, algal C:N, biovolume and N-specific RUE decreased towards the N-rich end of gradient metaecosystem, whereas the opposite was observed for most of the gradient for C:P, N:P and P-specific RUE. However, at highest N:P supply, unexpectedly low C:P, N:P, and P-specific RUE values were found, indicating that the low availability of P inhibited efficient use of N and biovolume production. Consequently, gradient metaecosystems had lower overall biovolume at the regional scale, but higher dissimilarity in species composition. Thus, the performance of phytoplankton in metaecosystems strongly depended on the stoichiometry of resource supply and spatial connectivity between patches.
Data from: Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum
Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation has been important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analyzed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signaling molecules. This study provides insight into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was likely present in the last common ancestor of animals.
Data from: Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load
Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ~150-fold, while the mutY mutations reduced the rate by ~40-60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined.
Data from: Dynamic social behaviour in a bacterium: Pseudomonas aeruginosa partially compensates for siderophore loss to cheats
Cooperation underlies diverse phenomena including the origins of multicellular life, human behaviour in economic markets and the mechanisms by which pathogenic bacteria cause disease. Experiments with microorganisms have advanced our understanding of how, when and why cooperation evolves, but the extent to which microbial cooperation can recapitulate aspects of animal behaviour is debated. For instance, understanding the evolution of behavioural response rules (how should one individual respond to another's decision to cooperate or defect?) is a key part of social evolution theory, but the possible existence of such rules in social microbes has not been explored. In one specific context (biparental care in animals), cooperation is maintained if individuals respond to a partner's defection by increasing their own investment into cooperation, but not so much that this fully compensates for the defector's lack of investment. This is termed 'partial compensation.' Here, I show that partial compensation for the presence of non-cooperating 'cheats' is also observed in a microbial social behaviour: the cooperative production of iron-scavenging siderophores by the bacterium Pseudomonas aeruginosa. A period of evolution in the presence of cheats maintains this response, whereas evolution in the absence of cheats leads to a loss of compensatory behaviour. These results demonstrate i) the remarkable flexibility of bacterial social behaviour; ii) the potential generality of partial compensation as a social response rule; and iii) the need for mathematical models to explore the evolution of response rules in multi-player social interactions.
Data from: The effect of static versus dynamic stimuli on visual processing of sexual cues in androphilic women and gynephilic men
Models of sexual response posit that attentional processing of sexual cues is requisite for sexual responding. Despite hypothesized similarities in the underlying processes resulting in sexual response, gender differences in sexual arousal patterns are abundant. One such gender difference relates to the stimulus features (e.g., gender cues, sexual activity cues) that elicit a response in men and women. In the current study, we examined how stimulus modality (static visual images versus dynamic audiovisual films) and stimulus features (gender, sexual activity, and nonsexual contextual cues) influences attentional (i.e., gaze) and elaborative (i.e., self-reported attraction, self-reported arousal) processing of sexual stimuli. Men's initial and controlled attention was consistently gender-specific (i.e., greater attention towards female targets), and this was not influenced by stimulus modality or the presence of sexual activity cues. In contrast, gender-specificity of women's attention patterns differed as a function of attentional stage, stimulus modality, and the features within the stimulus. Degree of specificity was positively predictive of self-reported attraction in both genders; however, it was not significantly predictive of self-reported arousal. These findings are discussed in the context of gendered processing of visual sexual information, including a discussion of implications for research designs.
Data from: Accurate measurements of dynamics and reproducibility in small genetic networks
Quantification of gene expression has become a central tool for understanding genetic networks. In many systems the only viable way to measure protein levels is by immunofluorescence, which is notorious for its limited accuracy. Using the early Drosophila embryo as an example, we show that careful identification and control of experimental error allows for highly accurate gene expression measurements. We generated antibodies in different host species, allowing for simultaneous staining of four Drosophila gap genes in individual embryos. Careful error analysis of hundreds of expression profiles reveals that less than ∼20% of the observed embryo-to-embryo fluctuations stem from experimental error. These measurements make it possible to extract not only very accurate mean gene expression profiles but also their naturally occurring fluctuations of biological origin and corresponding cross-correlations. We use this analysis to extract gap gene profile dynamics with ∼1 min accuracy. The combination of these new measurements and analysis techniques reveals a two-fold increase in profile reproducibility due to a collective network dynamics that relays positional accuracy from the maternal gradients to the pair-rule genes.
Data from: Theoretical models of the influence of genomic architecture on the dynamics of speciation
A long-standing problem in evolutionary biology has been determining whether and how gradual, incremental changes at the gene level can account for rapid speciation and bursts of adaptive radiation. Using genome-scale computer simulations, we extend previous theory showing how gradual adaptive change can generate nonlinear population transitions, resulting in the rapid formation of new, reproductively isolated species. We show that these transitions occur via a mechanism rooted in a basic property of biological heredity: the organization of genes in genomes. Genomic organization of genes facilitates two processes: (i) the buildup of statistical associations among large numbers of genes, and (ii) the action of divergent selection on persistent combinations of alleles. When a population has accumulated a critical amount of standing, divergently selected variation, the combination of these two processes allows many mutations of small effect to act synergistically and precipitously split one population into two discontinuous, reproductively isolated groups. Periods of allopatry, chromosomal linkage among loci, and large-effect alleles can facilitate this process under some conditions, but are not required for it. Our results complement and extend existing theory on alternative stable states during population divergence, distinct phases of speciation, and the rapid emergence of multilocus barriers to gene flow. The results are thus a step toward aligning population genomic theory with modern empirical studies.
Data from: SRUD: a simple non-destructive method for accurate quantification of plant diversity dynamics
1. Predicting changes in plant diversity in response to human activities represents one of the major challenges facing ecologists and land managers striving for sustainable ecosystem management. Classical field studies have emphasized the importance of community primary productivity in regulating changes in plant species richness. However, experimental studies have yielded inconsistent empirical evidence, suggesting that primary productivity is not the sole determinant of plant diversity. Recent work has shown that more accurate predictions of changes in species diversity can be achieved by combining measures of species' cover and height into an index of Space Resource Utilization (SRU). While the SRU approach provides reliable predictions, it is time-consuming and requires extensive taxonomic expertise. Ecosystem processes and plant community structure are likely driven primarily by dominant species (mass-ratio effect). Within communities, it is likely that dominant and rare species have opposite contributions to overall biodiversity trends. We therefore suggest that better species richness predictions can be achieved by utilizing SRU assessments of only the dominant species (SRUD), as compared to SRU or biomass of the entire community. 2. Here, we assess the ability of these measures to predict changes in plant diversity as driven by nutrient addition and herbivore exclusion. First, we tested our hypotheses by carrying out a detailed analysis in an alpine grassland that measured all species within the community. Next, we assessed the broader applicability of our approach by measuring the first three dominant species for five additional experimental grassland sites across a wide geographic and habitat range. 3. We show that SRUD outperforms community biomass, as well as community SRU, in predicting biodiversity dynamics in response to nutrients and herbivores in an alpine grassland. Across our additional sites, SRUD yielded far better predictions of changes in species richness than community biomass, demonstrating the robustness and generalizable nature of this approach. 4. Synthesis. The SRUD approach provides a simple, non-destructive and more accurate means to monitor and predict the impact of global change drivers and management interventions on plant communities, thereby facilitating efforts to maintain and recover plant diversity.
Data from: Dynamics of pre-choice and post-choice behaviour: rats approximate optimal strategy in a discrete-trial decision task
We simulate two types of environments to investigate how closely rats approximate optimal foraging. Rats initiated a trial where they chose between two spouts for sucrose, which was delivered at distinct probabilities. The discrete trial procedure used allowed us to observe the relationship between choice proportions, response latencies and obtained rewards. Our results show that rats approximate the optimal strategy across a range of environments that differ in the average probability of reward as well as the dynamics of the depletion-renewal cycle. We found that the constituent components of a single choice differentially reflect environmental contingencies. Post-choice behaviour, measured as the duration of time rats spent licking at the spouts on unrewarded trials, was the most sensitive index of environmental variables, adjusting most rapidly to changes in the environment. These findings have implications for the role of confidence in choice outcomes for guiding future choices.
Data from: Food provisioning alters infection dynamics in populations of a wild rodent
While pathogens are often assumed to limit the growth of wildlife populations, experimental evidence for their effects is rare. A lack of food resources has been suggested to enhance the negative effects of pathogen infection on host populations, but this theory has received little investigation. We conducted a replicated two-factor enclosure experiment, with introduction of the bacterium Bordetella bronchiseptica and food supplementation, to evaluate the individual and interactive effects of pathogen infection and food availability on vole populations during a boreal winter. We show that prior to bacteria introduction, vole populations were limited by food availability. Bordetella bronchiseptica introduction then reduced population growth and abundance, but contrary to predictions, primarily in food supplemented populations. Infection prevalence and pathological changes in vole lungs were most common in food supplemented populations, and are likely to have resulted from increased congregation and bacteria transmission around feeding stations. Bordetella bronchiseptica-infected lungs often showed protozoan co-infection (consistent with Hepatozoon erhardovae), together with more severe inflammatory changes. Using a multidisciplinary approach, this study demonstrates a complex picture of interactions and underlying mechanisms, leading to population-level effects. Our results highlight the potential for food provisioning to markedly influence disease processes in wildlife mammal populations.
Data from: Reserve size and fragmentation alters community assembly, diversity and dynamics
Researchers have disputed whether a single large habitat reserve will support more species than many small reserves. However, relatively little is known from a theoretical perspective about how reserve size affects competitive communities structured by spatial abiotic gradients. We investigate how reserve size affects theoretical communities whose assembly is governed by dispersal limitation, abiotic niche differentiation, and source-sink dynamics. Simulations were conducted with varying scales of dispersal across landscapes with variable environmental spatial autocorrelation. Landscapes were inhabited by simulated trees with seedling and adult stages. For a fixed total area in reserves, we found that small reserve systems increased the distance between environments dominated by different species, diminishing the effects of source-sink dynamics. As reserve size decreased, environmental limitations to community assembly became stronger, α-species richness decreased, and γ-richness increased. When dispersal occurred across short distances, a large reserve strategy caused greater stochastic community variation, greater α-richness, and lower γ-richness than in small reserve systems. We found that reserve size variation trades off between preserving different aspects of natural communities, including α versus γ-diversity. Optimal reserve size will depend on the importance of source-sink dynamics and the value placed on different characteristics of natural communities. Anthropogenic changes to the size and separation of remnant habitats can have far reaching effects on community structure and assembly.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.