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1,363 results for “phenotypic data”
Data from: Maranville JC, Baxter SS, Witonsky DB, Chase MA, Di Rienzo A. (2013) Genetic Mapping with Multiple Levels of Phenotypic Information Reveals Determinants of Lymphocyte Glucocorticoid Sensitivity.
<p>Genotype data for 88 African American indviduals in binary PLINK format published in </p> <p>Maranville JC, Baxter SS, Witonsky DB, Chase MA, Di Rienzo A. (2013) Genetic Mapping with Multiple Levels of Phenotypic Information Reveals Determinants of Lymphocyte Glucocorticoid Sensitivity. Am J Hum Genet. 93(4):735-743</p> <p> </p>
Phenotyping data from: Genetics of phenological development and implications for seed yield in lentil
<p>Using a historic collection of Australian lentil varieties released between 1988 and 2019, we show that genetic gain in yield (29 kg ha<sup>-1</sup> yr<sup>-1</sup>) associates with faster reproductive development. A focus on five loci related to reproductive development, the lentil <em>ELF3</em> ortholog <em>Sn</em>, two loci linked to clusters of lentil <em>FT</em> orthologs and two loci without proposed candidates in chromosomes 2 and 5, revealed the potential for introducing novel early flowering alleles into current breeding material for further phenological diversity with potential implications for yield.</p>
Data from: The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system
<p>A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defense, are excellent models to understand the link between vivid color pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which species share a conspicuous phenotype can provide an even better model for understanding the mechanisms of color production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which mimicry is produced in poison frogs. We assembled a 6.02 Gbp genome with a contig N50 of 310 Kbp, a scaffold N50 of 390 Kbp, and 85% of expected tetrapod genes. We leveraged this genome to conduct gene expression analyses throughout development of four color morphs of <em>R. imitator </em>and two color morphs from both <em>R. fantastica </em>and <em>R. variabilis </em>which <em>R. imitator</em> mimics. We identified a large number of pigmentation and patterning genes differentially expressed throughout development, many of them related to melanophores/melanin, iridophore development, and guanine synthesis. We also identify the pteridine synthesis pathway (including genes such as <em>qdpr </em>and <em>xdh</em>) as a key driver of the variation in color between morphs of these species, and identify several plausible candidates for coloration in vertebrates (e.g., <em>cd36, ep-cadherin, perlwapin</em>). Finally, we hypothesize that keratin genes (e.g., <em>krt8</em>) are important for producing different structural colors within these frogs.</p>
Data from: Phenotypic selection on an ornamental trait is not modulated by breeding density in a pied flycatcher population
<p>Most studies of phenotypic selection in the wild have focused on morphological and life-history traits and looked at abiotic (climatic) variation as the main driver of selection. Consequently, our knowledge of the effects of biotic environmental variation on phenotypic selection on sexual traits is scarce. Population density can be considered a proxy for the intensity of intra- and inter-sexual competition and could therefore be a key factor influencing the covariation between individual fitness and the expression of sexual traits. Here, we used an individual-based data set from a population of pied flycatchers (<em>Ficedula hypoleuca</em>) monitored over 24 years to analyse the effect of breeding density on phenotypic selection on dorsal plumage colouration, a heritable and sexually selected ornament in males of this species. Using the number of recruits as a fitness proxy, our results show overall stabilizing selection on male dorsal colouration, with intermediate phenotypes being favoured over extremely dark and dull individuals. However, our results did not support the hypothesis that breeding density mediates phenotypic selection on this sexual trait. We discuss the possible role of other biotic factors influencing selection on ornamental plumage.</p>
Summary-level data from meta-analysis of fat distribution phenotypes in UK Biobank and GIANT
<p>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</p> <p>Summary-level data as presented in:</p> <p>"Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry." Pulit, SL et al. bioRxiv, 2018. https://www.biorxiv.org/content/early/2018/04/18/304030</p> <p>**If you use these data, please cite the above preprint.</p> <p>If you have any questions or comments regarding these files, please contact me:</p> <p>Sara L Pulit<br> spulit@well.ox.ac.uk or s.l.pulit@umcutrecht.nl</p> <p>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</p> <p><strong>(1) Data files</strong></p> <p><em>i. whradjbmi.giant-ukbb.meta-analysis.combined.23May2018.txt</em><br> Meta-analysis of waist-to-hip ratio adjusted for body mass index (whradjbmi) in UK Biobank and GIANT data. Combined set of samples, max N = 694,649.</p> <p><em>ii. whradjbmi.giant-ukbb.meta-analysis.females.23May2018.txt</em><br> Meta-analysis of whradjbmi in UK Biobank and GIANT data. Female samples only, max N = 379,501.</p> <p><em>iii. whradjbmi.giant-ukbb.meta-analysis.males.23May2018.txt</em><br> Meta-analysis of whradjbmi in UK Biobank and GIANT data. Male samples only, max N = 315,284.</p> <p><em>iv. whr.giant-ukbb.meta-analysis.combined.23May2018.txt</em><br> Meta-analysis of waist-to-hip ratio (whr) in UK Biobank and GIANT data. Combined set of samples, max N = 697,734.</p> <p><em>v. whr.giant-ukbb.meta-analysis.females.23May2018.txt</em><br> Meta-analysis of whr in UK Biobank and GIANT data. Female samples only, max N = 381,152.</p> <p><em>vi. whr.giant-ukbb.meta-analysis.males.23May2018.txt</em><br> Meta-analysis of whr in UK Biobank and GIANT data. Male samples only, max N = 316,772.</p> <p><em>vii. bmi.giant-ukbb.meta-analysis.combined.23May2018.txt</em><br> Meta-analysis of body mass index (bmi) in UK Biobank and GIANT data. Combined set of samples, max N = 806,834.</p> <p><em>viii. bmi.giant-ukbb.meta-analysis.females.23May2018.txt</em><br> Meta-analysis of bmi in UK Biobank and GIANT data. Female samples only, max N = 434,794.</p> <p><em>ix. bmi.giant-ukbb.meta-analysis.males.23May2018.txt</em><br> Meta-analysis of bmi in UK Biobank and GIANT data. Male samples only, max N = 374,756.</p> <p><strong>(2) Data file format</strong></p> <p>CHR: Chromosome</p> <p>POS: Chromosomal position of the SNP, build hg19</p> <p>SNP: the dbSNP151 identifier of the SNP, followed by the first allele and second allele of the SNP, delimited with a colon. A small number of SNPs (<9,000) from the GIANT data had no dbSNP151 identifier, and are left as just an rsID. Note that these SNPs are also missing chromosome and position information (not provided in the GIANT data).</p> <p>Tested_Allele: the allele for which all association statistics are reported</p> <p>Other_Allele: the other allele at the SNP</p> <p>Freq_Tested_Allele: frequency of the tested allele</p> <p>BETA: the effect size of the tested allele</p> <p>SE: the standard error of the beta</p> <p>P: the p-value of the SNP, as reported from the inverse variance-weighted fixed effects meta-analysis</p> <p>N: the total sample size for this SNP</p> <p>INFO: the imputation quality (info score) of the SNP, as reported by UK Biobank. A number between 0 and 1 indicating quality of imputation (0, poor quality; 1, high quality or genotyped). Note that the summary-level GIANT data does not report info score, so SNPs appearing only in the GIANT analysis do not have info scores.</p>
data set related to article Broad phenotypic spectrum and genotype-phenotype correlations in GMPPB-related dystroglycanopathies: an Italian cross-sectional study
<p>This record contains raw data related to article Broad phenotypic spectrum and genotype-phenotype correlations in GMPPB-related dystroglycanopathies: an Italian cross-sectional study</p>
Zea mays MAGIC RIL population - field trial phenotyping data
<p>MIAPPE compliant ISA-tab files of the Zea mays MAGIC RIL population derived from eight genetically diverse founder lines.</p>
Zea mays MAGIC RIL population - growth chamber phenotyping data
<p>MIAPPE compliant ISA-tab files of 197 recombinant inbred lines of two different maize (Zea mays) populations including indepth phenotyping of the fourth leaf at later stages of development.</p>
Data from de Vega et al_Flora "Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant" [Dataset]
<p>Data from de Vega et al_Flora "Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant"</p>
BRESOV common bean ILs collection , phenotypic data
<p><strong><span>Dataset_ILS_2018</span></strong></p> <p><span>Dataset including phenotypic data recorded on the introgression line population (IL), in the multi-locations field trials performed in Spain, Romania, Italy in 2018 </span></p> <p><strong><span>Dataset_ILS_2019</span></strong></p> <p><span>Dataset including phenotypic data recorded on the introgression line population (IL), in the multi-locations field trials performed in Spain, Romania, Italy in 2019 </span></p> <p><strong><span>Dataset_ILS_2020</span></strong></p> <p><span>Dataset including phenotypic data recorded on the introgression line population (IL), in the multi-locations field trials performed in Spain, Romania, Italy in 2020</span></p>
Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data
The evolutionary dynamics of complex ecological traits – including multistate representations of diet, habitat, and behavior – remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains (CTMC) are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a pre-determined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories.
Data and code from: Phenotypic memory drives population growth and extinction risk in a noisy environment
<p>Random environmental fluctuations pose major threats to wild populations. As patterns of environmental noise are themselves altered by global change, there is growing need to identify general mechanisms underlying their effects on population dynamics. This notably requires understanding and predicting population responses to the color of environmental noise, i.e. its temporal autocorrelation pattern. Here, we show experimentally that environmental autocorrelation has a large influence on population dynamics and extinction rates, which can be predicted accurately provided that a memory of past environment is accounted for. We exposed near to 1000 lines of the microalgae <em>Dunaliella salina</em> to randomly fluctuating salinity, with autocorrelation ranging from negative to highly positive. We found lower population growth, and twice as many extinctions, under lower autocorrelation. These responses closely matched predictions based on a tolerance curve with environmental memory, showing that non-genetic inheritance can be a major driver of population dynamics in randomly fluctuating environments. </p>
Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion
Rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction and magnitude of phenotypic evolution during invasion has been underestimated. We explored the utility of niche-shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded from the northeastern coastline of Japan to North America, Europe and northwestern Africa within the last 100 years. A genetically-informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations and as predicted, non-native populations had greater tolerance for ecologically-relevant extreme heat (40ºC) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically-informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions, and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.
Data from: Recent chapters of Neotropical history overlooked in phylogeography: shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins
Establishing links between phenotypic and genotypic variation is a central goal of evolutionary biology, as they might provide important insights into evolutionary processes shaping genetic and species diversity in nature. One of the more intriguing possibilities is when no genetic divergence is found to be associated with conspicuous phenotypic divergence. In that case, speciation theory predicts that phenotypic divergence may still occur in the presence of significant gene flow—thereby resulting in little genomic divergence—when genetic loci underpinning phenotypes are under strong divergent selection. However, a finding of phenotypic distinctiveness with weak or no population genetic structure may simply result from low statistical power to detect shallow genetic divergences when small datasets are used. Here, we used a subgenomic dataset of 2386 ultraconserved elements to explore genome-wide divergence between two species of Antilophia manakins, which are phenotypically distinct yet evidently lack strong genetic differentiation according to previous studies based on a limited number of loci. Our results revealed clear population structure that matches the two phenotypes, supporting the idea that smaller datasets lacked the power to detect this recent divergence event (likely < 100 k ya). Indeed, we found little or no introgression between the species, as well as evidence of genome-wide divergence. One implication of our study is that the Araripe plateau may be a hotspot of cryptic-diverging forest Cerrado populations. Besides their use in biogeography, subgenomic datasets may help redefine local conservation programs by revealing cryptic population structure that may be key to population management.
Data from: Virulence phenotypes result from interactions between pathogen ploidy and genetic background
<p>Studying fungal virulence is often challenging and frequently depends on many contexts, including host immune status and pathogen genetic background. However, the role of ploidy has often been overlooked when studying virulence in eukaryotic pathogens. Since fungal pathogens, including the human opportunistic pathogen <i>Candida albicans</i>, can display extensive ploidy variation, assessing how ploidy impacts virulence has important clinical relevance. As an opportunistic pathogen, <i>C. albicans</i> causes non-lethal, superficial infections in healthy individuals, but life-threatening bloodstream infections in individuals with compromised immune function. Here, we determined how both ploidy and genetic background of <i>C. albicans</i> impacts virulence phenotypes in healthy and immunocompromised nematode hosts by characterizing virulence phenotypes in four near-isogenic diploid and tetraploid pairs of strains, which included both laboratory and clinical genetic backgrounds. We found that <i>C. albicans</i> infections decreased host survival and negatively impacted host reproduction, and we leveraged these two measures to survey both lethal and non-lethal virulence phenotypes across the multiple <i>C. albicans</i> strains. In this study, we found that regardless of pathogen ploidy or genetic background, immunocompromised hosts were susceptible to fungal infection compared to healthy hosts. Furthermore, for each host context, we found a significant interaction between <i>C. albicans</i> genetic background and ploidy on virulence phenotypes, but no global differences between diploid and tetraploid pathogens were observed.</p>
Data from: Macroevolutionary integration of phenotypes within and across ant worker castes
<p>Phenotypic traits are often integrated into evolutionary modules: sets of organismal parts that evolve together. In social insect colonies the concepts of integration and modularity apply to sets of traits both within and among functionally and phenotypically differentiated castes. On macroevolutionary timescales, patterns of integration and modularity within and across castes can be clues to the selective and ecological factors shaping their evolution and diversification. We develop a set of hypotheses describing contrasting patterns of worker integration and apply this framework in a broad (246 species) comparative analysis of major and minor worker evolution in the hyperdiverse ant genus Pheidole. Using geometric morphometrics in a phylogenetic framework, we inferred fast and tightly integrated evolution of mesosoma shape between major and minor workers, but slower and more independent evolution of head shape between the two worker castes. Thus, Pheidole workers are evolving as a mixture of intra- and inter-caste integration and rate heterogeneity. The decoupling of homologous traits across worker castes may represent an important process facilitating the rise of social complexity.</p>
Supplementary Data to: "A single nucleotide mutation in DUOX2 gene causes some of the panda's unique metabolic phenotypes"
<p>This file contains the data set associated with the manuscript entitled: "A single nucleotide mutation in the dual-oxidase 2 (<em>DUOX2</em>) gene causes some of the panda’s unique metabolic phenotypes", National Science Review, DOI: <a href="http://dx.doi.org/10.1093/nsr/nwab125">10.1093/nsr/nwab125</a></p>
Data and Results for: Cost-effective, high-throughput fruit phenotyping system for three-dimensional reconstruction of fruit form
<p>The dataset contains the raw data used for generating the results in the paper, and the reconstructed results at 1mm and 2mm voxel resolution.</p> <p><strong>Raw data</strong>: Samples are gathered into groups of five, DataObjects1-5.zip, ... , DataObjects56-59.zip.</p> <p>Once uncompressed, each directory holds the images and configuration information used for each sample. For instance, '1_obj' is for the first sample, and the 'data' folder has the image files by camera. In this case one camera was used, 'cam2', and there are 62 images. 'pattern_square_mm_external.txt', 'pattern_square_mm_internal.txt', and 'rotate_specification_file.txt' are all configuration files needed for the calibration step.</p> <p> </p> <p><strong>Results</strong>: Reconstructions results are in compressed folders 'reconstruction-results-1mm.zip' and 'reconstruction-results-2mm.zip' for 1 mm and 2 mm voxel resolutions, respectively. These results are three-dimensional model files than can be viewed with a variety of software, we have used the free MeshLab: https://www.meshlab.net/ .</p> <p> </p> <p> </p> <p> </p>
Phenotypic, genetic, and epigenetic data from 29 Serratia marcescens strains from an evolution experiment
<p>This dataset contains phenotypic, genetic, and epigenetic data from 29 <em>Serratia marcescens</em> strains from an evolution experiment. In a previous study (https://doi.org/10.1111/evo.12148), the bacterium <em>S. marcescens</em> was left to evolve from a common ancestor culture in replicated populations kept under different temperature regimes, and evolved clones were isolated and their phenotypes measured. Here, we randomly selected 28 evolved clones from this experiment, as well as the original reference strain, and used PacBio single molecule real-time (SMRT) sequencing to obtain genetic and epigenetic (N6-methyladenine modifications, m6A) data. The goal of our study was to obtain a detailed description of the methylation landscape of <em>S. marcescens</em> and to examine the potential contributions of genetic and epigenetic changes to phenotypic adaptation.</p>
Data for: Strong phenotypic trait correlations between mating partners do not result from assortative mating in wild great tits (Parus major)
<p>There is considerable debate about the occurrence of assortative mating between phenotypic traits measured within natural populations. Meta-analyses have implied that assortative mating occurs generally in natural populations but recent work indicates these conclusions largely result from biased data. Specifically, estimates of phenotypic correlations between mating partners do not solely result from non-random associations between individual-level traits of partners but also from other biological processes (joint phenotypic plasticity, indirect genetic effects), methodological practices (observer bias), and other unexplained residual correlations (e.g. correlated measurement error). This paper puts this critique to test. First, we estimated the overall phenotypic correlation between phenotypic traits of mating partners for a wild population of great tits. Second, we estimated various key variance components to reveal the extent to which phenotypic correlations between partners resulted from assortative mating, reversible plasticity, social partner effects, and methodological practices. We performed our analyses for a range of phenotypic traits (body mass, breathing rate, exploration behaviour, wing and tarsus length) to derive general conclusions not hinging on the specifics of the traits involved. Our analyses support the conclusion that patterns of assortative mating exist at first glance but occur because of the biasing effects of correlated residuals likely caused by a combination of phenotypic responses to unknown environmental factors or measurement error – not because of intrinsic patterns of assortative mating.</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.