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594 results for “Demographic data”
Data from: Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum
Eutrema salsugineum is a widely distributed species, which provide a good model to study long-distance dispersal and accumulation of deleterious mutations. Based on population genomic data, we clarified demographic history of E. salsugineum and showed how deleterious alleles accumulated.
Data from: Paternity assignment and demographic closure in the New Zealand southern right whale
The identification and characterisation of reproductively isolated subpopulations or 'stocks' is essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and 'gametic recapture' to examine the reproductive autonomy of southern right whales (Eubalaena australis) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother-calf pairs from skin biopsy samples, using sex-specific markers, 13 microsatellite loci and mtDNA haplotypes. We constructed DNA profiles for 314 adult males, representing 30% of the census male abundance of the NZ stock, previously estimated from genotypic mark-recapture modelling to be 1085 (95% CL 855, 1416). Under the hypothesis of demographic closure and the assumption of equal reproductive success among males, we predict: (1) the proportion of paternities assigned will reflect the proportion of the male population sampled and (2) the gametic mark-recapture (GMR) estimate of male abundance will be equivalent to the census male estimate for the NZ stock. Consistent with these predictions, we found that the proportion of assigned paternities equalled the proportion of the census male population size sampled. Using the sample of males as the initial capture, and paternity assignment as the recapture, the GMR estimate of male abundance was 1001 (95% CL 542, 1469), similar to the male census estimate. These findings suggest that right whales returning to the NZ calving ground are reproductively autonomous on a generational timescale, as well as isolated by maternal fidelity on an evolutionary timescale, from others in the Indo-Pacific region.
Data from: Identifying demographic and environmental drivers of recruitment and population growth in a cavity nesting sea duck population
Traits with the greatest proportional effects on fitness are typically conserved (Stearns 1992), and traits with larger temporal variation frequently play a dominant role in population dynamics (Cooch et al. 2001). We examined recruitment patterns and population growth in Common Goldeneyes (Bucephala clangula; hereafter goldeneye), using Pradel mark-recapture models from a long-term nest box study (1997-2010). Our objectives were to estimate recruitment (f) and population growth (λ) relative to recruitment origin group (in-situ or unknown), investigate environmental and density dependent effects on these parameters, and evaluate potential immigration patterns. We detected group-specific differences for f (in-situ: 0.47± 0.13 SE, unknown: 0.31 ± 0.04), and the proportion of boxes occupied by goldeneyes the year prior to recruitment had a significant negative effect on recruitment for the in-situ group (β = -1.04; 85% CI -1.29, -0.78), and a positive effect for the unknown group (β = 0.45; 85% CI 0.30, 0.61). The negative box occupancy effect in the year prior to recruitment, when in-situ yearling goldeneyes prospect for potential nest sites, suggests that local nesting densities may limit recruitment of locally hatched females. We identified two competitive models for λ, which averaged 1.04 ± 0.03 and included interactions between recruitment origin group and a linear temporal trend, and the proportion of ducklings marked two years prior. By evaluating all levels of marking effort on λ, we determined that even if all hatched ducklings were marked in a given year, the resulting in-situ λ was consistently lower than all observed population-level λs during the study, indicating that individuals produced outside of study area nest boxes contributed to λ. Though female goldeneyes are considered highly philopatric, our results suggest that female natal and breeding dispersal may be more prevalent than previously thought, and the spatial scale at which these processes occur requires further investigation.
Data from: Demographic, environmental and genetic determinants of mating success in captive koalas (Phascolarctos cinereus)
Many factors have been shown to affect mating behavior. For instance, genes of the major histocompatibility complex (MHC) are known to influence mate choice in a wide variety of vertebrate species. The genetic management of captive populations can be confounded if intrinsic mate choice reduces or eliminates reproductive success between carefully chosen breeding pairs. For example, the San Diego Zoo koala colony only has a 45% copulation rate for matched individuals. Herein, we investigated determinants of koala mating success using breeding records (1984-2010) and genotypes for 52 individuals at four MHC markers. We quantified MHC diversity according to functional amino acids, heterozygosity, and the probability of producing a heterozygous offspring. We then used categorical analysis and logistic regression to investigate both copulation and parturition success. In addition, we also examined age, day length, and average pairwise kinship. Our post-hoc power analysis indicates that at a power level of 1 – β = 0.8, we should have been able to detect strong MHC preferences. However, we did not find a significant MHC effect on either copulation or parturition success with one exception: pairs with lower or no production of a joey had significantly lower MHC functional amino acid diversity in the categorical analysis. In contrast, day length and dam age (or age difference of the pair) consistently had an effect on mating success. These findings may be leveraged to improve the success of attempted pairs, conserve resources, and facilitate genetic management.
Data from: Bayesian inference reveals positive but subtle effects of experimental fishery closures on marine predator demographics
Global forage-fish landings are increasing, with potentially grave consequences for marine ecosystems. Predators of forage fish may be influenced by this harvest, but the nature of these effects is contentious. Experimental fishery manipulations offer the best solution to quantify population-level impacts, but are rare. We used Bayesian inference to examine changes in chick survival, body condition and population growth rate of endangered African penguins Spheniscus demersus in response to eight years of alternating time-area closures around two pairs of colonies. Our results demonstrate that fishing closures improved chick survival and condition, after controlling for changing prey availability. However, this effect was inconsistent across sites and years, highlighting the difficultly of assessing management interventions in marine ecosystems. Nevertheless, modelled increases in population growth rates exceeded 1% at one colony; i.e. the threshold considered biologically meaningful by fisheries management in South Africa. Fishing closures evidently can improve the population trend of a forage-fish dependent predator – we therefore recommend they continue in South Africa and support their application elsewhere. However, detecting demographic gains for mobile marine predators from small no-take zones requires experimental time-frames and scales that will often exceed those desired by decision-makers.
Data and Code for Shriver et al. 2021, Quantifying the demographic vulnerabilities of dry woodlands to climate and competition using range-wide monitoring data
<p>Data and code for demographic analyses in Shriver et al. 2021. See paper and ReadMe for analysis description and further details. </p> <p>Shriver, R.K., C.B. Yackulic, D.M. Bell, J.B. Bradford. (2021)Quantifying the demographic vulnerabilities of dry woodlands to climate and competition using range-wide demographic models. Ecology. <a href="https://doi.org/10.1002/ecy.3425">https://doi.org/10.1002/ecy.3425</a></p> <p> </p>
Data from: Colonization and demographic expansion of freshwater fauna across the Hawaiian Archipelago
It is widely accepted that insular terrestrial biodiversity progresses with island age because colonization and diversification proceed over time. Here we assess whether this principle extends to oceanic island streams. We examined range-wide mtDNA sequence variation in four stream-dwelling species across the Hawaiian archipelago to characterize the relationship between colonization and demographic expansion, and to determine whether either factor reflects island age. We found that colonization and demographic expansion are not related and that neither correspond to island age. The snail Neritina granosa exhibited the oldest colonization time (~2.713 mya) and time since demographic expansion (~282 kya), likely reflecting a preference for lotic habitats most prevalent on young islands. Conversely, gobioid fishes (Awaous stamineus, Eleotris sandwicensis and Sicyopterus stimpsoni) colonized the archipelago only ~0.411-0.935 mya, suggesting ecological opportunities for colonization in this group were temporally constrained. These findings indicate that stream communities form across colonization windows, underscoring the importance of ecological opportunities in shaping island freshwater diversity.
MICCAI 2016 challenge dataset demographics data
<p>This dataset contains supplementary material for the 2016 MS segmentation challenge data article. It contains the full demographic data for the datasets opened to the public.</p>
Woodland Caribou demographic data and range boundaries
<p>As global climate change progresses, wildlife management will benefit from knowledge of demographic responses to climatic variation, particularly for species already endangered by other stressors. In Canada, climate change is expected to increasingly impact populations of threatened woodland caribou (<i>Rangifer tarandus caribou</i>) and much focus has been placed on how a warming climate has potentially facilitated the northward expansion of apparent competitors and novel predators. Climate change, however, may also exert more direct effects on caribou populations that are not mediated by predation. These effects include meteorological changes that influence resource availability and energy expenditure. Research on other ungulates suggests that climatic variation may have minimal impact on low-density populations such as woodland caribou because per-capita resources may remain sufficient even in "bad" years. We evaluated this prediction using demographic data from 21 populations in western Canada that were monitored for various intervals between 1994 and 2015. We specifically assessed whether juvenile recruitment and adult female survival were correlated with annual variation in meteorological metrics and plant phenology. Against expectations, we found that both vital rates appeared to be influenced by annual climatic variation. Juvenile recruitment was primarily correlated with variation in phenological conditions in the year prior to birth. Adult female survival was more strongly correlated with meteorological conditions and declined during colder, more variable winters. These responses may be influenced by the life history of woodland caribou, which reside in low-productivity refugia where small climatic changes may result in changes to resources that are sufficient to elicit strong demographic effects. Across all models, explained variation in vital rates was low, suggesting that other factors had greater influence on caribou demography. Nonetheless, given the declining trajectories of many woodland caribou populations, our results highlight the increased relevance of recovery actions when adverse climatic conditions are likely to negatively affect caribou demography.</p>
Data from: The demographic history of micro-endemics: Have rare species always been rare?
<p>Extinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (<em>N</em><sub><em>e</em></sub>) for each species and compared this to census population <em>(N</em><sub><em>c</em></sub>) sizes when known. In each case, <em>N</em><sub><em>e</em></sub> was an order of magnitude larger than <em>N</em><sub><em>c</em></sub> – a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes in <em>N</em><sub><em>e</em></sub> over time. Five out of ten species displayed significant population declines towards the present (68–90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascar's narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid.</p>
Data analysis from: Demographic consequences of changing body size in a terrestrial salamander
<p>Changes in climate can alter individual body size, and the resulting shifts in reproduction and survival are expected to impact population dynamics and viability. However, appropriate methods to account for size-dependent demographic changes are needed, especially in understudied yet threatened groups such as amphibians. We investigated individual and population-level demographic effects of changes in body size for a terrestrial salamander using capture-mark-recapture data. For our analysis, we implemented an integral projection model parameterized with capture-recapture likelihood estimates from a Bayesian framework. Our study combines survival and growth data from a single dataset to quantify the influence of size on survival while including different sources of uncertainty around these parameters, demonstrating how selective forces can be studied in populations with limited data and incomplete recaptures. We found a strong dependency of the population growth rate on changes in individual size, mediated by potential changes in selection on mean body size and on maximum body size. Our approach of simultaneous parameter estimation can be extended across taxa to identify eco-evolutionary mechanisms acting on size-specific vital rates, and thus shaping population dynamics and viability.</p>
Demographic data, disease characteristics, and laboratory findings for Association between polymorphisms within gene coding for tumor necrosis factor (TNF)-alpha with outcomes of treatment in sample of Iraqi patients with Ankylosing Spondylitis taking Etanercept
<p>Demographic data, disease characteristics, and laboratory findings for Association between polymorphisms within gene coding for tumor necrosis factor (TNF)-alpha with outcomes of treatment in sample of Iraqi patients with Ankylosing Spondylitis taking Etanercept</p>
Data from: Contrasting demographic responses to size-selective harvesting among neighboring wild fish populations
<p>Sustainable harvesting of wild populations relies on evidence-based knowledge to predict harvesting outcomes for species and the ecosystems they inhabit. Although harvesting may elicit compensatory density-dependence, it is generally size-selective, which induces additional pressures that are challenging to forecast. Furthermore, responses to harvest may be population-specific and whether generalizable patterns exist remains unclear.</p> <p>Taking advantage of Parks Canada's mandate to remove introduced brook trout (<em>Salvelinus fontinalis</em>) to restore alpine lakes in Canadian parks, we experimentally applied standardized size-selective harvesting rates (the largest ~64% annually) for three consecutive summers in five populations with different initial size structures. Four unharvested populations were used as controls.</p> <p>At reduced densities, harvested and control populations exhibited similar density-dependent increases in specific growth, juvenile survival, and earlier maturation. However, size-selective harvesting simultaneously induced changes to size and age structure that contrasted among harvested populations. Average body length decreased in three of five harvested populations, whereas it tended to increase in control populations over the three years. We also detected contrasting, population-specific changes in body length variability and ultimately in length- and age-at-harvest in harvested populations but not controls.</p> <p>Overall, populations with smaller, more homogeneous body sizes, and living at high densities were most resilient to size-selective harvesting, exhibiting the smallest change in size-at-age. In contrast, large-bodied populations exhibited more substantial size-structure changes following selective harvesting: large-bodied populations experienced either stabilizing or disruptive pressures, when initial length variability was high or low, respectively.</p> <p><em>Synthesis and application</em>: Our results show that within species, size-selective harvesting inherently leads to more risk and uncertainty when harvesting populations with larger and more varied body sizes than smaller-bodied populations with less range in body size. Our study supports prioritizing regulations that protect harvested populations with larger and more varied body sizes. Such a management strategy would reduce the likelihood of eliciting unpredictable or undesirable demographic changes to fish populations with these attributes.</p>
Dicerandra christmanii demographic data
<p>These data files consist of demographic measures taken on marked plants of the federally endangered <em>Dicerandra</em> <em>christmanii</em> from natural populations (in open gaps and roadsides), an augmented population, and introduced population. Data were collected from seven populations across two sites from 199 –2018 although populations were initiated in different years. </p>
Code and data for: Demographic resilience may sustain significant coral populations in a 2°C-warmer world.
<p>Data and Matlab code produced for the manuscript: Mason, R. A. B., Bozec, Y.-M., & Mumby, P. J. (2023). Demographic resilience may sustain significant coral populations in a 2°C-warmer world. <em>Global Change Biology</em>, 29(14): 4152-4160. <a href="https://doi.org/10.1111/gcb.16741">https://doi.org/10.1111/gcb.16741</a></p> <p>For questions about the contents of this repository, please contact robert.mason1@uqconnect.edu.au</p>
Epidemiological and Demographic Data From 150 Patients Diagnosed With Coronavirus Disease 2019 Pneumonia
ClinicalTrials.gov study NCT04430023. IPD Sharing: NO. Countries: 1. Publications: 3.
Demographic data collection in STEM organizations
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Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils
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Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history
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Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation
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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.