Find research datasets worth reusing

opencc-zeroOct 2022View details →

Data and code for: Social phenotype-dependent selection of social environment in wild great and blue tits: An experimental study

There is growing evidence that individuals actively assess the match between their phenotype and their environment when making habitat choice decisions (so-called matching habitat choice). However, to our knowledge, no studies have considered how the social environment may interact with social phenotype in determining habitat choice, despite habitat choice being an inherently social process and growing evidence for individual variation in sociability. We conducted an experiment using wild great and blue tits to understand how birds integrate their social phenotype and social environment when choosing where and how to feed. We used programmable feeders to (i) record social interactions and estimate social phenotype and (ii) experimentally manipulate the local density experienced by birds of differing social phenotype. By tracking feeder usage, we estimated how social environment and social phenotype predicted feeder choice and feeding behaviour. Both social environment and social phenotype predicted feeder usage, but a bird's decision to remain in a particular social environment did not depend on their social phenotype. In contrast, for feeding behaviour, responses to the social environment depended on social phenotype. Our results provide rare evidence of matching habitat choice and shed light on the dependence of habitat choice on between-individual differences in social phenotype.

opencc-zeroApr 2024View details →

EST-SSR genotyping data from: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: Genetic, phenotypic, and environmental insights

Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.

opencc-zeroApr 2024View details →

Data from: Associations between developmental stability, canalization and phenotypic plasticity in plants with temporally heterogeneous environmental experience

We subjected eight plant species to a first round of alternating inundation and drought vs. constantly moderate water treatments and a second round of water conditions. Fluctuating asymmetry (FA), intra- and inter-individual variations (CVintra and CVinter), and plasticity in traits were measured and correlations between variables were calculated for each species. Early temporally heterogeneous experience decreased the leaf size of half of the species, but had complex effects on leaf fluctuating asymmetry (FA) and inter-individual variation (CVinter) in traits immediately or in late conditions, with little effects on intra-individual variation (CVintra). There were several positive correlations between FA and CVinter, while there were correlations between CVinter and plasticity in early treatments, but negative ones in late treatments.

opencc-zeroMay 2024View details →

Lack of assortative mating might explain reduced phenotypic differentiation where two grasshopper species meet

Hybridization is an evolutionary process with wide-ranging potential outcomes, from providing populations with important genetic variation for adaptation to being a substantial fitness cost leading to extinction. Here, we focussed on putative hybridization between two morphologically distinct species of New Zealand grasshopper. We collected Phaulacridium marginale and Phaulacridium otagoense specimens from a region where mitochondrial introgression had been detected and where their habitat had been modified by introduced mammals eating the natural vegetation and by the colonization of many non-native plant species. In contrast to observations in the 1970s, our sampling of wild pairs of grasshoppers in copula provided no evidence of assortative mating with respect to species. Geometric morphometrics on the pronotum shape of individuals from areas of sympatry detected phenotypically intermediate specimens (putative hybrids), and the distribution of phenotypes in most areas of sympatry was found to be unimodal. These results suggest that hybridization associated with anthropogenic habitat changes has led to these closely related species forming a hybrid swarm, with random mating. Without evidence of hybrid disadvantage, we suggest a novel hybrid lineage might eventually result from the merging of these two species.

opencc-by-4.0May 2024View details →

Rapid Inference of Antibiotic Susceptibility Phenotype of Uropathogens using Metagenomic Sequencing with Neighbour Typing - RASE Database for EuSCAPE

RASE databases used for the prediction of antibiotic phenotype in the paper titled "Rapid Inference of Antibiotic Susceptibility Phenotype of Uropathogens using Metagenomic Sequencing with Neighbour Typing". A database for Klebsiella pneuomiae constructed from EuSCAPE isolates.

opencc-zeroMay 2024View details →

Phenotypic characterization of Histoplasma species

Histoplasmosis is an endemic mycosis that often presents as a respiratory infection in immunocompromised patients. Hundreds of thousands of new infections are reported annually around the world. The etiological agent of the disease, Histoplasma, is a dimorphic fungus commonly found in the soil where it grows as mycelia. Humans can become infected by Histoplasma through inhalation of its spores (conidia) or mycelial particles. The fungi transitions into the yeast phase in the lungs at 37°C. Once in the lungs, yeast cells reside and proliferate inside alveolar macrophages. Genomic work has revealed that Histoplasma is composed of at least five cryptic phylogenetic species that differ genetically. Three of those lineages have received new names. Here we evaluated multiple phenotypic characteristics (colony morphology, secreted proteolytic activity, yeast size and growth rate) of strains from five of the phylogenetic species of Histoplasma to identify phenotypic traits that differentiate between these species: H. capsulatum sensu stricto, H. ohiense, H. mississippiense, H. suramericanum, and an African lineage. We report diagnostic traits for three species. The other two species can be identified by a combination of traits. Our results suggest that 1) there are significant phenotypic differences among the cryptic species of Histoplasma, and 2) that those differences can be used to positively distinguish those species in a clinical setting and for further study of the evolution of this fungal pathogen.

opencc-zeroMay 2024View details →

Data from: Symbiont infection and psyllid haplotype influence phenotypic plasticity during host switching events

Many herbivorous insect species exhibit phenotypic plasticity when using multiple hosts, which facilitates survival in heterogeneous host environments. Physiological host acclimation is an important part of it, yet the effects of host acclimation on insect feeding behavior are not well studied, particularly for insect vectors of plant pathogens. We studied the combined effects of host acclimation and infection with a plant pathogenic symbiont on feeding behavior of Bactericera cockerelli, an oligophagous psyllid widespread in both crop and natural habitats that feeds primarily on Solanaceae and transmits an economically important plant pathogen, Candidatus Liberibacter solanacearum (CLso). We used a factorial design and the electrical penetration graphing technique to disentangle the effects of host acclimation, CLso infection, and psyllid haplotype on the within-plant feeding behavior of B. cockerelli during conspecific and heterospecific host switches. This approach allows to connect phenotypic plasticity with the role of B. cockerelli as a vector by quantifying the frequency and duration of behaviors involved in CLso transmission. We found significant reductions in multiple metrics of B. cockerelli feeding efficiency, exacerbated by infection with CLso, which could lead to reduced transmission of this pathogen. Psyllid genotype was also important; the Central haplotype exhibited less dramatic changes in feeding efficiency than the Western haplotype during heterospecific host switches. Our study shows that host acclimation and heterospecific host switching directly alter feeding behaviors underlying pathogen transmission, and that the magnitude of feeding efficiency reductions depends on both host genotype and infection status.

opencc-by-4.0May 2024View details →

Diseasome - Finding disease association based on Phenotypic and Genotypic clustering

The final processed phenotypic clustered data (output.zip) from Orphanet is also added along side the genotypic clustering data.

opencc-by-4.0May 2024View details →

Fluid flow drives phenotypic heterogeneity in bacterial growth and adhesion on surfaces

Raw data for the study reported by Hubert et al., Nature Communications 2024 (accepted). Each of the 4 folders within the archive, denoted 'Ulow', 'Low', 'Med', and 'High' contains 3 sets of raw experimental data, each corresponding to an experiment performed in the 'Ulow', 'Low', 'Med', and 'High' shear stress regime, in accordance with the folders' names. Each of these data sets is bundled into a single .avi video, consisting of raw images recorded at a 1/60 Hz acquisition frequency (i.e., 1 image per minute). The folder 'Supplementary_Software'contains Matlab and Python scripts used to treat the raw data, with a raw data sample. The file 'HOWTO_use_the_scripts.txt' explains how to use the scripts. Except for this HOWTO file, the files inside the various subfolders of folder 'Supplementary_Software' are not listed in the file tree below. Only the subfolders are listed. ./ ├── README_data_sets_and_treatment_scripts.txt (this file) ├── Ulow/  |     ├── Ulow_set1.avi  |     ├── Ulow_set2.avi  |     └── Ulow_set3.avi ├── Low/  |     ├── Low_set1.avi  |     ├── Low_set2.avi  |     └── Low_set3.avi ├── Med/  |     ├── Med_set1.avi  |     ├── Med_set2.avi  |     └── Med_set3.avi └── High/  |     ├── High_set1.avi  |     ├── High_set2.avi  |     └── High_set3.avi └── Supplementary_Software/     ├── HOWTO_use_the_scripts.txt     ├── step1_matlab/       |     ├── Pos0_100_every_1000/       |     ├── matlab_image_processing/       |     ├── images_treated_20201120_220854/       |     └── Outputs/     └── step2_python/             └── Outputs/

opencc-by-4.0Aug 2021View details →

Data and code for phenotypic, genetic and distribution analyses of the parthenogenetic grasshopper Warramaba virgo and its sexual progenitors

Includes raw data on phenotypic traits (critical thermal maximum, chill coma recovery, water loss and metabolic rate vs. temperature, mass of eggs, hatchlings and females, clutch sizes and lifetime reproductive output, development time, time to maturity, longevity), molecular traits (SNP, COI and microsatellite data) and distribution as well as code to analyse them.

Data from: Phenotypically plastic responses to environmental variation are more complex than life history theory predicts

For insects that exhibit wing polyphenic development, abiotic and biotic signals dictate the adult wing morphology of the insect in an adaptive manner such that in stressful environments the formation of a flight-capable morph is favored and in low stress environments a flightless morph is favored. While there is a relatively large amount known about the environmental cues that dictate morph formation in wing polyphenic hemipterans like planthoppers and aphids, whether those cues dictate the same morphs in non-hemipteran (i.e. cricket) wing polyphenic species has not been explicitly investigated. To experimentally test the generality of environmental cue determination of wing polyphenism across taxa with diverse life histories, in this study we tested the importance of food quantity, parasitic infection, and tactile cues on wing morph determination in the wing polyphenic sand field cricket, Gryllus firmus. Our results also show that certain stress cues, such as severe diet quantity limitation and parasitic infection, actually led to an increase in the production of flightless morph. Based on these findings, our results suggest that physiological and genetic constraints are important to an organism's ability to respond to environmental variation in an adaptive manner beyond simple life history trade-offs.

opencc-by-4.0Aug 2019View details →

Dataset 2. Variant Distribution of Majority Molecular Phenotype Classifications Relative to All Classifications

A variant may occur in multiple individuals, tissue types, or splice sites. A consensus (majority) molecular phenotype classification for the variant is displayed on ValidSpliceMut, generated by observing all affected cases and associated classifications. For each expression validated variant, the phenotypes are classified as per Figure 2 of Shirley et al. 2019  (<a href="https://doi.org/10.12688/f1000research.17204.3" target="_blank" rel="noopener">https://doi.org/10.12688/f1000research.17204.3</a>). The bins on the horizontal axis of these histograms represent the count of splicing variants with the most frequent classification divided by the total number of cases affected by a variant. Bar height represents the number of variants having the majority classification within the appropriate bin.  Below each histogram is a table that describes the distribution of majority molecular phenotypes in each bin. The three bins consist of mutations designated as variants that cause allele-specific alternative splicing (category 1), those that are likely aberrant (category 2) and mutations that are aberrant (category 3). For a full description of how these molecular phenotype classifications are determined, see Shirley et al. 2019. Figure 2 of the paper describes the algorithm we use to ensure that variants with no effect on splicing have been eliminated previous to this analysis. To gain more information about the mutations in a particular bin, an  data file has been provided for each of these figures. To identify which mutations occur in each bin, sort the data file in order of the `%Mol_Phenotype` column which was used to designate histogram bins. Once a mutation of interest has been found, download <a href="../records/3522192">Dataset 1 on Zenodo</a> (Filename: ‘ValidSpliceMut_TabDelimited_v4.txt’) and search for the mutation (mutation names will be identical). The mutation will appear in Dataset for however many patients the mutation was identified in (from the TCGA and ICGC Cancer Projects). From Dataset 1, users can acquire the mutation’s associated gene, its position within a gene, the Information-Theory based prediction that the mutation would have  on splicing, and the given evidence of splicing using the <a href="https://f1000research.com/articles/3-8">Veridical algorithm</a>. The latter provides how many reads were found in RNAseq data that supported an aberrant splicing event (exon skipping, intron inclusion, etc). Files/archives provided: 1 Supplementary figure to Shirley et al. F1000Research 2019, 7:1908. Dataset 2 contains six histograms and supporting tables (generated with GraphPad Prism v6.0). A variant may occur in multiple individuals, tissue types, or splice sites. Histogram bins show the fraction of  splicing molecular phenotype classifications relative to the major consensus phenotype among all cases for variants that are present  in at least 2, 3, 5, 10, 15, and 20 different tissue types. 2. Aggregated variant data/consensus phenotypes used to generate histograms, including tissue types. 3.  Software to generate histograms from variants validated in Dataset 1 (DOI <a href="../doi/10.5281/zenodo.1488210">10.5281/zenodo.1488210</a>).

opencc-by-4.0Oct 2013View details →

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.

Genotype data for 88 African American indviduals in binary PLINK format published in  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

Phenotyping data from: Genetics of phenological development and implications for seed yield in lentil

Using a historic collection of Australian lentil varieties released between 1988 and 2019, we show that genetic gain in yield (29 kg ha-1 yr-1) associates with faster reproductive development. A focus on five loci related to reproductive development, the lentil ELF3 ortholog Sn, two loci linked to clusters of lentil FT 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.

Phenotypic and genotypic analysis of drug resistance in M. tuberculosis isolates in Gansu, China

Tuberculosis has posed a serious threat to human health. It is imperative to investigate the geographic prevalence of tuberculosis and medication resistance, as this information is essential for informing strategies for its prevention and treatment. Drug resistance was identified using a proportion method. Drug-resistant genes and pathways were predicted using whole genome sequencing. The drug resistance range of bedaquiline was identified using the microporous plate two-fold dilution method, and drug resistance genes were studied using sequencing. The study revealed that 19.99% of the tuberculosis cases had multidrug resistance. The genes of M. tuberculosis are predominantly involved in the synthesis of ABC transporters, two-component systems, and bacterial secretion systems, as well as in energy production and conversion, and lipid transport and metabolism. The genes encode for 82.45% of carbohydrate-related enzymes such as glycoside hydrolases, glycosyl transferases, and carbohydrate esterases. The minimum inhibitory concentration (MIC) of bedaquiline against clinical strains was approximately 0.06 μg/mL, with identified mutations in drug-resistant genes Rv0678, atpE, and pepQ, specifically V152A, P62A, and T222N, respectively. The multidrug resistance tuberculosis development was attributed to the strong medication resistance exhibited. It was concluded that tuberculosis had presented a high level of drug resistance. Phenotypic resistance was related to genes, existing potential genetic resistance in M. tuberculosis. Bedaquiline was found to possess effective antibacterial properties against M. tuberculosis.

Data from: The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

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 R. imitator and two color morphs from both R. fantastica and R. variabilis which R. imitator 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 qdpr and xdh) 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., cd36, ep-cadherin, perlwapin). Finally, we hypothesize that keratin genes (e.g., krt8) are important for producing different structural colors within these frogs.

An efficient CRISPR-mediated genome editing system in diploid and polyploid Tragopogon (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution

Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of Tragopogon and obtained genome-edited T. porrifolius (2x) and T. mirus (4x) primary generation (T0) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (DFR) gene, which controls anthocyanin synthesis, in both T. porrifolius and T. mirus. All transgenic allotetraploid T. mirus individuals had at least one mutant DFR allele and 71.4% of the plants had all four DFR alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid Tragopogon. The anticipated absence of the anthocyanin was observed in both leaf and floral tissues from T. porrifolius and T. mirus mutants. In addition, the mutations were inherited in the T1 generation. This study demonstrates a highly efficient CRISPR platform producing genome-edited Tragopogon individuals that have successfully completed their life cycle. The approaches used and challenges faced in building the CRISPR system in Tragopogon provide a framework for building similar systems in other nongenetic models. Genome editing in Tragopogon paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, which holds enormous potential for both basic and applied research.

opencc-by-4.0Jun 2016View details →

Fig. 2 in Depigmented phenotypes inside a Salamandrina perspicillata population of the Campagna Romana (Latium, Italy)

Fig. 2 - Fosso del Barco course inside Macchia del Barco.

opencc-by-4.0Jun 2016View details →

Fig. 4 - Individuals 01-08 in Depigmented phenotypes inside a Salamandrina perspicillata population of the Campagna Romana (Latium, Italy)

Fig. 4 - Individuals 01-08: ventral view.