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1,226 results for “Intraspecific”
Data and code for: Rachel A Reeb, J Mason Heberling, & Sara E Kuebbing (2024). Cross-continental comparison of plant reproductive phenology shows high intraspecific variation in temperature sensitivity. AoB PLANTS, plae058
<p>Data and Analysis Code for: </p> <p>Rachel A Reeb, J Mason Heberling, Sara E Kuebbing (2024). Cross-continental comparison of plant reproductive phenology shows high intraspecific variation in temperature sensitivity. <em>AoB PLANTS</em>, plae058. <a href="https://doi.org/10.1093/aobpla/plae058">https://doi.org/10.1093/aobpla/plae058</a></p> <p>Includes two R markdown files ("climate_data_extraction_code.rmd" is the script for data extraction and cleaning and "Data_Analysis_V2.rmd" is the analysis script), the associated datasets (in .csv format), and the metadata file ("readme.txt").</p>
Non-genetically-based intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae
<p>We used next-generation sequencing to study DNA methylation and gene expression changes in plants from four clonal populations of the metallophyte moss <em>Scopelophila cataractae</em> experimentally exposed to either Cd or Cu. For this we performed reduced representation bisulfite DNA sequencing and RNA sequencing. </p>
Intraspecific variation in the sensitivity of bees to pesticides: a comparative analysis in Bombus terrestris and Osmia bicornis
<p>These files describe the archived CSV files associated with the publication "Intra-specific variation in sensitivity of Bombus terrestris and Osmia bicornis to three pesticides"</p> <p>By Alberto Linguadoca, Margret Jürison, Sara Hellström, Edward A. Straw1, Peter Šima, Reet Karise, Cecilia Costa, Giorgia Serra, Roberto Colombo, Robert J. Paxton, Marika Mänd, Mark J. F. Brown<br> </p>
Intraspecific variation in reproductive barriers between two closely-related Arabidopsis sister species
<p>Reproductive isolation (RI) is a critical component of speciation and varies strongly in timing and strength among different sister taxa, depending e.g.<em>,</em> on the geography of speciation and divergence time. However, these factors may also produce variation in timing and strength among populations within species. Here we tested for variation in the expression of RI among replicate population pairs between the sister taxa <em>Arabidopsis lyrata</em> subsp. <em>lyrata</em> and <em>A. arenicola</em>. While the former is predominantly outcrossing, the latter is predominantly selfing<em>.</em> We focused on intrinsic prezygotic and postzygotic RI as both species occur largely in allopatry. We assessed RI by performing within-population crosses and interspecific between-population crosses, and by raising offspring. RI was generally high between all interspecific population pairs, but it varied in timing and strength depending on population history. Prezygotic isolation was strongest between the closest-related population pair, while early postzygotic isolation was high for all other population pairs. Furthermore, the timing and strength of RI depended strongly on cross direction. Our study provides empirical support that reproductive barriers between species are highly variable among population pairs and asymmetric within population pairs, and this variation seems to follow patterns typically described across species pairs.</p>
The role of the intraspecific variability of hydraulic traits for modelling the plant water use in different European forest ecosystems: scripts, model output, and parameter files
<p>This repository contains the model outputs and R scripts used to process the data to analyze the impact of the plant hydraulic parameterization of the manuscript: "The role of the intraspecific variability of hydraulic traits for modelling the plant water use in different European forest ecosystems". The following is a detailed description of the content of this repository:</p> <p>model_output.zip: This compressed file contains the results of all the individual numerical experiments per experimental site as produced by the Comunity Land Model version 5. The files are stored in NETCDF format per year. The folder is arranged with subfolders containing the individual results from each experimental site as follows:</p> <ul> <li>rc: model output with the results of the resistant configuration of experiment 1 (RC)</li> <li>vc: model output with the results of the vulnerable configuration of experiment 1 (VC)</li> <li>k_dc: model output with the results of the default configuration used for experiments 1 and 2 (DC or DC<em>k</em><sub>max</sub>)</li> <li>k_rc: model output with the results of the low plant hydraulic conductance (L<em>k</em><sub>max</sub>) for experiment 2</li> <li>k_irc: model output with the results of the intermediate low plant hydraulic conductance (IL<em>k</em><sub>max</sub>) for experiment 2</li> <li>k_vc: model output with the results of the high plant hydraulic conductance (H<em>k</em><sub>max</sub>) for experiment 2</li> <li>k_ivc: model output with the results of the intermediate high plant hydraulic conductance (IH<em>k</em><sub>max</sub>) for experiment 2</li> <li>k_iirc: model output with the results of the additional intermediate low plant hydraulic conductance (IIL<em>k</em><sub>max</sub>) for experiment 2</li> <li>ko_dc: model output with the results of the best <em>k</em><sub>max</sub> and the default configuration of the PVC used in experiment 3</li> <li>ko_rc: model output with the results of the best <em>k</em><sub>max</sub> and the resistant configuration of the PVC used in experiment 3</li> <li>ko_vc: model output with the results of the best <em>k</em><sub>max</sub> and the vulnerable configuration of the PVC used in experiment 3</li> </ul> <p>The scripts were written for use in RStudio, and each contains a detailed description of the data requirements and outputs. Each script was developed to read directly the netcdf files of the model output and the csv files containing the transpiration estimates calculated from the SAPFLUXNET per experimental site (script 1).</p>
Raw data used in Kumar et al. 2020: Barley shoot biomass responds strongly to N:P stoichiometry and intraspecific competition, whereas roots only alter their foraging
<p>Raw data used in Kumar et al. 2020: Barley shoot biomass responds strongly to N:P stoichiometry and intraspecific competition, whereas roots only alter their foraging</p>
Fig. 2 in Intraspecific food resource partitioning in Brazilian silverside Atherinella brasiliensis (Atheriniformes: Atherinopsidae) in a tropical estuary, Brazil
Fig. 2. Box-plot of spatial and temporal variation of number of individuals (CPUE average ±SE) and Biomass (±SE) of A. brasiliensis collected Mamanguape river estuary in Brazil. Bold lines indicate medians, hinges indicate the 25th and 75th percentiles, whiskers indicate the largest and smallest observation within a distance of 1.5 the box size. White bar= Wet season and Dark Gray bar= Dry season.
Fig. 5 in Intraspecific food resource partitioning in Brazilian silverside Atherinella brasiliensis (Atheriniformes: Atherinopsidae) in a tropical estuary, Brazil
Fig. 5. Principal coordinate analysis ordination (PCO) coded by habitat (a) and size classes (b) for Atherinella brasiliensis in the Mamanguape River estuary, Brazil. Symbols Habitat: Mud flat (Full Black Triangle); Tidal Creek 1 (Gray Square); Tidal Creek 2 (Black Circle); Symbols size classes: Small juveniles (Open Black Square); Juveniles (Light Gray Circle) and Adults (Dark Gray Circle).
Fig. 7 in Intraspecific food resource partitioning in Brazilian silverside Atherinella brasiliensis (Atheriniformes: Atherinopsidae) in a tropical estuary, Brazil
Fig. 7. Feeding strategy for Atherinella brasiliensis in Mamanguape river estuary: A= Mudflat; B= Tidal Creek 1 and C= Tidal Creek 2. Food items: Cyc, Cyclopoida; Cal, Calanoida; Dec, Decapoda; Decl, Decapoda larvae; Hym, Hymnoptera; Egf, Fish eggs; Cer, Ceratopogonidae larvae; Ost, Ostracoda; Gas, Gastropoda; Pol, Polychaeta; Esc, Scale. (TL1= small juveniles; TL2= juveniles and TL3= adult).
Figure 1 in Intraspecific larval aggression in two species of Hyperini (Coleoptera: Curculionidae)
Figure 1. The number of fights observed in experiments with groups of Hypera postica larvae of various instars (L1–L4), in the presence (plain boxes) or absence (hatched boxes) of food (leaves of Medicago sativa). Filled circles and squares indicate the mean, boxes indicate confidence intervals, whiskers show the non-outlier range and empty circles represent outliers.
Figure 2 in Intraspecific larval aggression in two species of Hyperini (Coleoptera: Curculionidae)
Figure 2. The number of fights observed in experiments with mixed-instar groups of Hypera postica larvae in the presence or absence of food (leaves of Medicago sativa). Filled circles indicate the mean value, boxes show the confidence intervals, whiskers represent the nonoutlier range and empty circles represent outliers.
Figure 3. A in Intraspecific larval aggression in two species of Hyperini (Coleoptera: Curculionidae)
Figure 3. A summary of the possible behaviours of each instar of Hypera postica (L1, L2, L3, L4a and L4b).
Data from: Heat tolerance is more variable than cold tolerance across species of Iberian lizards after controlling for intraspecific variation
<ol> <li>The widespread observation that heat tolerance is less variable than cold tolerance ('cold-tolerance asymmetry') leads to the prediction that species exposed to temperatures near their thermal maxima should have reduced evolutionary potential for adapting to climate warming. However, the prediction is largely supported by species-level global studies based on single estimates of both physiological metrics per taxon.</li> <li>We ask if cold-tolerance asymmetry holds for Iberian lizards after accounting for intraspecific variation in critical thermal maxima (CT<i><sub>max</sub></i>) and minima (CT<i><sub>min</sub></i>). To do so, we quantified CT<i><sub>max</sub></i> and CT<i><sub>min</sub></i> for 58 populations of 15 Iberian lizard species (299 individuals). Then, we randomly selected one population from each study species (population sample = 15 CT<i><sub>max</sub></i> and CT<i><sub>min</sub></i> values), tested for variance homoscedasticity across species, and repeated the test for thousands of population samples as if we had undertaken the same study thousands of times, each time sampling one different population per species.</li> <li>The ratio of variances in CT<i><sub>max</sub></i> to CT<i><sub>min</sub></i> across species varied up to 16-fold depending on the populations chosen. Variance ratios show how much CT<i><sub>max</sub></i> departs from the cross-species mean compared to CT<i><sub>min</sub></i>, with a unitary ratio indicating equal variance of both thermal limits. Sampling one population per species was six times more likely to result in the observation of greater CT<i><sub>max</sub></i> variance ('heat-tolerance asymmetry') than cold-tolerance asymmetry. The null hypothesis of equal variance was twice as likely for cases of cold-tolerance asymmetry than for the opposite scenario.</li> <li>Range-wide, population-level studies that quantify heat and cold tolerance of individual species are urgently needed to ascertain the global prevalence of cold-tolerance asymmetry. While broad latitudinal clines of cold tolerance have been strongly supported, heat tolerance might respond to smaller-scale climatic and habitat factors hence go unnoticed in global studies. Studies investigating physiological responses to climate change should incorporate the extent to which thermal traits are characteristic of individuals, populations and/or species.</li> </ol>
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
<p>The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent‐coverage threshold to filter out false positives, (b) an internal‐standard DNA spike‐in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R<sup>2</sup> = .93, mitogenomes R<sup>2</sup> = .95) and a high repeatability across environmental‐sample replicates (barcodes R<sup>2</sup> = .94, mitogenomes R<sup>2</sup> = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species‐specific abundances, and phenology. SPIKEPIPE provides cost‐efficient and reliable quantification of eukaryotic communities.</p>
Data from: Assessing the contributions of intraspecific and environmental sources of infection in urban wildlife: Salmonella enterica and white ibis as a case study
Conversion of natural habitats into urban landscapes can expose wildlife to novel pathogens and alter pathogen transmission pathways. Because transmission is difficult to quantify for many wildlife pathogens, mathematical models paired with field observations can help select among competing transmission pathways that might operate in urban landscapes. Here we develop a mathematical model for the enteric bacteria Salmonella enterica in urban-foraging white ibis (Eudocimus albus) in south Florida as a case study to determine (i) the relative importance of contact-based versus environmental transmission among ibis and (ii) whether transmission can be supported by ibis alone or requires external sources of infection. We use biannual field prevalence data to restrict model outputs generated from a Latin hypercube sample of parameter space and select among competing transmission scenarios. We find the most support for transmission from environmental uptake rather than between-host contact and that ibis–ibis transmission alone could maintain low infection prevalence. Our analysis provides the first parameter estimates for Salmonella shedding and uptake in a wild bird and provides a key starting point for predicting how ibis response to urbanization alters their exposure to a multi-host zoonotic enteric pathogen. More broadly, our study provides an analytical roadmap to assess transmission pathways of multi-host wildlife pathogens in the face of scarce infection data.
Interspecific introgression and widespread intraspecific gene flow in a clade of tropical and subtropical seabirds
<p>The mechanisms that restrict gene flow between populations and facilitate population differentiation and speciation vary across the tree of life. In systems where physical barriers to gene flow are dynamic over time and space, such as many marine species, genetic introgression may be a major factor in the speciation process. In sympatric species of seabirds, hybridization has been frequently observed but few studies have investigated patterns of introgression. We used whole-genome sequence data to test for interspecific introgression between five pairs of tropical and subtropical seabird species and to test for gene flow within species across major land mass barriers and ocean basins. We found evidence for introgression between: blue-footed (<em>Sula</em> <em>nebouxii</em>) and Peruvian boobies (<em>S. variegata</em>); masked (<em>S. dactylatra</em>) and Nazca boobies (<em>S. granti</em>); and blue-footed and Nazca boobies. We found no evidence of introgression between blue-footed and brown boobies (<em>S. leucogaster</em>), or masked and brown boobies, despite observed hybridization between these species. We also found evidence for gene flow across several major land masses in three pantropical species: red-footed (<em>S. sula</em>), brown, and masked boobies. Finally, we report mixed evidence for ancient introgression between brown boobies and the ancestor of blue-footed, Peruvian, masked, and Nazca boobies. Our work indicates (1) that interspecific introgression has shaped contemporary booby diversity in the eastern Pacific, and (2) that contemporary physical barriers to gene flow between booby colonies are not absolute. Our findings contribute novel insights to the growing body of evidence that introgression is a widespread evolutionary process.</p>
Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex
<p>When using the data or code from this manuscript, please cite it as:</p><p><strong>Leiva FP</strong>, Santos M, Rezende E, & Verberk WCEP. 2021. Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex. Zenodo. <a href="https://doi.org/10.5281/zenodo.5120028">https://doi.org/10.5281/zenodo.5120028</a>.</p>
Solitary foundation or colony fission in ants: an intraspecific study shows that worker presence and number increase colony foundation success
<p>Datasets for the paper published in Oecologia entitled "Solitary foundation or colony fission in ants: an intraspecific study shows that worker presence and number increase colony foundation success"</p> <p>Script_article.R : R code to analyze the data</p> <p>Data.txt : Growth data</p> <p>donnees_survie.txt : Survival data</p> <p>donnees_presence_nid.txt : Data of the presence of queens in the nest</p>
Figure 5 in Junior synonymy of Mulloides armatus and intraspecific comparisons of the yellowstripe goatfish Mulloidichthys flavolineatus (Mullidae) using a comprehensive alpha-taxonomy approach
Figure 5. – Results of PCA for Mulloidichthys flavolineatus body shape showing (A) relationships between SL and the first principal component (PC1) and (B) relationships between the second to fourth principal components (PC2-4). The subspecies M. f. flavicaudus and populations of M. f. flavolineatus from selected regions are indicated by different symbols. The dashed line encloses M. f. flavicaudus and the dotted line encloses the population of M. f. flavolineatus from the entire Pacific.
Figure 4 in Junior synonymy of Mulloides armatus and intraspecific comparisons of the yellowstripe goatfish Mulloidichthys flavolineatus (Mullidae) using a comprehensive alpha-taxonomy approach
Figure 4. – Standard length against five morphometric characters and one meristic character in Mulloidichthys flavolineatus and the HT of M. armatus with distinction of M. f. flavicaudus and populations of M. f. flavolineatus from selected regions by different symbols. The hatched line indicates the minimum size for adult/subadult fish.
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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.