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5,538 results for “population data”
Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure
<p>Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (<em>Pinus pinaster</em> Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.</p>
Data from: Natural coral recovery despite negative population growth
<p>Demographic processes that ensure the recovery and resilience of marine populations are critical as climate change sends an increasing proportion on a trajectory of decline. Yet for some populations, recovery potential remains high. We conducted annual monitoring over 9-years (2012–2020) to assess the recovery of coral<em> </em>populations belonging to genus <em>Pocillopora</em>. These populations experienced a catastrophic collapse following a severe typhoon in 2009. From the start of the monitoring period, high initial recruitment led to the establishment of a juvenile population that rapidly transitioned to sexually mature adults, which dominated the population within six years after the disturbance. As a result, coral cover increased from 1.1% to 20.2% during this time. To identify key demographic drivers of recovery and population growth rates (λ), we applied kernel resampled Integral Projection Models (IPMs), constructing eight successive models to examine annual change. IPMs were able to capture reproductive traits as key demographic drivers over the initial 3 years, whilst individual growth was a continuous key demographic driver throughout the entire monitoring period. IPMs further detected a pulse of reproductive output subsequent to two further Category 5 typhoon events during the monitoring period, exemplifying key mechanisms of resilience for coral populations impacted by disturbance. Despite rapid recovery, (i.e., increased coral cover, individual colony growth, low mortality), IPMs estimated predominantly negative values of λ, indicating a declining population. Indeed, whilst λ translates to a change in the number of individuals, the recovery of coral populations can also be driven by an increase in the size of coral surviving colonies. Our results illustrate that accumulating long-term data of historical dynamics and applying IPMs to extract demographic drivers are crucial for future predictions that are based on comprehensive and robust understandings of ecological change. </p>
Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)
<p>Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.</p> <p>We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow <em>Salix herbacea</em> L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.</p> <p>We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. </p> <p>Synthesis: Our results suggest that sex ratio bias in <em>S. herbacea</em> is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of <em>Salix</em> may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.</p>
Data from: Effects of age, breeding strategy, population density, and number of neighbors on territory size and shape in Savannah Sparrows
<p>The size and shape of an animal's breeding territory are dynamic features influenced by multiple intrinsic and extrinsic factors and can have important implications for survival and reproduction. Quantitative studies of variation in these territory features can generate deeper insights into animal ecology and behavior. We explored the effect of age, breeding strategy, population density, and number of neighbors on the size and shape of breeding territories in an island population of Savannah Sparrows (<em>Passerculus sandwichensis</em>). Our dataset consisted of 407 breeding territories belonging to 225 males sampled over 11 years. We compared territory sizes to the age of the male territorial holder, the male's reproductive strategy (monogamy vs. polygyny), the number of birds in the study population (population density), and the number of immediate territorial neighbors (local density). We found substantial variation in territory size, with territories ranging over two orders of magnitude from 57 to 5727 m2 (0.0057 to 0.57 ha). Older males had larger territories, polygynous males had larger territories, territories were smaller in years with higher population density, and larger territories were associated with more immediate territorial neighbors. We also found substantial variation in territory shape, from near-circular to irregularly-shaped territories. Males with more neighbors had irregularly shaped territories, but the shape did not vary with male age, breeding strategy, or population density. For males that lived two years or longer, we found strong consistent individual differences in territory size across years, but weaker individual differences in territory shape, suggesting that size has high repeatability whereas shape has low repeatability. Our work provides evidence that songbird territories are highly dynamic and that their size and shape reflect both intrinsic factors (age and number of breeding partners) and extrinsic factors (population density and number of territorial neighbors).</p>
Interview Data: Nativism, Islamophobism and Islamism in the Age of Populism dataset
<h1><strong>Interview Data</strong></h1> <h2><strong>Nativism, Islamophobism and Islamism in the Age of Populism dataset</strong></h2> <p>Transcripts of 302 interviews conducted with self-identified Muslim youth of migrant origin and native youth with affiliation or sympathy with movements labeled far-right in Belgium, France, the Netherlands, and Germany.<a title="" href="#_ftn1" name="_ftnref1">[1]</a> Local researchers conducted the interviews using the same interview guide, including 17 questions. Interviews were not audio-recorded. The researchers took notes, verifying their transcriptions with the research participant during and after the interview. Originally, the research consisted 307 interviews but five participants (1 French native; 2 German Muslims; 2 German natives) did not want their interview transcriptions to be made public on the ERC data repository site. In accordance with our ethical guidelines, we anonymized the transcripts. The dataset also includes the summary output (as an excel file) of the values analysis of the 307 interviews. Please visit the attachment named Data Summary to learn more about our method of analysis and how to use the attached documents. As a complementary file, we hope that the additional excel sheet detailing the demographic characteristics of our research participants (sex, age, educational background, etc.) helps advance researchers’ understanding of our participant profile.</p> <p> </p> <p><strong>Additional information: </strong></p> <p>302 transcription files (zipped), 2 data summary files, 2 documentation files</p> <p> </p> <p><strong>Cadmus permanent link: </strong><a href="https://hdl.handle.net/1814/76159">https://hdl.handle.net/1814/76159</a></p> <p><strong>Series/Number: </strong>EUI; RSC; Research Data; 2023</p> <p><strong>Publisher: </strong>European University Institute</p> <p><strong>Keyword(s): </strong><a href="https://cadmus.eui.eu/discover?order=desc&rpp=10&sort_by=dc.date.issued_dt&query=%22Deprivation%22">Deprivation</a>, <a href="https://cadmus.eui.eu/discover?order=desc&rpp=10&sort_by=dc.date.issued_dt&query=%22Radicalism%22">Radicalism</a>, <a href="https://cadmus.eui.eu/discover?order=desc&rpp=10&sort_by=dc.date.issued_dt&query=%22Nativism%22">Nativism</a>, <a href="https://cadmus.eui.eu/discover?order=desc&rpp=10&sort_by=dc.date.issued_dt&query=%22Populism%22">Populism</a>, <a href="https://cadmus.eui.eu/discover?order=desc&rpp=10&sort_by=dc.date.issued_dt&query=%22Islamism%22">Islamism</a></p> <p><strong>Sponsorship and Funder information: </strong></p> <p>ERC Advanced Grant research project "Nativism, Islamophobism and Islamism in the Age of Populism: Culturalisation and Religionisation of what is Social, Economic and Political in Europe" (No: 785934). The project’s details and output can also be accessed at the project website, <strong><u> https://bpy.bilgi.edu.tr/en/</u></strong></p> <div><br> <div> <p><a title="" href="#_ftnref1" name="_ftn1">[1]</a> ERC Advanced Grant research project "Nativism, Islamophobism and Islamism in the Age of Populism: Culturalisation and Religionisation of what is Social, Economic and Political in Europe" (No: 785934). The project’s details and output can also be accessed at the project website, <a href="https://bpy.bilgi.edu.tr/en/">https://bpy.bilgi.edu.tr/en/</a> .</p> </div> </div>
Data from: Forecasting animal distribution through individual habitat selection: Insights for population inference and transferable predictions
<p>Habitat selection models frequently use data collected from a small geographic area over a short window of time to extrapolate patterns of relative abundance to unobserved areas or periods of time. However, these types of models often poorly predict how animals will use habitat beyond the place and time of data collection because space-use behaviors vary between individuals and are context-dependent. Here, we present a modelling workflow to advance predictive distribution performance by explicitly accounting for individual variability in habitat selection behavior and dependence on environmental context. Using global positioning system (GPS) data collected from 238 individual pronghorn, (<em>Antilocapra americana</em>), across 3 years in Utah, we combine individual-year-season-specific exponential habitat-selection models with weighted mixed-effects regressions to both draw inference about the drivers of habitat selection and predict space-use in areas/times where/when pronghorn were not monitored. We found a tremendous amount of variation in both the magnitude and direction of habitat selection behavior across seasons, but also across individuals, geographic regions, and years. We were able to attribute portions of this variation to season, movement strategy, sex, and regional variability in resources, conditions, and risks. We were also able to partition residual variation into inter- and intra-individual components. We then used the results to predict population-level, spatially and temporally dynamic, habitat-selection coefficients across Utah, resulting in a temporally dynamic map of pronghorn distribution at a 30x30m resolution but an extent of 220,000km2. We believe our transferable workflow can provide managers and researchers alike a way to turn limitations of traditional habitat selection models - variability in habitat selection - into a tool to understand and predict species-habitat associations across space and time.</p>
Fig. 2 in Morphology and Sequence Data of Mexican Populations of the Ciliate Parasite of Marine Fishes Trichodina rectuncinata (Ciliophora: Trichodinidae)
Fig. 2. Photomicrographs of silver-impregnated adhesive discs and diagrammatic drawings of the denticles of respective morphotypes studied in the present paper; a and a'. From Enneanectes reticulatus, San Carlos, Sonora. b and b'. From Enneanectes reticulatus, San Carlos, Sonora. c and c'. From Tomicodon zebra, Zihuatanejo, Guerrero. d and d'. From Tomicodon zebra, Cuatunalco, Oaxaca.
Fig. 3 in Morphology and Sequence Data of Mexican Populations of the Ciliate Parasite of Marine Fishes Trichodina rectuncinata (Ciliophora: Trichodinidae)
Fig. 3. Bayesian inference tree of sequences of the 18S gene of trichodinid species of the genus Trichodina and Trichodinella, emphasizing on Trichodina rectuncinata. Numbers near internal nodes show the support value. Codes: ♦ Cuatunalco; * Zihuatanejo; ● San Carlos.
Fig. 1 in Morphology and Sequence Data of Mexican Populations of the Ciliate Parasite of Marine Fishes Trichodina rectuncinata (Ciliophora: Trichodinidae)
Fig. 1. Map showing the location of Mexico, and localities where populations of Trichodina rectuncinata were obtained.
Figure S1 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure S1. Snail counts (y axis) at sites A (above) and B (below) for the three cohorts showing unmarked and recaptures separately for each visit: juveniles too small to mark, juveniles newly dotted, dotted juveniles recaptured, newly marked adult and subadult individuals, already marked adult and subadult individuals (recaptures).
Figure 9 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 9. Temperature and humidity profiles at sites A, B, and C between April and December 2017. TA = temperature at site A (three loggers), TB = temperature at site B (three loggers), TC = temperature at site C (three loggers). HA, HB, HC = humidity profile at sites A, B, and C, respectively. Some missing data are due to temporal failure of some loggers. Humidity loggers stopped to function completely in the middle of October at all three sites.
Figure 7 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 7. Minimum distances (in meters, x axis) of numbered individuals (y axis: absolute numbers of individuals) from sites A and B, over all subsequent observations.
Figure 6 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 6. Minimum distances (in meters, x axis) of numbered individuals (y axis: absolute numbers of individuals) from site A and B of all observations with a ~1-week interval.
Figure 3 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 3. Snail counts at site A (above) and site B (below); juv. small = small juveniles (too small to mark); juv. dotted = dotted individuals; subadults and adults = numbered subadults/adults.
Figure 8 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 8. Sum of MDs (in meters, x axis) over all subsequent observations (over the season) of numbered individuals (y axis: absolute numbers of individuals) from sites A and B.
Figure 2. M in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 2. M. subcristata shell-size classes: (A) small juveniles (too small to mark), appr. 8 mm shell height), (B) dotted juvenile, appr. 12 mm; (C) numbered adult, appr. 20 mm.
Figure 5 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 5. Population estimated according to Jolly-Seber for site A (above), site B (below). Y axis: estimated number of individuals.
Figure 1 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 1. Study area with three study sites (A, B, C). Note that due to the perspective view site B and C appear much smaller.
Data from: Widespread cultural change in declining populations of Amazon parrots
<p>This dataset of parrot call measurements and metadata is associated with the article "Widespread cultural change in declining populations of Amazon parrots" in Proceedings of the Royal Society B. The data was used to address change and stability in regional vocal dialects of yellow-naped amazon (<em>Amazona auropalliata</em>) contact calls recorded in Costa Rica over three sampling periods that spanned 22 years.</p>
Data - AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants
<p><strong>MSAs.zip </strong>Multiple sequences alignments generated by AlphaFold2 structure prediction of 7 engineered GFPs.</p> <p><strong>AF2_models_column_masking.zip </strong>AlphaFold2 models of the alternative conformations of 7 engineered GFPs.</p> <p><strong>MD_trajectories_PyMOL.zip</strong> Molecular dynamics trajectories (PyMOL sessions) of the alternative conformations of 7 engineered GFPs.</p> <p><strong>MD_analysis.zip </strong>Root mean square deviation and per-residue root mean square fluctuations along molecular dynamics simulations of 7 engineered GFPs.</p> <p><strong>rmsd_values.zip</strong> Root mean square deviation relative to crystallographic GFP structure for AlphaFold2 models and molecular dynamics frames (global and central alpha-helix)</p>
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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.