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594 results for “Demographic data”
Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments
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Data from: The influence of climate variability on demographic rates of avian Afro-palearctic migrants
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Data from: Environmental context determines the limiting demographic processes for plant recruitment across a species’ elevational range
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Data from: Demographic traits improve predictions of spatiotemporal changes in community resilience to drought
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Data in support of capturing functional strategies and compositional dynamics in vegetation demographic models
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Table S1: Demographic data and clinical conditions
<p>Table S1: Demographic data and clinical conditions. </p>
Census demographic data for the InMAP Source-Receptor Matrix (ISRM) dataset
<p>The InMAP Source-Receptor Matrix (ISRM) estimates the air quality impacts of emissions released from any source location in the contiguous United States to any receptor location. Specifically, the values in the ISRM dataset are the change in PM<sub>2.5</sub> concentration (µg m<sup>-3</sup>) in any receptor grid cell per unit of emissions (µg sec<sup>-1</sup>) in any source grid cell. ISRM was created from repeated runs of the Intervention Model for Air Pollution (<a href="http://spatialmodel.com/inmap/">InMAP</a>), isolating the impact of emissions from every grid cell in InMAP and from three emission heights representing ground-level, low-stack, and high-stack emissions. A file of the marginal impacts of emissions from each source location is also included ("marginal_values.csv"), which summarizes the estimates in ISRM by each source grid cell in terms of monetary damages ($ tonne<sup>-1</sup>), increased mortality (deaths tonne<sup>-1</sup>), and population exposure (population*µg m<sup>-3</sup> tonne<sup>-1</sup>).</p> <p>These files join US Census demographic information to the ISRM to facilitate future analyses. The original ISRM file can be found here: <a href="https://zenodo.org/record/3590127#.Xt0Z4GhKhPb">https://zenodo.org/record/3590127#.Xt0Z4GhKhPb</a></p>
Data from: Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of Howea in the face of high gene flow
The idea that populations must be geographically isolated (allopatric) to evolve into separate species has persisted for a long time. It is now clear that new species can also diverge despite ongoing genetic exchange, but few accepted cases of speciation in sympatry have held up when scrutinised using modern approaches. Here, we examined evidence for speciation of the Howea palms of Lord Howe Island, Australia, in light of new genomic data. We used coalescence-based demographic models combined with double digest restriction-site associated DNA sequencing of multiple individuals and provide support for previous claims by Savolainen et al. (Nature 441: 210–213, 2006) that speciation in Howea did occur in the face of gene flow.
Data for economic and demographic determinants of premium reserve in the Western Balkans
<p>All data are expressed as a percentage, except for GDP per capita, net wages, total population, life expectancy, expected years of education, average years of schooling, life and non-life premium, total premium, bank deposits, financial assets and deposits of insurance companies, which are expressed in absolute terms.</p> <p><strong>Source of data: </strong></p> <ol> <li>Data on Life and Non-life premium, Total (gross) premium, Premium reserve data, Financial assets and Deposits of insurance companies are collected from the official reports of insurance supervision agencies: Insurance Supervision Agency in Montenegro (<a href="http://www.ano.me/en/">http://www.ano.me/en/</a>), Croatian Financial Services Supervisory Agency (<a href="https://www.hanfa.hr/en/">https://www.hanfa.hr/en/</a>), National Bank of Serbia (<a href="https://www.nbs.rs/internet/english/">https://www.nbs.rs/internet/english/</a>, Insurance Supervision Agency of North Macedonia (<a href="http://aso.mk/en/?lang=en">http://aso.mk/en/?lang=en</a>) and Financial Supervisory Authority in Albania (<a href="https://amf.gov.al/">https://amf.gov.al/</a>).</li> <li>The economic indicators for the observed Western Balkan countries (GDP per capita, unemployment rate, inflation rate, net earnings and average effective deposit interest rate) are taken from the website Eurostat (<a href="https://ec.europa.eu/eurostat">https://ec.europa.eu/eurostat</a>) and Statista (<a href="https://www.statista.com/">https://www.statista.com/</a>) </li> <li>All demographic indicators, except for the expected and average years of schooling and education index, were collected from the Eurostat and UNDP database (<a href="https://ec.europa.eu/eurostat/data/database">https://ec.europa.eu/eurostat/data/database</a>; <a href="http://hdr.undp.org/en/countries/profiles/">http://hdr.undp.org/en/countries/profiles/</a> ).</li> <li>Data on expected and average school years were taken from the UNESCO Institute for Statistics (<a href="http://uis.unesco.org">http://uis.unesco.org</a>) , while the education index was obtained as a result of a calculation based on a formula published on the UNDP website (<a href="http://hdr.undp.org/en/content/education-index">http://hdr.undp.org/en/content/education-index</a>).</li> <li>Data on bond yield were collected from the website of European Commission (<a href="https://ec.europa.eu/">https://ec.europa.eu/</a>), i.e. from EC reports - EU Candidate Countries’ & Potential Candidates’ Economic Quarterly (CCEQ), except two data for Serbia (2006 and 2007) which were estimated by Makima extrapolation.</li> <li>Bank deposits data are taken from the official reports of banks' regulatory institutions: Central bank of Montenegro (<a href="https://www.cbcg.me/en">https://www.cbcg.me/en</a>), National bank of Serbia (<a href="https://www.nbs.rs/en/indeks/">https://www.nbs.rs/en/indeks/</a>), Croatian National bank (<a href="https://www.hnb.hr/en/home">https://www.hnb.hr/en/home</a>), National bank of the Republic of North Macedonia (<a href="https://www.nbrm.mk/pocetna-en.nspx">https://www.nbrm.mk/pocetna-en.nspx</a>); Bank of Albania (<a href="https://www.bankofalbania.org/home/">https://www.bankofalbania.org/home/</a>)</li> </ol> <p><strong>Description of columns:</strong></p> <p><strong>f1-</strong>GDPper capita;<strong> f2- </strong>Unemployment (%); <strong>f3-</strong>Inflation rate (%); <strong>f4-</strong> Net Wages €; <strong>f5-</strong> Deposit rate (%); <strong>f6-</strong> Population; <strong>f7-</strong> Female (%); <strong>f8-</strong> Population <15 (%); <strong>f9-</strong> Population 15-64 (%); <strong>f10-</strong> Dep old (%); <strong>f11-</strong> Dep young (%); <strong>f12-</strong> Urban population (%); <strong>f13-</strong>Life exp. (years); <strong>f14-</strong> Preschool enroll rate (%); <strong>f15-</strong> Elem school enroll rate (%); <strong>f16</strong>-High school enroll rate (%); <strong>f17-</strong> University enroll rate (%); <strong>f18-</strong> Expected years of schooling; <strong>f19-</strong> Avg. years of schooling; <strong>f20</strong>- Education Index (%); <strong>f21-</strong> Fertility rate (number of children to a woman); <strong>f22-</strong> Birth rate (per 1000 inhabitants); <strong>f23-</strong> Health costs (% GDP); <strong>f24-</strong>premium reserve per GDP,<strong> </strong></p> <p> <strong>i1-</strong> life premium €; <strong>i2</strong>- non-life premium €; <strong>i3</strong>- total premium €; <strong>i4</strong>- bond yield (%); <strong>i5a- </strong>bank deposits ( national currency);<strong> i5b- </strong>bank deposits €;<strong> i6a-</strong>financial assets in insurance (national currency)<strong>; i6b- </strong>financial assets in insurance €;<strong> i7a- </strong>deposits of insurers (national currency<strong>); i7b –</strong>deposit of insurers €</p>
A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data
<p>A common goal of population genomics and molecular ecology is to reconstruct the demographic history of a species of interest. A pair of powerful tools based on the sequentially Markovian coalescent have been developed to infer past population sizes using genome sequences. These methods are most useful when sequences are available for only a limited number of genomes and when the aim is to study ancient demographic events. The results of these analyses can be difficult to interpret accurately, because doing so requires some understanding of their theoretical basis and of their sensitivity to confounding factors. In this practical review, we explain some of the key concepts underpinning the pairwise and multiple sequentially Markovian coalescent methods (PSMC and MSMC, respectively). We relate these concepts to the use and interpretation of these methods, and we explain how the choice of different parameter values by the user can affect the accuracy and precision of the inferences. Based on our survey of 100 PSMC studies and 30 MSMC studies, we describe how the two methods are used in practice. Readers of this article will become familiar with the principles, practice, and interpretation of the sequentially Markovian coalescent for inferring demographic history.</p>
Data from: Demographic senescence in the aquatic plant Lemna gibba L. (Araceae)
Senescence is progressive, age-related bodily deterioration, accompanied at the population level by declines in average survival and fecundity (i.e., 'demographic senescence'). Demographic senescence of plants has been investigated in only a few species, including small, floating macrophytes in the genus Lemna (family Araceae, subfamily Lemnoideae – the 'duckweeds'). Unlike most plant species, Lemna ramets exhibit determinate growth, potentially rendering them more likely to experience demographic senescence. Here, our objective was to investigate senescence in a Lemna species not previously studied in this context, L. gibba L., toward the long-term goal of conducting cross-species comparative analyses. In a longitudinal lab study, we investigated a cohort of 334 individual L. gibba fronds, whose survival and reproduction we followed daily from birth (defined by the date a focal frond detached from its parent) to death (defined by the date a focal frond's last daughter detached). We fit survival data to exponential, Weibull, Gompertz, and logistic models, the first of which represents 'no senescence'. The logistic model was found to have the greatest support (AICC weight >0.99), indicating strong age-related declines in survival. We fit reproduction data using a generalized estimating equation approach, which showed a significant age-related decline in the predicted probability of daily reproduction – from 0.61 at age 3 days to 0.23 at age 52 days (i.e., after excluding the first two days of reproduction data to account for the initial, pre-reproductive phase of the L. gibba lifecycle). These age-related declines provide strong evidence that L. gibba does exhibit demographic senescence, consistent with evidence from congeneric species.
Data from: The double edged sword: the demographic consequences of the evolution of self-fertilisation
Phylogenies indicate that the transition from outcrossing to selfing is frequent, with selfing populations being more prone to extinction. The rates of transition to selfing and extinction, acting on different timescales, could explain the observed distributions of extant selfing species among taxa. However, phylogenetic and theoretical studies consider these mechanisms independently, i.e. transitions do not cause extinction. Here, we theoretically explore the demographic consequences of the evolution of self-fertilization. Deleterious mutations and mutations modifying the selfing rate are recurrently introduced and the number of offspring depends on individual fitness, allowing for a demographic feedback. We show that mutational meltdowns can be triggered in populations evolving near strict selfing. Populations having survived the demographic crash are more stable than ancestral outcrossing populations once deleterious mutations are purged. The relatively rapid time-scales in which extinctions occur indicate that during evolutionary transitions the accumulation of deleterious mutations may not be the cause of extinctions observed on longer time scales, which in turn could lead to the underestimation of transition rates from outcrossing to selfing.
Data from: Maintenance of deceptive gifts in a natural spider population: ecological and demographic factors
Alternative mating tactics are expected to occur predominantly when mate competition is intense, resources are in short supply, or as a result of asymmetric power relationships between individuals. Males of the nuptial gift-giving spider Pisaura mirabilis use a prevailing tactic of offering a nutritive gift (insect prey) and a deceptive tactic of offering a worthless gift (consumed prey) to prospective mates. If the male's tactic depends on pre-copulatory male-male competition, worthless gifts should occur primarily late in the season, when the operational sex ratio (OSR) becomes male-biased. If it depends on resource availability and/or post-copulatory sexual selection (sperm competition), worthless gifts should occur mostly early in the mating season, when prey availability is low and most females are unmated (i.e. post-copulatory sexual selection is weak). Nuptial gift construction correlated positively with prey availability and negatively with OSR, suggesting that males increase reproductive effort when resource and mate availability increase. We did not find evidence for body condition affecting male tactic use. Male size had a marked effect on the reproductive tactic employed. Males that matured early in the season were very small and employed mostly the nutritive gift tactic during their short life. Among the males that matured later and persisted through the season, relatively small males employed the worthless gift tactic whereas large males employed the nutritive gift tactic. We suggest that the existence of two distinct life history strategies among males (early small and late large size) interacts with environmental and demographic conditions to maintain the deceptive tactic.
Data from: Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program
While the goal of supplementation programs is to provide positive, population-level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive-born individuals are fully integrated into the natural population. In order to evaluate the long-term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook salmon (Oncorhynchus tshawytscha), we genotyped tissue samples spanning a 19-year period (1998-2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho USA. We expanded upon previous estimates of relative reproductive success (RRS) to include two full generations and used generalized linear models to determine if origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural-origin broodstock provided a long-term demographic boost to the population (mean of 4.56 times in the 1st generation and mean of 2.52 times in the 2nd generation). Overall when spawning in nature, hatchery-origin fish demonstrated a trend towards lower RS compared to natural-origin fish (p<0.05). However, when hatchery-origin fish successfully spawned with natural-origin fish, they had similar RS compared to natural by natural crosses (1st generation mean hatchery by natural cross RRS = 1.11 females, 1.13 males; 2nd generation mean hatchery by natural cross RRS = 1.03 females, 1.08 males). While origin, return year, and body length were significant predictors of fitness for both males and females (p<0.05), return day was significant for males but not females (p>0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long-term fitness effects on wild populations.
Data from: Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red-listed grasshopper
Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we employ genomic data (ddRADSeq) to test biologically-informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross-backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species, (b) distributional shifts resulted from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles, and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally-explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation (ABC) framework supported spatial configuration of topographic barriers to dispersal and human-driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model-based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.
Data from: Rapid genetic restoration of a keystone species exhibiting delayed demographic response
Genetic founder effects are often expected when animals colonize restored habitat in fragmented landscapes, but empirical data on genetic responses to restoration are limited. We examined the genetic response of banner-tailed kangaroo rats (Dipodomys spectabilis) to landscape-scale grassland restoration in the Chihuahuan Desert of New Mexico, USA. D. spectabilis is a grassland specialist and keystone species. At sites treated with herbicide to remove shrubs, colonization by D. spectabilis is slow and populations persist at low density for ≥10 yrs (≥6 generations). Persistence at low density and low gene flow may cause strong founder effects. We compared genetic structure of D. spectabilis populations between treated sites and remnant grasslands, and we examined how the genetic response to restoration depended on treatment age, area, and connectivity to source populations. Allelic richness and heterozygosity were similar between treated sites and remnant grasslands. Allelic richness at treated sites was greatest early in the restoration trajectory, and genetic divergence did not differ between recently colonized and established populations. These results indicated that founder effects during colonization of treated sites were weak or absent. Moreover, our results suggested founder effects were not mitigated by treatment area or connectivity. Dispersal is negatively density-dependent in D. spectabilis, and we hypothesize that high gene flow may occur early in the restoration trajectory when density is low. Our study shows genetic diversity can be recovered more rapidly than demographic components of populations after habitat restoration, and that founder effects are not inevitable for animals colonizing restored habitat in fragmented landscapes.
Data from: Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?
Interspecific interactions are contingent upon organism phenotypes, and thus phenotypic evolution can modify interspecific interactions and affect ecological dynamics. Recent studies have suggested that male-male competition within a species selects for capability to reproductively interfere with a closely related species. Here we examine the effect of past evolutionary history under different mating regimes on the demographic dynamics of interspecific competition in Callosobruchus seed beetles. We used previously established experimental evolution lines of C. chinensis that evolved under either forced lifelong monogamy or polygamy for 17 generations, and examined the demographic dynamics of competition between these C. chinensis lines and a congener, C. maculatus. Callosobruchus chinensis was competitively excluded by C. maculatus in all trials. Time series data analyses suggested that reproductive interference from C. chinensis was relatively more important in the trials involving polygamous C. chinensis than those involving monogamous C. chinensis, in accordance with the potentially higher reproductive interference capability of polygamous C. chinensis. However, the estimated signs and magnitudes of interspecific interactions were not fully consistent with this explanation, implying the evolution of not only reproductive interference but also other interaction mechanisms. Our study thus suggests multifaceted effects of sexually-selected traits on interspecific competitive dynamics.
Data from: The ecology of wildlife disease surveillance: demographic and prevalence fluctuations undermine surveillance
Wildlife disease surveillance is the first line of defence against infectious disease. Fluctuations in host populations and disease prevalence are a known feature of wildlife disease systems. However, the impact of such heterogeneities on the performance of surveillance is currently poorly understood. We present the first systematic exploration of the effects of fluctuations' prevalence and host population size on the efficacy of wildlife disease surveillance systems. In this study, efficacy is measured in terms of ability to estimate long-term prevalence and detect disease risk. Our results suggest that for many wildlife disease systems, fluctuations in population size and disease lead to bias in surveillance-based estimates of prevalence and overconfidence in assessments of both the precision of prevalence estimates and the power to detect disease. Neglecting such ecological effects may lead to poorly designed surveillance and ultimately to incorrect assessments of the risks posed by disease in wildlife. This will be most problematic in systems where prevalence fluctuations are large and disease fade-outs occur. Such fluctuations are determined by the interaction of demography and disease dynamics. Although particularly likely in highly fluctuating populations typical of fecund short-lived hosts, such fluctuations cannot be ruled out in more stable populations of longer-lived hosts. Synthesis and applications. Fluctuations in population size and disease prevalence should be considered in the design and implementation of wildlife disease surveillance, and the framework presented here provides a template for conducting suitable power calculations. Ultimately, understanding the impact of fluctuations in demographic and epidemiological processes will enable improvements to wildlife disease surveillance systems leading to better characterization of, and protection against endemic, emerging and re-emerging disease threats.
Data from: How well can body size represent effects of the environment on demographic rates? Disentangling correlated explanatory variables
Demographic rates are shaped by the interaction of past and current environments that individuals in a population experience. Past environments shape individual states via selection and plasticity, and fitness-related traits (e.g. individual size) are commonly used in demographic analyses to represent the effect of past environments on demographic rates. We quantified how well the size of individuals captures the effects of a population's past and current environments on demographic rates in a well-studied experimental system of soil mites. We decomposed these interrelated sources of variation with a novel method of multiple regression that is useful for understanding nonlinear relationships between responses and multicollinear explanatory variables. We graphically present the results using area-proportional Venn diagrams. Our novel method was developed by combining existing methods and expanding upon them. We showed that the strength of size as a proxy for the past environment varied widely among vital rates. For instance, in this organism with an income breeding life history, the environment had more effect on reproduction than individual size, but with substantial overlap indicating that size encompassed some of the effects of the past environment on fecundity. This demonstrates that the strength of size as a proxy for the past environment can vary widely among life-history processes within a species, and this variation should be taken into consideration in trait-based demographic or individual-based approaches that focus on phenotypic traits as state variables. Furthermore, the strength of a proxy will depend on what state variable(s) and what demographic rate is being examined; that is, different measures of body size (e.g. length, volume, mass, fat stores) will be better or worse proxies for various life-history processes.
Data from: Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data
Restriction-site associated sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq-specific biases remains unexplored. Here we assess in how far genotype-free methods of allele frequency estimation affect demographic inference from empirical RADSeq data. Using the well-studied pied flycatcher (Ficedula hypoleuca) as a study system, we compare allele frequency estimation and demographic inference from whole genome sequencing data with that from RADSeq data matched for samples using both genotype-based and genotype free methods. The demographic history of pied flycatchers as inferred from RADSeq data was highly congruent with that inferred from WGS data when allele frequencies were estimated directly from the read data. In contrast, when allele frequencies were derived from called genotypes, RADSeq-based estimates of most model parameters fell outside the 95% confidence interval (CI) of estimates derived from WGS data. Notably, more stringent filtering of genotypes tended to increase the discrepancy between parameter estimates from WGS and RADSeq data, respectively. The results from this study demonstrate the ability of genotype-free methods to improve AFS-based demographic inference from RADSeq data and highlight the need to account for uncertainty in NGS data regardless of sequencing method.
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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.