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617 results for “base population”
Data from: No evidence for MHC class I based disassortative mating in a wild population of great tits
Genes of the major histocompatibility complex (MHC) are regarded as a potentially important target of mate choice due to the fitness benefits that may be conferred to the offspring. According to the complementary genes hypothesis, females mate with MHC dissimilar males to enhance the immunocompetence of their offspring or to avoid inbreeding depression. Here, we investigate whether selection favours a preference for maximally dissimilar or optimally dissimilar MHC class I types, based on MHC genotypes, average amino acid distances and the functional properties of the antigen-binding sites (MHC supertypes); and whether MHC type dissimilarity predicts relatedness between mates in a wild great tit population. In particular, we explore the role that MHC class I plays in female mate choice decisions while controlling for relatedness and spatial population structure, and examine the reproductive fitness consequences of MHC compatibility between mates. We find no evidence for the hypotheses that females select mates on the basis of either maximal or optimal MHC class I dissimilarity. A weak correlation between MHC allele sharing and relatedness, and between MHC supertype sharing and relatedness suggests that MHC dissimilarity at functional variants may not provide an effective index of relatedness. Moreover the reproductive success of pairs did not vary with MHC dissimilarity. Our results provide no support for the suggestion that selection favours, or that mate choice realises, a preference for complimentary MHC types.
Data from: Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)
Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach, Random Forest, to detect markers linked to run timing across 14 populations from contrasting environments in the Columbia River and Puget Sound, USA. The approach permits detection of loci of small effect on the phenotype. Divergence between populations at these loci was then examined using both principle component analysis and FST outlier analyses, to determine whether shared genetic changes resulted in similar phenotypes across different lineages. Sequencing of 9107 RAD markers in 414 individuals identified 33 predictor loci explaining 79.2% of trait variance. Discriminant analysis of principal components of the predictors revealed both shared and unique evolutionary pathways in the trait across different lineages, characterized by minor allele frequency changes. However, genome mapping of predictor loci also identified positional overlap with two genomic outlier regions, consistent with selection on loci of large effect. Therefore, the results suggest selective sweeps on few loci and minor changes in loci that were detected by this study. Use of a polygenic framework has provided initial insight into how divergence in a trait has occurred in the wild.
Data from: Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations
Background: The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epigenetic variation and its influence on local adaptation in natural populations. Results: The structure and extent of the heritable methylation-based epigenetic variation were assessed within and among natural populations of Triticum turgidum ssp. dicoccoides. We used methylation sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) techniques, to assess the methylation status of random genomic CCGG sites and CCGG sites flanking transposable elements (TEs), respectively. Both techniques were applied to the DNA of 50 emmer accessions which were collected from five different geographically isolated regions. In order to ensure the assessment of heritable epigenetic variation, all accessions were grown under common garden conditions for two generations. In all accessions, the difference in methylation levels of CCGG sites, including CCGG sites that flanked TEs, were not statistically significant and relatively high, ranging between 46 and 76 %. The pattern of methylation was significantly different among accessions, such that clear and statistically significant population-specific methylation patterns were observed. Conclusion: In this study, we have observed population-unique heritable methylation patterns in emmer wheat accessions originating from five geographically isolated regions. Our data indicate that methylation-based epigenetic diversity might be eco-geographically structured and might be partly determined by climatic and edaphic factors.
Data from: Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population
Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual's genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F. This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F. Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.
Data from: Association of body mass index and age with incident diabetes in Chinese adults: a population-based cohort study
Objective. Type 2 diabetes mellitus is increasing in young adults, and greater adiposity is considered a major risk factor. However, whether there is an association between obesity and diabetes and how this might be impacted by age is not clear. Therefore, we investigated the association between body mass index (BMI) and diabetes across a wide range of age groups (20-30, 30-40, 40-50, 50-60, 60-70, ≥70 years old). Design. We performed a retrospective cohort study using healthy screening program data. Setting. A total of 211,833 adult Chinese persons > 20-years-old across 32 sites and 11 cities in China (Shanghai, Beijing, Nanjing, Suzhou, Shenzhen, Changzhou, Chengdu, Guangzhou, Hefei, Wuhan, Nantong) were selected for the study; these persons were free of diabetes at baseline. Primary and secondary outcome measures. Fasting plasma glucose levels were measured and information regarding the history of diabetes was collected at each visit. Diabetes was diagnosed as fasting plasma glucose ≥ 7.00 mmol/L and/or self-reported diabetes. Patients were censored at the date of diagnosis or the final visit, whichever came first. Results. With a median follow-up of 3.1 years, 4,174 of the 211,833 participants developed diabetes, with an age-adjusted incidence rate of 7.35 per 1,000 persons. The risk of incident diabetes increased proportionally with increasing baseline BMI values, with a 23% increased risk of incident diabetes with each kg/m2 increase in BMI (95%CI: 1.22, 1.24). Across all age groups, there was a linear association between BMI and the risk of incident diabetes, although there was a stronger association between BMI and incident diabetes in the younger age groups (age × BMI interaction, P < 0.0001). Conclusions. An increased BMI is also independently associated with a higher risk of developing diabetes in young adults and the effects of BMI on incident diabetes were accentuated in younger adults.
Data from: Variation in migration pattern, broodstock origin, and family productivity of coho salmon hatchery populations in British Columbia, Canada derived from parentage-based tagging.
In salmonid parentage-based tagging (PBT) applications, entire hatchery broodstocks are genotyped, and subsequently progeny can be non-lethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e. age). Inter- and intra-population variability in migration patterns, life history traits, and fishery contributions can be determined from PBT analysis of samples derived from both fisheries and escapements (portion of a salmon population that does not get caught in fisheries and returns to its natal river to spawn). In the current study of southern British Columbia coho salmon (Oncorhynchus kisutch) populations, PBT analysis provided novel information on intra-population heterogeneity among males in the total number of progeny identified in fisheries and escapements, the proportion of progeny sampled from fisheries versus escapement, the proportion of two-year old progeny (jacks) produced, and the within-season return time of progeny. Fishery recoveries of coho salmon revealed heterogeneity in migration patterns among and within populations, with recoveries from north and central coast fisheries distinguishing 'northern migrating' from 'resident' populations. In northern-migrating populations, the mean distance between fishery captures of sibs (brothers and sisters) was significantly less than the mean distance between non-sibs, indicating the possible presence of intra-population genetic heterogeneity for migration pattern. Variation among populations in productivity and within populations in fish catchability indicated that population selection and broodstock management can be implemented to optimize harvest benefits from hatcheries. Application of PBT provided valuable information for assessment and management of hatchery-origin coho salmon in British Columbia.
Data from: A trait-based approach to predict population genetic structure in bees
Understanding population genetic structure is key to developing predictions about species susceptibility to environmental change, such as habitat fragmentation and climate change. It has been theorized that life-history traits may constrain some species in their dispersal and lead to greater signatures of population genetic structure. In this study, we use a quantitative comparative approach to assess if patterns of population genetic structure in bees are driven by three key species-level life-history traits: body size, sociality, and diet breadth. Specifically, we reviewed the current literature on bee population genetic structure, as measured by the differentiation indices Nei's GST, Hedrick's G`ST, and Jost's D. We then used phylogenetic generalised linear models to estimate the correlation between the evolution of these traits and patterns of genetic differentiation. Our analyses revealed a negative and significant effect of body size on genetic structure, regardless of differentiation index utilized. For Hedrick's G`ST and Jost's D, we also found a significant impact of sociality, where social species exhibited lower levels of differentiation than solitary species. We did not find an effect of diet specialization on population genetic structure. Overall, our results suggest that physical dispersal or other functions related to body size are among the most critical for mediating population structure for bees. We further highlight the importance of standardizing population genetic measures to more easily compare studies and to identify the most susceptible species to landscape and climatic changes.
Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds
Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.
Differential influence of Slc7a11 expression and body condition on pheomelanin‐based pigmentation in two Eurasian nuthatch Sitta europaea populations with different predation risk
<p><span><span><span><span><span><span><span><span><span><span><span>The expression of the gene <i>Slc7a11</i>promotes the antioxidant capacity of cells by providing them with cysteine that can be used for the synthesis of glutathione (GSH), the most important intracellular antioxidant. In melanocytes, intracellular cysteine can also enter melanosomes and get incorporated in the pigment pheomelanin synthesis pathway, thus decreasing cysteine availability for GSH synthesis and potentially creating chronic oxidative stress. We thus hypothesized that a mechanism limiting the use of intramelanocytic cysteine for pheomelanin synthesis in environmental conditions generating oxidative stress may be physiologically advantageous and favored by natural selection. Here we searched for evidence of such a mechanism by comparing the influence of melanocytic <i>Slc7a11</i>expression on pheomelanin-based pigmentation in developing Eurasian nuthatch <i>Sitta europaea</i>nestlings from two populations differing in predation risk, a natural source of oxidative stress. Pheomelanin synthesis and pigmentation tended to increase with <i>Slc7a11</i>expression in the low-risk population as expected from the activity of this gene, but decreased with <i>Slc7a11</i>expression in the high-risk population. The same was not observed in the expression of five other genes influencing pheomelanin synthesis without affecting cysteine availability in melanocytes. The influence of body condition on the intensity of pheomelanin-based pigmentation also differed between populations, being positive in the low-risk population and negative in the high-risk population. The resulting pigmentation of birds was more intense in the high-risk population. These findings suggest that birds perceiving high predation risk may limit the use of cysteine for pheomelanin synthesis, which becomes independent of <i>Slc7a11</i>expression. Some birds may have thus evolved the ability to adjust their pigmentation phenotype to environmental stress.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Out-of-hospital endotracheal intubation experience, confidence, and confidence-associated factors among Northern Japanese emergency life-saving technicians: a population-based cross-sectional study
Objective: Clinical procedural experience and confidence are both important when performing complex medical procedures. Because out-of-hospital endotracheal intubation (ETI) is a complex intervention, we sought to clarify clinical ETI experience among prehospital rescuers as well as their confidence in performing ETI and confidence-associated factors. Design: Population-based cross-sectional study conducted from January to September 2017. Setting: Northern Japan, including eight prefectures. Participants: Emergency life-saving technicians (ELSTs) authorized to perform ETI. Outcome measures: Annual ETI exposure and confidence in performing ETI, according to a 5-point Likert scale. To determine factors associated with ETI confidence, differences between confident ELSTs (those scoring 4 or 5 on the Likert scale) and non-confident ELSTs were evaluated. Results: Questionnaires were sent to 149 fire departments; 140 agreed to participate. Among the 2821 ELSTs working at responding fire departments, 2620 returned the questionnaire (response rate, 92.9%); complete data sets were available for 2567 ELSTs (complete response rate, 91.0%). Of those 2567 respondents, 95.7% performed two or fewer ETI annually; 46.6% reported lack of confidence in performing ETI. Multivariable logistic regression analysis showed that years of clinical experience (adjusted odds ratio [AOR], 1.09; 95% confidence interval [CI], 1.05–1.13), annual ETI exposure (AOR, 1.79; 95% CI, 1.59–2.03), and the availability of ETI skill retention programs including regular simulation training (AOR, 1.31; 95% CI, 1.02–1.68) and operating room training (AOR, 1.44; 95% CI, 1.14–1.83) were independently associated with confidence in performing ETI. Conclusions: ETI is an uncommon event for most ELSTs and nearly half of respondents did not have confidence in performing this procedure. Because confidence in ETI was independently associated with availability of regular simulation and operating room training, standardization of ETI reeducation that incorporates such methods may be useful for prehospital rescuers.
Data from: Complementary and alternative asthma treatments and their association with asthma control: a population-based study
Objectives: Many patients with asthma spend time and resources consuming complementary and alternative medicines (CAMs). This study explores whether CAM utilization is associated with asthma control and the intake of asthma controller medications. Design: Population-based, prospective cross-sectional study Setting: general population residing in two census areas in the province of British Columbia, Canada. Recruitment was based on random-digit dialing of both landlines and cell phones. Participants: 486 patients with self-reported physician-diagnosis of asthma (mean age 52 years; 67.3% female). Primary and secondary outcome measures: We assessed CAM use over the previous 12 months, level of asthma control as defined by the Global Initiative for Asthma (GINA), and the self-reported intake of controller medications. Multivariate logistic regression was performed to study the relationship between any usage of CAMs (outcome), asthma control and controller medication usage, adjusted for potential confounders. Results: A total of 179 (36.8%) of the sample reported CAM usage in the past 12 months. Breathing exercises (17.7%), herbal medicines (10.1%), and vitamins (9.7%) were the most popular CAMs reported. After adjustment, female sex (OR: 1.66; 95% CI: 1.09-2.52) and uncontrolled asthma( vs. controlled asthma, OR: 2.25, 95% CI: 1.30-3.89) were associated with a higher likelihood of using any CAMs in the past 12 months. Controller medication use was not associated with CAM usage in general and in the subgroups defined by asthma control. Conclusion: Clinicians and policy makers need to be aware of the high prevalence of CAM use in patients with asthma and its association with lack of asthma control.
Data from: Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, i.e. the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic datasets to investigate the efficiency of an individual-based sampling scheme (ISS) in detecting isolation-by-distance and isolation-by-barrier patterns. Provided that pseudo-replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of inter-individual measures of genotypic dissimilarity may efficiently replace inter-population measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.
Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies
Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Data from: Evaluating the existence and benefit of major histocompatibility complex-based mate choice in an isolated owl population
<p>How mate preferences evolve in the first place has been a major conundrum for sexual selection. Some hypotheses explaining this assume fitness benefit derived from subsequent generations. Major Histocompatibility Complex (MHC)-based mate choice is a representative example of the mate choice that is associated with such trans-generational mechanisms. To provide evidences for fitness benefit of MHC-based mate choice, previous studies assessed the association between own MHC genotype and own fitness components. However, the association between MHC-based mate choice in the parental generation and fitness components in the resultant offspring generation has only rarely been measured in wild populations. Focusing on the isolated population of the monogamous Ryukyu Scops Owl (<i>Otus elegans interpositus</i>) on Minami-daito Island, Japan, we found evidence of MHC-based mate choice. However, we found no evidence of MHC-based mate choice increasing own reproductive success or offspring survival. This is a rare case study that directly examines the existence of the trans-generational indirect benefit of MHC-based mate choice for genetic compatibility from trans-generational data in a wild bird population. By investigating the fitness benefits of mate choice, this study serves to facilitate our understanding of the evolution of MHC-based mate choice.</p>
Data from: The burden of Hepatitis C virus infection in Punjab, India: a population-based serosurvey
Introduction: Hepatitis C virus (HCV) infection prevalence is believed to be elevated in Punjab, India; however, state-wide prevalence data are not available. An understanding of HCV prevalence, risk factors and genotype distribution can be used to plan control measures in Punjab. Methods: A cross-sectional, state-wide, population-based serosurvey using a multi-stage stratified cluster sampling design was conducted October 2013 to April 2014. Children aged >5 years and adults were eligible to participate. Demographic and risk behavior data were collected, and serologic specimens were obtained and tested for anti-HCV antibody, HCV Ribonucleic acid (RNA) on anti-HCV positive samples, and HCV genotype. Prevalence estimates and adjusted odds ratios for risk factors were calculated from weighted data and stratified by urban/rural residence. Results: 5,543 individuals participated in the study with an overall weighted anti-HCV prevalence of 3.6% (95% Confidence Interval [CI]: 3.0%-4.2%) and chronic infection (HCV Ribonucleic acid test positive) of 2.6% (95% CI: 2.0%-3.1%). Anti-HCV was associated with being male (adjusted odds ratio 1.52; 95% CI: 1.08-2.14), living in a rural area (adjusted odds ratio 2.53; 95% CI: 1.62-3.95) and was most strongly associated with those aged 40-49 (adjusted odds ratio 40-49 vs 19-29-year-olds 3.41; 95% CI: 1.90-6.11). Anti-HCV prevalence increased with each blood transfusion received (adjusted odds ratio 1.36; 95% CI: 1.10-1.68) and decreased with increasing education, (adjusted odds ratio 0.37 for graduate-level vs. primary school/no education; 95% CI: 0.16-0.82). Genotype 3 (58%) was most common among infected individuals. Discussion: The study findings, including the overall prevalence of chronic HCV infection, associated risk factors and demographic characteristics, and genotype distribution can guide prevention and control efforts, including treatment provision. In addition to high-risk populations, efforts targeting rural areas and adults aged >40 would be the most effective for identifying infected individuals.
Data from: A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations
Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.
Appendix of Integrating Population-based Patterns with Personal Routine to Re-engage Fitbit Use
<p>Appendix of Integrating Population-based Patterns with Personal Routine to Re-engage Fitbit Use</p>
Supplemental Materials - Performance Figures for "A Model for Predicting the (re)-occurrence of a ≥40% eGFR Decline in a large Population-based cohort of Persons with or At-Risk of Chronic Kidney Disease " paper
<p>The zip file contains performance metrics figures for each dynamic Bayesian Network (DBN) model, stratified by comorbidities, race, CKD stages, and ethnicity.</p> <p>Contains:</p> <ul> <li>Stratified: Bootstrapping of 1000 iterations and 1000 samples with stratified proportions (as in the original population of the test set) of rapid eGFR decliners and non-decliners.</li> </ul> <p> </p> <p>Second zip contains DBN structures as matrices for 2 periods study entry to entry period and entry period to year 1 for all sites in 2 excel files.</p>
Supplementary Data - Haplotype-based inference of recent effective population size in modern and ancient DNA samples
<p>This repository contains the simulated data analyzed in our manuscript titled "Haplotype-based Inference of Recent Effective Population Size in Modern and Ancient DNA Samples".The data is split into 7 datasets. </p><p><strong>- demographies.tar.gz</strong>: the simulated demographic models.<br><strong>- modern_data.tar.gz:</strong> simulated SNP-araray data. The genotypes were simulated under 4 demographic histories (see demographies.tar.gz) for 256 samples and under 10 different random seeds (Replicate 1-10). Additionally, Replicates 11 and 12 include simulations at larger sample sizes. Note that the results at lower sample sizes can be obtained by keeping the first N samples of the simulated files.<br><strong>- true_ibd.tar.gz :</strong> This dataset contains the IBD segments from the simulated modern_data (ground truth from ARGON simulator).<br><strong>- ancient_data.tar.gz</strong> dataset contains simulated aDNA data. The dataset contains data simulated at different coverages (MISSING_$M, where $M = exp(-coverage)), sample sizes, demographic models, and random seeds. Split into three parts. See below for instructions on how to reconstruct the dataset. <br><strong>- structure.tar.gz</strong> and<strong> admixture.tar.gz :</strong> contain the data simulated under more complex demographic histories involving 2 isolated populations (structure) or a single population undergoing a recent admixture event (admixtuer.tar.gz). The manuscript provides more details about the demographic histories.<br>- <strong>imputed.tar.gz</strong> dataset contains simulated imputed aDNA data. Each region was simulated independently. Each folder corresponds to a chromosome arm and contains:<br> - data.anc_array.npy: list of the SNPs included in the analysis (simulating a 1240k array)<br> - data.glimpse.vcf.gz: phased ancient population data as phased by GLIMPSE v1<br> - data.glimpse.vcf.gz.csi: index for the above VCF file<br> - data.imputed.vcf.gz: imputed ancient population data (unphased, including dosages and genotype posteriors)<br> - data.imputed.vcf.gz.csi: index file for the above VCF<br> - data.map.gz: genetic map for GLIMPSE (tab-separated format: pos chr cM)<br> - data.ref.tsv.gz: file used for calculating genotype likelihoods with BCFtools mpileup command to use as input for GLIMPSE (format: chromosome position ref_allele,alt_allele)<br> - data.ref.tsv.gz.tbi: index for the above file<br> - data.ref.vcf.gz: simulated sequencing data from the reference panel<br> - data.ref.vcf.gz.csi: index file for the above VCF<br> - data.target_ground_truth.vcf.gz: simulated sequencing data for the ancient population (ground truth)<br> - datalist.txt: list of genotype likelihood files for each target individual (to be used for merging into a single file)<br> - data.temp.map.gz: genetic map for data creation with msprime simulator (format: chr position rate(cM/Mb) cM)<br> - data.tree -> msprime simulator output containing all samples, both reference panel samples and ancient population samples<br> - data.vcf.gz: VCF containing ground truth sequencing data, phased genotypes for reference panel samples and for ancient population samples<br> - dataref.fa.fai: index for reference fasta file used during reads creation</p><p> </p><p>Note that some of the datasets have been split into multiple parts, for example admixed.tar.gz has been split into three different parts admixed.tar.gz-part-aa, admixed.tar.gz-part-ab, and admixed.tar.gz-part-ac<br>You can get the data by typing:</p><p>cat admixed.tar.gz.part-* > admixed.tar.gz</p><p><br> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.