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118 results for “environmental determinism”
Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams
<p>DNA were derived from fin tissue samples taken from individual trout captured from Little Jacks Creek, Big Jacks Creek , and Duncan Creek of the Owyhee mountains and Keithly Creek and Upper Mann Creek in the Hitt mountains of Western Idaho, United States. Fin tissues were collected from individual trout from each stream during monthly sampling events in June through October 2020. </p> <p><em>DNA Extraction:</em> Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.©). Small sections of fin tissue (≤ 25 mg) were collected from each sample. This was mixed with a digesting solution comprised of ultra-pure water, solid tissue buffer (Zymo Research Inc.©) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55°C in a water bath. We then aliquoted 100 µL of digestion supernatant and combined with 200 µL of genomic binding buffer (Zymo Research Inc.©). DNA was eluted in 50, 75, and 100 µL of elution buffer to determine which volume provided sufficient DNA concentration for genotyping. After it was determined all quantities produced suitable concentrations, going forward, 50 µL of elution buffer used.</p> <p><em>Genotyping:</em> Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery’s genetics research facility with the assistance of the Columbia River Intertribal Fish Commission (CRTFC). Genotyping protocols were as described in Campbell et al. (2015) and summarized below. First, samples were prepared for amplification via PCR by combining DNA extracts with a Qiagen Plus multiplex master mix and a species-specific pooled primer mix. This step added the Illumina sequencing primer sites to amplicons. Following the creation of the PCR cocktail, thermocycling was conducted for amplification. Amplified samples were then diluted 20-fold. Diluted samples were transferred to new 96-well PCR plates where two genetic indexes and barcodes provides a unique set of tagging primers to each well and plate. Tagged plates then underwent a second PCR step. After the second PCR, all DNA were transferred to Charm Biotech normalization plates where DNA was bound to wells, washed, and finally eluted. After normalization, all DNA was pooled together and a purification step using magnetized beads in two steps to selectively remove fragments of DNA that are both too large and too small for sequencing. Following purification, each plate was quantified via qPCR using Life Technologies QuantStudio 6 Flex Instrument (Life Technologies). Finally, sequencing was performed using an Illumina HiSeq 1500 instrument.</p> <p><strong>Ancillary peer-reviewed manuscripts:</strong><br> <em>Genotyping protocols</em><br> Campbell NR, Harmon SA, Narum SR. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour, 15: 855-867. https://doi.org/10.1111/1755-0998.12357<br> <em>SNP loci reference</em><br> Collins EE, Hargrove JS, Delomas TA, Narum SR. 2020. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecology and Evolution, 10(17): 9486-9502. https://doi.org/10.1002/ece3.6641 </p> <p><strong>Data Use</strong>:<br> <em>License</em>: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> <br> <em>Recommended Citation</em>: Wooding AP, Narum SR, Pradhan DS. 2022. Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7055582</p> <p>Funding for this project is provided by US National Science Foundation and Idaho EPSCoR through award: OIA-1757324 </p>
Fig. 3 in Environmental determinants of spatial and temporal variations in the transmission of Toxoplasma gondii in its definitive hosts
Fig. 3. Predicted relationships between NAO winter index and the probability of seropositivity for Toxoplasma gondii in all cats sampled; (a) juveniles and (b) adults. Points represent the observed seoprevalence values with 95% confidence intervals as whiskers. A median farm density (0.68 farm/km2) was used to calculate the predictions (full line). Minimal farm density (0 farm/km2) observed among sampled communes was used to calculate the minimal predictions of the model (dotted lines). High values of farm density (2 and 4 farms/km2) were used to calculate the maximal predictions of the model (dashed and dotted-dashed lines).
Fig. 2 in Environmental determinants of spatial and temporal variations in the transmission of Toxoplasma gondii in its definitive hosts
Fig. 2. Interannual variations in Toxoplasma gondii seroprevalence in the three types of cats standardised by age (bars) during the study period. Line segments represent the 95% confidence intervals for seroprevalence, and the numbers in brackets indicate the sample sizes. Wildcats (Felis s. silvestris), domestic cats (Felis s. catus) and hybrids are pooled.
Fig. 1 in Environmental determinants of spatial and temporal variations in the transmission of Toxoplasma gondii in its definitive hosts
Fig. 1. European wildcat (Felis s. silvestris) distribution in France (grey area; Léger et al., 2008; Say et al., 2012), and locations of samples from domestic cats (Felis s. catus), wildcats and their hybrids. Cat types are represented by different symbols (see the bottom left of the map). One location might correspond to several individuals (1, 2, 3, or 8), the size of the dot being proportional to the number (indicated at the right of the symbols) of individuals collected in each commune.
Fig. 2 in Environmental determinants affecting the occurrence of defoliator caterpillars on Eucalyptus (Myrtaceae) plantations in the Brazilian Amazonian region
Fig. 2. Average annual growth of Eucalyptus urophylla (Myrtaceae) trees (m3 of wood per ha per yr) as a function of the total number of Lepidoptera individuals collected per light trap (Almeirim Municipality, Pará State, and Laranjal do Jari Municipality, Amapá State, Brazil).
Fig. 3 in Environmental determinants affecting the occurrence of defoliator caterpillars on Eucalyptus (Myrtaceae) plantations in the Brazilian Amazonian region
Fig. 3. Total number of individuals of the 2 Lepidoptera primary pests, Misogada bleura (Lepidoptera: Notodontidae) and Sarsina violascens (Lepidoptera: Lymantriidae), collected with light traps in Eucalyptus urophylla (Myrtaceae) plantations as a function of the distance from the area of native vegetation (Almeirim Municipality, Pará State, and Laranjal do Jari Municipality, Amapá State, Brazil).
Fig. 1 in Environmental determinants affecting the occurrence of defoliator caterpillars on Eucalyptus (Myrtaceae) plantations in the Brazilian Amazonian region
Fig. 1. Number of Oxydia vesulia (Lepidoptera: Geometridae) and Sarsina violascens (Lepidoptera: Lymantriidae) adults collected with light traps in Eucalyptus urophylla (Myrtaceae) plantations as a function of the number of rotations of this plant in the same area. (Almeirim Municipality, Pará State, and Laranjal do Jari Municipality, Amapá State, Brazil).
FIGURE 1 in Taxonomic and functional turnover of Amazonian stream fish assemblages is determined by deforestation history and environmental variables at multiple scales
FIGURE 1 | Sampled sites and forest fragments in the Machado River basin, Brazil. The inset map of Brazil depicts the relative location of the study area (black) within the Madeira River basin (dark gray), inside the Amazon biome (light gray).
FIGURE 4 in Taxonomic and functional turnover of Amazonian stream fish assemblages is determined by deforestation history and environmental variables at multiple scales
FIGURE 4 | Explained variation of environmental contribution in turnover metrics partitioned by MRM and associated commonality analysis into pure local, shared and pure catchment components. RC = Raup-Crick; MPD = mean pairwise distance; MNTD = mean nearest taxon distance; all = all sampled streams; ref = streams with forested watersheds; new = streams with recently deforested watersheds; old = streams with historically deforested watersheds.
FIGURE 2 in Taxonomic and functional turnover of Amazonian stream fish assemblages is determined by deforestation history and environmental variables at multiple scales
FIGURE 2 | Distribution of sampling sites with (A) forest patches ranked according to the forest quality multimetric index and (B) effective forest cover. Non-forested area is white and is not included in the multimetric index calculation (or legend).
FIGURE 3 in Taxonomic and functional turnover of Amazonian stream fish assemblages is determined by deforestation history and environmental variables at multiple scales
FIGURE 3 | Standardized effect sizes for each taxonomic and functional turnover metric (mean and 95% confidence intervals). RC = Raup-Crick; MPD = mean pairwise distance; MNTD = mean nearest taxon distance; ref = streams with forested watersheds; new = streams with recently deforested watersheds; old = streams with historically deforested watersheds.
Linked collectors and determiners for: Estonian University of Life Sciences Institute of Agricultural and Environmental Sciences Mycological Herbarium.
Natural history specimen data linked to collectors and determiners held within, "Estonian University of Life Sciences Institute of Agricultural and Environmental Sciences Mycological Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1f917113-dd55-4000-9f80-6266fab1af03">https://bionomia.net/dataset/1f917113-dd55-4000-9f80-6266fab1af03</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1f917113-dd55-4000-9f80-6266fab1af03">https://gbif.org/dataset/1f917113-dd55-4000-9f80-6266fab1af03</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Estonian University of Life Sciences Institute of Agricultural and Environmental Sciences Entomological Collection.
Natural history specimen data linked to collectors and determiners held within, "Estonian University of Life Sciences Institute of Agricultural and Environmental Sciences Entomological Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1af83152-24f7-4df7-afbc-b213b62175bb">https://bionomia.net/dataset/1af83152-24f7-4df7-afbc-b213b62175bb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1af83152-24f7-4df7-afbc-b213b62175bb">https://gbif.org/dataset/1af83152-24f7-4df7-afbc-b213b62175bb</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Estonian University of Life Sciences Institute of Agricultural and Environmental Sciences Department of Plant Protection.
Natural history specimen data linked to collectors and determiners held within, "Estonian University of Life Sciences Institute of Agricultural and Environmental Sciences Department of Plant Protection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/91afc73f-a11a-4e8b-9313-ed056697cf05">https://bionomia.net/dataset/91afc73f-a11a-4e8b-9313-ed056697cf05</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/91afc73f-a11a-4e8b-9313-ed056697cf05">https://gbif.org/dataset/91afc73f-a11a-4e8b-9313-ed056697cf05</a>. Formatted as a Frictionless Data package.
Environmental and food web determinants of Lake Trout mercury concentrations in Ontario Lakes
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Data from: Potential drivers and implications of a balanced breeding sex ratio in a small population of an imperiled species with environmental sex determination
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Environmental determinants of leaf-litter ant community composition along an elevational gradient
Ant communities are extremely diverse and provide a wide variety of ecological functions in tropical forests. Here we investigated the abiotic factors driving ant composition turnover across an elevational gradient at Mont Itoupé, French Guiana. Mont Itoupé is an isolated mountain whose top is covered by cloud forests, a biogeographical rarity that is likely to be threatened according to climate change scenarios in the region. We examined the influence of six soil, climatic and LiDAR-derived vegetation structure variables on leaf-litter ant assembly (267 species) across nine 0.12-ha plots disposed at three elevations (ca. 400, 600 and 800m asl). We tested (a) whether species co-occurring within a same plot or a same elevation were more similar in terms of taxonomic, functional and phylogenetic composition, than species from different plots/elevations, and (b) which environmental variables significantly explained compositional turnover among plots. We found that the distribution of species and traits of ant communities along the elevational gradient was significantly explained by a turnover of environmental conditions, particularly in soil phosphorus and sand content, canopy height and mean annual relative humidity of soil. Our results shed light on the role exerted by environmental filtering in shaping ant community assembly in tropical forests. Identifying the environmental determinants of ant species distribution along tropical elevational gradients could help predicting the future impacts of global warming on biodiversity organization in vulnerable environments such as cloud forests.
Data from: Environmental gradients determine the potential for ecosystem engineering effects
Understanding processes that determine biodiversity is a fundamental challenge in ecology. At the landscape scale, physical alteration of ecosystems by organisms, called ecosystem engineering, enhances biodiversity worldwide by increasing heterogeneity in resource conditions and enhancing species coexistence across engineered and non-engineered habitats. Engineering-diversity relationships can vary along environmental gradients due to changes in the amount of physical structuring created by ecosystem engineering, but it is unclear how this variation is influenced by the responsiveness of non-structural abiotic properties to engineering. Here we show that environmental gradients determine the capacity for engineering to alter resource availability and species diversity, independent of the magnitude of structural change produced by engineering. We created an experimental rainfall gradient in an arid grassland where rodents restructure soils by constructing large, long-lasting burrows. We found that greater rainfall increased water availability and productivity in both burrow and inter-burrow habitats, causing a decline in local (alpha) plant diversity within both of these habitats. However, increased rainfall also resulted in greater differences in soil resources between burrow and inter-burrow habitats, which increased species turnover (beta diversity) across habitats and stabilized landscape-level (gamma) diversity. These responses occurred regardless of rodent presence and without changes in the extent of physical alteration of soils by rodents. Our results suggest that environmental gradients can influence the effects of ecosystem engineering in maintaining biodiversity via resource heterogeneity and species turnover. In an era of rapid environmental change, accounting for this interaction may be critical to conservation and management.
Environmental, sex-specific, and genetic determinants of infant social behavior in a wild primate
<p>Affiliative social bonds are linked to fitness components in many social mammals. However, despite their importance, little is known about how the tendency to form social bonds develops in young animals, or if the timing of development is heritable and thus can evolve. Using four decades of longitudinal observational data from a wild baboon population, we assessed the environmental determinants of an important social developmental milestone in baboons—the age at which a young animal first grooms a conspecific—and we assessed how the rates at which offspring groom their mothers develops during the juvenile period. We found that grooming development differs between the sexes: female infants groom at an earlier age and reach equal rates of grooming with their mother earlier than males. We also found that age at first grooming for both sexes is weakly heritable (h<sup>2</sup> = 0.043, 95% CI: 0.002 – 0.110). These results show that sex differences in grooming emerge at a young age; that strong, equitable social relationships between mothers and daughters begin very early in life; and that age at first grooming is heritable and therefore can be shaped by natural selection.</p>
Habitat area and environmental filters determine avian richness along an elevation gradient in mountain peatlands
<p>Globally, relationships between avian richness and elevation in mountain ecosystems typically reflect one of four well-documented patterns, but the mechanisms responsible for these patterns are poorly understood. We investigated which pattern best described bird species richness in peatlands of the Upper Bow Basin of the Canadian Rocky Mountains (1300 to 2000 m a.s.l.) and used a model competition framework to investigate possible mechanisms. Avian richness displayed a plateauing (cubic) relationship in response to increasing elevation (AICc weight = 0.48). Log richness was significantly positively related to log peatland area (R<sup>2</sup> = 0.42, p = 0.001); however, once we accounted for the richness-area relationship (area was not related to elevation (R<sup>2</sup> = 0.13, p = 0.083)), the richness-elevation relationship was best described by a negative linear model rather than a cubic model (AICc weight = 0.69, R<sup>2</sup> = 0.39). Consequently, we reject the neutral model of the mid-domain effect and conclude that peatland area and one or more environmental filters are simultaneously driving relationships between avian richness and elevation in Rocky Mountain peatlands. Multi-causality likely explains why researchers in different geographies observe inconsistent patterns between richness and elevation: drivers and interactions among drivers may vary spatially. Importantly, Natural Subregion was a stronger predictor of avian species richness than elevation per se (AICc weight = 0.96), suggesting that the responsible environmental filter(s) is relatively homogenous within ecological land classes (e.g., primary productivity) rather than directly variable with elevation (e.g., temperature). The results also lend insight into priorities for future research on richness-elevation patterns in mountain birds.</p>
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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.