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594 results for “Demographic data”
Dataset (raw questionnaire data and variable importance results) supplementing the publication "Does Gender Really Matter? How Demographics and Site Characteristics Influence Behavior and Attitudes of German Small-Scale Private Forest Owners"
<p>The dataset contains</p> <ul> <li>a translation of the questionnaire,</li> <li>the questionnaire raw data, and</li> <li>the results of the variable importance analysis</li> </ul> <p>used in the publication "Does Gender Really Matter? How Demographics and Site Characteristics Influence Behavior and Attitudes of Small-Scale Private Forest Owners".</p>
Silva, Harder et al. Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history Data
<p>Dataset used in the "Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history" paper by Silva, Harder et al.</p> <p>This dataset includes Fasta files for Simulated dataset and VCF files for both Empirical and Simulated datasets.</p>
Data from: Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species
<p>Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers - Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis - using a population genomics dataset of 23 562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.</p>
Data from: Integrating demographic niches and black spruce range expansion at subarctic treelines
<p>When investigating relationships between species' niches and distributions, niches can be divided demographically, resulting in unique niches for different life stages. This approach can identify changing substrate requirements throughout a species' life cycle. Using non-metric multidimensional scaling, we quantified microsite conditions associated with successful recruitment in the tundra landscape and successful seed production amongst adult trees of black spruce (<em>Picea mariana</em>) at subarctic treeline in Yukon, Canada to assess how life stage-specific requirements may impact the distribution of this widespread boreal tree species. Treeline ecotones in this region showed high heterogeneity in tundra microsites available for establishment. Black spruce exhibited changing microsite associations from germination to reproductive maturity, which were mainly driven by changes in plant community and soil moisture. These associations limit the microsites where individuals can establish and reproduce to a subset available within the heterogeneous landscape. Overall, we suggest that (1) substrates suitable for early recruitment are limited at the range edge; and (2) reproductive adults have a narrow niche, limiting successful seed production in adults and forming sink populations where suitable conditions are limited. Our multivariate assessment of microsite suitability can provide valuable insights into the spatial distribution of a species throughout its life cycle and identify life stage-specific constraints to range expansion.</p>
Data from: Demographic effects of a megafire on a declining prairie grouse in the mixed-grass prairie
<p>Recent studies have documented benefits of small, prescribed fire and wildfire for grassland-dependent wildlife, such as lesser prairie-chickens (<em>Tympanuchus</em> <em>pallidicintus</em>), but wildlife demographic response to the scale and intensity of megafire (wildfire > 40,000 ha) in modern fragmented grasslands remains unknown. Limited available grassland habitat makes it imperative to understand if increasing frequency of megafires could further reduce already declining lesser prairie-chicken populations, or if historical evolutionary interactions with fire make lesser prairie-chickens resilient. To evaluate lesser prairie-chicken demographic response to megafires, we compared lek counts, nest density, and survival rates of adults, nests, and chicks before (2014–2016) and after (2018–2020) a 2017 megafire in the mixed-grass prairie of Kansas, USA (Starbuck fire ~254,000 ha). There was a 67% decline in attending males on leks post-fire and a 46% decline in occupied leks post-fire. Despite population declines as indicated by lek counts, adult female breeding season survival (Ŝ) was similar pre- (Ŝ <span>= </span>0.65 ± 0.08 [SE]) and post-fire (0.61 ± 0.08), as was chick survival (pre-fire: 0.23 ± 0.07; post-fire: 0.27 ± 0.11). Nest survival appeared lower post-fire (pre-fire: 0.38 ± 0.06; post-fire: 0.20 ± 0.06), <span>but did not differ at the 95% confidence interval.</span> Nest density of marked females declined 73% in areas burned by megafire. Although lesser prairie-chickens persisted in the study area and we documented minimal effects on most demographic rates, reduced lesser prairie-chicken abundance and reproductive output suggests full recovery may take >3 years. Increased propensity for megafire resulting from suppression of smaller fires, compounded by climate change and woody encroachment, may impose a short-term (3-5 year) threat to already declining lesser prairie-chicken populations.</p>
Data for Apalachicola Bay oyster demographic analysis
<p>Processed data describing the number and lengths of oysters sampled from long-term fisheries independent sampling in Apalachicola Bay, Florida. Original (raw) data collected by Florida Fish and Wildlife Conservation Commission and Florida Department of Agriculture and Consumer Services.</p>
Data for: Using a demographic model to project the long-term effects of fire management on tree biomass in Australian savannas
<p>Tropical savannas are characterised by high primary productivity and high fire frequency, such that much of the carbon captured by vegetation is rapidly returned to the atmosphere. Hence, there have been suggestions that management-driven reductions in savanna fire frequency and/or severity could significantly reduce greenhouse gas emissions and sequester carbon in tree biomass. However, a key knowledge gap is the extent to which savanna tree biomass will respond to modest shifts in fire regimes due to plausible, large-scale management interventions. Here, we: (1) characterise relationships between the frequency and severity of fires and key demographic rates of savanna trees, based on long-term observations in vegetation monitoring plots across northern Australia; (2) use these relationships to develop a process-explicit demographic model describing the effects of fire on savanna tree populations; and (3) use the demographic model to address the question: to what extent is it feasible, through the strategic application of prescribed burning, to increase tree biomass in Australian tropical savannas? Our long-term tree monitoring dataset included observations of 12,344 tagged trees in 236 plots, monitored for between 3 and 24 years. Analysis of this dataset showed that frequent high-severity fires significantly reduced savanna tree recruitment, survival and growth. Our demographic model suggested that: (1) despite the negative effects of frequent high-severity fires on demographic rates, savanna tree biomass appears to be suppressed by only a relatively small amount by contemporary fire regimes, characterised by a mix of low- to high-severity fires; and (2) plausible, management-driven reductions in the frequency of high-severity fires are likely to lead to increases in tree biomass of about 11.0 t DM ha<sup>–1</sup> (95% confidence interval: -1.2–20.8) over a century. Accounting for this increase in carbon storage could generate significant carbon credits, worth on average three times those generated annually by current greenhouse gas (methane and nitrous oxide) abatement projects, and has the potential to significantly increase the economic viability of fire/carbon projects, thereby promoting ecologically sustainable management of tropical savannas in Australia and elsewhere. This growing industry has the potential to bring much-needed economic activity to savanna landscapes, without compromising important natural and cultural values.</p>
Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)
<p>Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (<em>Plectropomus</em> <em>leopardus</em> [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that <em>P. leopardus</em> in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10–120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.</p>
Data and code for: Generation and applications of simulated datasets to integrate social network and demographic analyses
<p class="MsoNormal"><span>Social networks are tied to population dynamics; interactions are driven by population density and demographic structure, while social relationships can be key determinants of survival and reproductive success. However, difficulties integrating models used in demography and network analysis have limited research at this interface. We introduce the R package genNetDem for simulating integrated network-demographic datasets. It can be used to create longitudinal social networks and/or capture-recapture datasets with known properties. It incorporates the ability to generate populations and their social networks, generate grouping events using these networks, simulate social network effects on individual survival, and flexibly sample these longitudinal datasets of social associations. By generating co-capture data with known statistical relationships it provides functionality for methodological research. We demonstrate its use with case studies testing how imputation and sampling design influence the success of adding network traits to conventional Cormack-Jolly-Seber (CJS) models. We show that incorporating social network effects in CJS models generates qualitatively accurate results, but with downward-biased parameter estimates when network position influences survival. Biases are greater when fewer interactions are sampled or fewer individuals are observed in each interaction. While our results indicate the potential of incorporating social effects within demographic models, they show that imputing missing network measures alone is insufficient to accurately estimate social effects on survival, pointing to the importance of incorporating network imputation approaches. genNetDem provides a flexible tool to aid these methodological advancements and help researchers test other sampling considerations in social network studies.</span></p>
cultural heritage elements in Andalusia and demographic data sorted by urban category
<p>Dataset concerning cultural heritage elements and demographic data in Andalusia at the municipality level, as they appear on SIMA (Sistema de Información Multiterritorial de Andalucía), March 2023. They have been sorted by urban category, depending on the number of inhabitants of each municipality: less than 1.000 inhabitants, 1.000 to 10.000 inhabitants, 10.000 to 100.000 inhabitants, and more than 100.000 inhabitants.</p>
Data from: Demographic consequences of an extreme heatwave are mitigated by spatial heterogeneity in an annual monkeyflower
<p>This repository includes three different datasets as well as associated readme files. One dataset contains fitness data for individuals planted within a common garden experiment planted near the Browder Ridge Trailhead, Oregon USA in 2019. The second dataset contains fecundity data from 12 populations in the Central Oregon Cascades in 2018 and 2019. The final dataset contains demographic and phenological data from eleven populations in the Central Oregon Cascades in 2019. </p>
Data from: Hidden demographic impacts of fishing and environmental drivers of fecundity in a sea turtle population
<p><span>Fisheries bycatch is a critical threat to sea turtle populations worldwide, particularly because turtles are vulnerable to multiple gear types. The Canary Current is an intensely fished region, yet there has been no demographic assessment integrating bycatch and population management information of the globally significant Cabo Verde loggerhead turtle (<em>Caretta</em> <em>caretta</em>) population. Using Boa Vista island (Eastern Cabo Verde) subpopulation data from capture-recapture and nest monitoring (2013–2019), we evaluated population viability and estimated regional bycatch rates (2016–2020) in longline, trawl, purse-seine, and artisanal fisheries. We further evaluated current nesting trends in the context of bycatch estimates, existing hatchery conservation measures, and environmental (net primary productivity) variability in turtle foraging grounds. We projected that current bycatch mortality rates would lead to the near extinction of the Boa Vista subpopulation. Bycatch reduction in longline fisheries and all fisheries combined would increase finite population growth rate by 1.76% and 1.95%, respectively. Hatchery conservation increased hatchling production and reduced extinction risk, but alone it could not achieve population growth. Short-term increases in nest counts (2013–2021), putatively driven by temporary increases in net primary productivity, may be masking ongoing long-term population declines. When fecundity was linked to net primary productivity, our hindcast models simultaneously predicted these opposing long-term and short-term trends. Consequently, our results showed conservation management must diversify from land-based management. The masking effect we found has broad-reaching implications for monitoring sea turtle populations worldwide, demonstrating the importance of directly estimating adult survival and that nest counts might inadequately reflect underlying population trends.</span></p>
Colony-level coral demographic data from Japan & Australia (2016-2019)
<p>The persistent exposure of coral communities to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2016-2019), we explored spatial variation across the short- and long-term dynamics of competitive, stress-tolerant, and weedy assemblages to evaluate how thermal variability mediates the structural composition of coral communities. Here this dataset contains the raw colony-level data collected during these annual surveys, detailing the size, survival, and recruitment of coral colonies within a series of permenant plots arranged throughout the reef communities of Okinawa, Kochi (both Japan), the Solitary Islands Marine Park, and Heron Island (both Australia). This data set facilitates the comparison of coral population dynamics between tropical and subtropical ecoregions and between different taxonomic and morpho-functional groups.</p>
Data from: Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced
<p><span><em>Vicia</em> <em>sepium</em></span><span> (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese <em>V. sepium</em> lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese <em>V. sepium</em> is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5,000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese <em>V. sepium</em> is not introduced but is native.</span></p>
Data from: Demographically explicit scans for barriers to gene flow using gIMble
<p>Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Here we implement a composite likelihood approach for the quantification of barriers to gene flow. This analytic framework captures background selection and selection against locally maladaptive alleles (i.e. genomic barriers) in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. We have implemented genomewide IM blockwise likelihood estimation (gIMble) as a modular tool, which includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied sister species pair of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analysis uncovers both large effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of polygenic barrier architecture.</p>
Supplementary data for: "The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches"
<p>Supplementary data to https://doi.org/10.1101/2023.06.01.543285</p>
Genotype data for: Demographic and genetic consequences of a steelhead supplementation program
<p>Supplementation of naturally-spawning populations by the addition of hatchery-spawned individuals is commonly conducted for recovery of threatened and endangered populations and to support harvest opportunities. We present an analysis of steelhead, the anadromous form of Rainbow Trout (<em>Oncorhynchus</em> <em>mykiss</em>), returning to an integrated supplemented population in Southwest Washington over the course of 15 years. The goal of the supplementation program was to evaluate whether use of a juvenile captive broodstock and an integrated paradigm could be used to increase adult returns while avoiding negative genetic impacts to the population. Estimates of relative reproductive success (RRS) for fish spawned in the hatchery ranged from 2.4 for hatchery-origin females to 6.4 for natural-origin males, indicating that fish spawned in the hatchery produced more returning adult progeny than did fish allowed to spawn in the natural environment. We observed a slight reduction in reproductive success (RS) for hatchery-origin (relative to natural-origin) fish when spawning in the natural environment, but the difference was non-significant for males and marginally significant for females. In contrast to the relatively weak relationship between RS and origin (male P = 0.347, η<sup>2</sup> = 0.008; female P = 0.066, η<sup>2</sup> = 0.037), we observed a strong relationship between RS and return year (male P < 0.001, η<sup>2</sup> = 0.896; female P < 0.001, η<sup>2</sup> = 0.867) (i.e., hatchery- and natural-origin fish did well or poorly together each year). Hatchery-origin fish exhibited reduced genetic diversity, as well as evidence of increased temporal population structure among hatchery fish. We suspect the latter is an artifact of cultural practices that reduce diversity in age at smoltification. We conclude that the program was successful in achieving an increase in adult return, but not in avoiding negative genetic effects on the population, and that any lasting impacts of supplementation remain to be determined.</p>
Data from: A hierarchical population model for the estimation of latent prey abundance and demographic rates of a nomadic predator
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Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species
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Data from: Demographic costs and benefits of natural regeneration during tropical forest restoration
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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.