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1,068 results for “demographic”
R Data for CPBS Report 23SDSU01 - Urban Demographic Shift of Pedestrian and Bicyclist Collisions, Equity, and Police Enforcement
<p>Data for the statistical program R.</p>
Data from: Less favorable climates constrain demographic strategies in plants
Correlative species distribution models are based on the observed relationship between species' occurrence and macroclimate or other environmental variables. In climates predicted less favourable populations are expected to decline, and in favourable climates they are expected to persist. However, little comparative empirical support exists for a relationship between predicted climate suitability and population performance. We found that the performance of 93 populations of 34 plant species worldwide – as measured by in situ population growth rate, its temporal variation and extinction risk – was not correlated with climate suitability. However, correlations of demographic processes underpinning population performance with climate suitability indicated both resistance and vulnerability pathways of population responses to climate: in less suitable climates, plants experienced greater retrogression (resistance pathway) and greater variability in some demographic rates (vulnerability pathway). While a range of demographic strategies occur within species' climatic niches, demographic strategies are more constrained in climates predicted to be less suitable.
Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers
The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.
Data from: Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot
The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (FIS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies.
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.
An unexpected genetic diversity pattern and a complex demographic history of a rare medicinal herb, Chinese asparagus (Asparagus cochinchinensis) in Korea
Range-wide population studies of wide spread species are often associated with complex diversity patterns resulting from genetically divergent evolutionary significant units (ESUs). The compound evolutionary history creating such a pattern of diversity can be inferred through molecular analyses. Asparagus cochinchinensis, a medicinally important perennial herb, is in decline due to overharvesting in Korea. Eight A. cochinchinensis populations in Korea and three neighboring countries (China, Japan and Taiwan) were examined using nine nuclear microsatellite loci and three chloroplast microsatellite loci to characterize molecular diversity patterns. The average within-population diversity was limited likely due to long-term bottlenecks observed in all eight populations. High pairwise FST values indicated that the populations have largely diverged, but the divergences were not correlated with geographic distances. Clustering analyses revealed a highly complex spatial structure pattern associated with two ESUs. Approximate Bayesian Computation (ABC) suggest that the two ESUs split about 21,000 BP, were independently introduced to Korea approximately 1,800 years ago, and admixed in secondary contact zones. The two ESUs found in our study may have different habitat preferences and growth conditions, implying that the two genetically divergent groups should be considered not only for conservation and management but also for breeding programs in agricultural areas.
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.
Complex multi-predator effects on demographic habitat selection and community assembly in colonizing insects
<p>Running the gauntlet of predators consumes critical time and energy resources, as all species are vulnerable to one or, typically, more predators at some life stage. Prey employ a vast array of mechanisms to avoid predation, and predators, likewise, come in a bewildering variety. Thus, defensive adaptations are rarely one size fits all. Considerable work has addressed multi-predator consumptive effects, but we now know that non-consumptive effects of predators can dramatically impact individuals, (meta)populations, and (meta)communities. However, little is known regarding the community-wide dynamics of non-consumptive effects generated by multiple predators. Predator avoidance by choosing a patch that is free of a particular predator or predators can be the most effective strategy if conditions at colonization are a reliable predictor of absence, which is often true for fish in freshwater systems. We experimentally manipulated composition of the predator assemblage in aquatic mesocosms in a substitutive design, with zero, one, two, or three caged predatory fish species (one benthic, one pelagic, and one surface fish) at constant density and biomass, and assayed responses of naturally colonizing aquatic insects. We addressed three related questions; first, how do members of a diverse assemblage of colonizing aquatic insects respond to this variation in species and species combinations, second, do individual species (and higher taxa), respond differently to single vs multiple predator species (species richness), and third how do any responses to fish species and species combinations, and effects on species richness, translate into community-wide changes in the composition of colonists. Prey had varied responses to specific predators or combinations of predators, resulting in distinct community composition across treatments and higher β-diversity with predators. Prey showed emergent multi-predator effects, where certain species only responded to predator species combinations, but not to any individual predator, and stronger effects of multiple predator vs single predator treatments, despite strong responses to individual predators in many taxa. Habitat selection effects can range from the individual to the metacommunity, and the dynamics of habitat selection in response to predators is a complex function of predator identity, density, richness, species composition, and patch spatial context.</p>
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>
OHSU 2019-2020 utilization of ambulatory telehealth and office visits by patient demographics
<p>The COVID-19 pandemic and subsequent expansion of telehealth may be exacerbating inequities in ambulatory care access due to institutional and structural barriers. We conduct a repeat cross-sectional analysis of ambulatory patients to evaluate for demographic disparities in the utilization of telehealth modalities. The ambulatory patient population at Oregon Health & Science University (Portland, OR) is examined from June 1 through September 30, in 2019 (reference period) and in 2020 (study period). We first assess for changes in demographic representation and then evaluate for disparities in the utilization of telephone and video care modalities using logistic regression. Between the 2019 and 2020 periods, patient video utilization increased from 0.2% to 31%, and telephone use increased from 2.5% to 25%. There was also a small but significant decline in the representation males, Asians, Medicaid, Medicare, and non-English speaking patients. Amongst telehealth users, adjusted odds of video participation were significantly lower for those who were Black, American Indian, male, prefer a non-English language, have Medicaid or Medicare, or older. A large portion of ambulatory patients shifted to telehealth modalities during the pandemic. Seniors, non-English speakers, and Black patients were more reliant on telephone than video for care. The differences in telehealth adoption by vulnerable populations demonstrate the tendency towards disparities that can occur in the expansion of telehealth and suggest structural biases. Organizations should actively monitor the utilization of telehealth modalities and develop best-practice guidelines in order to mitigate the exacerbation of inequities.</p>
Perceived fairness and perceived transparency of AI systems according to system's characteristics, personality traits and demographic characteristics
<p>We collected data of 3197 users' fairness perception regarding various configurations of a AI-based system in the recruitment domain, as well as, the demographic and personally characteristics of the participants.</p> <p>The dataset includes the following columns:</p> <p><strong>:System characteristics</strong></p> <p> :Certification</p> <p>Uncertificated system (U)</p> <p>Certificated system (C)</p> <p>:Input data</p> <p>High quality input data (H)</p> <p>Low quality input data (L)</p> <p>:Output</p> <p>Positive outcome (P)</p> <p>Borderline outcome (B)</p> <p>Negative outcome (N)</p> <p>:Explanation style</p> <p>Control- no explanation (CON)</p> <p>Case-based (CAS)</p> <p>Certification-based (CER)</p> <p>Demographic-based (DEM)</p> <p>Input influence-based (INP)</p> <p>Sensitivity-based (SEN)</p> <p><strong>:Demographic characteristics</strong></p> <p>:Gender</p> <p>Female</p> <p>Male</p> <p>:Age</p> <p>18-34</p> <p>35-50</p> <p>50+</p> <p>:Residence</p> <p>Unites states of America</p> <p>India</p> <p>Other</p> <p>:Education level</p> <p>High school degree or less</p> <p>Bachelor's degree</p> <p>Master's or doctoral degree</p> <p>:Employment status</p> <p>Not employed</p> <p>Employed</p> <p>:Income level</p> <p>Above average</p> <p>Average</p> <p>Below average</p> <p><strong>:Personality characteristics</strong></p> <p>(TIPI questionnaire)</p> <p>Extraverted, enthusiastic</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Critical, quarrelsome</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Dependable, self-disciplined</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Anxious, easily upset</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Open to new experiences, complex</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Reserved, quiet</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Sympathetic, warm</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Disorganized, careless</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Calm, emotionally stable</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p>Conventional, uncreative</p> <p>1-7 (1= disagree strongly up to 7= agree strongly)</p> <p><strong>:Participants responses</strong></p> <p>:Fairness evaluation</p> <p>The participants were requested to report their level of perceived fairness (their view about the fairness of the system - at what level they consider the system as a fair system) on a 6-point Likert scale, from "Extremely fair" (represented as 3) to "Extremely unfair" (represented as -3). The option of "neither fair or unfair" (represented as 0) was excluded from the scale.</p> <p>:Transparency evaluation</p> <p>the participants were requested to report their level of perceived transparency (their understanding why the system produced the specific output - at what level they understand why this output was given) on a 6-point Likert scale, from " Thoroughly understand" (represented as 3) to " Thoroughly don't understand" (represented as -3). The option of "neither understand or don't understand" (represented as 0) was excluded from the scale.</p> <p>:Output Expectation</p> <p>The participants were requested to report their expectation for the specific output based on the input they received according to the system's scale, 5-point Likert scale from "Strongly recommended" (represented as 2) to "Strongly not recommended" (represented as -2).</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.
Demographic History and Genomic Targets of Positive Selection in Giant Gough Mice
<p>A key challenge in understanding how natural selection operates is to identify the mutations and genes that make it possible. Positive selection on beneficial mutations distorts linked variation by altering the site frequency spectrum, the configuration of haplotypes, and population differentiation. By comparing patterns of sequence variation to neutral predictions across genomes, the targets of positive selection can be located. We applied this logic to an unusual population of house mice that shows phenotypic and ecological hallmarks of selection. Mice from Gough Island are twice the body size of mainland mice, eat live seabirds, maintain a very high population density, and inhabit an environment without predators or humans. We used massively parallel short-read sequencing to survey the genomes of 14 Gough Island mice. We computed a set of summary statistics to capture diverse aspects of variation across these genome sequences, used approximate Bayesian computation to reconstruct a null demographic model, and then applied machine learning to estimate the posterior probability of positive selection in each region of the genome. We conducted parallel analyses on genome sequences from 8 mice from Germany, treating them as representatives of a mainland reference population. A few thousand 5kb windows show strong evidence for positive selection in Gough Island mice but not in German mice. Genic regions and the X chromosome contain disproportionate shares of these selection windows. Over-represented gene ontologies in selection windows emphasize neurological themes. Inspection of genomic regions harboring many selection windows with high posterior probabilities pointed to genes with known effects on exploratory behavior and body size as potential targets. Some genes in these regions have missense mutations and/or putative regulatory mutations with large differences between Gough Island mice and German/French mice in the frequency of the derived allele; these are candidates for adaptive variants. Our results provide a genomic portrait of adaptation to island conditions and position Gough Island mice as a powerful system for understanding the genetic component of natural selection.</p>
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>
Figure 3 in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 3. Map of cluster membership and posterior probability for each cluster based on the GENELAND analysis. A, the estimated cluster membership represents the modal cluster assignment of each pixel, and the rest of the inset maps show the posterior probability of individuals of Octodontomys gliroides in Argentina, Bolivia, and Chile. Black dots represent sampling localities. The three clusters are: B, populations of northern and central Bolivia; C, populations from northern Chile, central and southern Bolivia, and northern Argentina; and D, the remaining Argentinian populations and one population from southern Bolivia. The white area represents a probability between 90 and 100% for sampling localities to belong to their respective cluster.
Figure 5 in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 5. Map, showing the putative barriers (major rivers, lakes, salt flats, the Atacama Desert, and the mountain chains of the Andes) that separate the populations of Octodontomys gliroides.
Figure 4 in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 4. Pairwise mismatch distribution (left) and Bayesian skyline plots (right), depicting the demographic history for the entire sample (A and B), lineage A (C and D), and lineage B (E and F). For mismatch distributions, black circles represent the observed distribution of pairwise differences and white circles represent the theoretical expected distribution under a population expansion model. For the skyline plot, black lines represent median estimates, whereas the dotted lines represent the upper and lower 95% credible intervals. The x-axis of Bayesian skyline figures is the time per million years before the present and the y-axis is the estimated effective population size (Ne).
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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.
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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
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