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65 results for “population source”
Variant, Metabolite and Source Data for: Population genomics uncover loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)
<p>These files contain the variant and metabolome for a collection of 220 tef (<em>Eragrsotis tef)</em> accessions from an ethiopian diversity panel. The accessions were assembled and managed by the Ethiopian Institute of Agricultural Research (EIAR, Ethiopia). The variant data was produced at the John Innes Centre (UK). The metabolome data was produced at Aberystwyth University (UK). These dataset are described in Jones et al. (2024), <em>bioRxiv</em>, https://doi.org/10.1101/2024.09.30.615331. The source data for main figures in the publication are also included.</p> <p>The submission contains</p> <ol> <li>EIAR_filtered.vcf.gz: This is the variant data obtained from alignment of Illumina reads from all 220 teff accessions to the reference assembly of tef (Dabbi). Low quality variants were filtered out. This variant data was used for constructing the phylogenetic relationship between the accessions. The samples names corresponds to the DNA code in Supplementary Table S10 (Jones et al, 2024).</li> <li>pooled_EIAR_filtered.vcf.gz: After the phylogentic analysis described above, reads from accessions that were found to be genetically redundant were pooled before variant calling. This file was used for the SNP GWAS analysis. The samples names corresponds to the DNA code in Supplementary Table S10 (Jones et al, 2024).</li> <li> Metabolite_Profile.xlxs (source data for Figure 5): This file contains m/z feature intensities from untargeted metabolite fingerprinting using Flow Infusion Electrospray High-resolution Mass Spectrometry (FIE-HRMS). The sample names contains a combination of Location code and Plot number in Supplementary Table S10 e.g AT plot 1, CD plot 1, DZ plot 1, where AT, CD and DZ represent Alem Tena, Chefe Donsa and Debre Zeit, respectively. The data was used for the partial least squares discriminant analysis and differentially accumulated metabolites analysis presented in Figure 5.</li> <li>Source data: Numerical source data for graphs and charts in Figures 3 - 7.</li> <li>Tsedey TT2 Sequence from Improved Assembly: The 4A and 4B sequences around the TT2 orthologue in tef from the improved PacBio-based chromosome-scale assembly of tef. These sequences were used for plotting the LTR Copia alignments presented in Supplementary Figure 9. We thank Corteva for pre-publication access to this improved Tsedey genome assembly.</li> </ol>
Supplementary material for "Productivity drives the dynamics of a red kite source population that depends on immigration"
<p>Data files, code and custom functions for all analyses and figures presented in the paper. The seven data files are provided in csv format (CMRJuvRing.csv, CMRJuvDraht.csv, CMRAdDraht.csv, CMRAdSat.csv, RingRecoveries.csv, Bruten.csv, Condition.csv). The code file (RedKiteCode.txt) and the function file (Custom_functions.txt) are space delineated text files. The code file is written for R, but some models are run in JAGS from R. The code file also contains descriptions of the data files and code for data management.</p> <p> </p>
An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion
<ol> <li>Many African large carnivore populations are declining due to decline of the herbivore populations on which they depend. The densities of apex carnivores like the lion and spotted hyena correlate strongly with prey density, but competitive subordinates like the African wild dog benefit from competitive release when the density of apex carnivores is low, so the expected effect of a simultaneous decrease in resources and dominant competitors is not obvious. </li> <li>Wild dogs in Zambia's Luangwa Valley Ecosystem occupy four ecologically similar areas with well-described differences in the densities of prey and dominant competitors, due to spatial variation in illegal offtake.</li> <li>We used long-term data to fit a Bayesian integrated population model (IPM) of the demography and dynamics of wild dogs in these four regions. The IPM used Leslie projection to link a Cormack-Jolly-Seber model of area-specific survival (allowing for individual heterogeneity in detection), a zero-inflated Poisson model of area-specific fecundity, and a state-space model of population size that used estimates from a closed mark-capture model as the counts from which (latent) population size was estimated.</li> <li>The IPM showed that both survival and reproduction were lowest in the region with the lowest density of preferred prey (puku, <em>Kobus vardonii</em>, and impala, <em>Aepyceros</em> <em>melampus</em>), despite little use of this area by lions. Survival and reproduction were highest in the region with the highest prey density, and intermediate in the two regions with intermediate prey density. The population growth rate (λ) was positive for the population as a whole, strongly positive in the region with the highest prey density, and strongly negative in the region with the lowest prey density.</li> <li>It has long been thought that the benefits of competitive release protect African wild dogs from the costs of low prey density. Our results show that the costs of prey depletion overwhelm the benefits of competitive release and cause local population decline where anthropogenic prey depletion is strong. Because competition is important in many guilds and humans are affecting resources of many types, it is likely that similarly fundamental shifts in population limitation are arising in many systems.</li> </ol>
Home and hub: pet trade and traditional medicine impact reptile populations in source locations and destinations
<p>The pet trade and Traditional Chinese Medicine (TCM) consumption are major drivers of global biodiversity loss. Tokay geckos (<em>Gekko gecko</em>) are among the most traded reptile species worldwide. In Hong Kong, pet and TCM markets sell tokay geckos while wild populations also persist. To clarify connections between trade sources and destinations, we compared genetics and stable isotopes of wild tokays in local and nonlocal populations to dried individuals from TCM markets across Hong Kong. We found that TCM tokays are likely not of local origin. Most wild tokays were related to individuals in South China, indicating a probable natural origin. However, two populations contained individuals more similar to distant populations, indicating pet trade origins. Our results highlight the complexity of wildlife trade impacts within trade hubs. Such trade dynamics complicate local legal regulation when endangered species are protected, but the same species might also be non-native and possibly damaging to the environment.</p>
Home and hub: pet trade and traditional medicine impact reptile populations in source locations and destinations
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An individual-based model trained on multiple data sources estimates population connectivity and facilitates aggregation of harvest management units
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An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion
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Individual multilocus genotypes of three translocated and two source populations of Arnica montana in southern Belgium
<p>Individual multilocus genotypes based on nine microsatellite loci measured in the framework of a genetic monitoring of translocated populations of the critically endangered Arnica montana. See Van Rossum et al. (2020) in Molecular Ecology for more details.</p>
Data from: Plant community response to switchgrass (Panicum virgatum) population source in establishing prairies
Ecological restoration and revegetation efforts entail the translocation of native plant populations. Risks associated with these efforts include failure of translocated populations to establish or, conversely, such strong establishment that they excessively dominate the recipient community. The role that selective breeding plays in mediating these risks is unclear but of increasing importance as efforts to restore and establish multifunctional grasslands also increase. In a three-year, spatially replicated study, we seeded experimental prairie communities with either domesticated (cultivar) or undomesticated strains of Panicum virgatum (switchgrass), a North American C4 species under development as a biomass crop. We evaluated the composition, performance, and diversity of the recipient plant communities and compared the performance of cultivar and undomesticated switchgrass in those communities. We found little evidence that switchgrass population source affected community response. Switchgrass cultivars modestly exceeded undomesticated strains with respect to stand establishment, third-year stand density, and aboveground biomass; effect size and significance differed among sites. Our results suggest that including cultivars in ecological restorations and multifunctional grasslands may enhance success of switchgrass establishment with little risk of impairing the composition or diversity of plant communities for up to three years, as reflected in the measures used here. However, the incorporation of undomesticated switchgrass into multifunctional grasslands may enhance landscape-scale genetic variation and mitigate risks associated with gene flow between translocated and local wild switchgrass populations; more research on these dynamics is needed.
Replication data for Anterior Cruciate Ligament Injury: identifying information sources and risk factor awareness among the general population
<p>Creating awareness about a disorder is important for prevention from the perspective of public health. However, for sports injuries, like the anterior cruciate ligament (ACL) injury, there is no study which has investigated the awareness of risk factors for the injury and prevention methods among the general population, to the best of our knowledge. The sources of information among the population are also unclear. The purpose of present study was to identify these aspects of public awareness about the ACL injury.</p> <p>A questionnaire was randomly distributed among the general population registered with a web based questionnaire supplier, to recruit 900 participants who were aware about the ACL injury. The questionnaire consisted of two parts: Question 1 asked them about their sources of information regarding the ACL injury; Question 2 asked them about the risk factors for ACL injury. Multivariate logistic regression was used to determine the information sources that provide a good understanding of the risk factors.</p> <p>The leading source of information for ACL injury was television (57.0%). However, the results of logistic regression analysis revealed that television was not an effective medium to create awareness about the risk factors, among the general population. Instead “Lecture by a coach”, “Classroom session on Health”, and “Newspaper” were significantly effective in creating a good awareness of the risk factors (p < 0.001).</p>
Chinese Reference Population: open-source age-dependent computational phantoms of reference Chinese population
<p>The<strong> Chinese Reference Population (CRP)</strong> phantoms dataset encompass <strong>30 phantoms</strong> available in both voxel and NURBS formats, with age in 0, 1, 2, 3, 4, 5, 6, 8, 10, 12, 15, 18 years and adult male and female, as well as 4 pregnant women and fetus in early pregnancy, first trimester, second trimester and third trimester.</p> <ul> <li><strong>Voxelized phantoms</strong> are accessible in NII format :<strong> <em>"XXX.nii", which could be opened in AMIDE software.</em></strong></li> <li>Excel file<strong> </strong>containing<strong> organ masses and other descriptive information </strong>:<strong> <em>"CRP_descriptive_Info.xlsx"</em></strong></li> <li>In the application of F18−FDG dose calculation, <strong>organ absorbed doses per unit activity administered </strong>is provided in an Excel file :<strong> <em>"Application_F18-FDG.xlsx"</em></strong></li> </ul> <p>All data are stored on Zenodo and can be publicly accessed.</p>
Dataset to study the population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources
<p>During colonial times, Nile tilapia <em>Oreochromis niloticus</em> (Linnaeus, 1758) was introduced in non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focussing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridisation. Using RAD sequencing (27 611 SNPs), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, stressing their ability to interbreed and the potential threat they cause to the genetic integrity of native tilapias. Populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity with Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge to avoid introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.</p>
Source population and time spent in captivity affect survival and reproduction of long-distance translocated northern bobwhites
<p>Northern bobwhites (<em>Colinus virginianus</em>) have become a species of great conservation priority because of widespread and ongoing population declines. Long-distance translocations are becoming increasingly used to access a source population with densities high enough to support translocation. Two key uncertainties exist regarding the efficacy of long-distance translocations: choosing a source population with adaptations that will be successful in a novel environment and mitigating the stress response common during the translocation process. We translocated bobwhites from the South Texas Plains and the Floridian Coastal Plain to a recipient site in the Floridian Coastal Plain in 2021 and 2022 to compare the survival and productivity of bobwhites translocated from two different source populations. We also evaluated how varying holding times during the translocation process influenced the success of the translocated individuals. Breeding season survival, nest propensity, and fecundity were greater for Florida resident and Florida translocated bobwhites relative to Texas translocated bobwhites. We observed high rates of mortality during the transport and holding processes, but holding time did not affect breeding season survival of Texas translocated bobwhites. Both nest success and fecundity of Texas translocated bobwhites were negatively affected by holding time. Bobwhites translocated long distances may have the adaptive capacity to be successful in novel environments, but the consequences of translocation stress can be detrimental. Future translocation planning should consider choosing source populations from similar ecoregions to simultaneously decrease translocation distances and potential stress from translocation.</p>
Population in Jakarta 2022 (Source form: Central Bureau of Statistics)
<p>The population pyramid graph above illustrates the population distribution in Jakarta in 2022. The 0-4 age group has a larger population compared to several age groups above it. The 30-34 age group has a slightly larger male population (388,746) than the female population (431,768). For the 65+ age group, the male and female populations are relatively balanced with slightly more females.</p> <p>This population pyramid shows a young population structure, with a wider base in the younger age group (0-19 years) and then starting to narrow in the older age group. This is an indication that Jakarta still has a fairly young population with the potential for a large population in the future.</p>
Genomic analyses point to a low evolutionary potential of prospective source populations for assisted migration in a forest herb
<p>Climate change is increasingly impacting temperate forest ecosystems and many forest herbs might be unable to track the changing climate due to dispersal limitation. Forest herbs with a low adaptive capacity may therefore benefit from conservation strategies that mitigate dispersal limitation and evolutionary constraints, such as assisted migration. However, assisted migration strategies rarely consider evolutionary constraints of potential source populations that may jeopardize their success. In cases where climate adaptation is overshadowed by competing evolutionary processes, assisted migration is unlikely to support adaptation to future climates. Using a combination of population and landscape genomic analyses, we disentangled local adaptation drivers and quantified the adaptability and vulnerability to climate change of the self-incompatible deciduous forest herb <em>Primula</em> <em>elatior</em>. Southern populations displayed a sharp genetic turnover, and a considerable amount of local adaptation under diversifying selection was discovered. However, most of the outlier loci could not be linked to climate variables (71%) and were likely related to other local adaptation drivers, such as photoperiodism. Furthermore, specific adaptations to climate extremes, such as drought stress, could not be detected. This is in line with the typical occurrence of forest herbs in buffered climatic conditions, which can be expected to reduce selection pressures imposed by climate. Finally, populations in the south of the distribution area had increased sensitivity to climate change due to a reduced adaptive capacity and a moderate genetic offset, while central European populations were sensitive due to a high genetic offset. We conclude that assisted migration from southern source populations could bear significant risk due to nonclimatic maladaptation and a low adaptive capacity. Regional admixture and restoration of ecological connectivity to increase the adaptive capacity, and assisted range expansion to suitable habitat in the north might be more appropriate mitigation strategies.</p>
Source Data: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans
<p>Source data for manuscript titled: 'No evidence for a common blood microbiome based on a population study of 9,770 healthy humans' (https://www.biorxiv.org/content/10.1101/2022.07.29.502098v1)</p>
Sources of coaster brook trout (Salvelinus fontinalis) revealed by genomic analysis of brook trout populations along Minnesota's shoreline with Lake Superior
<p>Knowledge of population-level relationships and how these relationships pertain to different life history forms is critical to developing effective management plans for native trout, char, and salmon. In the Lake Superior basin, identifying effective restoration strategies for coaster brook trout (<em>Salvelinus</em> <em>fontinalis</em>), a lake-inhabiting form of brook trout, is hampered by limited information on genetic connectivity and source-sink dynamics among brook trout populations. Here, we infer these relationships by surveying 8,178 single nucleotide polymorphisms in 234 brook trout from seven rivers along the Minnesota shoreline with Lake Superior, including from reaches above and below natural waterfalls that prevent upstream movement. We identified well-differentiated above-barrier populations that supply brook trout to below-barrier reaches. We also compared within-river brook trout to 26 coaster brook trout from Lake Superior. We identified at least four source populations for these coaster brook trout, three of which were located within rivers. Additionally, we estimated N<sub>E</sub> for within-river populations and detected a decline across recent generations, with the most recent estimates approaching critical thresholds. Finally, comparisons with 94 domestic brook trout representing nine hatchery strains revealed a lack of domestic introgression into wild populations, demonstrating the importance of natural reproduction to population persistence. Our results offer novel insights into sources of coaster brook trout and highlight the role of within-river populations in supporting the coaster life history. Management efforts focused on instream restoration may be more important to rehabilitating coaster brook trout than previously thought, and are urgently needed given the population-level conservation status reported here.</p>
High prevalence of lipopolysaccharide mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections
<p>Chronic, highly antibiotic-resistant infections in cystic fibrosis (CF) lungs contribute to increasing morbidity and mortality. <em>Pseudomonas</em> <em>aeruginosa</em>, a common CF pathogen, exhibits resistance to multiple antibiotics, contributing to antimicrobial resistance (AMR). These bacterial populations display genetic and phenotypic diversity, but it is unclear how this diversity affects susceptibility to bacteriocins. R-pyocins, i.e. bacteriocins produced by <em>P. aeruginosa</em>, are phage-tail-like antimicrobials. R-pyocins have potential as antimicrobials, however, recent research suggests the diversity of <em>P. aeruginosa</em> variants within CF lung infections leads to varying susceptibility to R-pyocins. This variation may be linked to changes in lipopolysaccharide (LPS), acting as the R-pyocin receptor. Currently, it is unknown how frequently R-pyocin-susceptible strains are in chronic CF lung infection, particularly when considering the heterogeneity within these strains. In this study, we tested R2-pyocin susceptibility of 139 <em>P. aeruginosa</em> variants from 17 sputum samples of seven CF patients and analyzed LPS phenotypes. We found that 83% of sputum samples did not have R2-pyocin-resistant variants, while nearly all samples contained susceptible variants. There was no correlation between LPS phenotype and R2-pyocin susceptibility, though we estimate that about 76% of sputum-derived variants lack an O-specific antigen, 40% lack a common antigen, and 24% have altered LPS cores. The absence of a correlation between LPS phenotype and R-pyocin susceptibility suggests LPS packing density may play a significant role in R-pyocin susceptibility among CF variants. Our research supports the potential of R-pyocins as therapeutic agents, as many infectious CF variants are susceptible to R2-pyocins, even within diverse bacterial populations.</p>
Temporal variability in effective size (Ne) identifies potential sources of discrepancies between mark recapture and close kin mark recapture estimates of population abundance
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Heterogenous susceptibility to R-pyocins in populations of Pseudomonas aeruginosa sourced from cystic fibrosis lungs
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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.