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5,828 results for “Traits”
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery
<p>Datasets for "Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery", Eid et al., <em>Nature Communications. </em></p>
Frugivoria: an open trait database of birds and mammals exhibiting frugivory in moist montane Neotropical forest
Biodiversity in many areas is rapidly shifting and declining as a consequence of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor, and conserve biodiversity hotspots. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the functional trait information required to evaluate functional diversity is often lacking and is difficult to harmonize across disparate data sources. Biodiversity hotspots are particularly lacking in this information. To address this knowledge gap, we compiled Frugivoria, a trait database containing dietary, life-history, and morphological traits as well as IUCN conservation status, for mammals and birds exhibiting frugivory, which are important for seed dispersal, an essential ecosystem service. Accompanying Frugivoria is an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyze traits in space. This version of Frugivoria encompasses species in moist montane forests of Central and South America. Compared with existing trait databases, Frugivoria adds 25 species (reclassifying 199 to align with the most recent taxonomic changes), adds new traits such as observed and inferred range size, habitat specialization, and body size, and also fills gaps in trait categories from other databases such as diet category, home range size, generation time, and longevity. Overall, Frugivoria adds 2,045 new trait values for mammals and 4,022 for birds, and includes a total of 17,454 trait entries with minimums and maximums reported for certain traits. Frugivoria and its workflow enables researchers to quantify relationships between traits and the environment, as well as spatial trends in functional diversity, contributing to basic knowledge and applied conservation of frugivores
Stachewicz et al. 2021: Trait correlation, phylogenetic signal in Carabidae morphology (repackaging of occurrences published by the NEON Biorepository Data Portal)
Stachewicz JD, Fountain-Jones NM, Koontz A, Woolf H, Pearse WD, Gallinat AS. 2021. Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology bioRxiv 02.12.431029; doi: https://doi.org/10.1101/2021.02.12.431029 Many NEON samples and specimens used in this work resulted from NEON prototype data and will not be archived in the Biorepository. See the appendices in the above linked article for a full list of NEON samples and specimens and their associated collection data. Additionally, see appendices of above linked article for specimen-level morphological trait measurements and genetic sequence data.
Phenotypic trait variation of Herminium monorchis in the Qinghai-Tibetan Plateau with grazing intensity and climatic conditions
This data set contains raw data supporting the research entitled “Livestock grazing outweighs climate in driving trait variation of a widespread alpine plant” (currently under peer review), which documents how phenotypic traits of a widespread herbaceous plant in the Qinghai-Tibetan Plateau, Herminium monorchis, vary with grazing intensity and environmental conditions.
Seasonal trends in leaf level physiological parameters, obtained through gas exchange, reflectance spectroscopy and, functional trait analysis
This data package contains leaf level gas exchange, reflectance spectroscopy, and functional trait measurements collected in six common deciduous tree species across the full 2021 growth season (May -October) at the Black Rock Forest in Cornwall, New York, USA. Branches were sampled predawn using the shotgun method of branch retrieval, and re-cut under water to preserve hydraulic function before transport to the lab. Gas exchange data included in this package are stomatal response curves (irradiance response) which can be used to estimate stomatal slope and intercept. Spectroscopic data are full-range (350 – 2500 nm) leaf reflectance spectra collected on all leaves sampled for gas exchange and traits. Leaf level trait measurements include leaf mass per area (LMA), leaf dry matter content (LDMC), elemental nitrogen and carbon expressed on a per mass basis, and fitted values of Asat, Vcmax, and Rdark scaled to a reference temperature of 25C. Data from these three data tables (stomatal responce, spectra, leaf traits) can be cross referenced using the unique SampleID. Additional data tables include stomatal anatomy (stomatal density, length, and width of the guard cells), hydraulic properties estimated from pressure volume curves (relative water deficit at the turgor loss point), and predawn water potential for all sampled branches. Site level data includes the dGPS location of each sampled tree, its species, and DBH. Each tabular data file (*.csv) is accompanied by a data description (*_dd.csv) which includes relevant metadata (unit, definition, data type). Copies of all raw instrument output (spectroradiometer, LICOR, pressure chamber) and included as .zip files.
canopy herbivory and leaf traits of tree communities in tropical montane rainforests of southern Ecuador
This dataset contains herbivory data estimated as leaf area loss [cm²] and [%] and several leaf traits measured either conventionally or via spectral sensing-based techniques from canopies of tree communities in tropical montane rainforests of the Andes in southern Ecuador between February and March in 2019. The data were used by Schön et al. (in prep) to evaluate whether leaf traits are valuable indicators of canopy herbivory mainly caused by arthropods and further, whether chemical leaf traits estimated via spectral sensing-based techniques have similar strong relations to herbivory as leaf traits measured conventionally. Herbivory was estimated with the software WinFOLIA ™ 2019a from scanned mature and sun-exposed leaves of tree canopies. Spectral sensing-based leaf traits comprising secondary plant metabolites and both structural and nutritional cell components were estimated from leaves with an OceanOptics spectrometer HDX. Conventionally measured leaf traits comprising morphological and nutritional traits were derived by applying both elemental and morphometrical analyses (e.g., ICP analysis, a digital micrometer and penetrometer). For detailed descriptions of the methodology see Schön et al. (in prep), Homeier et al. (2021), and Limberger et al. (2021). Research was conducted by the subprojects A1, B1, and B4 within the framework of the RESPECT project (Environmental changes in biodiversity hotspot ecosystems of South Ecuador: RESPonse and feedback effECTs) funded by the DFG with the grant numbers: BE1780/51-1, BE1780/51-2, Ho3296/6-1, FA 925/11-1, FA 925/11-2, FA 925/16-1, BR1293/17-1.
Leaf traits plus growth and dieback data for cloud forest epiphytes in a cloud exclusion treatment at Wayqecha Biological Station, Peru
Morphological traits [specific leaf area, stomatal length and density, leaf thickness, cuticle thickness and hydrenchymal layer thickness] and physiological traits [stomatal conductance, minimum leaf conductance and foliar water uptake capacity] along with pressure volume curves were measured at the Wayqecha Biological Station, Peru. Vascular epiphytes were sampled from a control plot and fog reduction treatment plot constructed from two 30 m tall aluminum towers, 40 m apart with panels of polyethylene mesh strung between the towers. Measurements of leaf morphological traits were taken in June-July 2022 in the control and treatment plots to assess plasticity to fog reductionin the fifth year of the experiment. Samples of branches and leaves for each individual approximately 1-2 meters off the ground were collected in the plot, close enough to the curtain to maximize any effects of fog interception. Growth and dieback data were also collected species of vascular and non-vascular epiphytes attached to wooden transplant boards in the control and treatment plot in 2017. Rates of growth and dieback were recorded for vascular epiphytes from 2017-2019 and for non-vascular epiphytes from 2018-2019. The 2017 data collection took place in November while data for 2018 and 2019 were collected in June.
Fungal traits associated with soil organic matter formation, Harvard Forest, Petersham MA, 2020-2023
Soil microbes are a major source of organic residues that accumulate as soil organic matter (SOM), the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive SOM formation and stabilization; however, whether certain microbial traits consistently predict SOM accumulation across different functional pools (e.g., total vs. stable SOM) is unresolved. To address these uncertainties, we incubated individual species of fungi in SOM-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their SOM formation potentials. We find that the formation of different SOM functional pools is associated with distinct fungal traits, and that ‘multifunctional’ species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote SOM formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary (high/low) trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex SOM.
Relyea, R. A., and K. L. Yurewicz. 2002. Predicting community outcomes from pairwise interactions: Integrating density- and trait-mediated effects. Oecologia 131:569-579.
Understanding how species interactions shape the structure of ecological communities based on pairwise comparisons has been a difficult undertaking for ecologists because effects in reassembled communities can be different than simple density-mediated interactions would suggest. Part of this complexity occurs because many species change their behavior and morphology with different predators and competitors and, thus, change their per-capita interaction rates (i.e. trait-mediated interactions). Our objective was to use a simple experimental community of two predators (larval dragonflies, Anax longipes, and larval salamanders, Ambystoma tigrinum), two prey (larval green frogs, Rana clamitans, and larval bullfrogs, R. catesbeiana), and a shared prey resource to determine whether we can predict interactions in a reassembled community by combining our knowledge of density- and trait-mediated interactions,. We combined pairwise laboratory experiments on predation rates and predator-induced behaviors with a mesocosm experiment to examine density- and trait-mediated effects. We used a factorial combination of no predators, caged Anax (to induce anti-predator traits without changing prey density), and lethal Anax crossed with no predators, caged Ambystoma, and lethal Ambystoma. The species interactions in the reassembled community were qualitatively predictable based on the pairwise experiments. Lethal Anax preyed upon Ambystoma and green frogs while lethal Ambystoma only preyed upon green frogs. Anax also reduced the activity of the green frogs; this caused a decrease in salamander predation on green frogs, a decrease in green frog acquisition of resources, and an increase in bullfrog acquisition of resources. Ambystoma had no effect on green frog activity, no effect on resource acquisition by green frogs, and no effect on resource acquisition by bullfrogs. These results suggest that we can better understand how species interact in natural communities if we have a more deta
Relyea, R. A. 2000. Trait-mediated indirect effects in larval anurans: Reversing competition with the threat of predation. Ecology 81:2278-2289.
Ecologists recently have been focusing on the role that trait-mediated indirect effects can have on community structure and composition. To date, this work has primarily focused on the effects of predator-induced behavioral plasticity on communities. However, predator-induced morphological plasticity, which has been documented in many taxa, might also lead to trait-mediated indirect effects. Here, I examined how predators altered the behavior and morphology of larval wood frogs (Rana sylvatica) and leopard frogs (R. pipiens) and how these phenotypic changes altered the outcome of competition between the two species. Competition in the absence of caged predators was asymmetric; when reared separately, leopard frogs grew more than wood frogs, but when competing (without predators), wood frogs grew faster than leopard frogs. The presence of caged predators reversed the outcome of competition between the two anuran prey. In the presence of larval dragonflies (Anax spp.) or caged mudminnows (Umbra limi), leopard frogs grew faster than wood frogs while total tadpole biomass production remained unchanged. Thus, there was a predator-mediated indirect effect. Because predators alter both the behavior and morphology of larval anurans and both of these traits are known to affect resource consumption and growth, both are potential mechanisms to explain the change in competitive outcome. Changes in behavior were not related to changes in growth, but changes in morphology (specifically mouth width and tail length) were related to changes in growth. When competitors were added (without predators), wood frogs increased their mouth width by 10% and their tail length by 3%, while leopard frogs increased their mouth width by 5% and did not change their tail length. The greater increase in mouth width for wood frogs should increase their forage intake, since tadpoles feed by scraping periphyton; the importance of a 3% longer tail in competitive ability is unknown. The presence of the p
Selected trait data for the most abundant phytoplankton, zooplankton, benthic invertebrates, and fishes of the Upper San Francisco Estuary
This data set includes selected trait data from published literature and online databases for the most common phytoplankton, zooplankton, benthic invertebrate, and fish taxa at long term monitoring stations in the Upper San Francisco Estuary, which includes the Sacramento-San Joaquin River Delta, Suisun Bay, and Grizzly Bay.
DroughtNet: Establishing the International Drought Experiment at Cedar Creek tIDE (trait IDE): Aboveground Biomass
Droughts are forecast to become increasingly frequent and intense in many regions worldwide, likely impacting community structure, ecosystem functioning, and ecosystem services. The International Drought Experiment (IDE) is a coordinated, multi-site drought experiment requiring only a moderate investment of time and resources by investigators. This coordinated, distributed experiment will quantify the impacts of extreme drought across a wide range of terrestrial ecosystems based on a common experimental design and a comparable suite of measurements. We aim to establish two stand-alone experiments following the IDE design at Cedar Creek. Precipitation reduction shelters will be established during spring 2017 to simulate a 1 in 100 year dry event, which at our site corresponds to removing 43% of annual precipitation. The tIDE (trait IDE) study will be established in e248 plots in the Big Biodiversity experiment field. The three precipitation treatments described above will be applied at the subplot level and fully crossed with the two current irrigation treatments (ambient or ambient plus ~2 cm per week of irrigation) and with two of the current fertilization treatments (unamended or 14 g N m-2), with six true replicate plots for each of the 12 treatment combinations, for a total of 72 subplots. Standard measurements across these two experiments and all other DroughtNet sites will include peak aboveground biomass clipping, soil carbon and nitrogen content, plant community composition from % cover, plant traits, and meteorological measurements (daily precipitation, air temperature). Many sites will also measure light availability, root biomass, soil moisture, and decomposition rates of tea bags and tongue depressors. Pre-treatment data will be collected during 2016. The experiment is expected to have minimal impacts on Cedar Creek and on other projects.
DroughtNet: Establishing the International Drought Experiment at Cedar Creek tIDE (trait IDE): Percent Cover
Droughts are forecast to become increasingly frequent and intense in many regions worldwide, likely impacting community structure, ecosystem functioning, and ecosystem services. The International Drought Experiment (IDE) is a coordinated, multi-site drought experiment requiring only a moderate investment of time and resources by investigators. This coordinated, distributed experiment will quantify the impacts of extreme drought across a wide range of terrestrial ecosystems based on a common experimental design and a comparable suite of measurements. We aim to establish two stand-alone experiments following the IDE design at Cedar Creek. Precipitation reduction shelters will be established during spring 2017 to simulate a 1 in 100 year dry event, which at our site corresponds to removing 43% of annual precipitation. The tIDE (trait IDE) study will be established in e248 plots in the Big Biodiversity experiment field. The three precipitation treatments described above will be applied at the subplot level and fully crossed with the two current irrigation treatments (ambient or ambient plus ~2 cm per week of irrigation) and with two of the current fertilization treatments (unamended or 14 g N m-2), with six true replicate plots for each of the 12 treatment combinations, for a total of 72 subplots. Standard measurements across these two experiments and all other DroughtNet sites will include peak aboveground biomass clipping, soil carbon and nitrogen content, plant community composition from % cover, plant traits, and meteorological measurements (daily precipitation, air temperature). Many sites will also measure light availability, root biomass, soil moisture, and decomposition rates of tea bags and tongue depressors. Pre-treatment data will be collected during 2016. The experiment is expected to have minimal impacts on Cedar Creek and on other projects.
Climate Change Across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest: growth and enzyme activity traits of soil fungi isolated from CCASE in July 2017, grown under a common garden experiment in the laboratory that mimicked CCASE soil temperature treatments
Projections for the northeastern U.S. indicate that mean air temperatures will rise and snowfall will become less frequent, causing more frequent soil freezing. To test fungal responses to these combined chronic and extreme soil temperature changes, we conducted a laboratory-based common garden experiment with soil fungi that had been subjected to different combinations of growing season soil warming, winter soil freeze/thaw cycles, and ambient conditions for four years in the field. We found that fungi originating from field plots experiencing a combination of growing season warming and winter freeze/thaw cycles had inherently lower activity of acid phosphatase, but higher cellulase activity, that could not be reversed in the lab. In addition, fungi quickly adjusted their physiology to freeze/thaw cycles in the laboratory, reducing growth rate and potentially reducing their carbon use efficiency. Our findings suggest that less than four years of new soil temperature conditions in the field can lead to physiological shifts by some soil fungi, as well as irreversible loss or acquisition of extracellular enzyme activity traits by other fungi. These findings could explain field observations of shifting soil carbon and nutrient cycling under simulated climate change. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits
Climate change will increase soil drying, altering microbial communities via increasing water stress and decreasing resource availability. The responses of these microbial communities to changing environments is likely governed by physiological tradeoffs between high yield, resource acquisition, and stress tolerance (Y-A-S framework). We leveraged a unique field experiment that manipulates both drought and carbon availability across two years and three land uses, and we used both metagenomic and bioassay indicators of the three microbial community traits to test the following hypotheses: 1. Drought increases microbial allocation to stress tolerance functions, at the expense of growth and resource acquisition. 2. Because microbes are resource-limited under drought, increased carbon will enable greater expression of stress tolerance. 3. All three key life history traits described in the YAS framework will trade off, especially when resources are limited. Drought did increase microbial physiological investment in stress tolerance (measured via trehalose production), but we saw few other changes in microbial communities under drought. Carbon addition increased resource acquisition (measured via enzyme activity and resource acquisition gene abundance) and stress tolerance (trehalose assay), but did so in both drought and average rainfall environments. We found no evidence of trait tradeoffs, as we found no significant negative correlations between traits (measured via bioassay and metagenomics). In summary, we found C addition, and to a lesser extent, drought, both altered microbial community function and functional genes. However, resources did not alter drought response in a way that was consistent with theory of life history tradeoffs.
LTM01 Herbarium and grassland sites leaf trait measurements at Konza Prairie
Using herbarium specimens spanning 133 years and field-collected measurements, we assessed intraspecific trait (leaf structure and stomata) variability from grass species in the Great Plains of North America. We focused on two widespread, closely-related grasses from tribe Paniceae: Dichanthelium oligosanthes subsp. scribnerianum (C3) and Panicum virgatum (C4). Thirty-one specimens per taxon were sampled from local herbaria from the years 1887 – 2013 to assess trait responses across time to changes in atmospheric [CO2] and growing season precipitation and temperature. In 2021 and 2022, the species were measured from eight grasslands sites to explore how traits vary spatially across natural continental precipitation and temperature gradients. For temporal trends, we predicted Δ13C would decrease in D. oligosanthes and exhibit no change in P. virgatum. Dichanthelium oligosanthes is a C3 species, which we predict will respond to increased [CO2] concentrations by increasing its WUE to either conserve water while maintaining the same rates of photosynthesis or increase photosynthesis and maintain the same rates of water loss, thus decreasing Δ13C. We did not expect Δ13C of P. virgatum to respond over time because discrimination in C4 species is minimally affected by [CO2]. We also predicted both grasses will increase tissue C:N ratios and decrease stomatal density and stomatal lengths on both sides of the leaves in response to increased [CO2] over time. Lastly, we hypothesized %N and δ15N would decrease for both taxa. Because both taxa are widely distributed across North America and are known to exhibit variation in leaf morphology, we expected specific leaf area (SLA) to be greater in areas with warmer temperatures but not be correlated with differences in precipitation. We expect leaf dry matter content (LDMC) to increase with greater precipitation and decrease with higher temperatures.
LPT01 Leaf physiological and structural traits of encroaching shrub species at Konza Prairie
A variety of leaf-level physiological and structural traits were collected on seven species of encroaching shrubs at Konza Prairie Biological Station during the summer of 2022. Shrub species spanned an order of magnitude in abundance. These data were used to assess if the most abundant encroaching species at Konza Prairie have common growth forms and physiology or unique traits that differentiate their carbon- and water-use strategies. Measurements included A-Ci response curves, light response curves, pressure-volume curves, specific leaf area, leaf dry matter content, leaf carbon and nitrogen content, leaf 13C and wood density. All measurements were collected on the same shrub individuals.
Plant functional traits in the black sand extended growing season experiment, 2023.
Climate change is predicted to affect the alpine at a more rapid rate than other ecosystems. One predicted consequence is earlier snowmelt, which the Niwot Ridge LTER site Black Sand experiment aimed to replicate. Black sand was hand-spread across the early snowmelt treatment to cause a more rapid snowmelt than in the control plots. Sand was still spread across the control plots after snowmelt to control for the effects of the sand on vegetation. Each treatment also contained ITEX chambers which raised the temperature of individual plots. Within this larger experiment, we measured plant functional traits to see if they varied across the four treatments: control, control + ITEX, early snowmelt, and early snowmelt + ITEX.
Turf Transplant Bistort traits, 2024 - ongoing.
The Turf Transplant Experiment was set up in the summer of 2024. Paired experimental sites were established in two tundra community types - dry meadow and moist meadow - with one site of each community type pair in a lower elevation/warmer area and one site in a higher elevation/cooler area. Subplot turfs (25 cm^2) were transplanted (1) between sites of the same community type at different elevations/temperatures, (2) between plots within the same site or (3) left in place as non-transplant controls. This data package contains trait measurements on Bistort individuals.
SEV-LTER Plant Traits Database
This dataset contains measurements of morphological (leaf, stem, root, and seed), nutrient, and isotopic traits for plant species growing in the Sevilleta National Wildlife Refuge. Approximately 104 species were sampled in or near four core sites of the SEV-LTER (core_blue, core_black, core_creosote, and core_PJ) plus the Sevilleta Field Station between 2017 and 2021. In addition, seed masses were measured from a 2016-era seed collection provided by Jenny Noble and added to the dataset; for these, site = NA.
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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.