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1,068 results for “demographic”
Demographic consequences of changes in environmental periodicity
<p>The fate of natural populations is mediated by complex interactions among vital rates, which can vary within and among years. While the effects of random, among-year variation in vital rates have been studied extensively, relatively little is known about how periodic, non-random variation in vital rates affects populations. This knowledge gap is potentially alarming as global environmental change is projected to alter common periodic variations, such as seasonality. We investigated the effects of changes in vital-rate periodicity on populations of three species representing different forms of adaptation to periodic environments: the yellow-bellied marmot (<em>Marmota flaviventer</em>), adapted to strong seasonality in snowfall; the meerkat (<em>Suricata suricatta</em>), adapted to inter-annual stochasticity as well as seasonal patterns in rainfall; and the dewy pine (<em>Drosophyllum lusitanicum</em>), adapted to fire regimes and periodic post-fire habitat succession. To assess how changes in periodicity affect population growth, we parameterized periodic matrix population models and projected population dynamics under different scenarios of perturbations in the strength of vital-rate periodicity. We assessed the effects of such perturbations on various metrics describing population dynamics, including the stochastic growth rate, log λ<sub>S</sub>. Overall, perturbing the strength of periodicity had strong effects on population dynamics in all three study species. For the marmots, log λ<sub>S</sub> decreased with increased seasonal differences in adult survival. For the meerkats, density dependence buffered the effects of perturbations of periodicity on log λ<sub>S</sub>. Finally, dewy pines were negatively affected by changes in natural post-fire succession under stochastic or periodic fire regimes with fires occurring every 30 years, but were buffered by density dependence from such changes under presumed more frequent fires or large-scale disturbances. We show that changes in the strength of vital-rate periodicity can have diverse but strong effects on population dynamics across different life histories. Populations buffered from inter-annual vital-rate variation can be affected substantially by changes in environmentally-driven vital-rate periodic patterns; however, the effects of such changes can be masked in analyses focusing on inter-annual variation. As most ecosystems are affected by periodic variations in the environment such as seasonality, assessing their contributions to population viability for future global-change research is crucial.</p>
Long-term demographic trends and spatio-temporal distribution of past human activity in Central Europe: Comparison of archaeological and palaeoecological proxies (datasets and R scripts)
<p>This digital archive is an outcome of the paper Kolář J., Macek M., Tkáč P., Novák D. & V.Abraham: Long-term demographic trends and spatio-temporal distribution of past human activity in Central Europe: Comparison of archaeological and palaeoecological proxies. Quaternary Science Reviews, 2022</p>
Demographics
<p>Dataset for presentation entitled "Reconstruction effects in wh-slifting: Experimental evidence"</p>
Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana
<p><em>This folder contains data & code used for the study "Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana"</em></p> <p>All data analyzed in the study are stored in the folder "data":</p> <ul> <li>"pheno_file.csv": the main phenotypic file corresponding to the experiment with paired plants used to estimate Indirect Genetic Effects.</li> <li>"pheno_file_single_plants.csv": phenotypic file with measurements of plant biomasses in the absence of competition (single plants)</li> <li>"call_method_75_TAIR9.csv": genomic data (SNPs) for each accession from the RegMap panel (ref [1])</li> <li>"Data_geo_RegMap_accessions.csv": geographic localization of each accession from the RegMap panel (ref [2])</li> <li>"igeGWAS_scores.csv": Genome-Wide Association Study (GWAS) results reporting for each SNP from the RegMap panel the p-value and estimated effect sizes of their direct and indirect genetic effects</li> <li>"1001_accessions_info.csv": geographic localization and admixture group for each accession from the 1001 genomes project (ref [3])</li> <li>"snp_data_all_samples.txt": allelic value of each accession from the 1001 genomes project at the eleven top SNPs associated with IGE</li> <li>"sample_names.txt": names of accessions listed in the file "snp_data_all_samples.txt"</li> <li>"climatic_data.csv": climatic data for each accessions from the 1001 genomes project (ref [4])</li> <li>"candidate_genes_all.csv": list of all genes (and associated GO terms) with a non-synonymous, nonsense, or frameshift mutation in close proximity (distance < half LD decay distance) and high linkage (r2>0.5) with a SNP significantly associated with IGE</li> <li>"genes.coord.bed": list of all genes in a +- 500 kb around top IGE SNPs and their coordinates</li> <li>"AllGenes_fst.GeneID.txt": pairwise Fst computed between each pair of admixture groups, for all genes annotated in the genome of A. thaliana</li> </ul> <p>"ABBA_BABA" subfolder contains ABBA_BABA statistics computed for each individual chromosome (Chr1-Chr5) using genomic windows of 20 kb with at least 250 SNPs per windows. ABBA-BABA statistics were computed using custom python scripts from https://github.com/simonhmartin/genomics_general</p> <p><br> "GEA" subfolder contains Genome-Environment Association results, with one file per chromosome x climatic variable. Climatique variable are indexed, following the order listed in the file "Climatic_variables.txt" within the subfolder "GEA". GEA analysis were run with the gemma program: https://github.com/genetics-statistics/GEMMA.</p> <p><br> "LD_IGE_SNPs" subfolders contains the list of SNPs located at +- 2Mb of a significant IGE SNP (one file per IGE SNP, named "SNPalias_LDSimplified.csv") and their linkage (r2) with the IGE SNP. It also contains the file "LD_windows_sizes.csv" with the half LD decay distances for all significant IGE SNP.</p> <p>All analysis performed to produce the tables and figures presented in the study (main manuscript & supplementary information) were done with the R script "Arabidopsis_IGE_analysis.R", which uses "manhattan_custom.R" as a source function to produce custom manhattan plots.</p> <p> </p> <p><strong>REFERENCES:</strong></p> <p>[1] Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, et al. 2012. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44: 212–216.</p> <p>[2] Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. 2011. Source verification of mis-identified Arabidopsis thaliana accessions. The Plant Journal 67: 554–566.</p> <p>[3] 1001 Genomes Consortium. 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491.</p> <p>[4] Ferrero-Serrano Á, Assmann SM. 2019. Phenotypic and genome-wide association with the local environment of Arabidopsis. Nature Ecology & Evolution 3: 274–285.</p>
Data from: Island-wide characterization of agricultural production challenges the demographic collapse hypothesis for Rapa Nui (Easter Island)
<p>Communities in resource-poor areas face health, food production, sustainability, and overall survival challenges. Consequently, they are commonly featured in global debates surrounding societal collapse. Rapa Nui (Easter Island) is often used as an example of how over-exploitation of limited resources resulted in a catastrophic population collapse. A vital component of this narrative is that the rapid rise and fall of pre-contact Rapanui population growth rates was driven by the construction and overexploitation of once extensive rock gardens. However, the extent of island-wide rock gardening, while key for understanding food systems and demography, must be better understood. Here, we use shortwave infrared (SWIR) satellite imagery and machine learning to generate an islandwide estimate of rock gardening and re-evaluate prior population size models for Rapa Nui. We show that the extent of this agricultural infrastructure is substantially less than previously claimed and likely could not have supported the large population sizes that have been assumed.</p>
SSP1 and SSP3 population projections with demographic categories
<p>Demographic projections for the Shared Socioeconomic Pathways SSP1 and SSP3 scenarios with demographic breakdown for "young", "adult" and "old" populations, defined as <15 years old, 15-65 years old, and >65 years old, at 10 year intervals. Projections are calculated combining SSP population projections, UN WPP country wide demographic trends, and SEDAC demographic spatial distributions.</p> <p> </p> <p>The "interp" version of the files includes linear interpolationed values for each grid cell for every year.</p>
Fig. 1 in Demographic And Morphometric Parameters Of The Yellow-Necked Mouse (Apodemus Flavicollis) In Late Autumn-Early Spring In Lithuania
Fig. 1. Dynamics of the age structure of A. flavicollis population in October–April 2004–2009. RESULTS
Figure 2 in Effects of dams on demographic structures of amphidromous fish and crustacean species in Caribbean rivers
Figure 2. – Individual number histograms of each species broken down by size classes (mm) (left chart) and cohort extraction (right chart) downstream of the Grand Carbet River in March. Right chart: red curves are each cohort extracted by the model; green curve is the cumulative individual number in the modelled age groups.
Figure 1 in Effects of dams on demographic structures of amphidromous fish and crustacean species in Caribbean rivers
Figure 1. – Map of Guadeloupe with the three sampled rivers (bold lines) and study sites: downstream and upstream the water intakes (●) and the first riffle from the mouth of the rivers (Ì).
Figure 7 in Effects of dams on demographic structures of amphidromous fish and crustacean species in Caribbean rivers
Figure 7. – Individual number histograms of each species broken down by size classes (mm) for the three stations (top chart) and porosity chart of the Moreau River water intake (bottom chart). Bottom chart: dotted black line indicates 50% crossing; dotted grey lines indicate the mean crossing rate for these size classes. The size of the downstream and upstream populations of Macrobrachium faustinum and M. heterochirus are too small and fragmented to be presented.
Figure 4 in Effects of dams on demographic structures of amphidromous fish and crustacean species in Caribbean rivers
Figure 4. – Individual number histograms of each species broken down by size classes (mm) (left chart) and cohort extraction (right chart) downstream of the Moreau River in June. Right chart: red curves are each cohort extracted by the model; green curve is the cumulative individuals' number in the modelled age groups. No Macrobrachium heterochirus were caught.
Figure 6 in Effects of dams on demographic structures of amphidromous fish and crustacean species in Caribbean rivers
Figure 6. – Individual number histograms of each species broken down by size classes (mm) for the three stations (top chart) and porosity chart of the Pérou River water intake (bottom chart). Bottom chart: arrow indicates the optimal size at crossing; dotted black line indicates 50% crossing; dotted grey lines indicate the mean crossing rate for these size classes. The size of the downstream and upstream population of Macrobrachium faustinum is too small and fragmented to be presented.
Comparative Study of Demographic Profile and Health Condition among Transgender and Cisgender in India
<p>This data set respresents data on Transgender and Cisgender Community including their demographic profile and health condition living in Varanasi District of Uttar Pradesh State in India. The data was collected with ethical permission and consent of respondents. This work is thesis related. The given data is according to survey conducted in the concern area. </p>
Fig. 2 in Temporal and demographic blood parasite dynamics in two free-ranging neotropical primates
Fig. 2. Individual infection status by parasite by year. Strength and thickness of lines are scaled to the number of individuals that took a given infection trajectory from one year to the next. Two diagonal lines span 2012‾2014 because those individuals were not sampled in 2013. The + symbols represent every infection or non-infection found across all individuals in the study.
Fig. 3 in Temporal and demographic blood parasite dynamics in two free-ranging neotropical primates
Fig. 3. Parasite species richness by species, age class and sex. Colors represent females (black) and males (gray).
Fig. 1 in Temporal and demographic blood parasite dynamics in two free-ranging neotropical primates
Fig. 1. Annual prevalence of single- and co-infections by species. Prevalence indicated for each parasite (dark gray), and each pairwise combination of parasites (light gray). Numbers near the top of each bar show the exact prevalence; black lines indicate 95% confidence intervals; dots indicate expected levels of co-infection (refer to Section 3.2). M-D is co-occurrence of M. mariae and Dipetalonema spp., D-T is Dipetalonema spp. and T. minasense, and M-T is M. mariae and T. minasense.
Common20LS: A Lexical Simplification Dataset with Demographic Information
<p>Common20LS is a dataset for the task of Lexical Simplification that contains demographic information about the annotators. It consists on 20 Lexical Simplification problems annotated by 262 people. Each annotated instance is composed of a sentence, a target complex word or phrase, and a set of simplifications suggested by humans ranked by simplicity.</p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (16S rRNA gene sequencing data)
<p>Microbiome data accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for alpha- and beta- diversity, as well as for individual taxa both in binary and quantitative phenotypic representation. Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (Metadata)
<p>Associated demographic, lifestyle, environmental and biochemical metadata accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
Fig. 5 in Gastrointestinal parasites of a reintroduced semi-wild plains bison (Bison bison bison) herd: Examining effects of demographic variation, deworming treatments, and management strategy
Fig. 5. The average sum of FECs counts by year, demonstrating and increasing trend in FECs between 2015 and 2019. Black horizontal lines denote median values, while the top and bottom of boxes denote the upper and lower interquartile ranges (75th and 25th percentiles). Extending "whiskers" denote values of 1.5 times the interquartile range; points outside of this range constitute outliers.
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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.