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5,828 results for “Traits”
Fungal Divergent Actin: Trait mapping and function hypothesis
<p>This projects investigates the potential new function of a divergent actin form mainly found in fungal species (Fungal Divergent Actin (FDA)) using trait mapping and association analysis as a novel strategy to generate hypotheses about protein function. We use the ProteinCartography pipeline (https://doi.org/10.57844/arcadia-a5a6-1068), combined with trait mapping and trait association analysis to generate hypotheses about the function of FDA. </p> <p>The overall idea is to identify a working set of fungal species for which we are able to confidently determine the presence or absence of fungal divergent actin, gather fungal trait information for these species (ecological traits, structural traits, genetic traits etc...) and determine whether there is any correlation between the presence/absence of FDA and one of the fungal trait. Any correlation between FDA presence/absence and fungal trait can then be used to infer hypothesis about the function of FDA.</p> <p>Our approach is divided into four main steps:</p> <p>- Step 1: Expanding the initial set of fungal species that possess FDA</p> <p>- Step 2: Defining the 'working set of species' (set of fungal species for which we can determine their FDA status (presence or absence))</p> <p>- Step 3: Curating fungal trait information</p> <p>- Step 4: Statistical modeling of the association of FDA and chosen fungal traits</p> <p> </p> <p>In this upload, we provide files that are parts of Steps 1 & 2:</p> <p> - ProteinCartography folder of the ProteinCartography run for the FDA proteins: fungal_divergent_actins_PC.zip</p> <p> - .csv table of all fungal proteins and associated species in Uniprot that have available structure in AlphaFold: Fungi_prot_uniprot.csv</p> <p> </p> <p><strong>ProteinCartography run: fungal_divergent_actins_PC.zip</strong></p> <p><em>(Step 1 - Expanding the initial set of fungal species that possess FDA)</em></p> <p>The aim of the first step, is to detect as many fungal species as possible that possess FDA. For this, we used ProteinCartography (https://doi.org/10.57844/arcadia-a5a6-1068), to screen for protein that have similar structures than the previously identified Fungal Divergent Actin (REF actin pub) and expand the original cluster of FDA.</p> <p>After identifying 6 representative sequences of Fungal Divergent Actins, we used each of the six proteins as input proteins for "Search Mode'' of the pipeline ProteinCartography. Full details on the ProteinCartography pipeline can be found in the GitHub repository and accompanying pub (https://doi.org/10.57844/arcadia-a5a6-1068).</p> <p>The fungal_divergent_actins_PC.zip contains all the inputs and outputs of the ProteinCartography run:</p> <ul> <li>fasta and pdb files for all 6 input proteins</li> <li>configuration file for the ProteinCatography run</li> <li>all output files (including main files presented in the Pub: similarity matrix, semantic analysis and aggregated_features_pca_umap in the subfolder output/clusteringresults</li> </ul> <p> </p> <p><strong>Uniprot list of fungal protein with available structure: </strong>Fungi_prot_uniprot.csv</p> <p><em>(Step 2 - Defining the 'working set of species')</em></p> <p>The aim of Step 2 is to identify the list of fungal species for which we can confidently determine the FDA presence/absence status. While ProteinCartography allows us to identify species that possess FDA, we also need to be able to confidently tell when a species doesn't possess FDA. Thus, the working set is defined as the set of species for which the presence or absence of FDA was putatively established.</p> <p>Because ProteinCartography relies on protein structures available in UniProt and AlphaFold, we decided to define our working set as any fungal species that has a minimum of 6000 protein structures in AlphaFold. Then we consider that any species of this set that is not part of the extended cluster does not possess FDA.</p> <p>Fungi_prot_uniprot.csv is the list of fungal proteins and associated species that have structure avaialable in AlphaFold from UniProt. This serves as the initial file to eventually count the number of proteins with available structures per species and identify the working set of fungal species - To obtain this list we conducted an 'Advanced search' in UniProt using the following query: </p> <ul> <li>'Fungi' in Taxonomy field </li> <li>' * ' for the field AlphaFoldDB cross-reference (found within the Cross reference /3D structure field)</li> </ul>
Local adaptation in trait-mediated trophic cascades dataset
<p>Predator-induced changes in prey foraging can indirectly influence community dynamics by increasing the abundance of basal resources via a trait-mediated trophic cascade. The strength of these cascades may be altered by eco-evolutionary relationships between predators and prey, but the role of basal resources has received limited attention. We hypothesized that the strength of trait-mediated trophic cascades may be shaped by selection from trophic levels above and below prey. Our field and laboratory experiments utilized snails (<em>Nucella lapillus</em>)<em> </em>from two regions in the Gulf of Maine (GoM) that vary substantially in basal resource (e.g., barnacles, mussels) availability and invasion history with the predatory green crab, <em>Carcinus maenas</em>. <em>Nucella</em> from both regions were provided with mussels as a basal resource and exposed to the presence or absence of green crab risk cues. In both experiments, <em>Nucella</em> from the northern GoM, where basal resources are scarce, displayed weaker responses to risk cues than southern <em>Nucella</em>. In the lab, however, northern <em>Nucella</em> foraged more than southern snails under risk, but foraging rates among the two regions did not differ without risk. Our results suggest that adaptation to basal resource availability may contribute to geographic variation in the strength of trait-mediated trophic cascades.</p>
FLAMITS: FLAMmability plant traiTS database
<p><span>FLAMITS database</span> contains 19,972 records of 40 flammability variables (classified according to the measured component of flammability). For each record, relevant details of the flammability experiment are included, such as the burning device, the ignition source, and the burned plant part. In addition, FLAMITS compiles taxonomic and functional data of the studied species and information on the study site (locality, geographic coordinates, biome, biogeographic realm, and fire activity). We compiled data from 295 studies located in 39 countries and distributed across 12 biomes worldwide over the last 62.5 years (1961 to 15th May 2023). The dataset has 1790 plant taxa from 186 families, 833 genera, and 1790 species.</p>
Data and code for: Regional and local variability in the morphometric traits of two emblematic seagrass species (Zostera marina and Zostera noltei) along the French coast
<p>We present here the raw data and scripts to reproduce the results presented in the preprint "Regional and local variability in the morphometric traits of two emblematic seagrass species (Zostera marina and Zostera noltei) along the French coast" available on Zenodo. </p> <p> </p> <p>Preprin abstract:</p> <p><em><span>Zostera marina</span></em><span> and <em>Zostera noltei</em> are two foundation species that play a crucial role in the functioning of coastal ecosystems. They occur in a wide range of environmental conditions over a large geographical area in the northern hemisphere. The aim of this study was to investigate the scales of variability in the dynamics of these two species in relation to environmental conditions in four sites along the French coasts. We used community trajectory analysis, a multivariate statistical approach that allows quantitative measures and comparisons of ecosystem temporal trajectories. We found a significant effect of latitude and tidal regime on the seasonal dynamics of the two species. Populations from the southernmost microtidal site showed a seasonal stability in their morphometric traits and a good resistance to present-day climatic conditions. In the meso- and macrotidal regime sites, hydrodynamics and light have led to very different ecological strategies. On the one hand, high tidal currents increased shoot density and root biomass, while on the other hand, low light and less current favoured the development of long leaves to optimise photosynthesis. Finally, significant variation in meadow development was also observed at the local scale, which requires further investigation to identify the specific drivers. Our discussion suggests that special attention should be paid to interpreting the dynamics of these species according to the scale of observation, and that this diversity of variation scales should be taken into account in conservation measures. In a global context of seagrass bed decline, our study suggests some avenues of research to improve our understanding of seagrass species ecology in order to properly assess the state of coastal waters.</span></p>
High sexual display trait diversity without measured genetic divergence in a montane hybrid zone involving young species (Habronattus americanus subgroup, Araneae, Salticidae)
<p>Genetic introgression, allele exchange across species boundaries, is a commonly recognized feature of animal evolution. Under such a paradigm contemporary contact zones provide first-hand and complementary insight into the geographic, phenotypic, and genetic details of introgression. Also, when mate choice phenotypes are conspicuous and variable in hybrids, contact zones provide potential insight into how sexual selection interacts with species boundary maintenance, particularly when postzygotic reproductive isolation is weak. The <em>Habronattus</em> <em>americanus</em> subgroup includes several recently evolved jumping spider species, with an estimated age of about 200,000 years, and substantial evidence for hybridization and introgression. We explored a contact zone involving <em>H. americanus</em> (Keyserling, 1885) and <em>H. kubai</em> (Griswold, 1979) on Mount Shasta, California, in alpine habitats that would have been unavailable (under ice) at the Last Glacial Maximum. We characterized morphological diversity within the contact zone, including the fine-scale geographic distribution of hybrid and parental individuals, and assessed genetic variation using ddRADseq data. Combined results indicate a lack of measured genomic differentiation between specimens with distinct morphologies, including individuals with phenotypes of the parental species. We identified a diverse array of hybrid morphologies, with phenotypic evidence for backcrossing, essentially forming a phenotypic bridge between parental taxa. The study area is characterized by more hybrid than parental individuals, with a significantly larger number of red-palped morphologies than white and/or yellow-palped morphologies; the novel, white-palped phenotype is perhaps transgressive. Overall, these results contribute to a better understanding of the expected ebb and flow of lineage interactions during the early stages of speciation.</p>
Decoupling of uptake and transport-related traits in absorptive roots across coexisting herbaceous species in alpine meadows
<div>The anatomical structure of roots determines their function. Coexisting species complementarily forage nutrients by roots themselves (e.g., root strategy) and their fungal partners (e.g., mycorrhizal strategy), leading to a tradeoff between root strategy and mycorrhizal strategy. However, few studies have specifically evaluated whether and how the root anatomical structures are involved in this tradeoff, especially for species in alpine ecosystems limited by extreme climate.Here, absorptive root anatomical and chemical traits and three key root traits commonly associated with nutrient foraging strategies, i.e., root strategy indicated by first-order root length and root branching intensity and mycorrhizal strategy indicated by arbuscular mycorrhizal fungal colonization, were examined across 68 herbaceous species in alpine meadows of the Tibetan Plateau.We observed that absorptive roots with higher branching intensity had more protoxylem poles, thinner cortices and smaller cortical cells, whereas absorptive roots with higher mycorrhizal colonization and longer first-order roots consistently had thicker cortices and larger cortical cells. Unexpectedly, root cortical traits responsible for nutrient uptake were decoupled from stelar traits specialized in water and nutrient transportation. The decoupling may be related to the non-coordinated changes in soil water and nutrient availability in the meadows of the Tibetan Plateau. In addition, we found that root cortical thickness and stelar radius increased at a similar rate rather than well-reported different rates with increasing root diameter. Our results demonstrate that root internal makeup plays an integral role in forming the diverse nutrient foraging strategies in belowground. These findings provide new insights into our understanding of plant coexistence and responses of alpine meadows to climate change on the Tibetan Plateau.</div>
Data from: Intraspecific leaf trait variation mediates edge effects on litter decomposition rate in fragmented forests
<p>There is strong trait dependence in species-level responses to environmental change and their cascading effects on ecosystem functioning. However, there is little understanding of whether intraspecific trait variation (ITV) can also be an important mechanism mediating environmental effects on ecosystem functioning. This is surprising, given that global change processes such as habitat fragmentation and the creation of forest edges drive strong trait shifts within species. On 20 islands in the Thousand Island Lake, China, we quantified intraspecific leaf trait shifts of a widely distributed shrub species, <em>Vaccinium carlesii</em>, in response to habitat fragmentation. Using a reciprocal transplant decomposition experiment between forest edge and interior on 11 islands with varying areas, we disentangled the relative effects of intraspecific leaf trait variation vs. altered environmental conditions on leaf decomposition rates in forest fragments. We found strong intraspecific variation in leaf traits in response to edge effects, with a shift towards recalcitrant leaves with low specific leaf area and high leaf dry matter content from forest interior to the edge. Using structural equation modelling, we showed that such intraspecific leaf trait response to habitat fragmentation had translated into significant plant afterlife effects on leaf decomposition, leading to decreased leaf decomposition rates from the forest interior to the edge. Importantly, the effects of intraspecific leaf trait variation were additive to and stronger than the effects from local environmental changes due to edge effects and habitat loss. Our experiment provides the first quantitative study showing that intraspecific leaf trait response to edge effects is an important driver of the decrease in leaf decomposition rate in fragmented forests. By extending the trait-based response-effect framework towards the individual level, intraspecific variation in leaf economics traits can provide the missing functional link between environmental change and ecological processes. These findings suggest an important area for future research on incorporating ITV to understand and predict changes in ecosystem functioning in the context of global change.</p>
Phylogeny and climate explain contrasting hydraulic traits in different life forms of 150 woody Fabaceae species
<ol> <li>The contrasting hydraulic traits observed among different plant life forms are shaped by entangled environmental and evolutionary processes. However, we lack an understanding of the relative importance of life form, climate and phylogeny in explaining the variance of hydraulic traits.</li> <li>We analyzed seven hydraulic traits and eleven climatic variables of 150 Fabaceae species representing three life forms from 62 sites worldwide, using phylogenetic comparative analyses and variance partitioning.</li> <li>The phylogenetic signal found in most traits disappeared after considering life form, indicating that phylogenetic conservatism in traits originated from the divergence among life forms. The trait-climate relationships were also phylogenetically dependent, implying that trait responses are driven by climate and phylogeny together. Variance partitioning showed that phylogeny and climate explained greater trait variation than life form did.</li> <li> <em>Synthesis. </em>The climate-driven hydraulic trait responses in Fabaceae still existed with phylogeny being considered, suggesting that this large family may be particularly sensitive to climate change.<em> </em>Our results emphasize the need to include phylogeny in plant hydraulic adaptation studies under future climate change.</li> </ol>
Micro- and macroclimate interactively shape diversity, niches, and traits of Orthoptera communities along elevational gradients
<p>Temperature is one of the main drivers shaping species diversity and assembly processes. Yet, site-specific effects of the local microclimate on species and trait compositions of insect communities have rarely been assessed along macroclimatic temperature clines. Bavarian Alps, Germany Bayesian joint species distribution models were applied to investigate how ecological and morphological traits drive variation in the climatic niches of 32 Orthoptera species on 93 grassland sites with contrasting microclimatic conditions along a steep elevational macroclimatic gradient in an Alpine region in Central Europe. Species richness and abundance decreased along the elevational macroclimatic gradient, and both benefitted from warm microclimate. Interactive effects of elevation and microclimate on the abundance were, however, species-specific, and partly mediated by traits: Warm microclimatic conditions facilitated the occurrence of demanding xerophilic and late-hatching species, resulting in marked community dissimilarities at mid-elevations where colder sites harboured only a subset of the species. The latter mainly occurred at low elevations together with long-winged species. Abundance peaks of non-xerophilic species were further upslope when microclimate was warm. Intraspecifically, the body sizes and wing lengths of the larger females, but not the males, decreased with elevation akin the community mean, and brown colour morphs were more frequent at sites with warm microclimate. Our nuanced results reveal that trait-dependent responses of species to microclimate play a key role in the assembly and structuring of insect communities along macroclimatic gradients. Since microclimate preferences changed with elevation, we conclude that species temperature niches are narrower than the elevational range suggests and both macro- and microclimatic conditions must be considered when predicting species responses to climate change. Microclimatic contrasts among sites at similar elevations enhanced species turnover mediated by moisture preferences and phenology, highlighting the importance of mountains for conservation as climatic refugia where species with diverging niches can persist in proximity.</p>
Moss functional trait ecology: Trends, gaps, and biases in the current literature
<p>Functional traits are critical tools in plant ecology for capturing organism-environment interactions based on trade-offs as well as making links between organismal and ecosystem processes. While broad frameworks for functional traits have been developed for vascular plants, we lack the same for bryophytes, despite an escalation in the number of bryophyte functional trait studies conducted in the last 45 years and an increased recognition of the ecological roles bryophytes play across ecosystems. In this review, we compiled data from 282 published articles (10005 records) focusing on functional traits measured in mosses, and sought to (a) examine trends in types of traits measured, (b) capture taxonomic and geographic breadth of trait coverage, (c) reveal biases in coverage in the current literature, and (d) develop a bryophyte-function index (BFI) to describe completeness of current trait coverage and identify global gaps to focus research efforts. The most commonly measured response traits (those related to growth/reproduction in individual organisms) and effect traits (those that directly affect community/ecosystem scale processes) fell into the categories of morphology (e.g. leaf area, shoot height) and nutrient storage/cycling, and our BFI revealed that these data were most commonly collected from temperate and boreal regions of Europe, North America and east Asia. However, fewer than 10% of known moss species have available functional trait information. Our synthesis revealed that there is a need for research on traits related to ontogeny, sex, and intraspecific plasticity, and on co-measurement of traits related to water-relations and bryophyte-mediated soil processes. </p>
Trait-based mechanistic approach highlights global patterns and losses of herbivore biomass functional diversity
<ol> <li>Mammalian herbivores play a pivotal role in Earth System processes by affecting biogeochemical cycles and ecosystem functioning, potentially leading to significant repercussions on atmosphere-biosphere feedbacks. Global dynamic models of mammalian populations can improve our understanding of their ecological role at large scales and the consequences of their extinctions. However, such models are still lacking and mammals are poorly integrated in Earth System science.</li> <li>We developed a mechanistic global model of terrestrial herbivore populations simulated with 37 functional groups defined through the analysis of eco-physiological traits across all extant herbivores (2599 species). We coupled this model with a global vegetation model to predict herbivores' maximum potential biomass in pre-industrial and at present-day and to study the environmental drivers explaining the distribution of herbivore biomass. Present-day biomass was estimated by accounting for anthropogenic activity causing habitat and range losses.</li> <li>We show that natural ecosystems could have sustained a potential wild herbivore wet biomass of 330 Mt [95% CI 245–417], comprised of 193 Mt [95% CI 177–208] by large species (body mass > 1–10 kg, depending on functional group) and 138 Mt [95% CI 68-209] by small species. We estimate that the remaining present-day large herbivores biomass is 82 Mt [95% CI 32–133], reduced by 57% due to anthropogenic activity; consequently, small herbivores currently dominate global herbivore biomass with 98 Mt (95% CI 91–106, -29%). Losses vary greatly across climatic zones and functional groups, suggesting that size is not the only discriminant feature of biomass decline.</li> <li>Actual evapotranspiration is the most important driver of total, large, and small herbivore biomass and explains 64%, 59%, and 49% of its variation, respectively. Distribution of modeled and observed large herbivores' biomass suggested a high dependency on energy and water with more biomass in hot and wet areas. These results challenge the notion that large herbivore biomass peaks primarily in ecosystems with intermediate precipitation levels such as savannas.</li> <li>Outside Africa and the Tropics, pre-industrial biomass hotspots occur in areas today dominated by humans; this could undermine the recovery of larger species biomass in certain areas. These herbivore biomass estimates provide a quantitative benchmark for setting conservation and rewilding goals at large spatial scales. The herbivore model and functional classification create new opportunities to integrate mammals into Earth System science and models.</li> </ol>
Short and long-term effects of endogenous cortisol on personality traits and behavioral syndromes
<p>Animals express consistent individual differences in some behaviours, termed animal personality but behaviours can also considerably vary within individuals, within minutes or hours, due to environmental stimuli. Consistent among-individual variation is often assumed to be mediated by hormonal mechanisms. Hormones are also involved in flexible and fast responses towards environmental stimuli. Even though basic mechanisms by which hormones regulate behaviours are known, much of the quantitative patterns underlying hormone-behaviour interactions within and among individuals, remain unclear. Here, we conducted two experiments to investigate the immediate, short-term effects of experimentally elevated cortisol titres on well-known animal personality traits (Experiment 1) and the potential long-term effects of such experimentally elevated cortisol titres (Experiment 2) in the medium-sized cavy (<em>Cavia aperea</em>). Therefore, we tested how personality traits related to stress-coping, novelty seeking and social behaviour react within hours towards elevated cortisol. In Experiment 2, we tested if a three-weeks elevation of cortisol affects the same personality traits after cessation of the hormone treatment. We investigated effects on the mean levels of behaviours, i.e., the personality type, the temporal consistency, i.e., repeatability and among-individual correlations of traits. In experiment 1, we found cortisol to lead to more aggressive behaviour and more passive stress-coping while other traits were unaffected. In experiment 2, we found no long-term persisting effects. Both measured hormones, cortisol and testosterone, showed correlations to several personality traits, these correlations were, however, unaffected by the cortisol treatment. Animals receiving the cortisol treatment showed higher repeatability, for one stress-coping trait and lower repeatability for testosterone concentration. Interestingly, sexes differed only in few mean trait expressions but showed different correlation structures across traits. Taken together, our data indicate that personality traits in adult individuals are very consistent and only react via short-term fluctuations towards internal hormonal signals.</p>
Supplementary data for Inter-provenance variability and phenotypic plasticity of wood and leaf traits related to hydraulic safety and efficiency in seven European beech (Fagus sylvatica L.) provenances differing in yield
<p>Dataset and supplementary file for <strong>Inter-provenance variability and phenotypic plasticity of wood and leaf traits related to hydraulic safety and efficiency in seven European beech (<em>Fagus sylvatica</em> L.) provenances differing in yield </strong>paper.</p> <p>The ANFS_data file includes individual level measurements of xylem safety and efficiency traits, leaf traits and growth among 7 provenances planted at two common garden sites in Germany and Slovakia. More details related to the methodology might be found in the published paper by Kurjak et al. 2024.</p> <p>The ANFS_supplementary file includes the test for differences in distance to tip between sites and provenances, based on the branch diameter-branch length scaling.</p>
Length-mass allometries of larval mosquitoes and aquatic dipterans: differences between taxa, traits and methods
<p>Body mass underpins many ecological processes at the level of individuals, populations and communities. Often estimated in arthropods from linear traits such as body length or head width, these relationships can vary even between closely related taxa. Length-mass relationships of mosquito (Diptera: Culicidae) larvae are poorly known, despite the importance of this taxon to disease and aquatic ecology. To fill this gap, we measured ontogenetic changes in linear traits (body length, head width and thorax width) and dry and wet masses, and estimated length- and width-mass relationships in larvae of three Culicidae species inhabiting different niches: the tropical <em>Aedes</em> <em>albopictus</em> (Skuse, 1894), the temperate <em>Culex</em> <em>pipiens</em> (Linnaeus, 1758) and the snowmelt <em>Ochlerotatus</em> <em>punctor</em> (Kirby, 1837). We compared these data with published length-weight allometries of other larval aquatic dipterans. We show that thorax width and body length, but not head width, reliably predict body mass for the three mosquito species. The length-mass allometry slopes in aquatic dipterans vary considerably between and within families but are independent of phylogeny, specimen handling, preservation techniques, and data fitting method. However, slope estimates become less precise with decreasing sample size and size range. To obtain reliable estimates of the allometric slopes, we recommend using data on all larval stages for intraspecific allometries and a wide range of species for interspecific allometries. We also caution against indiscriminately using of length-mass allometries obtained for other taxa or collected at lower taxonomic resolution, e.g. when using length-mass relationships to estimate biomass production at a given site. </p>
Effects of leaf litter traits on terrestrial isopod and millipede consumption, assimilation and growth
<ol> <li>Nutrient cycling through leaf litter consumption is an essential ecological function performed by macrodetritivorous invertebrates such as isopods and millipedes. Leaf litter consumption rates can vary greatly depending on the environment, consumer identity, and litter traits, but generalizations about the effects of plant traits on macrodetritivore leaf litter consumption, assimilation and growth are not well established and mostly indirectly inferred.</li> <li>We conducted a systematic search of the global literature and obtained 456 standardized measures from laboratory experiments of relative consumption (RCR), assimilation (RAR) and growth (RGR) rates of terrestrial isopods and millipedes, extracted from 56 different articles. We investigated if commonly measured leaf traits, plant functional groups, prior microbial conditioning of leaves, and climatic conditions affected these rates. We obtained data on commonly measured leaf traits from the TRY global plant trait database, inferred plant functional groups from taxonomic groupings, and obtained climatic data from information reported within articles.</li> <li>RCR, RAR and RGR varied greatly among macrodetritivore and plant species, but overall, there were no differences between isopods and millipedes. Microbial conditioning of litter greatly increased RCR. Plant functional group was an important predictor of RCR, with eudicot trees and forbs being consumed in greater quantities than magnoliid trees and grasses. Fresh leaf N:P ratio had a positive effect on RAR, and leaf N and C:N ratio had positive and negative effects on RGR respectively, while climatic variables had weak effects on the three rates.</li> <li>Our work shows that plant traits (both those associated with plant functional groups and commonly measured leaf traits) exert strong effects on resource processing rates by terrestrial macrodetritivores. Further, prior microbial conditioning of leaf litter has a large and globally consistent positive effect on macrodetritivore litter consumption, suggesting that they may consume little, if any, freshly senesced leaf material when microbially conditioned litter is available. Our results suggest that, where extremes of temperature or precipitation do not occur, variables reflective of food quality (leaf traits and microbe conditioning) are more important drivers of macrodetritivore leaf litter consumption than are extrinsic climatic variables.</li> </ol>
QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat
<p>The mapping population comprises of 180 RILs developed from a cross between GW322 and KAUZ.</p> <p><strong>Phenotypic data</strong><br>Phenotypic evaluation was conducted across two consecutive crop seasons (2021-22 and 2022-23) under late sown irrigation (LSIR) and late sown restricted irrigation (LSRI) conditions at ICAR-IARI, New Delhi. Various physiological and agronomic traits of importance were measured. The component traits of yield including days to heading (DH), normalized difference vegetation index (NDVI), SPAD chlorophyll content (SPAD), plant height (PH), spike length (SL), thousand-grain weight (TGW), grain weight per spike (GWPS), biomass (BM) and grain yield per plot (PY) were measured under heat and combined stress conditions.</p> <p><strong>Genotypic data</strong><br>DNA was isolated from 21-day-old seedlings using the CTAB method (Murray and Thompson, 1980). DNA quality check was done using 0.8% agarose gel electrophoresis. The Axiom Breeders' array containing 35K Single Nucleotide Polymorphism (SNP) was employed for the genotyping of RILs and parents.</p>
SquamBase 1.0 – a dataset of squamate species traits
<p><strong>Motivation</strong>: I present a database that contains information on multiple key traits for all 11,744 recognized species of squamates worldwide. The database encompasses key traits and hopefully a reasonably comprehensive picture of available public knowledge. I present a comprehensive description of the sources and rationale leading to the assignment of each particular trait state for each species. Hopefully, the dataset can serve the scientific community and promote research and understanding of the group, comparisons with other taxa, and assessment of conservation needs. Furthermore, gaps in our knowledge of squamate traits become readily apparent and will hopefully lead to further study and even better knowledge.</p> <p><strong>Main types of variables contained</strong>: morphological, ecological, life history, geographic and conservation-related traits</p> <p><strong>Spatial</strong> <strong>location</strong>: Global</p> <p><strong>Time period</strong>: Late Holocene to recent</p> <p><strong>Major taxa and level of measurement</strong>: Squamata, species</p> <p><strong>Software format</strong>: .xlsx</p>
Females pay little attention to variation in male display traits in a jumping spider with dimorphic males
<p><span>Dimorphic male alternative reproductive strategies typically involve divergent suites of morphological and behavioral traits to maximize reproductive success. Most instances of these strategies typically follow similar patterns of a larger, territorial or aggressive male morph and a smaller, satellite male morph. The genetically determined male morphs of the jumping spider, <em>Maevia</em> <em>inclemens</em>, have evolved dramatically different secondary sexual traits and courtship behavior, but do not seem to fit the classic mold of male alternative reproductive strategies. In the past several decades, advances have been made to better understand the different reproductive strategies between the morphs and how females (or predators) perceive them differently. However, the specific information content and function of their dimorphic morphological traits, and whether female aggression is an important factor in their evolution, is still not clearly understood. We tested two hypotheses for alternative mating strategies in <em>M. inclemens</em>. Tufted males have three tufts of setae above their eyes that may signal their mate quality. Striped males have contrasting black-and-white striped legs that may function as an aggression deterrent. We manipulated tuft length and the presence/absence of leg stripes and paired a single male with an unmated female in no-choice mating behavior experiments to quantify mating success, female receptivity, female aggression, and reproductive output. We found little support for our focal hypotheses. However, our models suggested that male body condition is more likely to influence mating interactions than variation in the target traits we manipulated. Our robust negative results allow us to critically revise our hypotheses to better understand the unique and perplexing male dimorphism of <em>M. inclemens</em> that deviates from current theory.</span></p>
Data from: Manipulation of soil mycorrhizal fungi Influences floral display traits
<p>Most plants form root hyphal relationships with mycorrhizal fungi, especially arbuscular mycorrhizal fungi (AMF). These associations are known to positively impact plant biomass and competitive ability. However, less is known about how mycorrhizae may impact other ecological interactions, such as those mediated by pollinators.</p> <p>We performed a meta-regression of studies that manipulated AMF and measured traits related to pollination, including floral display, rewards, visitation, and reproduction, extracting 63 studies with 423 effects.</p> <p>On average, the presence of mycorrhizae was associated with positive effects on floral traits. Specifically, we found impacts of AMF on floral display, pollinator visitation and reproduction, and a positive but non-significant impact on rewards. Studies manipulating mycorrhizae with fungicide tended to report contrasting results, possibly because fungicide destroys both beneficial and pathogenic microbes.</p> <p>Our study highlights the potential for relationships with mycorrhizal fungi to play an important, yet underrecognized role in plant-pollinator interactions. With heightened awareness of the need for a more sustainable agricultural industry, mycorrhizal fungi may offer the opportunity to reduce reliance on inorganic fertilizers. At the same time, fungicides are now ubiquitous in agricultural systems. Our study demonstrates indirect ways in which plant-belowground fungal partnerships could manifest in plant-pollinator interactions.</p>
Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing
<p>Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (<em>Pungitius pungitius</em>) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components, and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogenous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.