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Figure 5 in Removal of historical taxonomic bias and its impact on biogeographic analyses: a case study of Neotropical tardigrade fauna
Figure 5. Tanglegram of consensus tree exhibiting the similarity between all biogeographic provinces from biogeographic regions and transitions zones (Andean region (AR), South American transition zone (SATZ), Neotropical region (NR), and Mexican transition zone (MTZ)) for all data ('false cosmopolitan' and 'indigenous species', on the left) and only 'indigenous data' (on the right). Each province is connected to itself by a dark grey line. The consensus tree was obtained by resampling (1000×) the row order with the 'recluster' package (Dapporto et al. 2020). Each province is coloured according to their area of origin: provinces from the AR are coloured blue, provinces from the SATZ are coloured light green, provinces from the NR are coloured pink, and provinces from the MTZ are coloured purple. Branches of provinces that appear unrelated to any other are bold and red-coloured. Provinces without any records of 'indigenous species' are not present in the tanglegram. Provinces without any records of tardigrade species were excluded from the clustering analysis.
Table 2 in Removal of historical taxonomic bias and its impact on biogeographic analyses: a case study of Neotropical tardigrade fauna
<p><b>Table 2.</b> Extrapolated richness of limnoterrestrial and freshwater tardigrade species and standard error for each region and transition zone. Estimations were made with all data (‘false cosmopolitan’ and ‘indigenous species’) and only ‘indigenous data for comparison. Estimations were made using the Jackknife1 estimator (based on: Burnham and Overton 1978, 1979).</p><table><tbody><tr><th><b>Area</b></th><th><b>Dataset</b></th><th><b>Number of provinces with at least one record</b></th><th><b>Total number of provinces</b></th><th><b>Observed richness</b></th><th><b>Estimated richness</b></th><th><b>Standard error</b></th></tr></tbody><tbody><tr><th>Neotropical region</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>33</td><td>50</td><td>186</td><td>282.969</td><td>29.094</td></tr><tr><td>‘Indigenous data’</td><td>29</td><td>50</td><td>96</td><td>157.793</td><td>19.499</td></tr><tr><th>Andean region</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>7</td><td>9</td><td>105</td><td>159.857</td><td>31.489</td></tr><tr><td>‘Indigenous data’</td><td>7</td><td>9</td><td>43</td><td>68.714</td><td>14.154</td></tr><tr><th>South America transition zone</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>6</td><td>7</td><td>66</td><td>102.666</td><td>25.011</td></tr><tr><td>‘Indigenous data’</td><td>3</td><td>7</td><td>26</td><td>41.330</td><td>12.995</td></tr><tr><th>Mexican transition zone</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>5</td><td>5</td><td>41</td><td>65.800</td><td>14.881</td></tr><tr><td>‘Indigenous data’</td><td>4</td><td>5</td><td>11</td><td>19.250</td><td>5.068</td></tr></tbody></table>
Figure data for "Antarctic sea ice surface temperature bias in atmospheric reanalyses induced by the combined effects of sea ice and clouds"
<p>Data supporting figures in the paper "Antarctic sea ice surface temperature bias in atmospheric reanalyses induced by the combined effects of sea ice and clouds" published at <em>Communications Earth & Environment. </em></p>
Data for the manuscript "The impact of dealiasing biases on bird and insect data products of C-band weather radars and consequences for aeroecological applications" by Weisshaupt et al.
<p>Netcdf files of the analyses in the manuscript "The impact of dealiasing biases on bird and insect data products of C-band weather radars and consequences for aeroecological applications" by Weisshaupt et al. containing flight directions, flight speeds and animal densities in 200-m height layers between 0-1 km from four single PRF and one dual-PRF scans from 10 Finnish polarimetric C-band weather radars between 1-30 Sept 2022 and from the Kankaanpää weather radar between 10 Sept – 30 Oct 2023 and 10 April - 10 June 2024. Bird and insect echoes were identified by the classifier developed by Mäkinen, T., J. Ritvanen, S. Pulkkinen, N. Weisshaupt, and J. Koistinen, 2022: Bayesian Classification of Nonmeteorological Targets in Polarimetric Doppler Radar Measurements. <em>J. Atmos. Oceanic Technol.</em>, <strong>39</strong>, 1561–1578, <a href="https://doi.org/10.1175/JTECH-D-21-0177.1" target="_blank" rel="noopener">https://doi.org/10.1175/JTECH-D-21-0177.1</a>.</p> <p>File names indicate the PRF mode, processing mode (either untreated ("raw") or dealiased ("no_classif")), date and a 5-letter radar id.</p>
Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs
<div> <div> <h2>Abstract</h2> <a href="https://github.com/christabel-bucao/fish-variability-across-organs/#abstract"></a></div> <p>Phenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variation is gene expression. As for other phenotypes, the range of accessible expression variation is limited and biased by different evolutionary and developmental constraints. Gene expression variability broadly refers to the tendency of a gene to vary in expression (i.e., between individuals or cells) due to stochastic fluctuations or differences in genetic, epigenetic, or environmental factors, separately from the differences between e.g. organs. Variability due to biomolecular stochasticity (transcriptional ‘noise’) and cell-to-cell heterogeneity has been well-studied in isogenic populations of unicellular organisms such as bacteria and yeasts. However, for more complex organisms with multiple cells, tissues, and organs sharing the same genetic background, the interplay between inter-individual expression variability, gene and organ function, and gene regulation remains an open question. In this study, we used highly multiplexed 3’-end Bulk RNA Barcoding and sequencing (BRB-seq) to generate transcriptome profiles spanning at least nine organs in outbred individuals of three ray-finned fish species: zebrafish, Northern pike, and spotted gar. For each condition, we measured expression variation per gene independent of mean expression level. We observed that lowly variable genes are enriched in cellular housekeeping functions whereas highly variable genes are enriched in stimulus-response functions. Furthermore, genes with highly variable expression between individuals evolve under weaker purifying selection at the coding sequence level, indicating that intra-species gene expression variability predicts inter-species protein sequence divergence. Genes that are broadly expressed across organs tend to be both highly expressed and lowly variable between individuals, whereas organ-biased genes are typically highly variable within their top organ of expression. For genes with organ-biased expression profiles, we inferred differences in selective pressure on gene regulation depending on their top organ. We found that genes with peak expression in the brain have low inter-individual expression variability across non-nervous organs, suggesting stabilizing selection on regulatory evolution of brain-biased genes. Conversely, liver-biased genes have highly variable expression across organs, implying weaker regulatory constraints. These patterns show that gene regulatory mechanisms evolved differently based on constraints on the primary organ.</p> <h2>Directory Structure</h2> </div> <ul> <li> <p><code>config/</code>: Contains YAML file indicating package versions for conda environment</p> </li> <li> <p><code>data/</code>: Contains input data</p> <ul> <li><code>counts/</code>: Contains counts and UMI-deduplicated counts. Currently under embargo and will be made available upon acceptance for publication.</li> <li><code>gene_metadata/</code>: Contains gene biotype information from Ensembl</li> <li><code>sample_metadata/</code>: Contains sample metadata files for each species</li> <li><code>selectome/</code>: Contains selection statistics from the <a href="https://selectome.org/" rel="nofollow">Selectome</a> database<br><br></li> </ul> </li> <li> <p><code>results/</code>: Contains output files sorted by subfolders labeled after each step of the analysis pipeline. Only R notebook HTML files are available on the Git repository, please check Zenodo for R data files.</p> <ul> <li><code>run_pipeline.Rdata</code>: Contains all parameters used for each step of the analysis pipeline<br><br></li> </ul> </li> <li> <p><code>workflow/</code>: Contains scripts used for the analysis pipeline</p> <ul> <li><code>analysis/</code>: Contains all steps of the analysis pipeline, available as .Rmd files</li> <li><code>functions/</code>: Contains all functions used for analysis/</li> <li><code>renv/</code>: Used for package management in R</li> <li><code>run_pipeline.R</code>: Runs all the steps under analysis/</li> <li><code>run_go_figure.sh</code>: Runs <a href="https://gitlab.com/evogenlab/GO-Figure" rel="nofollow">GO-Figure!</a> 1.0.0 (downloaded separately)</li> <li><code>demultiplex_brbseq_fastq.sh</code>: Used for demultiplexing BRB-seq fastq files using <a href="https://github.com/DeplanckeLab/BRB-seqTools">BRB-seqTools</a> 1.6.1 (downloaded separately) for uploading to NCBI SRA</li> <li><code>rename_fastq_files.sh</code>: Used for renaming demultiplexed fastq files by mapping each barcode to their corresponding sample name</li> <li><code>renv.lock</code>: Lockfile for managing R package versions. Run <code>renv::restore()</code> to set up the R environment based on packages specified in the lockfile. All package versions used are also specified in the output HTML files under results/.</li> </ul> </li> </ul> <div> <h2>Species Codes</h2> </div> <ul> <li><strong>LOC</strong>: <em>Lepisosteus oculatus</em> (spotted gar)</li> <li><strong>ELU</strong>: <em>Esox lucius</em> (Northern pike)</li> <li><strong>DRE</strong>: <em>Danio rerio</em> (zebrafish)</li> </ul>
Data from: Scale-specific sex-biased dispersal in the Valais shrew unveiled by genetic variation on the Y chromosome, autosomes, and mitochondrial DNA
We investigated sex-specificities in the evolutionary processes shaping Y chromosome, autosomes and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of population structure that were not consistent across maternal, paternal and bi-parentally inherited markers. Differentiation on a Y microsatellite was lower than expected from the comparison with autosomal microsatellites and mtDNA, and it was mostly due to genetic variance among populations within valleys, while the opposite was observed on other markers. In addition, there was no pattern of isolation-by-distance for the Y, while there was strong isolation-by-distance on mtDNA and autosomes. We use a hierarchical island model of coancestry dynamics to discuss the relative roles of the micro-evolutionary forces that may induce such patterns. We conclude that sex-biased dispersal is the most important driver of the observed genetic structure, but with an intriguing twist: it seems that dispersal is strongly male-biased at large spatial scale, while it is mildly biased in favour of females at local scale. These results add to recent reports of scale-specific sex-biased dispersal patterns, and emphasize the usefulness of the Y chromosome in conjunction with mtDNA and autosomes to infer sex-specificities.
Data from: Increased male bias in eider ducks can be explained by sex-specific survival of prime-age breeders
In contrast to theoretical predictions of even adult sex ratios, males are dominating in many bird populations. Such bias among adults may be critical to population growth and viability. Nevertheless, demographic mechanisms for biased adult sex ratios are still poorly understood. Here, we examined potential demographic mechanisms for the recent dramatic shift from a slight female bias among adult eider ducks (Somateria mollissima) to a male bias (about 65% males) in the Baltic Sea, where the species is currently declining. We analysed a nine-year dataset on offspring sex ratio at hatching based on molecularly sexed ducklings of individually known mothers. Moreover, using demographic data from long-term individual-based capture-recapture records, we investigated how sex-specific survival at different ages after fledgling can modify the adult sex ratio. More specifically, we constructed a stochastic two-sex matrix population model and simulated scenarios of different survival probabilities for males and females. We found that sex ratio at hatching was slightly female-biased (52.8%) and therefore unlikely to explain the observed male bias among adult birds. Our stochastic simulations with higher survival for males than for females revealed that despite a slight female bias at hatching, study populations shifted to a male-biased adult sex ratio (> 60% males) in a few decades. This shift that was driven by prime reproductive-age individuals (≥5-year-old), with sex-specific survival of younger age classes playing a minor role. Hence, different age classes contributed disproportionally to population dynamics. We argue that an alternative explanation for the observed male dominance among adults - sex-biased dispersal - can be considered redundant and is unlikely, given the ecology of the species. The present study highlights the importance of considering population structure and age-specific vital rates when assessing population dynamics and management targets.
Data from: Diversifying selection and color-biased dispersal in the asp viper
Background: The presence of intraspecific color polymorphism can have multiple impacts on the ecology of a species; as a consequence, particular color morphs may be strongly selected for in a given habitat type. For example, the asp viper (Vipera aspis) shows a high level of color polymorphism. A blotched morph (cryptic) is common throughout its range (central and western Europe), while a melanistic morph is frequently found in montane populations, presumably for thermoregulatory reasons. Besides, rare atypical uniformly colored individuals are known here and there. Nevertheless, we found in a restricted treeless area of the French Alps, a population containing a high proportion (>50%) of such specimens. The aim of the study is to bring insight into the presence and function of this color morph by (i) studying the genetic structure of these populations using nine microsatellite markers, and testing for (ii) a potential local diversifying selection and (iii) differences in dispersal capacity between blotched and non-blotched vipers. Results: Our genetic analyses support the occurrence of local diversifying selection for the non-blotched phenotype. In addition, we found significant color-biased dispersal, blotched individuals dispersing more than atypical individuals. Conclusion: We hypothesize that, in this population, the non-blotched phenotype possess an advantage over the typical one, a phenomenon possibly due to a better background matching ability in a more open habitat. In addition, color-biased dispersal might be partly associated with the observed local diversifying selection, as it can affect the genetic structure of populations, and hence the distribution of color morphs.
Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
Data from: Females know better: sex-biased habitat selection by the European wildcat
The interactions between animals and their environment vary across species, regions, but also with gender. Sex‐specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex‐specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex‐specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use‐availability framework using radio‐telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid‐range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex‐biased behavioral patterns may contribute to the resilience of wildcats' genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats' habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex‐related differences in environmental preferences.
Data from: Harnessing stratigraphic bias at the section scale: conodont diversity in the Homerian (Silurian) of the Midland Platform, England
Fossil abundance and diversity in geological successions are subject to bias arising from shifting depositional and diagenetic environments, resulting in variable rates of fossil accumulation and preservation. In simulations, this bias can be constrained based on sequence-stratigraphic architecture. Nonetheless, a practical quantitative method of incorporating the contribution of sequence-stratigraphic architecture in community palaeoecology and diversity analyses derived from individual successions is missing. As a model of faunal turnover affected by the stratigraphic bias, we use the 'Mulde event', a postulated mid-Silurian interval of elevated conodont turnover, which coincides with global eustatic sea-level changes and which has been based on regionally constrained observations. We test whether conodont turnover is highest at the boundary corresponding to the 'event' and post-'event' interval against the alternative that conodont turnover reflects habitat tracking and peaks at facies shifts. Based on the previously documented, parasequence-level stratigraphic framework of sections in the northern and central part of the Midland Platform, the relative controls of sequence-stratigraphic architecture, time and depositional environment over conodont distribution are evaluated using permutational multivariate analysis of variance. The depositional environment controls the largest part of variability in conodont assemblage composition, whereas the postulated 'Mulde event', or genuine temporal change in conodont diversity, cannot be detected. Depending on the binning of the stratigraphic succession, contrasting diversity and turnover patterns can be produced. The simple approach proposed here, emulating partitioning of β diversity into spatial and temporal components, may help to constrain the stratigraphic bias, even at the scale of an individual section.
Data from: Taxonomic identification bias does not drive patterns of abundance and diversity in theropod dinosaurs
<p>The ability of palaeontologists to correctly diagnose and classify new fossil species from incomplete morphological data is fundamental to our understanding of evolution. Different parts of the vertebrate skeleton have different likelihoods of fossil preservation and varying amounts of taxonomic information, which could bias our interpretations of fossil material. Substantial previous research has focused on the diversity and macroevolution of non-avian theropod dinosaurs. Theropods provide a rich dataset for analysis of the interactions between taxonomic diagnosability and fossil preservation. We use specimen data and formal taxonomic diagnoses to create a new metric, the Likelihood of Diagnosis (LoD), which quantifies the diagnostic likelihood of fossil species in relation to bone preservation potential. We use this to assess whether a taxonomic identification bias impacts the non-avian theropod fossil record. We find the patterns of differential species abundance and clade diversity are not a consequence of their relative diagnosability. Although there are other factors that bias the theropod fossil record, our results suggest patterns of relative abundance and diversity for theropods might be more representative of Mesozoic ecology than often considered.</p>
Data from: Wide range screening of algorithmic bias in word embedding models using large sentiment lexicons reveals underreported bias types
<p>Concerns about gender bias in word embedding models have captured substantial attention in the algorithmic bias research literature. Other bias types however have received lesser amounts of scrutiny. This work describes a large-scale analysis of sentiment associations in popular word embedding models along the lines of gender and ethnicity but also along the less frequently studied dimensions of socioeconomic status, age, physical appearance, sexual orientation, religious sentiment and political leanings. Consistent with previous scholarly literature, this work has found systemic bias against given names popular among African-Americans in most embedding models examined. Gender bias in embedding models however appears to be multifaceted and often reversed in polarity to what has been regularly reported. Interestingly, using the common operationalization of the term bias in the fairness literature, novel types of so far unreported bias types in word embedding models have also been identified. Specifically, the popular embedding models analyzed here display negative biases against middle and working-class socioeconomic status, male children, senior citizens, plain physical appearance and intellectual phenomena such as Islamic religious faith, non-religiosity and conservative political orientation. Reasons for the paradoxical underreporting of these bias types in the relevant literature are probably manifold but widely held blind spots when searching for algorithmic bias and a lack of widespread technical jargon to unambiguously describe a variety of algorithmic associations could conceivably be playing a role. The causal origins for the multiplicity of loaded associations attached to distinct demographic groups within embedding models are often unclear but the heterogeneity of said associations and their potential multifactorial roots raises doubts about the validity of grouping them all under the umbrella term bias. Richer and more fine-grained terminology as well as a more comprehensive exploration of the bias landscape could help the fairness epistemic community to characterize and neutralize algorithmic discrimination more efficiently.</p>
Data from: Divergent estimates of herd-wide caribou calf survival: ecological factors and methodological biases
Population monitoring is a critical part of effective wildlife management, but methods are prone to biases that can hinder our ability to accurately track changes in populations through time. Calf survival plays an important role in ungulate population dynamics and can be monitored using telemetry and herd composition surveys. These methods, however, are susceptible to unrepresentative sampling and violations of the assumption of equal detectability, respectively. Here we capitalized on 55 herd-wide estimates of woodland caribou (Rangifer tarandus caribou) calf survival in Newfoundland, Canada using telemetry (n = 1,175 calves) and 252 herd-wide estimates of calf:cow ratios (C:C) using herd composition surveys to investigate these potential biases. These data included 17 herd-wide estimates replicated from both methods concurrently (n = 448 calves and n =17 surveys) which we used to understand which processes and sampling biases contributed to disagreement between estimates of herd-wide calf survival. We used Cox proportional hazards models to determine if estimates of calf mortality risk were biased by the date a calf was collared. We also used linear mixed effects models to determine if estimates of C:C ratios were biased by survey date and herd size. We found that calves collared later in the calving season had a higher mortality risk and that C:C tended to be higher for surveys conducted later in the autumn. When we used these relationships to modify estimates of herd-wide calf survival derived from telemetry and herd composition surveys concurrently, we found that formerly disparate estimates of woodland caribou calf survival now overlapped (within a 95% confidence interval) in a majority of cases. Our case study highlights the potential of under-appreciated biases to impact our understanding of population dynamics and suggests ways that managers can limit the influence of these biases in the two widely applied methods for estimating herd-wide survival.
Delineating the ligand-receptor interactions that lead to biased signaling at the mu-opioid receptor
<p>Dataset for the manuscript entitled "Delineating the ligand-receptor interactions that lead to biased signaling at the mu-opioid receptor."</p>
A promising novel judgment bias test to evaluate affective states in dogs (Canis familiaris)
<p>Datasets generated and analysed during the current study.</p>
Salient objects dominate the central fixation bias when orienting towards images
<p>Data and stimulus material from:</p> <p>Wolf, C., & Lappe, M. (2021). Salient objects dominate the central fixation bias when orienting towards images. Journal of Vision</p> <p>For questions please contact chr.wolf[at]wwu.de</p>
Example data for bias-restrained ensemble refinement in gmxapi 0.2
<p>Input files are provided for running bias-restrained ensemble refinement using gmxapi 0.2 as described in the accompanying manuscript, doi:10.1101/2021.07.18.452496. </p>
Identifying contributors to PM2.5 simulation biases of chemical transport model using fully connected neural networks
<p>The processed data and codes in the study are included. </p> <p><strong>Source data:</strong></p> <p>The training and testing dataset is composed of observed and simulated data of pollutants and meteorology in the BTH and YRD regions in the whole year of 2015. The processed datasets used for training are named as "dataset_BTH" and "dataset_YRD" in the folder.</p> <ul> <li><em>The hourly observed pollution data</em> are from China National Urban Air Quality Real-time Release Platform of the National Environmental Monitoring Station</li> <li><em>The hourly simulated pollutants data</em> comes from the output of WRF-CMAQv5.2 (spatial resolution of 27 km).</li> <li><em>Meteorological observation data</em> is provided by China Meteorological Data Service Centre</li> <li><em>The meteorological simulation data</em> comes from the simulation results of the WRF model</li> </ul> <p><strong>Codes:</strong></p> <ul> <li>preprocessing of raw CMAQ data, observed pollution data and meteorological data</li> <li>bulid and train process of fully connected neural networks</li> <li>calculation of correlation between variables</li> <li>feature selection method</li> <li>contribution analysis</li> </ul>
Data from: Density-dependent sex-biased development of macroptery in a water strider
<p>In wing-polymorphic insects, wing morphs differ not only in dispersal capability but also in life history traits because of trade-offs between flight capability and reproduction. When the fitness benefits and costs of producing wings differ between males and females, sex-specific trade-offs can result in sex differences in the frequency of long-winged individuals. Furthermore, the social environment during development affects sex differences in wing development, but few empirical tests of this phenomenon have been performed to date. Here, I used the wing-dimorphic water strider <i>Tenagogerris euphrosyne</i> to test how rearing density and sex ratio affect the sex-specific development of long-winged dispersing morphs (i.e., sex-specific macroptery). I also used a full-sib, split-family breeding design to assess genetic effects on density-dependent, sex-specific macroptery. I reared water strider nymphs at either high or low densities and measured their wing development. I found that long-winged morphs developed more frequently in males than in females when individuals were reared in a high-density environment. However, the frequency of long-winged morphs was not biased according to sex when individuals were reared in a low-density environment. In addition, full-sib males and females showed similar macroptery incidence rates at low nymphal density, whereas the macroptery incidence rates differed between full-sib males and females at high nymphal density. Thus complex gene-by-environment-by-sex interactions may explain the density-specific levels of sex bias in macroptery, although this interpretation should be treated with some caution. Overall, my study provides empirical evidence for density-specific, sex-biased wing development. My findings suggest that social factors as well as abiotic factors can be important in determining sex-biased wing development in insects.</p>
ScienceDex guides
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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.