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Figure 4 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 4. Pearson's correlation analysis between the volume of the horizontal capture web (cm3) and the number of inquiline spiders associated with the web for the spider Aglaoctenus lagotis in two vegetation fragments (JKW: John Kennedy Woodland; PCC: Pica-Pau Country Club) in Araguari, Minas Gerais, Brazil.
Figure 3 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 3. Simple linear regressions between the sheet area of the web and the cephalothorax length of Aglaoctenus lagotis individuals in two vegetation fragments (JKW: John Kennedy Woodland; PCC: Pica-Pau Country Club) in Araguari, Minas Gerais, Brazil. The correlation is positive for both sites (p <0.0001).
Figure 1 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 1. Map of the municipality of Araguari, Minas Gerais, Brazil. 1. The John Kennedy Woodland (JKW; 18°38′35″ S, 48°11′19″ W). 2. The Permanent Preservation Area of the Pica- Pau Country Club (PCC; 18°36′38″ S, 48°11′17″ W).
Figure 2 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 2. Schematic diagram of the methodology used to measure the volume of the capture web of Aglaoctenus lagotis. See the text for details of the calculation.
Figure 6 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 6. Vertical distribution of the prosome length ratios of the copepods (PLOkhotsk: PLOyashio) (left) and temperature anomalies (°C: TOkhotsk – TOyashio) (right) between the Okhotsk Sea (St. OK24) and Oyashio region (St. 19) evaluated by IONESS from October to November 1996. The vertical distribution of each copepod is calculated by daily duplicate samples in the Okhotsk Sea (symbols and bars indicate the means and standard deviations of D50%, respectively). For inter-oceanic comparison, the dashed lines in each panel indicate that the positions of values of both regions are equal.
Figure 1 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 1. Location of the sampling stations in the Okhotsk Sea and Oyashio region from September to December in 1996–1998. ○: closing net sampling, ●: closing net and IONESS sampling.
Fig. 2 in Distribution patterns of selected insect populations on their host plants - an ecological study
Fig. 2: Illustration of those insects with their preferred host plants studied in the present contribution: (a) greenfly on the leaves of the common hazel, (b) mealybug on the leaves of the chervil, (c) sap beetle on the leaves of the nettle.
Fig. 1 in Distribution patterns of selected insect populations on their host plants - an ecological study
Fig. 1: (a) Basic types of distribution patterns in the animal kingdom: (1) regular distribution, (2) aggregated (clotted) distribution, (3) random distribution; (b) graphical method for the determination of the distribution pattern produced by a given animal population.
Fig. 3 in Distribution patterns of selected insect populations on their host plants - an ecological study
Fig. 3: Graphical determination of the distribution patterns of those species introduced in Fig. 2: (a) greenfly on the common hazel, (b) mealybug on the chervil, (c) sap beetle on the nettle.
Data from: Maintenance of deceptive gifts in a natural spider population: ecological and demographic factors
Alternative mating tactics are expected to occur predominantly when mate competition is intense, resources are in short supply, or as a result of asymmetric power relationships between individuals. Males of the nuptial gift-giving spider Pisaura mirabilis use a prevailing tactic of offering a nutritive gift (insect prey) and a deceptive tactic of offering a worthless gift (consumed prey) to prospective mates. If the male's tactic depends on pre-copulatory male-male competition, worthless gifts should occur primarily late in the season, when the operational sex ratio (OSR) becomes male-biased. If it depends on resource availability and/or post-copulatory sexual selection (sperm competition), worthless gifts should occur mostly early in the mating season, when prey availability is low and most females are unmated (i.e. post-copulatory sexual selection is weak). Nuptial gift construction correlated positively with prey availability and negatively with OSR, suggesting that males increase reproductive effort when resource and mate availability increase. We did not find evidence for body condition affecting male tactic use. Male size had a marked effect on the reproductive tactic employed. Males that matured early in the season were very small and employed mostly the nutritive gift tactic during their short life. Among the males that matured later and persisted through the season, relatively small males employed the worthless gift tactic whereas large males employed the nutritive gift tactic. We suggest that the existence of two distinct life history strategies among males (early small and late large size) interacts with environmental and demographic conditions to maintain the deceptive tactic.
Data from: Ecological specialization in populations adapted to constant versus heterogeneous environments
Populations vary in their degree of ecological specialization. An intuitive, but often untested, hypothesis is that populations evolving under greater environmental heterogeneity will evolve to be less specialized. How important is environmental heterogeneity in explaining among-population variation in specialization? We assessed juvenile viability of 20 Drosophila melanogaster populations evolving under one of four regimes: (i) a salt-enriched environment, (ii) a cadmium-enriched environment, (iii) a temporally varying environment, and (iv) a spatially varying environment. Juvenile viability was tested in both the original selective environments and a set of novel environments. In both the original and novel environments, populations from the constant cadmium regime had the lowest average viability and the highest variance in viability across environments but populations from the other three regimes were similar. Our results suggest that variation in specialization among these populations is most simply explained as a pleiotropic by-product of adaptation to specific environments rather than resulting from a history of exposure to environmental heterogeneity.
Data from: Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations
Next generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850,275 raw reads were obtained averaging 355 bp in length. Reads were assembled, post processing, into 16,681 unique contigs with an N50 of 898 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were annotated based on comparison to the Arabidopsis thaliana genome (TAIR10). Contigs were identified that exhibit high similarity to genes associated with natural variation in flowering time and freezing tolerance in other plant species and will facilitate future studies aimed at elucidating the molecular basis of clinal life history variation and adaptive differentiation in H. maximiliani. Large numbers of gene-associated simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) also were identified that can be deployed in mapping and population genomic analyses.
Data from: The interrelationship among economic activities, environmental degradation, material consumption, and population health in low-income countries: a longitudinal ecological study
Objectives: The theory of ecological unequal exchange explains how trade and various forms of economic activity create the problem of environmental degradation, and lead to the deterioration of population health. Based on this theory, our study examined the inter-relationship among economic characteristics, ecological footprints, CO2 emissions, infant mortality rates and under-5 mortality rates in low-income countries. Design: A longitudinal ecological study design. Setting: Sixty-six low-income countries from 1980 to 2010 were included in the analyses. Data for each country represented an average of 23 years (N=1497). Data sources: Data were from the World Development Indicators, UN Commodity Trade Statistics Database, Global Footprint Network and Polity IV Project. Analyses: Linear mixed models with a spatial power covariance structure and a correlation that decreased over time were constructed to accommodate the repeated measures. Statistical analyses were conducted separately by sub-Saharan Africa, Latin America and other regions. Results: After controlling for country-level sociodemographic characteristics, debt and manufacturing, economic activities were positively associated with infant mortality rates and under-5 mortality rates in sub-Saharan Africa. By contrast, export intensity and foreign investment were beneficial for reducing infant and under-5 mortality rates in Latin America and other regions. Although the ecological footprints and CO2 emissions did not mediate the relationship between economic characteristics and health outcomes, export intensity increased CO2 emissions, but reduced the ecological footprints in sub-Saharan Africa. By contrast, in Asia, the Middle East and North Africa, although export intensity was positively associated with the ecological footprints and also CO2 emissions, the percentage of exports to high-income countries was negatively associated with the ecological footprints. Conclusions: This study suggested that environmental protection and economic development are important for reducing infant and under-5 mortality rates in low-income countries.
Data from: Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis
The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we used double-digest restriction site-associated DNA (ddRAD) sequencing to identify 1861 genomewide, quality-filtered single-nucleotide polymorphism (SNP) loci for C. funebralis collected from three northern and three southern California sites (15 individuals per population). Considering all SNPs, there was no evidence for genetic differentiation among populations or regions (average FST = 0.0042). However, outlier tests revealed 34 loci putatively under divergent selection between northern and southern populations, and structure and SNP tree analyses based on these outliers show clear genetic differentiation between geographic regions. Three of these outliers are known or hypothesized to be involved in stress granule formation, a response to environmental stress such as heat. Combined with previous work that found thermally tolerant southern populations show high baseline expression of stress response genes, these results further suggest that thermal stress is a strong selective pressure across C. funebralis populations. Overall, this study increases our understanding of the factors constraining local adaptation in marine organisms, while suggesting that ecologically driven, strong differentiation can occur at relevant loci in a species with planktonic larvae.
Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species
Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum); patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated ddRAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning.
Supplementary material 1 from: Topping CJ, Duan X (2024) Managing large and complex population operations with agent-based models: The ALMaSS Population_Manager. Food and Ecological Systems Modelling Journal 5: e117593. https://doi.org/10.3897/fmj.5.117593
The code documentation for the ALMaSS Population_Manager class
Figure 2 from: Topping CJ, Duan X (2024) Managing large and complex population operations with agent-based models: The ALMaSS Population_Manager. Food and Ecological Systems Modelling Journal 5: e117593. https://doi.org/10.3897/fmj.5.117593
Figure 2 The time step processes. The three parts of the time step (BeginStep, Step, EndStep) process can run in multithreaded mode for each object 1 to n, extant at that time and are separated by customisable methods for reporting or list management by the Population_Manager class.
Figure 1 from: Topping CJ, Duan X (2024) Managing large and complex population operations with agent-based models: The ALMaSS Population_Manager. Food and Ecological Systems Modelling Journal 5: e117593. https://doi.org/10.3897/fmj.5.117593
Figure 1 The current class hierarchy for beetle population managers, starting with the parent class Population_Manager_Base.
Figure 3 from: Topping CJ, Duan X (2024) Managing large and complex population operations with agent-based models: The ALMaSS Population_Manager. Food and Ecological Systems Modelling Journal 5: e117593. https://doi.org/10.3897/fmj.5.117593
Figure 3 Change in the maximum and minimum sizes and population numbers for two scenarios using the Theoretical1 species, N = do nothing, Rand = randomise the execution order.
Supplementary material 1 from: Marinovska PG, Todorova TI, Boyadzhiev KP, Pisareva EI, Tomova AA, Parvanova PN, Dimitrova M, Chankova SG, Petrova VY (2022) Cellular susceptibility and oxidative stress response to menadione of logarithmic, quiescent, and nonquiescent Saccharomyces cerevisiae cell populations. In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 127-138. https://doi.org/10.3897/biorisk.17.77320
Figure S1
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.