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262 results for “environmental variation”
Detecting local variations across metazoan communities in backreef depressions of Reunion Island (Mascarene Archipelago) through environmental DNA survey
<p>The back-reef depressions, or lagoons, of Reunion Island (western Indian Ocean) host a high abundance of organisms living amongst the coral reefs and are critical sites for artisanal fishing, tourism, and shoreline stability for the island. Over time, increasing degradation of Reunionese reefs has been observed due to overexploitation, beach erosion and eutrophication. Efforts to mitigate the impact of these pressures on aquatic organisms include biodiversity surveys primarily performed through visual censuses that can be logistically complex and may unintentionally overlook organisms. Surveys integrating environmental DNA (eDNA) collections have provided rapid biodiversity assessments, while helping to circumvent some limitations of visual surveys. The present study describes the results of an exploratory eDNA survey, which aims to characterize metazoan communities of four Reunionese lagoons located along the west coast of the island. As eDNA surveys first require deliberate study design and optimization for each new context, we sought to establish a modernized workflow implementing specialized equipment to collect and preserve samples to facilitate future studies in these lagoons. During the austral summer of 2023, samples were pumped directly from surface and bottom depths at each site through self-preserving filters which were then processed for DNA metabarcoding using regions of the 12S ribosomal RNA (12S), small ribosomal subunit 18S (18S) and Cytochrome Oxidase I (COI) genes. The survey detected high species richness that varied by site, and in a single collection period, recovered the presence of 60 teleost families and numerous invertebrate taxa, including members of the coral faunal community that are less studied in Reunion. Distinct biological communities were observed at each site, and within a single lagoon, suggesting that these differences are due to site-specific factors (e.g., environmental variables, geographic distance, etc.). Although continued protocol optimization is needed, the present findings demonstrate the successful application of an eDNA-based survey for biodiversity assessment within Reunionese lagoons.</p>
Dataset _ Influence of the seasonal variation of environmental conditions on biogas upgrading in an outdoors pilot scale high rate algal pond
<p>This is the dataset used for the publication of the journal article title<em> “</em><strong>Influence of the seasonal variation of environmental conditions on biogas upgrading in an outdoors pilot scale high rate algal pond”. </strong>In this dataset there is all the information collected in the experimentation process.</p>
Data on specialist and generalist herbivory, environmental variation, and phytochemical similarity from the Atlantic Rainforest of Brazil: 2013-2014
What: These are data on specialist and generalist herbivory from naturally occurring Piper plants as well as environmental data collected in 10 m diameter plots across sites in the Atlantic Rainforest of Brazil. Data also include chemical similarity calculated as the Morisita similarity index for species in a given plot and chemical modules that demonstrate classes of compounds that group together and influence herbivory. Why: Data were collected to understand factors that influence herbivory and tropical forest richness with a particular focus on secondary chemistry metabolomics. Where: Field sites include São Bento de Sapucaí (-22.8758, -45.8581), Parque Nacional de Itatiaia (-22.3698, -44.6285), Parque Estadual de Intervales (-24.3088, -48.2736), and Parque Estadual de Serra do Mar - Núcleo Pincinguaba (-23.6200, -46.7222). When: Data were collected in the field from Dec 2013 – May 2014. How: Field data were collected in 10 m diameter plots centered on randomly located Piper plants. Chemical data come from 1H-NMR metabolomics.
Phenotypic plasticity in response to fine-grained environmental variation in predation.
1. In nature, organisms experience environmental variability at coarse-grained (inter-generational) and fine-grained (intra-generational) scales and a common response to environmental variation is phenotypic plasticity. The emphasis of most empirical work on plasticity has been on examining coarse-grained variation with the goal of understanding the costs and benefits of plastic responses in response to a particular environment. 2. In this study, we investigated the effects of fine-grained variation in predation on the inducible defences of larval wood frogs (Rana sylvatica) by widely altering the density and feeding schedule of caged predators (Dytiscusspp.) while holding average predation constant. 3. We found that predator cues induced change in tadpole behaviour, morphology, and mass. Surprisingly, however, temporal variation in predation did not cause the tadpoles to alter their activity (compared to a constant predation treatment) or mass. Temporal variation in predation did alter tadpole tail depth, but only when experiencing our most extreme variation treatment in which the predators were fed once every 8 days. Under these conditions, the predator-induced tadpole tail was less extreme compared to environments containing constant predation. 4. While a number of previous studies have examined behavioural responses of prey to temporal variation in predation risk without holding average predation constant, this appears to be the first test of temporal variation per se. As in previous studies of organism responses to temporal variation in resources, our results suggest that fine-grained environmental variability can affect the expression of phenotypically plastic traits, but our tadpoles appear to be generally unresponsive to this finegrained variation for many of their traits.
Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities
<p>Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by the environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. For this purpose, we generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high Arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more likely reflect interactive associations. Our results indicate that positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.</p>
Neglected patterns of variation in transgenerational plasticity: The importance of different sources of environmental variation differs across ages and sexes in a cyprinid fish
<p>Adaptive transgenerational plasticity (TGP) requires individuals to integrate environmental experience across multiple sources. However, few empirical studies have considered that the relative relevance of certain sources might vary across ontogeny and sexes.</p> <p>Here, we address this knowledge gap by studying inducible antipredator defenses, one of the most convincing examples of TGP. We assessed individual and combined effects of perceived high predation risk in mothers, fathers, caring males and personal environments on the morphology of juvenile, adult male and adult female cyprinids Pimephales promelas.</p> <p>Parental rather than personal environmental experience determined morphological defense expression across ages and sexes, likely because parents had a longer sampling period.</p> <p>In juveniles and adult males, egg-mediated environmental experience outweighed sperm-mediated environmental experience in the induction of body shape differences, likely because eggs can transmit information beyond epigenomes. However, in adult females, where body shape responses can be interpreted as life-history plasticity, information from egg and sperm were equally important, likely resulting from different integration mechanisms between morphological and life-history plasticity.</p> <p>The importance of care-mediated relative to gamete-mediated variation changed between juveniles and adult males, likely because they represent short- and long-term environmental experience, respectively. Instead, in adult females, both sources were again equally important, potentially owing to lag-times of life-history plasticity. Parental care intensity only contributed marginally to defense formation.</p> <p>These results highlight age- and sex-specific prioritization of different environmental experiences so as to generate optimal phenotypes.</p>
Data from: Environmental variation associated with topography explains butterfly diversity along a tropical elevation gradient
<p>Few studies have evaluated the role of topography on the diversity patterns of biological communities along elevation gradients. We evaluated the influence of microclimate and vegetation structure associated with topographic variation on the richness and composition of species of different families of butterflies on a mountain located in a dry enclave (Chicamocha River Canyon) in the northern Andes, Colombia. We captured butterflies over four months at 18 elevations (300 to 1500 m a.s.l.) in two topographic positions (riverbed and hillslope) using an entomological net and traps baited with fermented fruit. In general, butterfly richness increased with elevation in both topographic positions. However, the richness-elevation relationship changed with butterfly family. The riverbed and hillslope sites host different assemblages of butterflies, and this pattern that was consistent for most families. In the riverbed, two sets of species are recognized along the elevation gradient (one below 700 m a.s.l. and the other above 1000 m a.s.l.), mainly owing to species replacement. On the hillslopes there was no clear pattern of grouping associated with elevation. Microclimate differences between the riverbed and hillslope sites along the elevation gradient were related to the vegetation structure and explained the variation in butterfly species composition. Our results highlight the role of topography not only by explaining the response of species richness and composition to environmental variation determined by elevation, but also as a factor that must be considered in the planning and management of biodiversity conservation in the mountains.</p>
Data from: Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
<blockquote> <p>While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast <i>trn</i>L region (10-143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the <i>trn</i>L sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the <i>specificity</i> of assignments made by the <i>trn</i>L primers, and improves the <i>accuracy</i> of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.</p> </blockquote>
Data from: Environmental drivers of population-level variation in the migratory and diving ontogeny of an Arctic top predator
<p>The development of migratory strategies that enable juveniles to survive to recruitment is critical for species that exploit seasonal niches. For animals that forage via breath-hold diving this requires a combination of both physiological and foraging skill development. Here, we assess how migratory and dive behaviour develop over the first months of life for a migratory Arctic top predator, the harp seal, tracked using animal-borne satellite relay data loggers. We reveal similarities in migratory movements and differences in diving behaviour between juveniles from breeding populations in the Northwest Atlantic and Greenland Sea. In both regions, periods of resident and transient behaviour during migration were associated with proxies for food availability; sea ice concentration and water depth. However, while ontogenetic development of dive behaviour was similar for both groups of juveniles over the first 25 days, after this time Greenland Sea animals performed shorter and shallower dives and were more closely associated with sea ice than Northwest Atlantic animals. Together, these results highlight the role of both intrinsic and extrinsic factors in shaping early-life behaviour. Differences in the environmental conditions experienced during early-life may shape how populations respond to the rapid changes occurring in the Arctic ocean ecosystem.</p>
Dataset: Environmental conditions and male quality traits simultaneously explain variation of multiple colour signals in male lizards
<p>Dataset and R code associated with the following publication:</p> <p>Badiane et al. (2022), Environmental conditions and male quality traits simultaneously explain variation of multiple colour signals in male lizards. Journal of Animal Ecology, in press</p> <p>This dataset includes the following files:</p> <p>- An excel file containing the reflectance spectra of all individuals from all the study populations</p> <p>- An excel file containing the variables collected at the individual and population levels</p> <p>- Two R scripts corresponding to the analyses performed in the publication</p>
Fig. 6 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig. 6: Spatial variation of copepod demographic class density: copepod nauplii, copepodit and adult males and females along the west and east coasts of Djerba Island.
Fig 8 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig 8: Correlation matrix (Pearson test) for biological variables in relation to abiotic variables determined along the west and east coasts of Djerba Island.
Fig. 4 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig. 4: Spatial variations of microphytoplankton abundance, microphytoplankton groups, dominant species, species richness and species diversity index along the west and east coasts of Djerba Island.
Fig. 7 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig. 7: Principal component analysis (PCA) (axis I and II) of microphytoplankton and zooplankton communities' abundance and selected environmental variables along the west and east coasts of Djerba Island.
Fig. 3 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig. 3: Spatial variations of nutrient concentrations: nitrite (NO -), nitrate (NO -), ammonium (NH +), total nitrogen (T- 2 3 4 N), orthophosphate (PO 3-), total phosphate (T-P), N/P ratio, 4 and silicate along the west and east coasts of Djerba Island.
Fig. 1 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig. 1: Location of sampling stations along the western and eastern coasts of Djerba Island. The grey contour lines in the maps show the position of the isobaths and the numbers in parenthesis indicate the depths of these isobaths. Table 1. Sampling date, depth, latitude and longitude of sampled stations.
Fig. 1 in Spatial variation of summer microphytoplankton and zooplankton communities related to environmental parameters in the coastal area of Djerba Island (Tunisia, Eastern Mediterranean) Abstract
Fig. 1: Location of sampling stations along the western and eastern coasts of Djerba Island. The grey contour lines in the maps show the position of the isobaths and the numbers in parenthesis indicate the depths of these isobaths.
Fig. 1. Percival environmental chambers housing Eumaeus atala. A in Life history variations and seasonal polyphenism in Eumaeus atala (Lepidoptera: Lycaenidae)
Fig. 1. Percival environmental chambers housing Eumaeus atala. A) Interior view of fabric housing cages in the Percival chambers and B) plastic 'deli-box' larval cages inside with host plant material and young Eumaeus atala larvae.
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.
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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.