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11,506 results for “Dynamics”
Data from: Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector
The dynamics of association between pathogens and vectors can strongly influence epidemiology. It has been proposed that wilt disease epidemics in cucurbit populations are sustained by persistent colonization of beetle vectors (Acalymma vittatum) by the bacterial phytopathogen Erwinia tracheiphila. We developed a qPCR method to quantify E. tracheiphila in whole beetles and frass and used it to assess pathogen acquisition and retention following variable exposure to infected plants. We found that (i) E. tracheiphila is present in frass in as little as three hours after feeding on infected plants and can be transmitted with no incubation period by vectors given brief exposure to infected plants, but also by persistently colonized vectors several weeks following exposure; (ii) duration of exposure influences rates of long-term colonization; (iii) frass infectivity (assessed via inoculation experiments) reflects bacterial levels in frass samples across time; and (iv) vectors rarely clear E. tracheiphila infections, but suffer no apparent loss of fitness. These results describe a pattern conducive to the effective maintenance of E. tracheiphila within cucurbit populations.
Data from: The evolutionary dynamics of sexually antagonistic mutations in pseudoautosomal regions of sex chromosomes
Sex chromosomes can evolve gene contents that differ from the rest of the genome, as well as larger sex differences in gene expression compared with autosomes. This probably occurs because fully sex-linked beneficial mutations substitute at different rates from autosomal ones, especially when fitness effects are sexually antagonistic (SA). The evolutionary properties of genes located in the recombining pseudo-autosomal region (PAR) of a sex chromosome have not previously been modelled in detail. Such PAR genes differ from classical sex-linked genes by having two alleles at a locus in both sexes; in contrast to autosomal genes, however, variants can become associated with gender. The evolutionary fates of PAR genes may therefore differ from those of either autosomal or fully sex-linked genes. Here, we model their evolutionary dynamics by deriving expressions for the selective advantages of PAR gene mutations under different conditions. We show that, unless selection is very strong, the probability of invasion of a population by an SA mutation is usually similar to that of an autosomal mutation, unless there is close linkage to the sex-determining region. Most PAR genes should thus evolve similarly to autosomal rather than sex-linked genes, unless recombination is very rare in the PAR.
Data from: Contrasting effects of spatial heterogeneity and environmental stochasticity on population dynamics of a perennial wildflower
Understanding how variation in growth, survival and reproduction affect population dynamics is a fundamental question in ecology. Although the effects of among-year variation (environmental stochasticity) are well understood, the effects of among-site variation (spatial heterogeneity) are less clearly defined. I evaluated the effects of spatial and temporal variation on the population dynamics of Pulsatilla patens, pasqueflower, a perennial prairie forb. I conducted a 10-year demographic monitoring study, and quantified vital rate variation among sites and years using generalized linear models. I incorporated vital rate functions using this variation into integral projection models for stochastic and spatially heterogeneous environments. I also explored the effects of temporal and spatial autocorrelation, by exploring model predictions over the range of possible values for temporal autocorrelation and local seed dispersal. Vital rates varied more among years than among sites. However, environmental stochasticity and spatial heterogeneity had similar magnitude effects on population dynamics. These effects were also qualitatively different: environmental stochasticity reduced population growth rates relative to the average, whereas spatial heterogeneity increased population growth rates. Spatial autocorrelation and negative temporal autocorrelation led to higher population growth rates, although environmental stochasticity still reduced growth rates for all autocorrelation values, and spatial heterogeneity increased growth rates for all autocorrelation values. Some form of autocorrelation would be necessary for model projections to match observed population trends. Synthesis. Spatial heterogeneity is as important as environmental stochasticity for population dynamics, but it is much less often incorporated into population projection models. This study points to a number of interesting avenues for future research into the roles of spatial heterogeneity and spatiotemporal variation for long-term population dynamics.
Data from: The role of fish life histories in allometrically scaled food-web dynamics
1. Body size determines key ecological and evolutionary processes of organisms. Therefore, organisms undergo extensive shifts in resources, competitors and predators as they grow in body size. While empirical and theoretical evidence show that these size-dependent ontogenetic shifts vastly influence the structure and dynamics of populations, theory on how those ontogenetic shifts affect the structure and dynamics of ecological networks is still virtually absent. 2. Here, we expand the Allometric Trophic Network (ATN) theory in the context of aquatic food webs to incorporate size-structure in the population dynamics of fish species. We do this by modifying a food web generating algorithm, the niche model, to produce food webs where different fish life-history stages are described as separate nodes which are connected through growth and reproduction. Then, we apply a bioenergetic model that uses the food webs and the body sizes generated by our niche model to evaluate the effect of incorporating life-history structure into food web dynamics. 3. We show that the larger the body size of a fish species respective to the body size of its preys, the higher the biomass attained by the fish species and the greater the ecosystem stability. We also find that the larger the asymptotic body size attained by fish species the larger the total ecosystem biomass, a result that holds true or both the largest fish in the ecosystem and each fish species in the ecosystem. 4. This work provides an expanded ATN theory that generates food webs with life-history structure for chosen species. Our work offers a systematic approach for disentangling the effects of increasing life-history complexity in food-wed models.
Data from: Health trajectories reveal the dynamic contributions of host genetic resistance and tolerance to infection outcome
Resistance and tolerance are two alternative strategies hosts can adopt to survive infections. Both strategies may be genetically controlled. To date, the relative contribution of resistance and tolerance to infection outcome is poorly understood. A bioluminescent Listeria monocytogenes (Lm) infection challenge model on four genetically diverse mouse strains was used to study the genetic determination and dynamic contributions of host resistance and tolerance to listeriosis, a serious food-borne infectious disease in humans. Conventional statistical analyses revealed significant genetic variation in both resistance and tolerance, but could not capture the time-dependent relative importance of either strategy. These limitations were overcome by the development of novel statistical tools to analyse individual infection trajectories portraying simultaneous changes in infection severity and health. Based on these tools, early expression of resistance followed later by expression of tolerance, emerged as important hallmarks for surviving Lm infections. Trajectory analysis further revealed that survivors and non-survivors follow distinct infection paths, which are also genetically determined, and provided new survival thresholds as objective endpoints in infection experiments. Future studies may use trajectories as novel traits for mapping and identifying genes that control infection dynamics and outcome. A Matlab script for user-friendly trajectory analysis is provided.
Supplementary material 3 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Table S3
Figure 1 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Figure 1 Geographic location of the study sites A the location of Armero and Cambao in Colombia B Armero C Cambao. Abbreviations: F = forest, ES = early succession, P = pasture. Maps courtesy of DIVA-GIS 7.5 and Google Earth Image 2020. For more details, see the online map at https://www.google.com/maps/d/u/3/edit?mid=1le-kQOQFh8RumUibWP3D8ghtxVvGM-eF&usp=sharing
Figure 3 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Figure 3 Non-metric multidimensional scaling ordination of carabid beetle assemblages at Armero (Colombia). Wet and dry season catches were analyzed and plotted separately. The catch in five of the ten forest samples returned zero individuals, and were removed from the analysis. The ellipses indicate 1 SD of the weighted average of site scores of forest (dotted line), early succession (long dashed line), and pasture (solid line). Abbreviations of the significant environmental vectors: soiltemp = soil temperature, airtemp = air temperature, litterdepth = leaf litter depth (cm), canopy = percentage canopy cover. Stress value 0.06.
Supplementary material 2 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Table S2
Figure 5 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Figure 5 Generalized Linear Mixed Model predicted (mean ± SE) number of individuals of Calosoma alternans, genus Megacephala and the remaining carabid beetle species collected from Armero and Cambao combined across the three habitat types (forest, early succession, and pasture). Note different y-axis scales.
Supplementary material 1 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Table S1
Figure 4 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Figure 4 Generalized Linear Model predicted (mean ± SE) number of individuals of Calosoma alternans and the remaining carabid beetle species collected from Armero across the three habitat types (forest, early succession, and pasture). Note different y-axis scales.
Figure 2 from: Ariza GM, Jácome J, Esquivel HE, Kotze DJ (2021) Early successional dynamics of ground beetles (Coleoptera, Carabidae) in the tropical dry forest ecosystem in Colombia. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 877-906. https://doi.org/10.3897/zookeys.1044.59475
Figure 2 Rarefaction and extrapolation richness curves for carabid beetles from Armero (A–C), and Armero and Cambao combined (D–F) A, D comparison of richness between habitats using sample-size-based curves B, E sample completeness curves C, F comparison of richness using coverage-based curves. Abbreviations: F = forest, ES = early succession, P = pasture. Numbers in parentheses denote sample sizes and the observed Hill number (q = 0) (A, D), sample size and the estimated sample coverage (B, E), and the estimated sample coverage and the observed Hill number (q = 0) (C, F), respectively.
Data from: A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data
Our understanding of macroevolutionary patterns of adaptive evolution has greatly increased with the advent of large-scale phylogenetic comparative methods. Widely used Ornstein-Uhlenbeck (OU) models can describe an adaptive process of divergence and selection. However, inference of the dynamics of adaptive landscapes from comparative data is complicated by interpretational difficulties, lack of identifiability among parameter values and the common requirement that adaptive hypotheses must be assigned a priori. Here we develop a reversible-jump Bayesian method of fitting multi-optima OU models to phylogenetic comparative data that estimates the placement and magnitude of adaptive shifts directly from the data. We show how biologically informed hypotheses can be tested against this inferred posterior of shift locations using Bayes Factors to establish whether our a priori models adequately describe the dynamics of adaptive peak shifts. Furthermore, we show how the inclusion of informative priors can be used to restrict models to biologically realistic parameter space and test particular biological interpretations of evolutionary models. We argue that Bayesian model-fitting of OU models to comparative data provides a framework for integrating of multiple sources of biological data–such as microevolutionary estimates of selection parameters and paleontological timeseries–allowing inference of adaptive landscape dynamics with explicit, process-based biological interpretations.
Data from: Dynamical state transitions into addictive behaviour and their early-warning signals
The theory of critical transitions in complex systems (ecosystems, climate, etc.), and especially its ability to predict abrupt changes by early-warning signals based on analysis of fluctuations close to tipping points, is seen as a promising avenue to study disease dynamics. However, the biomedical field still lacks a clear demonstration of this concept. Here, we used a well-established animal model in which initial alcohol exposure followed by deprivation and subsequent reintroduction of alcohol induces excessive alcohol drinking as an example of disease onset. Intensive longitudinal data (ILD) of rat drinking behaviour and locomotor activity were acquired by a fully automated drinkometer device over 14 weeks. Dynamical characteristics of ILD were extracted using a multi-scale computational approach. Our analysis shows a transition into addictive behaviour preceded by early-warning signals such as instability of drinking patterns and locomotor circadian rhythms, and a resultant increase in low frequency, ultradian rhythms during the first week of deprivation. We find evidence that during prolonged deprivation, a critical transition takes place pushing the system to excessive alcohol consumption. This study provides an adaptable framework for processing ILD from clinical studies and for examining disease dynamics and early-warning signals in the biomedical field.
Data from: Impaired hippocampal place cell dynamics in a mouse model of the 22q11.2 deletion
Hippocampal place cells represent the cellular substrate of episodic memory. Place cell ensembles reorganize to support learning but must also maintain stable representations to facilitate memory recall. Despite extensive research, the learning-related role of place cell dynamics in health and disease remains elusive. Using chronic two-photon Ca2+ imaging in hippocampal area CA1 of wild-type and Df(16)A+/− mice, an animal model of 22q11.2 deletion syndrome, one of the most common genetic risk factors for cognitive dysfunction and schizophrenia, we found that goal-oriented learning in wild-type mice was supported by stable spatial maps and robust remapping of place fields toward the goal location. Df(16)A+/− mice showed a significant learning deficit accompanied by reduced spatial map stability and the absence of goal-directed place cell reorganization. These results expand our understanding of the hippocampal ensemble dynamics supporting cognitive flexibility and demonstrate their importance in a model of 22q11.2-associated cognitive dysfunction.
Spatial dynamics of pathogen transmission in communally roosting species: Impacts of changing habitats on bat-virus dynamics
<p>1. The spatial organisation of populations determines their pathogen dynamics. This is particularly important for communally roosting species, whose aggregations are often driven by the spatial structure of their environment.</p> <p>2. We develop a spatially explicit model for virus transmission within roosts of Australian tree-dwelling bats (<i>Pteropus</i> spp.), parameterised to reflect Hendra virus. The spatial structure of roosts mirrors three study sites, and viral transmission between groups of bats in trees was modelled as a function of distance between roost trees. Using three levels of tree density to reflect anthropogenic changes in bats habitats, we investigate the potential effects of recent ecological shifts in Australia on the dynamics of zoonotic viruses in reservoir hosts.</p> <p>3. We show that simulated infection dynamics in spatially structured roosts differ from that of mean-field models for equivalently sized populations, highlighting the importance of spatial structure in disease models of gregarious taxa. Under contrasting scenarios of flying-fox roosting structures, sparse stand structures (with fewer trees but more bats per tree) generate higher probabilities of successful outbreaks, larger and faster epidemics, and shorter virus extinction times, compared to intermediate and dense stand structures with more trees but fewer bats per tree. These observations are consistent with the greater force of infection generated by structured populations with less numerous but larger infected groups, and may flag an increased risk of pathogen spillover from these increasingly abundant roost types.</p> <p>4. Outputs from our models contribute insights into the spread of viruses in structured animal populations, like communally roosting species, as well as specific insights into Hendra virus infection dynamics and spillover risk in a situation of changing host ecology. These insights will be relevant for modelling other zoonotic viruses in wildlife reservoir hosts in response to habitat modification and changing populations, including coronaviruses like SARS-CoV-2. </p>
Improving intra- and inter-annual GPP predictions by using individual-tree inventories and leaf growth dynamics
<p>Carbon sequestration is a key ecosystem service provided by forests. Inventory data based on individual trees are considered to be the most accurate method for estimating forest productivity. However, estimations of forest photosynthesis itself from inventory data remains understudied, particularly when considering the growth and development of individual trees under the background of global change. Here, we used the leaf growth process with phenology and non-structural carbohydrates (NSC) storage to revise an individual-tree based carbon model, FORCCHN. This model couples leaf development and biomass to quantify gross primary productivity (GPP) in the forests, where growth is decoupled from photosynthesis in daily step. The model was initialized with inventory-based forest data rather than the more widely used satellite-based data. We tested the model against measured aboveground woody biomass, growth of leaf biomass, daily gross ecosystem exchange (GEE), and yearly GEE at five representative forest sites in the Northern Hemisphere. We also compared the results from the original model and the revised model at five forest sites. Including leaf growth dynamics and inventory-based initialization improved the predicted performance (r2) of GPP by an average of 33%. Synthesis and applications. Our results suggest that the appropriate vegetation data sources (i.e. inventory or satellite selection) and the effective predictions of the growth process should be considered when developing future carbon cycle models and forest carbon estimation options. Applying and improving such carbon models to evaluate carbon sequestration is an important part of forest carbon sink management.</p>
Metabolic contrast agent produced from transported solid 13C-glucose hyperpolarized via Dynamic Nuclear Polarization
<p>Magnetic Resonance Imaging combined with hyperpolarized <sup>13</sup>C-labelled metabolic contrast agents produced via dissolution Dynamic Nuclear Polarization can, non-invasively and in real-time, report on tissue specific aberrant metabolism. However, hyperpolarization equipment is expensive, technically demanding and needs to be installed on-site for the end-user. In this work, we provide a robust methodology that allows remote production of the hyperpolarized <sup>13</sup>C-labelled metabolic contrast agents. The methodology, built on photo-induced thermally labile radicals, allows solid sample extraction from the hyperpolarization equipment and several hours’ lifetime of the <sup>13</sup>C-labelled metabolic contrast agents at appropriate storage/transport conditions. Exemplified with [U-<sup>13</sup>C, d<sub>7</sub>]-D-glucose, we remotely produce hyperpolarized <sup>13</sup>C-labelled metabolic contrast agents and generate above 10,000-fold liquid-state Magnetic Resonance signal enhancement at 9.4 T, keeping on-site only a simple dissolution device.</p>
Data from: A signature of dynamic biogeography: enclaves indicate past species replacement
Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future.
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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.