Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk

sushie.molqtl.weights.tar.gz contains ancestry-specific eQTL and pQTL weights trained on mRNA and protein levels measured in American European, American African, and American Hispanic ancestries from TOPMed-MESA and GENOA studies. Column “a1” is the counting allele. mesa.*.fusion.tar.gz contains the weights in FUSION format. sushie_real_data_results.tar.gz contains all the real data analyzed in the sushie project. sushie_sim_data_results.tar.gz contains all the sim data analyzed in the sushie project. sushie_analysis_codes.tar.gz contains all the codes and scripts to generate and analyze these data.

opennotspecifiedAug 2024View details →

Animal Diversity Web: ADW Traits & image objects from Quaardvark Tool

This morphometry and life history dataset for size characteristics of birds is from undergraduate students who contributed to the Animal Diversity Web. Traits and images are harvested using ADW__s Quaardvark data download tool.

opencc-zeroOct 2023View details →

The effects of water-stress, temperature, and plant traits on the outbreak potential of a specialist and generalist spider mite species (Acari: Tetranychidae)

The host-generalist two-spotted spider mite [Tetranychus urticae (Acari: Tetranychidae); TSM] and host-specialist Banks grass mite [Oligonychus pratensis (Acari: Tetranychidae); BGM] are common pests of corn (Zea mays L.) in the arid western United States. Climate warming and decreased precipitation may promote conditions favored by these spider mites. However, rapid evolution of spider mite resistance to commercially available acaricides is driving the need for alternative solutions for managing outbreaks. Planting of drought-tolerant corn hybrids has been proposed to be a dual-purpose strategy for mitigating water deficits for irrigation and reducing leaf conditions favorable for BGM outbreaks. However, understanding of the mechanisms responsible for reducing the BGM in the field is lacking, and determining whether outbreaks of the TSM can also be averted using drought-tolerant corn is a pressing concern. We conducted a two-year field study testing a drought-tolerant corn hybrid and an analogous drought-susceptible hybrid under water-stress with artificially-infested spider mite populations. Drought-tolerant corn had larger stem diameter, more massive cobs, and greater leaf water mass compared to the drought-susceptible corn under water stress. We also found that the BGM populations were reduced on drought-tolerant plants under water-stress, as expected, but we found an opposite trend in the TSM. Lastly, water-stressed leaves were warmer, transpired less, and had higher carbon concentration, which contributed to larger investment in eggs and growth in the BGM. We anticipate that further evaluation of irrigation and crop drought-tolerance in management of agriculture systems for multiple pest species will be increasingly impactful in arid regions.

opencc-zeroOct 2023View details →

Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits

Shade tolerance is a central concept in forest ecology and strongly influences forest community dynamics. However, the plant traits and conditions conferring shade tolerance are yet to be resolved. We propose that shade tolerance is shaped not only by responses to light but also by a species' defense and recovery functional traits, soil microbial communities, and interactions of these factors with light availability. We conducted a greenhouse experiment for three temperate species in the genus Acer that vary in shade tolerance. We grew newly germinated seedlings in two light levels (2% and 30% sun) and controlled additions of microbial filtrates using a wet-sieving technique. Microbial filtrate treatments included: <20 µm, likely dominated by pathogenic microbes; 40-250 µm, containing arbuscular mycorrhizal fungi (AMF); combination, including both filtrate sizes; and sterilized combination. We monitored survival for nine weeks and measured fine root AMF colonization, hypocotyl phenolics, stem lignin, and stem+root nonstructural carbohydrates (NSC) at three-week intervals. We found that differences in seedling survival between low and high light only occurred when microbes were present. AMF colonization, phenolics, and NSC generally increased with light. Phenolics were greater with <20 µm microbial filtrate, suggesting that soil-borne pathogens may induce phenolic production and NSC was greater with 40-250 µm filtrate, suggesting that mycorrhizal fungi may induce NSC production. Across species, microbe treatments, and light availability, survival increased as phenolics and NSC increased. Therefore, shade tolerance can be explained by interactions among soil-borne microbes, seedling traits, and light availability, providing a more mechanistic and trait-based explanation of shade tolerance and thus forest community dynamics.

opencc-by-nc-2.5Oct 2023View details →

STraDa: A Singer Traits Dataset

What is STraDa? STraDa is a dataset that was presented at the late breaking demo session of ISMIR 2023. The detailed description of the dataset is in README.md. STraDa is large-scale music audio dataset that contains singers' metadata, tracks' metadata, IDs for downloading audios of 30s (preview parts) by using <a href="https://developers.deezer.com/api">Deezer API</a>. This dataset could be used for various MIR tasks, such as singer identification, singer recognition, singer gender/age detection, genre classification, language classification. The training set contains 25194 excerpts of 30s, and 5264 singers. The testing set contains 200 songs from 200 singers that are balanced across two genders, 5 languages and 4 age groups (5 song/gender/language/age group), that could be used for bias analysis.   What does STraDa contain? An important feature of STraDa is that each track only has a single lead singer, which improves the accuracy of annotations. The annotations in the training set are gathered and cross-validated from 4 different data sources: <a href="https://www.deezer.com/en/">Deezer</a>, <a href="https://www.wikidata.org/wiki/Wikidata:Main_Page">Wikidata</a>, <a href="https://musicbrainz.org">musicbrainz</a>, <a href="https://www.discogs.com">discogs</a>.  The testing set is curated and annotated manually to ensure perfect accuracy. Singers' metadata contains gender, birth year and active country. Tracks' metadata contains genre, language and release date.   What could STraDa be used for? STraDa could be used for singer identification, singer recognition, singer gender/age detection, song genre/language identification. The balance in the testing set could enable bias analysis.   Dataset use This dataset is only available for conducting non-commercial research related to audio analysis under license Creative Commons Attribution Non Commercial 2.5 Generic. It's important to note that data under this license are data contained in STraDa, not applicable to audios. We do NOT grant permission for any modification, generation or manipulation using these audios. We wholeheartedly welcome researchers to use STraDa for their own research purpose. Please send an email to ykong@deezer.com if you have any questions about the data. Citation If you use STraDa, please cite following paper: <pre>@inproceedings{kong2024stradasingertraitsdataset, title={STraDa: A Singer Traits Dataset}, author={Yuexuan Kong and Viet-Anh Tran and Romain Hennequin}, booktitle={Interspeech 2024}, year={2024} }</pre>

Data from: Functional trait plasticity diverges between sexes in African cichlids: a contribution toward ecological sexual dimorphism?

Phenotypic plasticity enables development to produce multiple phenotypes in response to environmental conditions. Plasticity driven variation has been suggested to play a key role in adaptive divergence, and plasticity itself can evolve. However, the interaction of plasticity with the multiple levels involved with adaptive divergence is less understood. For example, sexual dimorphism can contribute to adaptive variation through ecological sexual dimorphism (ESD), but the contribution of plasticity to this phenomenon is unknown. Therefore, to determine the potential contribution of plasticity to ESD, we used the adaptive radiation of Malawi cichlids. Two mouthbrooding species (Labeotropheus fuelleborni and Tropheops "Red Cheek", hereafter LF and TRC respectively) with differences in foraging tactics underwent foraging experiments using benthic and limnetic treatments while accounting for sex. Plasticity in craniofacial shape and three functionally important traits were measured. Plasticity was shown, but without any sex-based differences in shape. However, for mechanical advantage traits of the mandible sex by diet interactions were found. This suggests that ESD, may be influenced by phenotypic plasticity that diverges between sexes. Given the involvement of the mandible in parental care in cichlids this may indicate that sexual divergence in plasticity may trade-off against maternal care tactics.

Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech

Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1,087 adult trees, seeds, one-year-old seedlings, and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilising selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.

Trait data for common garden Primula elatior

<ol> <li>Climate change and the resulting increased drought frequencies pose considerable threats to forest herb populations, particularly where additional environmental challenges jeopardize responses to selection. Specifically, habitat fragmentation may impede climate adaptation through its impact on the distribution of adaptive genetic variation, and cause evolutionary shifts in mating systems. </li> <li>To assess how habitat fragmentation disrupts climate adaptation, we conducted a common garden experiment with Primula elatior offspring originating from 24 populations sampled along a latitudinal gradient with varying climate and landscape characteristics. We then quantified a range of vegetative, regulatory, and reproductive traits under distinct soil moisture regimes to evaluate imprints of local adaptation and phenotypic plasticity. Additionally, we conducted a more extensive field campaign in 60 populations along the same latitudinal gradient to evaluate the potential evolutionary breakdown of reciprocal herkogamy.</li> <li>For large, connected populations, our results demonstrated an evolutionary shift from a strategy in southern populations that seems aligned with drought avoidance — where plants minimize their exposure to dry conditions and optimize photosynthesis — to a drought tolerance strategy in northern populations, where plants adapted to function despite water scarcity. However, habitat fragmentation disrupted climate clines and the adaptive responses to drought stress in key traits related to growth, biomass allocation and water regulation. Additionally, our findings indicate the onset of evolutionary breakdown in reciprocal herkogamy and divergence in other key flower traits. The disruption of climate clines, drought responses, and adaptations in mating systems contributed to a substantially diminished flowering investment across the distribution range, with the most pronounced effects observed in southern fragmented populations. </li> <li> Synthesis: We present novel empirical evidence of how habitat fragmentation disrupts climate adaptation and drought tolerance in a wide range of traits along the range of the forest herb Primula elatior. These findings emphasize the need to account for habitat fragmentation while designing effective conservation strategies in order to preserve and restore resilient meta-populations of forest herbs amidst ongoing global changes.</li> </ol>

Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability

Though not often examined together, both plant-soil feedbacks (PSFs) and functional traits have important influences on plant community dynamics and could interact. For example, seedling functional traits could impact seedling survivorship responses to soils cultured by conspecific versus heterospecific adults. Furthermore, levels of functional traits could vary with soil culturing source. In addition, these relationships might shift with light availability, which can affect trait values, microbe abundance, and whether mycorrhizal colonization is mutualistic or parasitic to seedlings. To determine the extent to which functional traits mediate PSFs via seedling survival, we conducted a field experiment. We planted seedlings of four temperate tree species across a gradient of light availability and into soil cores collected beneath conspecific (sterilized and live) and heterospecific adults. We monitored seedling survival twice per week over one growing season, and we randomly selected subsets of seedlings to measure mycorrhizal colonization and phenolics, lignin, and NSC levels at three weeks. Though evidence for PSFs was limited, Acer saccharum seedlings exhibited positive PSFs (i.e., higher survival in conspecific than heterospecific soils). In addition, soil microbes had a negative effect on A. saccharum and Prunus serotina seedling survival, with reduced survival in live versus sterilized conspecific soil. In general, we found higher trait values (measured amounts of a given trait) in conspecific than heterospecific soils and higher light availability. Additionally, A. saccharum survival increased with higher levels of phenolics, which were higher in conspecific soils and high light. Quercus alba survival decreased with higher AMF colonization. We demonstrate that functional trait values in seedlings as young as three weeks vary in response to soil source and light availability. Moreover, seedling survivorship was associated with trait values for two species, despite both drought and heavy rainfall during the growing season that may have obscured survivorship-trait relationships. These results suggest that seedling traits could have an important role in mediating the effects of local soil source and light levels on seedling survivorship and thus plant traits could have an important role in PSFs.

opencc-by-4.0Nov 2023View details →

Arnica montana functional traits in 27 sites - Monts d'Ardeche, France - 2021

In 27 sites in southeastern France, we measured vegetative and reproductive functional traits of arnica of interest for harvesters, and recorded management actions (grazing; mowing) and ecological variables (including height of surrounding vegetation and tree cover). We examined their effects on plant traits with linear mixed models, and used path analysis to test if the effects of human management on traits are mediated by the height of surrounding vegetation. The data presented here, accompanied by the Material and Methods of the corresponding publication in Annals of Botany Plants contains all the necessary information to reproduce the analysis. This data is linked to the following accepted article in Annals of Botany Plants : Locqueville, J., Violle, C., McKey, D., Caillon, S. and Coq, S. (2023) A feedback loop between management, intraspecific trait variation and harvesting practices. Annals of Botany Plants, accepted manuscript.

opencc-zeroDec 2022View details →

Raw data and Matlab code for: Convergence in carnivorous pitcher plants reveals a mechanism for composite trait evolution

Composite traits involve multiple components that, only when combined, gain a new synergistic function. Thus, how they evolve remains a puzzle. We combined field experiments, microscopy, chemical analyses and laser Doppler vibrometry with comparative phylogenetic analyses to show that two carnivorous Nepenthes pitcher plant species convergently evolved identical adaptations in three distinct traits to acquire a new, composite trapping mechanism. Comparative analyses suggest that this new trait arose convergently via 'spontaneous coincidence' of the required trait combination, rather than directional selection in the component traits. Our results indicate a plausible mechanism for composite trait evolution and highlight the importance of stochastic phenotypic variation as a facilitator of evolutionary novelty.

Wood trait preferences of Neotropical xylophagous beetles

Tree life history strategies are correlated with functional plant traits, such as wood density, moisture content, bark thickness, and nitrogen content; these traits affect the nutrients available to xylophagous insects. Cerambycid beetles feed on substrates that vary in these traits, but little is known about how they affect community composition. The goal of this project is to explore the community composition of two cerambycid subfamilies (Cerambycinae and Lamiinae) according to the wood traits in the wood they eat. In a salvage project conducted adjacent to the Panama Canal, trees were felled and exposed to Cerambycidae for oviposition. Disks from branches of differing thickness from the same plant individuals were used to calculate wood density, moisture content, and bark thickness in the field; nitrogen data were acquired offsite. Thick and thin branches tended to differ in wood trait values; therefore, data were analyzed separately in subsequent analyses. In thin branches, cerambycid abundance and species richness were higher in samples with less dense, moister wood, and thicker bark. Thick branches showed similar trends, but the wood traits accounted for little variability in beetle abundance or species richness. There were no significant regressions between beetle data and nitrogen. Cerambycines emerged more slowly, and from denser, drier wood, than lamiines. Cerambycines might be more drought-tolerant than lamiines, and therefore more resistant to the longer, more severe dry seasons that are predicted to occur due to climate change.

opengpl-3.0-or-laterSep 2023View details →

Genome Database: Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

This repository contains the dataset used in the publication "Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers," which is currently under revision. A pre-print can be found <a href="https://doi.org/10.1101/2022.12.29.522137">here</a>. The database is based on previously published work to create a genomic database of honeybee gut microbes by Kirsten Ellegaard (2021), found <a href="https://zenodo.org/records/4661061">here.</a>The zipped folder deposited here after unzipping, should contain the following files and directories:<ul><li>honeybee_genome.fasta : fasta file containing the host (Apis mellifera) genome sequence</li><li>beebiome_db : fasta file of 198 concatenated genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier</li><li>beebiome_red_db : fasta file of 39 species representative genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier to be used for the analysis of intra-specific variation</li><li>fna_files : directory containing genome sequence files and concatenated files where the concatenated files contain one fasta entry renamed to the genome identifier and all contigs concatenated into one entry</li><li>ffn_files : directory containing one file per genome listing the nucleotide sequence of all the predicted genes</li><li>faa_files : directory containing one file per genome listing the amino acid sequence of all the predicted genes</li><li>bed_files : directory containing bed files where the location of each of the predicted genes are indicated based on their position in the concatenated genome file</li><li>single_ortho : directory containing one file per phylotype listing all the single-copy orthogroups (OGs) identified by orthofinder where each line represents an OG id followed by a list of genes from each of the genomes of that phylotype that belong to that OG and the corresponding sequences of these genes can be found in the ffn file belonging to the respective genome</li><li>red_bed_files : directory containing bed files for species representative genomes that only list the positions genes that belong to the core orthogroups of their phylotype</li></ul>Further information about how this genome database was used to analyze strain-level diversity can be found in the publication and accompanying code repository.

Native herbivore browsing alters plant physical and chemical traits in a eucalypt forest understory

Macropods exhibit selective herbivory on plant traits within and between species and hence can alter plant trait variation. In this study we asked, what are the effects of macropod herbivory on intraspecific variation in plant traits of forest understorey species? We tested the effects of herbivory by macropods on eight plant traits, in nine understorey species using a herbivore exclusion experiment. Generalised linear mixed models were used to test for differences between herbivory treatments in trait means as well as variation within species and at the community level. Macropod herbivory resulted in differences in either the mean trait value or trait variance within a species for seven of the eight tested plant traits. Macropod exclusion resulted in larger dimensions of size for most species, as well as changes in specific leaf area, moisture content, and carbon content of leaves. Further, community-weighted means of specific leaf area, moisture content, and leaf nitrogen were lower in the presence of macropods. Plant trait variance was altered for three of the seven community weighted traits. This study demonstrates a mechanism through which macropods can drive changes in the traits of understorey plant species. Plant traits have been linked to various larger scale ecological processes including ecosystem flammability, nutrient cycling, response to global change and habitat suitability for other organisms. Therefore, herbivore-induced changes in plant trait variation and community composition could have important flow on effects for other environmental processes and hence should be considered in management decisions regarding fire-prone ecosystems.

Functional traits and related environmental variables of 28 populations of Nuphar lutea

This dataset includes 31 leaf functional traits, 2 genetic diversity metrics and 4 leaf reflectance measures on 28 wild populations of yellow water lily (Nuphar lutea). For each population (plot) coordinates, water depth, specific conductivity, nitrate, sediment organic matter and sediment total phosphorus contents are provided as well. The populations were located in 4 different lake systems in central and northern Italy. All the information on the methodology used to collect the data and can be found in the related paper.

Trait overdispersion in dragonflies reveals the role and drivers of competition in community assembly across space and season

Our understanding of how biotic interactions influence animal community assembly is largely restricted to local systems due to the difficulty of obtaining ecologically meaningful assemblage data across large spatial extents. Here, we used thousands of spatio-phenologically high-resolution assemblages across three distinct European regions together with a functional diversity approach to understand community assembly of dragonflies and damselflies (Odonata), an insect group characterized by a pronounced competitive reproductive biology. We found that adult dragonfly, but not damselfly, assemblages were consistently composed of species morphologically more different than expected by chance based on the traits that enhance their inter-specific reproductive encounters. These results provide consistent evidence for the role of competition in the assembly of animal communities, which we interpret is most likely caused by the territorial reproductive biology of dragonflies. Support for competition varied both spatially and seasonally following theoretical expectations, as it was strongest in locations and seasonal moments with low thermal stress (i.e. warm conditions) and high niche packing. Our study illustrates how spatio-temporal diversity patterns arise from variation in assembly processes.

Data from: Larval diet and temperature alter mosquito immunity and development: using body size and developmental traits to track carry-over effects on longevity

Background: Estimating arbovirus transmission potential requires a mechanistic understanding of how environmental factors influence the expression of adult mosquito traits. While preimaginal exposure to environmental factors can have profound effects on adult traits, tracking and predicting these effects remains challenging. Methods: Using Aedes albopictus and a structural equation modelling approach, we explored how larval nutrition and temperature jointly affect development rate and success, body size, and whether these metrics capture carry-over effects on adult longevity. Additionally, we investigated how larval diet and temperature affect the baseline expression of ten immune genes. Results: We found that larval development success was primarily determined by diet, while temperature and diet both affected development rate, pupal wet weight, and wing length. Effects of diet on both morphometric measures and their relationships to adult longevity were asymmetrical, with wing length having a positive association and pupal weight a negative association. Larval diet indirectly affected adult longevity, and the time to pupation was negatively correlated with longevity. The expression of eight immune genes from Toll, JAK-STAT, and Imd pathways was enhanced in mosquitoes with higher nutrition. Conclusions: Our results highlight deficiencies from using a single body size measure to capture carry-over effects on adult traits. Further studies of larval development rate under varying environmental conditions and its potential for tracking carry-over effects on vectorial capacity are warranted.

opencc-zeroDec 2023View details →

Morphological, ecological and territorial traits for 525 Hylinae frog species

This dataset includes data on 15 morphological, ecological and territorial variables (columns) for 525 Hylinae frog species (rows), as well as cites of the references from which data were retrieved, complete references and description of variables

opencc-zeroDec 2023View details →

Nitrogen redistribution and seasonal trait fluctuation facilitate plant N conservation and ecosystem N retention

<ol> <li>Low available soil nitrogen (N) limits plant productivity in alpine regions, and alpine plants thus resorb and reallocate N from senescing tissues to conserve this limited N during the nongrowing season. However, the destination and extent of N redistribution during plant senescence among above- and below-ground organs, let alone other processes of translocation outside of plants and into the soil components, remain poorly understood. </li> <li>Utilizing the 15N stable isotope as a tracer, we quantified N redistribution among above- and below-ground plant organs and different soil components during senescence in an alpine meadow ecosystem, and explored the relationship between 15N among plant-soil N pools with seasonal fluctuations of plant functional traits.</li> <li>We found a substantial depletion of 15N in fine roots (-40% ± 2.8%) and aboveground tissues (-51% ± 5.1%), and an enhanced 15N storage primarily in coarse roots (+79% ± 27%) and soil organic matter (+37% ± 10%) during plant senescence. In parallel, we observed a temporal variation in plant functional traits, representing a shift from more acquisitive to more conservative strategies as the growing season ends, such as higher coarse root N and coarse root to fine root ratio. The seasonal trait variations were highly correlated with the 15N retention in coarse roots and soil organic matter. Particularly, 15N retention in particulate and mineral-associated organic matter increased by 30% ± 12% and 24% ± 9%, respectively, suggesting a potential pathway through which fine root and microbial mortality contribute to 15N redistribution into soil N pools during senescence.</li> <li> Synthesis. N redistribution and seasonal plant trait fluctuation facilitate plant N conservation and ecosystem N retention in the alpine system. This study suggests a coupled aboveground-belowground N conserving strategy that may optimize the temporal coupling between plant N demand and ecosystem N supply in N-limited alpine ecosystems. </li> </ol>