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308 results for “density dependence”
Data package supporting manuscript "Widespread Heterogeneity in Density-Dependent Mortality of Nearshore Fishes"
This repository contains the complete data synthesis and analysis pipeline for a global meta-analysis on density-dependent mortality in reef fishes. We estimated mortality parameters (α and β) from >30 ecological studies and explored how ecological traits, experimental methods, and phylogenetic history explain variation in density dependence. It comprises eight data tables in csv format, three .tre files for phylogenetic trees (see method document for data sources), and the zipped code folder (including 12 R scripts) to ensure transparent, end-to-end reproducibility of data processing, analysis, and visualization. This package supports the manuscript “Widespread Heterogeneity in Density-Dependent Mortality of Nearshore Fishes” by Stier & Osenberg (Ecology Letters).
Generalization of a density-dependent ecosystem function in dominant aquatic macroinvertebrates
<div> <div> <p>This Zenodo record contains the supporting data and code for the publication 'Generalization of a density-dependent ecosystem function in dominant aquatic macroinvertebrates', published in Oikos (<a title="DOI to publication" href="https://doi.org/10.1111/oik.10774">https://doi.org/10.1111/oik.10774</a>). The data are described in detail in the corresponding publication. The data archive contains a ReadMe file, two text files with the empirical data, and a corresponding R script for analysis. All required data to reproduce the full analysis from the original publication are provided.</p> <p>In order to reproduce the analysis and figures, run <code>DensityDependenceAnalysis20240319.R</code>. Make sure that your working directory is the actual folder containing the data files <code>Data_Field.txt</code> and <code>Data_Lab.txt</code>. If run in Rstudio, this should happen automatically. Else this is easily achieved by (re)starting R (or R Studio) by double-clicking the R script file from the folder. The script will produce all the figures from the paper, organized in a folder <code>AnalysisYYYYMMDD</code> and two subfolders <code>CheckFigs</code> and <code>SuppFigs</code>. Figures are prepared as pixel graphics (PNG).</p> </div> </div>
Density-dependent effects of exotic brook trout on aquatic communities in mountain lakes revealed by environmental DNA and morphological taxonomy
Invasion of non-native fishes threatens freshwater biodiversity worldwide. Yet, detailed estimates of population demography for invasive species, that estimate population size and body size of the invasive species, are rarely integrated in evaluating aquatic community responses. Our study capitalized on detailed brook trout population demographic data collected for a replicated whole lake ecosystem experiment involving experimental harvesting of exotic brook trout in nine mountain lakes. We applied environmental DNA (eDNA) metabarcoding and morphological taxonomy to examine the response of crustacean zooplankton and macroinvertebrate communities to gradients in brook trout effective density and lake elevation. Density-dependent effects of brook trout on crustacean zooplankton and macroinvertebrate communities were detected even decades after their first introductions (between 1926 and 1980). However, they were moderated by environmental factors such as elevation, lake maximum depth and dissolved organic carbon. Elevation was important in structuring crustacean zooplankton and macroinvertebrate community composition. While there were differences in explanatory variables when describing communities characterized by eDNA metabarcoding and morphological taxonomy, the principal environmental factors that structured the communities were similar. Our paper highlights persisting density-dependent impacts of exotic trout on invertebrate communities even decades after first introduction, and it considers the conservation implications for lake restoration.
Influence of cockle bioturbation on microphytobenthic primary producers: habitat and density-dependent effect
The purpose of this study was to better understand the non-trophic interactions of benthic macrofauna, especially through their bioturbation activity, on microphytobenthos (MPB), which remain poorly studied and understood. For this purpose, a mesocosm experiment was performed, using the common cockles Cerastoderma edule. This species plays a key role in coastal ecosystem, especially impacting sediment characteristics and biogeochemistry through their bioturbation, including sediment reworking and bioirrigation. For the first time, bioturbation rates, biogeochemical fluxes at the sediment-water interface and MPB biomass and photosynthetic variables were measured at the same time. The effect of cockles density and sediment type were also investigated. This mesocosm experiment took place at the marine station of Arcachon. Experimental units consisted of PVC tubes filled with 2 types of sediment (medium sand or fine sand; samples in Arachon Bay and Baie des Veys in France). Then, 4 density of cockles were added in triplicate (0, 288, 720 and 1,297 ind. m-2), for each sediment type. The whole design was repeated twice, because in one of them luminophores were added at the top to measure sediment reworking, and could interfere with fluorescence measurement of MPB variables. All experimental units were incubated 6 days into a big tank, with artificial tide and light. Dissolved tracers were added into the natural seawater (close system) to measure bioirrigation rates of cockles. After 6 days, regarding experimental units with luminophores, they were slices and porewater was extracted to quantify bioturbation rates. Regarding units without luminophores, surface biomass and photosynthetic parameters of MPB were first measured in all unit with an IMAGING PAM. Then, oxygen and nutrient fluxes at the sediment water interface were measured using incubations. And finally, the first centimeter was sliced to measure total MPB biomass. This study demonstrated that bioturbation intens
Density-dependent demography of creosote bush (Larrea tridentata) along grass-shrub ecotones.
The encroachment of woody plants into grasslands is a global phenomenon with implications for biodiversity and ecosystem function. Understanding and predicting the pace of expansion and the underlying processes that control it are key challenges in the study and management of woody encroachment. Theory from spatial population biology predicts that the occurrence and speed of population expansion should depend sensitively on the nature of conspecific density dependence. If fitness is maximized at the low-density encroachment edge then shrub expansion should be "pulled" forward. However, encroaching shrubs have been shown to exhibit positive feedbacks, whereby shrub establishment modifies the environment in ways that facilitate further shrub recruitment and survival. In this case there may be a fitness cost to shrubs at low density causing expansion to be "pushed" from behind the leading edge. We studied the spatial dynamics of creosotebush (Larrea tridentata), which has a history of encroachment into Chihuahuan Desert grasslands over the past century. We used demographic data from observational censuses and seedling transplant experiments to test the strength and direction of density dependence in shrub fitness along a gradient of shrub density at the grass-shrub ecotone. We also used seed-drop experiments and wind data to construct a mechanistic seed dispersal kernel, then connected demography and dispersal data within a spatial integral projection model (SIPM) to predict the dynamics of shrub expansion. The SIPM predicted that, contrary to expectations based on potential for positive feedbacks, the shrub encroachment wave is "pulled" by maximum fitness at the low-density front. However, the predicted pace of expansion was strikingly slow (ca. 8 cm/yr), and this prediction was supported by independent re-surveys of the ecotone showing little to no change in spatial extent of shrub cover over 12 years. Encroachment speed was acutely sensitive to seedling recruitment,
Dataset: Environment effects on X-ray absorption spectra with quantum embedded real-time Time-dependent density functional theory approaches
<p>This dataset collects the outputs from real-time TDDFT simulation of X-ray absorption of halides in model systems, using the frozen density embedding (FDE) and block-orthogonalized Manby-Miller embedding (BOMME), as well as processing tools and scripts used to carry out the calculations.</p>
Data from: Multifaceted density dependence: Social structure and seasonality effects on Serengeti lion demography
<p>This dataset contains the data and R scripts to estimate the survival, transition, and detection probabilities (Lions_Survival_Transition_MultistateCMRModel.zip) as well as the probability of reproduction and recruitment to 1 year old (Lions_Reproduction_Recruitment_GLMM.zip) in a population of African lions (<em>Panthera leo</em>) monitored between 1984 and 2014 in the Serengeti National Park, Tanzania.</p> <p>We assessed the season-specific effects of density measures at the intra- (number of females in a pride and male coalition size) and extra-group levels (number of nomadic coalitions in the home range of a group) using a Bayesian multistate capture-mark-recapture model for the survival and transition rates and Bayesian generalized linear mixed models for reproduction probability and recruitment. <br><br>The README file further describes each uploaded file.</p>
MCR LTER: Coral Reef: Density-dependence data for Edmunds, et al., Ecology 2018
This dataset contains coral cover data describing the context within which denisty-dependence (DD) was measured on the island of Moorea, French Polynesia, including data describing the benthic community, diameters of Pocillopora spp. measured in photoquadrats, surveys of corals and recruits. These data correspond to figures 1 through 3 in the manuscript by PJ Edmunds, L. Bramanti, and H.R. Nelson, 'Density-dependence mediates coral community structure', Ecology, 99(11), 2018, pp. 2605-2613. This ata set was revised on 27 November 2018. The data managed for Fig. 3 were missing values for two quadrats used in the analysis (quadrats 24 and 9). In this data revision, the values from the missing quadrats have been included. The reefs of Mo’orea, French Polynesia, provide the opportunity to study DD of coral population growth, because coral assemblages in this location responded to declines in abundance with high recruitment and an increase in cover during which recruitment of pocilloporid corals was inversely associated with density. This study tests for DD in this system, first, by describing the context within which it operates: coral cover changed from 46% in 2005, to less than 1% in 2010 following an outbreak of a corallivorous sea star and a cyclone, and then increased to 74% by 2017, in large part through inverse density- associated pocilloporid recruitment. Second, a test for DD of recruitment was conducted by decreasing Pocillopora spp. cover from 33% to 19%: one year later, the density of Pocillopora spp. recruits was 1.65-fold higher in the low versus high cover treatment. Finally, the effects of DD were investigated by comparing simulated and empirical distributions of pocilloporid colonies: as predicted by DD, small colonies were randomly distributed, while large colonies were uniformly distributed. Together these results demonstrate DD of population regulation for Pocillopora spp. corals, thus revealing the potential importance of this ecological principle i
Evolution under pH stress and high population densities leads to increased density-dependent fitness in the protist Tetrahymena thermophila
<p>Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist species <em>Tetrahymena thermophila</em>, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (<em>r<sub>0</sub></em>). Overall, evolution at low pH led to the convergence of <em>r<sub>0</sub></em> and intraspecific competitive ability (<em>α</em>) across the four genotypes. Given the strong correlation between <em>r<sub>0</sub></em> and <em>α</em>, we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase in <em>r<sub>0</sub></em> , or decrease of <em>α</em>, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.</p> <p> </p>
Data from: How density dependence, genetic erosion, and the extinction vortex impact evolutionary rescue
<p>Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation, and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity, and the fixation of maladaptive alleles, hindered adaptation, and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.</p>
Per capita sperm metabolism is density-dependent
<p>From bacteria to metazoans, higher-density populations have lower <em>per capita</em> metabolic rates than lower-density populations. This relationship between density and metabolism was actually first proposed 100 years ago and was focused on spermatozoa but contemporary studies of sperm metabolism specifically assume that sperm concentration has no effect on metabolism. We did a systematic review to estimate the relationship between sperm aerobic metabolism and sperm concentration, for 203 estimates spanning 49 species, from protostomes to humans from 89 studies. We found strong evidence that <em>per capita </em>metabolic rates are concentration-dependent: both within- and among-species, sperm have lower metabolisms in dense ejaculates but increase their metabolism when diluted. On average, a 10-fold decrease in sperm concentration increased <em>per capita</em> metabolic rate by ~60%. Metabolic plasticity in sperm may be an adaptive response but this requires further testing.</p>
Data and R code from: Relics of beavers past: time and population density drive scale-dependent patterns of ecosystem engineering
<p><span>Like many ecological processes, natural disturbances exhibit scale-dependent dynamics that are largely a function of the magnitude, frequency, and scale at which they are assessed. Ecosystem engineers create patch-scale disturbances that affect ecological processes, yet we know little about how these effects scale across space or vary through time. Here, we investigate how patch disturbances by beavers (<i>Castor canadensis</i>), ecosystem engineers renowned for their pond-creation behavior, affect ecological processes across space and time. We evaluated how beaver population recovery influenced surface water dynamics in relation to population density over 70 years across multiple spatial scales (pond, watershed, and regional) in northern Minnesota. Surface water area was positively related to population density at the watershed scale; however, despite variation in beaver densities (and therefore surface water area) at the watershed scale, regional-scale surface water area was stable through time. This stability appears to have been driven by asynchronous beaver density fluctuations among watersheds, combined with the increasing importance of abandoned ponds. Beavers initially created and occupied larger ponds with greater surface water area, but through time shifted towards occupying smaller ponds. As ponds accumulated on the landscape proportionally more surface water was stored within abandoned ponds, which offset the smaller size of occupied ponds. Beaver engineering—driven by density-dependent mechanisms and the legacy effects from abandoned ponds—not only follows general patterns of patch disturbance dynamics by creating a spatial mosaic of patches, but the organism-created mosaic also appears to generate ecological stability at greater spatial scales. We suggest restoring beavers to landscapes is a viable method for increasing surface water storage and will ultimately help advance numerous conservation and rewilding objectives. Our study demonstrates that ecosystem engineering effects can be scale-dependent, indicating researchers should evaluate the ecological impact of engineers across diverse spatiotemporal scales to fully understand their functional roles in ecosystems.</span></p>
Environment and density-dependency explain the fine-scale distribution of tree recruits before and after thinning
<p>Dataset used in the article "Environment and density-dependency explain the fine-scale distribution of tree recruits before and after thinning" in PeerJ</p>
Density-dependent selection and the maintenance of colour polymorphism in barn owls
<p>The capacity of natural selection to generate adaptive changes is according to the Fundamental Theorem of Natural Selection proportional to the additive genetic variance in fitness. In spite of its importance for development of new adaptations to a changing environment, processes affecting the magnitude of the genetic variance in fitness-related traits are poorly understood. Here we show that the red-white colour polymorphism in female barn owls is subject to density-dependent selection at the phenotypic and genotypic level. The diallelic melanocortin-1 receptor (MC1R) gene explained a large amount of the phenotypic variance in reddish colouration in the females (R^2 = 59.8 %). Red individuals (RR genotype) were selected for at low densities, while white individuals (WW genotype) were favoured at high densities and were less sensitive to changes in density. We show that this density-dependent selection favours white individuals and predicts fixation of the white allele in this population at longer time scales without immigration or other selective forces. Still, fluctuating population density will cause selection to fluctuate and periodically favour red individuals. These results suggest how balancing selection caused by fluctuations in population density can be a general mechanism affecting the level of additive genetic variance in natural populations.</p>
Asymmetric density-dependent competition does not contribute to the maintenance of sex in a mixed population of sexual and asexual Potamopyrgus antipodarum
<p>Asexual reproduction is expected to have a two-fold reproductive advantage over sexual reproduction, owing to the cost of producing males in sexual subpopulations. The persistence of sexual females thus requires an advantage to sexual reproduction, at least periodically. Here we tested the hypothesis that asexual females are more sensitive to limited resources. Under this idea, fluctuations in the availability of resources (<em>per capita</em>) could periodically favor sexual females when resources become limited. We combined sexual and asexual freshwater snails (<em>Potamopyrgus antipodarum</em>) together in nylon mesh enclosures at three different densities in an outdoor mesocosm. After one month, we counted the brood size of fertile female snails. We found that fecundity declined significantly with increasing density. However, sexual females did not produce more offspring than asexual females at any of the experimental densities. Our results thus suggest that the cost of sexual reproduction in <em>P. antipodarum</em> is not ameliorated by periods of intense resource competition.</p>
Data from: Density-dependence produces spurious relationships among demographic parameters in a harvested species
<p>1. Harvest of wild organisms is an important component of human culture, economy, and recreation, but can also put species at risk of extinction. Decisions that guide successful management actions therefore rely on the ability of researchers to link changes in demographic processes to the anthropogenic actions or environmental changes that underlie variation in demographic parameters. </p> <p>2. Ecologists often use population models or maximum sustained yield curves to estimate the impacts of harvest on wildlife and fish populations. Applications of these models usually focus exclusively on the impact of harvest and often fail to consider adequately other potential, often collinear, mechanistic drivers of the observed relationships between harvest and demographic rates. In this study, we used an integrated population model and long-term data (1973-2016) to examine the relationships among hunting and natural mortality, the number of hunters, habitat conditions, and population size of blue-winged teal (Spatula discors), an abundant North American dabbling duck with a relatively fast-paced life history strategy.</p> <p>3. Over the last two and a half decades of the study, teal abundance tripled, hunting mortality probability increased slightly (< 0.02), and natural mortality probability increased substantially (> 0.1) at greater population densities. We demonstrate strong density-dependent effects on natural mortality and fecundity as population density increased, indicative of compensatory harvest mortality and compensatory natality. Critically, an analysis that only assessed the relationship between survival and hunting mortality would spuriously indicate depensatory hunting mortality due to multicollinearity between abundance, natural mortality, and hunting mortality. </p> <p>4. Our findings demonstrate that models that only consider the direct effect of hunting on survival or natural mortality can fail to accurately assess the mechanistic impact of hunting on population dynamics due to multicollinearity among demographic drivers. This multicollinearity limits inference and may have strong impacts on applied management actions globally.</p>
Density dependence maintains long-term stability despite increased isolation and inbreeding in the Florida Scrub-Jay
<p>Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understanding how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively-breeding Florida Scrub-Jays (<em>Aphelocoma coerulescens</em>) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival, and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.</p>
Figure 1 in Host instars preference, density-dependent parasitism and behavioral perspective of parasitoids (Aphidius colemani, Aphidius matricariae and Aphelinus abdominalis) in Aphis glycines and Aphis gossypii
Figure 1: Comparison of parasitoids (Ad.colemani, Ad.matricariae and Al.abdominalis) on different ages (nymphal instars) of the(A) As.glycines (n= 30) and (B) As. gossypii (n= 30).
Fig. 3 in Diversity and density-dependence relationship between hymenopteran egg parasitoids and the corn leafopper (Hemiptera: Cicadellidae) in maize agroecosystem vs. teosinte wild habitat
Fig. 3. Relationship between the number of exposed Dalbulus maidis eggs and number of Anagrus virlai within the crop maize habitat on (A) maize sentinel plants, and (B) teosinte sentinel plants.
Fig. 1 in Diversity and density-dependence relationship between hymenopteran egg parasitoids and the corn leafopper (Hemiptera: Cicadellidae) in maize agroecosystem vs. teosinte wild habitat
Fig. 1. Relationship between the number of exposed Dalbulus maidis eggs and number of adult parasitoids (of any species) found in the crop maize habitat on (A) maize sentinel plants, and (B) teosinte sentinel plants.
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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.