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FIGURE 2 in Dispersion of hooks on the anal fins of primary and secondary males in Brycon orbignyanus (Characiformes: Bryconidae): a secondary sexual trait for breeder selection
FIGURE 2 | Details regarding the fins of Brycon orbignyanus. A, C and E. Rays without hooks. B, D and F. Rays with hooks. b: base. fb: first fork. r: rays. rs: rays with hooks. s: hooks. sg: rays segment. st: hooks cusp. tb: terminal bifurcation. Scales: A and B. 1 cm; C and D. 200 µm; E. 100 µm; F. 50 µm.
FIGURE 4 in Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon
FIGURE 4 | Standard length frequency histograms and the corresponding von Bertalanffy growth function for Calophysus macropterus (sexed and unsexed individuals combined) in (A, B) the upper Putumayo River and in (C) the AMU (the Amazonas, lower Marañón and Ucayali rivers).
FIGURE 3 in Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon
FIGURE 3 | Mean monthly GSI values (circles) of Calophysus macropterus females between 2013 and 2017 in relation with the water level (dotted line) in the upper Putumayo River (A) and the Amazonas, lower Marañón and Ucayali rivers (B).
FIGURE 2 in Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon
FIGURE 2 | Size frequency distribution of Calophysus macropterus females and males caught over the study period in the Putumayo River (A) and the Amazonas, lower Marañón and Ucayali rivers (B).
FIGURE 1 in Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon
FIGURE 1 | Geographic location of biological monitoring points for Calophysus macropterus at Puerto Leguízamo in the Putumayo River (Colombia) and Iquitos (Amazonas, lower Marañón and Ucayali rivers, AMU).
FIGURE 5 in Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon
FIGURE 5 | Standard length at first sexual maturity for males (black triangles) and females (white circles) of Calophysus macropterus (A) in the upper Putumayo River and (B) in AMU (the Amazonas, lower Marañón and Ucayali rivers).
FIGURE 7 in Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon
FIGURE 7 | Standard length-converted catch curves (SL) and mortality estimates for Calophysus macropterus (A) females, (B) males and all individuals (sexed and unsexed) combined (C) in the Amazonas, lower Marañón and lower Ucayali rivers, calculated from the VBGF parameters at a mean temperature of 27°C. Z, M and F represent the instantaneous rates of total, natural and fishing mortality, respectively. E is the exploitation rate (E = F.Z-1). Black dots = data points in the curve on which the regression was fitted.
Single-cell and spatial transcriptomics delineate molecular traits and immunosuppressive landscape during histological progression of lung adenocarcinoma
<p>Two specimens of lung adenocarcinoma, each corresponding to the lepidic and solid histologic patterns as confirmed through histologic scrutiny, were procured in accordance with standard surgical protocols. These specimens underwent a process of formalin fixation and were subsequently encapsulated within paraffin-embedded tissue blocks. The specimens were then sectioned and subjected to hematoxylin and eosin (H&E) staining to facilitate subsequent imaging at a resolution of 40x (equivalent to 0.25 micron/pixel) via the use of Aperio GT450 scanners. The tissue slides were then conveyed to the Genomics core, where following the decoverslipping of the tissue, the Visium CytAssist device was employed to transfer transcriptomic probes from the original glass slides to capture areas on Visium slides measuring 11mm x 11mm. Comprehensive transcriptomic profiling was achieved post mRNA permeabilization, through poly(A) capture and probe hybridization. The resultant libraries were sequenced utilizing the Illumina Novaseq 6000, using paired-end sequencing with a read length of 150 base pairs.</p>
F I G U R E 1 A in Linking plant functional traits to biodiversity under environmental change
F I G U R E 1 A diagram of the linkage between functional traits and biodiversity at multiple ecological scales. Across different scales, the diagram includes the response of functional traits to different environmental conditions, interactions under shifts in community structure and ecosystem functioning, which affect species' survival or extinction, and thus biodiversity. The diagram is constructed following a bottom‐up logic based on individual traits and aims to facilitate future trait‐diversity models to predict biodiversity responses under environmental change.
Table 1 in Review Of Bryophyte Functional Traits In Ecological Studies
<p><b>Table 1.</b> Overview of main bryophyte functional traits according to van Zuijlen et al. (2023).</p><table><tbody><tr><th>Biological traits</th><th><b>Ecological traits</b></th></tr></tbody><tbody><tr><th>generation length</th><td>aquatic species</td></tr><tr><th>growth form</th><td>epiphytic species or not</td></tr><tr><th>life form</th><td>how strong species are bound to forest habitats</td></tr><tr><th>life strategy</th><td>major habitat class “Artificial/Terrestrial”</td></tr><tr><th>peristome</th><td>major habitat class “Forest”</td></tr><tr><th>permanent protonema</th><td>major habitat class “Grassland”</td></tr><tr><th>rhizoids</th><td>major habitat class “Rocky areas”</td></tr><tr><th>r or K strategy</th><td>major habitat class “Shrubland”</td></tr><tr><th>length of the seta</th><td>major habitat class “Wetlands”</td></tr><tr><th>sexual condition</th><td>indicator value – moisture</td></tr><tr><th>sporophyte frequency</th><td>indicator value – heavy metal tolerance</td></tr><tr><th>shoot size</th><td>indicator value – continentality</td></tr><tr><th>spore size</th><td>indicator value – light</td></tr><tr><th>deciduous branches or stem tips</th><td>indicator value – nutrients</td></tr><tr><th>bulbils</th><td>indicator value – salt tolerance</td></tr><tr><th>gemmae</th><td>indicator value – temperature</td></tr><tr><th>deciduous leaves or leave fragments</th><td>substrate class: dead animal carcass or dung</td></tr><tr><th>tubers</th><td>substrate class: bark of living phanerophyte</td></tr><tr><th>size of vegetative propagule</th><td>substrate class: epiphytic on non­woody living substrate</td></tr><tr><th></th><td>substrate class: rock</td></tr><tr><th></th><td>substrate class: soil</td></tr><tr><th></th><td>substrate class: deadwood</td></tr></tbody></table>
Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer
<p><strong>Exposure expression quantitative trait loci (e2QTL)</strong></p> <p>The analysis of e2QTL allows for the identification of context-specific eQTL effects (Kim-Hellmuth et al. (2017), PMID: 28814792). To evaluate how inter-individual genetic variability influences the regulation of DNA damage-induced apoptosis, we performed e2QTL analysis of CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.</p> <p><code>eQTL_DNA_damage_induced_apoptosis.csv:</code> eQTL data. FastQTL was used to analyze cis-eQTL within a 1 MB window of a gene’s transcription start site. Filtering and normalization of expression data was performed as described by the Genotype Tissue Expression (GTEx) project (The GTEx Consortium (2015), PMID: 25954001) including 60 PEER factors, top 3 genotype PCs and sex as covariates. Genotypes were filtered by PHWE > 10-6 and MAF > 5 %. Adjusted p-values were generated using 1,000 to 10,000 permutations. Variant IDs (CHR:POS:REF:ALT) are based on GRCh38.</p> <p><code>e2QTL_DNA_damage_induced_apoptosis.csv:</code> e2QTL data. The most significant variant for each analyzed gene was determined based on eQTL data to calculate e2QTL in a z-test that were corrected for multiple testing using Bonferroni correction as described by Kim-Hellmuth et al. (2017). Variant IDs (CHR:POS:REF:ALT) are based on GRCh38.</p> <p> </p>
Inbreeding depression, functional traits and phenotypic plasticity in an endangered tree species from Congo basin with a mixed mating system
<h3><span>Inbreeding depression, functional traits and phenotypic plasticity in an endangered tree species from Congo basin with a mixed mating system</span></h3> <h1><a name="_Hlk166486742"></a><strong><span>Abstract</span></strong></h1> <p><span><span>1. Most tree species can suffer from inbreeding depression (ID), which they escape by reproducing predominantly through outcrossing. A remarkable exception is <em>Pericopsis elata</em>, an African timber species naturally producing 54% of self-fertilized seeds in the eastern Congo Basin. This species is highly logged and suffers from a deficit of natural regeneration, so that silviculture is needed for its sustainable management. While selecting good genetic material can increase the value of plantations, we lack fundamental biological knowledge on the effect of inbreeding and competition on growth potential, variability in leaf traits and phenotypic plasticity. We hypothesize that ID in <em>P. elata</em> could result from the expression of deleterious mutations affecting functional traits, or from a reduction of adaptive phenotypic plasticity in inbred genotypes.</span></span></p> <p><span><span>2. To test our hypotheses, 540 <em>P. elata</em> seedlings were monitored for 4 years in a Nelder-type device located in the DRC, in which trees were planted along concentric circles to generate a density gradient. Nine leaf morphological traits (including specific leaf area, stomata density and size), eight leaf chemical traits, diameter, and total height were measured regularly, while paternity analyses allowed distinguishing inbred and outbred plants. To explain the observed ID on growth, we tested whether inbreeding affected leaf traits and/or their plasticity expressed across years, across the density gradient or across sunlight exposure. </span></span></p> <p><span><span>3. Outbred plants grew faster than inbred ones, demonstrating ID for each level of competition. Despite the significant correlation found between specific leaf area and growth, and the impact of planting density, plant age, and leaf exposure to sunlight on multiple traits, mean leaf trait values did not differ according to inbreeding. However, </span></span><span><span>a few leaf traits (chlorophyl content, </span></span><span><span>maximum stomatal water vapor conductance</span></span><span><span>, and leaf fresh mass) showed significantly higher plasticity in outbred than inbred plants. </span></span></p> <p><span><span>4. Synthesis: the observed ID on growth was not explained by a direct effect of inbreeding on the mean values of functional traits but possibly by a reduction of phenotypic plasticity with inbreeding. Additional studies on the interplay between ID, functional traits and plasticity should be conducted at the intra-specific level to identify general patterns<em>.</em></span></span></p> <p><span><strong><span>Key-words : </span></strong></span><span><span>Inbreeding depression, phenotypic plasticity, silviculture, functionals traits, <em>Pericopsis elata</em>, mating system, Nelder device.</span></span></p>
Open database on traits and phylogenetic data on European pollinators
<p>(subtitle) data on wild bees, hoverflies and butterflies</p> <p>(abstract) This dataset was produced in the framework of the work package 1 (task 2) of the Horizon EU project Safeguard. The dataset encompassess trait data for three groups of pollinators: wild bees, hoverflies and butterflies, as well as phylogenetic data extracted from the GenBank. Information on traits comes from different literature sources, as well as direct measurements in collections and published databases. Some of the traits are common accross different species groups, while some traits are unique for particular group.</p> <p>(method) Litherature search and direct measurments on specimens.</p> <p>(dataset) This dataset compiles trait data for European wild bee, hoveverfly and butterfly species, and includes different categorical or numerical values for particular traits. It also contains phylogenetic information for species.</p>
Fig. 3. Character state maps for four traits. A in Phylogenetic revision of Dennstaedtioideae (Dennstaedtiaceae: Polypodiales) with description of Mucura, gen. nov.
Fig. 3. Character state maps for four traits. A, Spore shape: monolete (blue), trilete (yellow); B, Sorus position: abaxial (blue), marginal (yellow). C, Chromosome base number: 43 or 86 (light blue), 34 (blue), 46 or 47 (light green), 29 (green), 44 (pink), 30 (red), 31 (light orange), 32 (orange), 48 (light purple), 28 (purple), 56 (yellow), 26 (brown), 52 (magenta), 38 (aquamarine); D, Perpispore morphology: prominent ridges (light blue), prominent ridges and verrucae (blue), prominent ridges, verrucae + irregular reticles (light green), verrucae (orange), verrucae and ridges (green), regular reticles (pink), regular reticles + tubercles (red), echinae (purple), baculae (light yellow), ornamented verrucae (brown), rodlets (yellow), tubercles (aquamarine), rugulae (light brown). White circles indicate taxa for which character state data is missing.
Fig. 2. Character state maps for four traits. A in Phylogenetic revision of Dennstaedtioideae (Dennstaedtiaceae: Polypodiales) with description of Mucura, gen. nov.
Fig. 2. Character state maps for four traits. A, Abaxial indusium present (blue) vs. absent (yellow); B, Adaxial indusium present (blue) vs. absent (yellow); C, Epipetiolar buds present (blue) vs. absent (yellow); D, Leaf buds present (blue) vs. absent (yellow). White circles indicate taxa for which character state data is missing.
Data from: Show me you care: female mate choice based on egg attendance rather than male or territorial traits
Female mate choice is often based on male traits, including signals or behaviors, and/or the quality of a male's territory. In species with obligate paternal care, where care directly affects offspring survival, females may also base their mate choices on the quality of a sire's care. Here, we quantified male reproductive success in a natural population of the glassfrog Hyalinobatrachium cappellei, a species with male parental care, to determine the influence of territory quality, male traits, and paternal care behaviors on female mate choice. We found that attending males have a higher chance of gaining new clutches than non-attending males. Our results indicate that females do not select males based only on body condition, calling persistence, or territory traits. Instead, our findings support the hypothesis that females choose males based on care status. Indeed, males already attending a clutch were 70% more likely to obtain another clutch, and the time to acquire an additional clutch was significantly shorter. We also found that males adjust their parental care effort in response to genetic relatedness, by caring only for their own offspring; however, remaining close to unrelated clutches serves as a strategy to attract females and increase chances of successful mating. Thus, males that establish territories that already contain clutches benefit from the signal eggs provide to females.
Temporal dynamics of biodiversity effects and light-use related traits in two intercropping systems
<p>Dataset for "Temporal dynamics of biodiversity effects and light-use related traits in two intercropping systems"</p>
Drought stress triggers differential survival and functional trait responses in the establishment of Arnica montana seedlings
<ul> <li>The establishment and survival of seedlings are critical stages in the life cycle of plants and therefore usually well timed to humid and favourable conditions. Climate projections suggest that the threatened mountain grassland species <em>Arnica montana</em> may be increasingly exposed to drought stress. However, studies that focus on the species’ early development are missing. We evaluated impacts of drought-induced stress on <em>A. montana</em> seedlings in their early establishment phase and identified traits for the species’ fitness decline.</li> <li>In a greenhouse experiment, we tested the response of <em>A. montana</em> seedlings to different drought levels (moderate, strong, extreme). To assess their fitness under increasing drought, we evaluated the survival of the seedlings based on four senescence stages and measured the performance of above- and belowground morphological and physiological functional traits.</li> <li><em>Arnica montana</em> seedlings showed high resistance to drought. Senescence accelerated and survival declined only under strong and extreme drought conditions. However, the seedlings’ vegetative performance decreased even with moderate drought, as indicated by smaller values of most leaf traits and some root traits. Physiological trait response was less sensitive.</li> <li>Drought stress hinders the establishment and survival of <em>A. montana</em> seedlings. Following the functional trait responses to drought and their associations with survival, we suggest declining leaf length, leaf width, and leaf number as sensitive traits that can lead to a decline performance.</li> </ul>
Data from: Environmental conditions during development affect sexual selection through trait-fitness relationships
<p>Sexual selection can be shaped by spatial variation in environmental features among populations. Differences in sexual selection among populations generated through the effects of the environment could be shaped via four paths: differences in mean absolute fitness, differences in the means or variances of phenotypes, or differences in the absolute fitness-trait function relationship. Because sexual selection only occurs during the adult life stage, most studies have focused on identifying environmental features that influence these metrics of fitness and trait distributions among adults. However, these adult features could also be affected by environmental factors experienced in early life stages that then shape the trajectory for sexual selection during the adult life stage. Here we investigated how among-population variation in environmental conditions during the juvenile (larval) stage of two species of <i>Enallagma</i> damselflies shapes sexual selection on male body size. We found that environmental factors related to predation pressures, lake primary productivity, and habitat availability have a role in shaping spatial variation in sexual selection. This acts mainly through how the environment affects absolute fitness-body size associations, not spatial variation in mean fitness or body size means and variances. These results demonstrate that the underpinnings of sexual selection in the wild can arise from environmental conditions during pre-reproductive life stages.</p>
LT-Brazil: A database of leaf traits across biomes and vegetation types in Brazil
<p><span>Motivation: Leaf traits represent an important component of plant functional strategies, and those related to carbon fixation and nutrient acquisition form the leaf economics spectrum. However, observations of functional leaf traits are underrepresented in tropical regions in comparison with those in temperate areas. Brazil, a country with continental scale and vast biodiversity is a timely example, where many biomes are impacted by human activities and climate change. However, leaf traits relevant to understand vegetation responses to these impacts remain poorly quantified for many species found in the country. We compiled an extensive data set of four functional leaf traits for native woody species occurring in the Brazilian territory. In addition to trait observations, sampling dates and geo-references were compiled and climatic parameters and soil properties of each sampling site were extracted from several databases.</span></p> <p><span>Main types of variables contained: The LT-Brazil data set contains 3479, 1216, 775, and 775 clean observations of leaf mass per area, leaf nitrogen (N) concentration per unit mass, leaf phosphorus (P) concentration per unit mass, and leaf N : P ratio, respectively, from native woody species, encompassing information of biome, vegetation, taxonomic data, geographical coordinates, climatic parameters, as well as soil properties.</span></p> <p><span>Spatial location and grain: We compiled trait observations from 223 sites under native vegetation distributed in all main biomes (i.e., Amazônia, Caatinga, Cerrado, Mata Atlântica, Pampa, and Pantanal) across the Brazilian territory.</span></p> <p><span>Time period and grain: The data represent information published and/or sampled during the last 25 years.</span></p> <p><span>Major taxa and level of measurement: Our compilation was focused on trait data observed for native woody species, excluding monocots, palm trees, herbs, and hemiparasitic plants. Thus, 108, 478, and 1321 botanical families, genera, and species were included, covering <em>c.</em> 9% of the woody angiosperm flora of Brazil.</span></p> <p>Software format: Data are provided as comma-separated value (.csv) files.</p>
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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.