Find research datasets worth reusing

opencc-zeroApr 2024View details →

Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale

Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the Late Miocene and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity due to them experiencing stronger environmental seasonality than forest species. We quantified seasonality using environmental niche modelling, and surveyed the degree of plasticity in a key wing pattern element (eyespot size) using museum specimens. We show that species occurring in highly seasonal environments display strong plasticity, while species in less seasonal or aseasonal environments exhibit surprisingly variable degrees of plasticity, including strong to no plasticity. Furthermore, eyespot size plasticity has a moderate phylogenetic signal and the ancestral Bicyclus likely exhibited some degree of plasticity. We propose hypotheses to explain the range of plasticity patterns seen in less seasonal environments, and generate testable predictions for the evolution of plasticity in Bicyclus. Our study provides one of the most compelling cases showing links between seasonality and phenotypic plasticity on a macroevolutionary scale and the potential role of plasticity in facilitating the colonization of novel environments.

opencc-zeroApr 2024View details →

Data from: Phenotypic plasticity and the effects of thermal fluctuations on specialists and generalists

Classical theories predict that relatively constant environments should generally favor specialists, while fluctuating environments should select for generalists. However, theoretical and empirical results have pointed out that generalist organisms might on the contrary perform poorly under fluctuations. In particular, if generalism is underlaid by phenotypic plasticity, performance of generalists should be modulated by the temporal characteristics of environmental fluctuations. Here, we used experiments in microcosms and a mathematical model to test whether the period or autocorrelation of thermal fluctuations mediate links between the level of generalism and the performance of organisms under fluctuations. In the experiment, thermal fluctuations consistently impeded performance compared to constant conditions. However, the intensity of this effect depended on the level of generalism: while the more specialists strains performed better under fast or negatively autocorrelated fluctuations, plastic generalists performed better under slow or positively autocorrelated fluctuations. Our model suggests that these effects of fluctuations on organisms' performance may result from a time delay in the expression of plasticity, restricting its benefits to slow-enough fluctuations. This study points out the need to further investigate the temporal dynamics of phenotypic plasticity to better predict its fitness consequences under environmental fluctuations.

opencc-by-4.0Apr 2024View details →

Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome

DIfferential splicing analysis dataset generate using MAJIQ v2.5.1 pipeline accompanying the following manuscript: Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome.

opencc-by-4.0Apr 2024View details →

Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data

This repository contains raw and processed data of the original datasets generated for Lee et al. "Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data". The files Dilution_3_ROI02.ome.tiff, Dilution_3_ROI02_mask.ome.tiff, st_reclustered_expr_data.h5ad contain raw data (as ome tiff), a mesmer-generated segmentation mask, and single-cell quantification in anndata format of the cell pellet data generated for the study. The file tonsil-for-zenodo.tar.gz contains all raw and processed data of the IMC data of the 16 human tonsil ROIs: <ul> <li>imc contains raw tiff stacks of the acquisition</li> <li>mask contains mesmer-generated masks</li> <li>channel.yml contains channel info</li> <li>exp_mat/dc/ contains single cell quantifications using mesmer segmentation</li> </ul>

opencc-by-4.0Nov 2024View details →

Chromosomal instability degrades developmental phenotypes essential for anti-GD2 immunotherapy outcomes in high-risk neuroblastoma

Childhood Cancer Data Initiative (CCDI) dbGaP Study Accession: phs002431

opencc-by-sa-4.0Nov 2024View details →

Wheat breeding phenotyping and yield dataset

This is a wheat breeding phenotyping and yield dataset, including canopy height (CH, m), canopy volume (CV, m3), and leaf area index (LAI) collected in the field; vegetation index (VI) generated by multispectral data acquired by UAV remote sensing; trial site weather (Weather); and yield (Yield, kg). The data comes from field trials. Data acquisition and processing are described in the relevant part of the manuscript. This dataset will be continuously updated in the future to help breeders carry out their work efficiently and accelerate the breeding process of excellent varieties.

opencc-by-4.0Jun 2024View details →

E. coli ribosome phenotypes for antimicrobial susceptibility testing

This repository contains the anonymised images, masks, and metadata for "Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing in Escherichia coli". Code for training neural networks using these images can be found at <a href="https://github.com/KapanidisLab/ribosome_phenotype_classification">https://github.com/KapanidisLab/ribosome_phenotype_classification</a>. The data contains fluorescence microscopy images of E. coli MG1655 and clinical isolates, details of which can be found in the manuscript.

opencc-by-4.0Aug 2024View details →

Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes

Dataset of multi-well plate reader files related to the analysis of the growth of C. difficile isolates on differnet carbon substrates.  Data Collection. This dataset accompanies an mSystems article which is available at <a href="https://doi.org/10.1128/msystems.01075-24">https://doi.org/10.1128/msystems.01075-24</a>. The "Materials and Methods" section in this article fully describes the biological nature of these samples and how the samples were processed and analyzed.   Repository Content. The amiga folders contains both the raw data (see data and mapping sub-folders), intermediate outpus (see dervied sub-folders), and final outputs (see figures and summary sub-folders). Each amiga folder corresponds to a single working directory analyzed by the <a href="https://github.com/firasmidani/amiga">AMiGA</a> software. For the amiga-biolog directory, the notes sub-folder also includes text files related to flagging plates and wells for quality issues. Data Organization. Growth plate data are organized by the following experiments.  <ul> <li>biolog</li> <li>validation</li> <li>ribotype-255</li> <li>clade-5</li> <li>yeast-extract-biolog</li> <li>yeast-extract-validation</li> </ul> Data Analysis. Code used for manipulating and analyzing these samples is also publicly available on GitHub (<a href="https://github.com/firasmidani/cdiff-biolog-growth">https://github.com/firasmidani/cdiff-biolog-growth</a>) under the GNU GPL-3.0 license. The scripts in "analyze-code" can be used to analyze all data and the scripts in the "generate-figures" folder can be used to reproduce all figures included in the manuscript. See the GitHub repository for instructions on how to do so.

opencc-by-4.0May 2024View details →

Data from: Genomic, phenotypic, and environmental correlates of speciation in the midwife toads (Alytes)

This package includes the following :  <ul> <li>A matrix of 5,111 SNPs genotyped in the subgenus Alytes (Ao_complex_5111loci.str)</li> <li>A matrix of 3,535 SNPs genotyped in A. o. lusitanicus, A. o. pertinax and A. cisternasii (OC_3535loci.str)</li> <li>A matrix of 15,211 SNPs genotyped in A. o. pertinax and A. dickhilleni (OD_15211loci.str)</li> <li>SNP matrices (.str), Q estimates and environemental suitability estimates (Q_transect_xxx.txt), distances along transects (dist_transect_xxx.txt), hzar inputs (Input_HZ_xxx.csv), lists of diagnostic loci (HZ_xxx_diag_loci.csv) and R commands (HZ_xxx.r), as used to analyze the hybrid zones coded as CAN, HUE, POR, MAD, GAL, PYR</li> <li>Locus-by-locus cline parameters for the eight hybrid zones considered (Clines_HZ_xxx.csv) and R commands used for vizualization (Clines.Display.r)</li> <li>Occurrence records of Alytes (Occurence_dataset.csv)</li> <li>Bioacoustic dataset (Bioacoustic_dataset.csv), and the R commands used for analyses (Bioacoustics.r)</li> <li>Morphometric dataset, including raw measurements (Morphometric_dataset.csv), the input file for GroupStruct (Morphometric_dataset_naked.csv), the size-corrected measurements (Morphometric_dataset_corrected.csv), and the R commands used for analyses (Morphometrics.r)</li> <li>Environemental dataset (Environemental_dataset.csv), and the R commands used for analyses (Environmental.r)</li> </ul>

opencc-zeroOct 2021View details →

Habitat fragmentation induces rapid phenotypic divergence of migratory and isolated sticklebacks

The adaptive capacity of many organisms is seriously challenged by human-imposed environmental change, which currently happens at unprecedented rates and magnitudes. For migratory fish, habitat fragmentation is a major challenge that can compromise their survival and reproduction. Therefore, it is important to study if fish populations can adapt to such modifications of their habitat. Here, we study whether originally anadromous three-spined stickleback populations (Gasterosteus aculeatus; 'migrants') changed in behavior and morphology in response to human-induced isolation. We made use of a natural field-experiment, where the construction of pumping stations and sluices in the 1970s unintendedly created replicates of land-locked stickleback populations ('resident') in the Netherlands. For two years, we systematically tested populations of residents and migrants for differences in morphology and behavioral traits (activity, aggressiveness, exploration, boldness and shoaling) in lab-based assays. We detected differences between migrant and resident populations in virtually all phenotypic traits studied: compared to the ancestral migrants, residents were smaller in size, had fewer and smaller plates and were significantly more active, aggressive, exploratory and bolder and shoaled less. Despite large ecological differences between 2018 and 2019, results were largely consistent across the two years. Our study shows that human-induced environmental change has led to the rapid and consistent morphological and behavioral divergence of stickleback populations in about 50 generations. Such changes may be adaptive but this remains to be tested.

opencc-zeroOct 2021View details →

Data from: Axes of multivariate sexual signal divergence among incipient species: concordance with selection, genetic variation, and phenotypic plasticity

Sexual signaling traits are often observed to diverge rapidly among populations, thereby playing a potentially key early role in the evolution of reproductive isolation. While often assumed to reflect divergent sexual selection among populations, patterns of sexual trait diversification might sometimes be biased along axes of standing additive genetic variation and covariation among trait components. Additionally, theory predicts that environmentally-induced phenotypic variation might facilitate rapid trait evolution, suggesting that patterns of divergence between populations should mirror phenotypic plasticity within populations. Here we evaluate the concordance between observed axes of multivariate sexual trait divergence and predicted divergence based on (1) interpopulation variation in sexual selection, (2) additive genetic variances, and (3) temperature-related phenotypic plasticity in male courtship song among geographically isolated populations of the Hawaiian swordtail cricket, Laupala cerasina, which exhibit sexual isolation due sexual signaling traits. The major axis of multivariate divergence, dmax, accounted for 76% of variation among population male song trait means, and was moderately correlated with interpopulation differences in directional sexual selection based on female preferences. However, the majority of additive genetic variance was largely oriented away from the direction of divergence, suggesting that standing genetic variation may not play a dominant role in the patterning of signal divergence. In contrast, the axis of phenotypic plasticity strongly mirrored patterns of interpopulation phenotypic divergence, which is consistent with a role for temperature-related plasticity in facilitating instead of inhibiting male song evolution and sexual isolation in these incipient species. We propose potential mechanisms by which sexual selection might interact with phenotypic plasticity to facilitate the rapid acoustic diversification observed in this species and clade.

opencc-zeroNov 2021View details →

Data From: Fit and fatty freshwater fish: Contrasting polyunsaturated fatty acid phenotypes between hybridizing stickleback lineages

Long-chain polyunsaturated fatty acids are biologically important lipids that are unevenly distributed between and throughout environments. This heterogeneity can affect the evolution of metabolic processes, as populations adapt to the resource landscape that they encounter. Here, we compare fatty acid phenotypes of stickleback over two time scales of evolutionary divergence: between two lineages with different metabolic capacities for fatty acid synthesis (i.e. different copy number of the fatty acid desaturase gene; FADS2) that independently colonized European freshwaters during the Pleistocene and Holocene; and between two ecotypes within each lineage that have diverged more recently (~150 years) in different habitats (i.e. lake and stream). We measured fatty acid profiles of wild-caught and lab-reared fish for each lineage and ecotype combination after rearing lab fish on a diet deficient in omega-3 long-chain polyunsaturated fatty acids. Since these lineages hybridize in nature, we also measured profiles of lab-reared hybrids and backcrosses raised on the same deficient diet. Wild fish showed strong compositional differences in fatty acids between habitats, lineages, and sexes. Common garden fish had generally lower polyunsaturated fatty acid levels than wild fish, and females had lower omega-6:omega-3 than males. Fish from the lineage with fewer FADS2 copies also had lower levels of docosahexaenoic acid. Overall, we document divergence in fatty acid phenotypes between stickleback lineages with different histories of freshwater colonization, and between ecotypes in the early stages of adaptive population divergence.

opencc-zeroNov 2021View details →

Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae

The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: Berndtia and Thoracica: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear-phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts. Key words: adaptive host invasion, larval phenotypes, coral barnacle, barnacle phylogeny

opencc-zeroNov 2021View details →

Phenotype and QTL mapping data from: Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover

Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defense polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (Trifolium repens). This widespread species displays a well-studied chemical defense polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F2 mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL X E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL co-localization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favored early investment in flowering at the cost of multi-year survival in the southernmost site vs. delayed flowering and multi-year persistence in the northern environments. Our findings demonstrate that multi-locus genetic tradeoffs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.

opencc-by-4.0Apr 2021View details →

Transposable elements mark a repeat-rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus).

This upload contains the relevant data (alignments, trees, html TE landscape files, and datasheets) used in the manuscript: "The importance of repeat-rich regions in the migratory phenotypes of the willow warbler (Phylloscopus trochilus): transposable elements as a marker."

Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species

The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in Primula vulgaris and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (CYPᵀ), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in CYPᵀ. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in P. vulgaris. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.

Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism

Locusts exhibit one of nature's most spectacular examples of complex phenotypic plasticity, in which changes in density cause solitary and cryptic individuals to transform into gregarious and conspicuous locusts forming large migrating swarms. We investigated how these coordinated alternative phenotypes might have evolved by studying the Central American locust and three closely related non-swarming grasshoppers in a comparative framework. By experimentally isolating and crowding during nymphal development, we induced density-dependent phenotypic plasticity and quantified the resulting behavioural, morphological, and molecular reaction norms. All four species exhibited clear plasticity, but the individual reaction norms varied among species and showed different magnitudes. Transcriptomic responses were species-specific, but density-responsive genes were functionally similar across species. There were modules of co-expressed genes that were highly correlated with plastic reaction norms, revealing a potential molecular basis of density-dependent phenotypic plasticity. These findings collectively highlight the importance of studying multiple reaction norms from a comparative perspective.

Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high elevation hypoxia

In response to a warming climate, many montane species are shifting upslope to track the emergence of preferred temperatures. Characterizing patterns of variation in metabolic, physiological and thermal traits along an elevational gradient, and the plastic potential of these traits, is necessary to understand current and future responses to abiotic constraints at high elevations, including limited oxygen availability. We performed a transplant experiment with the upslope-colonizing common wall lizard (Podarcis muralis) in which we measured nine aspects of thermal physiology and aerobic capacity in lizards from replicate low- (400 m above sea level, ASL) and high-elevation (1700 m ASL) populations. We first measured traits at their elevation of origin and then transplanted half of each group to extreme high elevation (2900 m ASL; above the current elevational range limit of this species), where oxygen availability is reduced by ∼25% relative to sea level. After 3 weeks of acclimation, we again measured these traits in both the transplanted and control groups. The multivariate thermal–metabolic phenotypes of lizards originating from different elevations differed clearly when measured at the elevation of origin. For example, high-elevation lizards are more heat tolerant than their low-elevation counterparts (counter-gradient variation). Yet, these phenotypes converged after exposure to reduced oxygen availability at extreme high elevation, suggesting limited plastic responses under this novel constraint. Our results suggest that high-elevation populations are well suited to their oxygen environments, but that plasticity in the thermal–metabolic phenotype does not pre-adapt these populations to colonize more hypoxic environments at higher elevations.

Phenotypic and Genetic data for "Evolution of fruit and seed traits during almond naturalization"

1- Cultivated plant species often naturalize and enter wild communities in a process known as feralization. To successfully feralize, crops must overcome ecological barriers and may undergo selection on certain traits, diverging phenotypically and genetically from their crop ancestors. In spite of the agronomic and ecological relevance of crop feralization, the eco-evolutionary dynamics driving it remain understudied. 2- In this paper, we evaluated phenotypic and genotypic differentiation in fruit and seed traits during the naturalization of the almond tree (Prunus dulcis (Mill.) D.A. Webb) in SE Iberia and evaluated the potential role of natural selection in this process. To do so, we investigated patterns of genetic divergence between cultivated and feral populations using functional (the cyanogenesis Sk gene) and neutral (17 SSR loci) markers and analyzed morphological and biochemical traits in kernels of 342 individuals from 15 cultivated and 24 feral populations. 3- We detected very little genetic differentiation in neutral markers between cultivated and feral populations. The majority of the observed genetic variation was due to differences within each type. Conversely, the recessive allele sk responsible for seed toxicity was significantly more frequent in feral populations. Phenotypic differentiation between cultivated and naturalized almond populations was also significant. Feral almond kernels were smaller and lighter, had denser and more resistant shells (endocarps) and more toxic seeds. Selection analyses indicated that these genetic and phenotypic patterns might be driven by directional selection on fruit and seed traits, potentially linked to defense against predation. 4- Synthesis. Our findings indicate that almond naturalization is consistent with strong directional selection on fruits and seeds, leading to smaller and more toxic seeds encased in harder endocarps. Accordingly, we propose that feralization of this crop is, at least to some degree, driven by adaptive evolution of dispersal and recruitment traits.