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445 results for “abiotic”
Supporting code, tables and data for: Megafrugivores as fading shadows of the past: Extant frugivores and the abiotic environment as the most important determinants of the distribution of palms in Madagascar
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Data from: Beyond abiotic decay: Fiddler crabs accelerate plastic fragmentation in pollution hotspots
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Abiotic environments can modify the penetrance of transgene-based lethality systems for insect population control
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Abiotic and biotic contexts shape the effect of disturbance on non-native plant invasion
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Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses
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Abiotic conditions shape spatial and temporal morphological variation in North American birds
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Effects of surface mulches on abiotic properties of drip-irrigated xeric landscapes in central Arizona-Phoenix
The primary objective of this project is to study Effects of Surface Mulches on Abiotic Properties of Drip-Irrigated Xeric Landscapes Soil moisture (Li 2003, van Wesemael et al 1996). Vegetative mulches such as green waste compost and pine bark chips also reduce evaporation and increase soil moisture (Brady and Weil 2002, Pickering et al 1998). Mulches increase water infiltration into the soil profile by preventing soil crust formation (Brady and Weil 2002). Mulch improves soil structure, reduces soil erosion and reduces surface compaction by protecting soil aggregates from beating rain and direct solar radiation (Brady and Weil 2002, Borland 1990, Li 2003). Mulch buffers soil temperature extremes (Brady and Weil 2002, Li 2003, Montague et al 1998 and 2000, Pickering et al 1998). .
Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment and/or DFTD. We employ genetic-environment association analyses using a RAD-capture panel including 6,886 SNPs from 3,286 individuals sampled pre- and post-disease arrival. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD were not detected post disease arrival. Several post-DFTD candidate loci were associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by the strong selection resulting from the rapid onset of DFTD.
Data from: Evolutionary constraint on low elevation range expansion: defense-abiotic stress tolerance tradeoff in crosses of the ecological model Boechera stricta
Most transplant experiments across species geographic range boundaries indicate that adaptation to stressful environments outside the range is often constrained. However, the mechanisms of these constraints remain poorly understood. We used extended generation crosses from diverged high and low elevation populations. In experiments across low elevation range boundaries, there was selection on the parental lines for abiotic stress tolerance and resistance to herbivores. However, in support of a defense-tolerance tradeoff, extended generation crosses showed non-independent segregation of these traits in the lab across a drought-stress gradient and in the field across the low elevation range boundary. Genotypic variation in a marker from a region of the genome containing a candidate gene (MYC2) was associated with change in the genetic tradeoff. Thus, using crosses and forward genetics, we found experimental genetic and molecular evidence for a pleiotropic tradeoff that could constrain the evolution of range expansion.
Data from: Biomass–density relationships of plant communities deviate from the self‐thinning rule due to age structure and abiotic stress
<p>A pertinent debate in plant ecology centers around the generality of the self-thinning rule. However, studies focused on highly simplified settings such as even-aged monospecific populations or optimal conditions. This neglects the fact that most natural communities, to which the classical self-thinning slope is often applied, are age-structured, composed of multiple species and exposed to various types of abiotic stress.</p> <p>With the help of an individual-based model, we relax these simplified assumptions and systematically test for changes in the biomass–density relationships of uneven-aged, functionally diverse plant communities across a complete stress gradient, using excessive to insufficient soil water as a case study.</p> <p>We show that frequent recruitment, which resulted in an uneven-aged community, and stress intensity caused predictable changes in the entire biomass–density trajectory. Increasing stress resulted in steeper (more negative) slopes and increased the intercept in the classical self-thinning section irrespective of excessive or insufficient soil water as a stress type. Recruitment steepened the slope, too and enabled a novel section in the biomass–density trajectory. This novel section represented a quasi-steady state of the density-dependent dynamics of new generations which occurred locally within patches of recruitment. At the community level, the slope of the biomass–density relationship at quasi-steady state had a significantly flatter slope of −1.1 under optimal soil water conditions. Functional diversity showed little impact on density-dependent mortality. Namely, it resulted in an earlier onset of mortality but not in changes in the values of the slope and intercept.</p> <p>We conclude that the classical −3/2 slope is not useful to describe the biomass–density relationship in natural and semi-natural plant communities. The magnitude and direction of variation in the slope are related to the age–structure and abiotic stress intensity in the plant community.</p>
Biotic and abiotic drivers of plant-pollinator community assembly across wildfire gradients
<p>1. Understanding how abiotic disturbance and biotic interactions determine pollinator and flowering-plant diversity is critically important given global climate change and widespread pollinator declines. To predict responses of pollinators and flowering-plant communities to changes in wildfire disturbance, a mechanistic understanding of how these two trophic levels respond to wildfire severity is needed.</p> <p>2. We compared site-to-site variation in community composition (β-diversity), species richness, and abundances of pollinators and flowering plants among landscapes with no recent wildfire (unburned), mixed-severity wildfire, and high-severity wildfire in three sites across the Northern Rockies Ecoregion, USA. We used variation partitioning to assess the relative contributions of wildfire, other abiotic variables (climate, soils, topography), and biotic associations among plant and pollinator composition to community assembly of both trophic levels.</p> <p>3. Wildfire disturbance generally increased species richness and total abundance, but decreased β-diversity, of both pollinators and flowering plants. However, reductions in β-diversity from wildfire appeared to result from increased abundances following fires, resulting in higher local species richness of pollinators and flowers in burned than unburned landscapes. After accounting for differences in abundance, standardized effect sizes of β-diversity were higher in burned than unburned landscapes, suggesting that wildfire enhances non-random assortment of pollinator and flowering-plant species among local communities.</p> <p>4. Wildfire disturbance mediated the relative importance of mutualistic associations to β-diversity of pollinators and flowering plants. The influence of pollinator β-diversity on flowering-plant β-diversity increased with wildfire severity, whereas the influence of flowering-plant β-diversity on pollinator β-diversity was greater in mixed-severity than high-severity wildfire or unburned landscapes. Moreover, biotic associations among pollinator and plant species explained substantial variation in β-diversity of both trophic levels beyond what could be explained by wildfire and all other abiotic and spatial factors combined.</p> <p>5. Synthesis: Wildfire disturbance and plant-pollinator interactions both strongly influence the assembly of pollinator and flowering-plant communities at local and regional scales. However, biotic interactions were generally more important drivers of community assembly in disturbed than undisturbed landscapes. As wildfire regimes continue to change globally, predicting its effects on biodiversity will require a deeper understanding of the ecological processes that mediate biotic interactions among linked trophic levels.</p>
Data from: Abiotic and biotic context dependency of perennial crop yield
<p>Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass—<i>Thinopyrum intermedium</i>-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (<i>Silphium intregrifolium</i>), and alfalfa (<i>Medicago sativa</i>). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both <i>Silphium</i> and alfalfa strongly benefit from AM fungi. The presence of native prairie AM fungi had a greater benefit to <i>Silphium </i>in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of <i>Silphium</i> and alfalfa. This study identifies importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.</p>
Tree phenology and abiotic variables 1998-2017 at Ngogo, Kibale National Park, Uganda
<p>Fruit production in tropical forests varies considerably in space and time, with important implications for frugivorous consumers. Characterizing temporal variation in forest productivity is thus critical for understanding adaptations of tropical forest frugivores, yet long-term phenology data from the tropics, in particular from African forests, are still scarce. Similarly, as the abiotic factors driving phenology in the tropics are predicted to change with a warming climate, studies documenting the relationship between climatic variables and fruit production are increasingly important. Here we present data from 19 years of monitoring the phenology of 20 tree species at Ngogo in Kibale National Park, Uganda. Our aims were to characterize short- and long-term trends in productivity and to understand the abiotic factors driving temporal variability in fruit production. Short-term (month-to-month) variability in fruiting was relatively low at Ngogo, and overall fruit production increased significantly through the first half of the study. Among the abiotic variables we expected to influence phenology patterns (including rainfall, solar irradiance, and average temperature), only average temperature was a significant predictor of monthly fruit production. We discuss these findings as they relate to the resource base of the frugivorous vertebrate community inhabiting Ngogo.</p>
Data from: The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)
The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 Myr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.
Data from: Evolutionary relationships can be more important than abiotic conditions in predicting the outcome of plant-plant interactions
Positive and negative plant–plant interactions are major processes shaping plant communities. They are affected by environmental conditions and evolutionary relationships among the interacting plants. However, the generality of these factors as drivers of pairwise plant interactions and their combined effects remain virtually unknown. We conducted an observational study to assess how environmental conditions (altitude, temperature, irradiance and rainfall), the dispersal mechanism of beneficiary species and evolutionary relationships affected the co-occurrence of pairwise interactions in 11 Stipa tenacissima steppes located along an environmental gradient in Spain. We studied 197 pairwise plant–plant interactions involving the two major nurse plants (the resprouting shrub Quercus coccifera and the tussock grass S. tenacissima) found in these communities. The relative importance of the studied factors varied with the nurse species considered. None of the factors studied were good predictors of the co-ocurrence between S. tenacissima and its neighbours. However, both the dispersal mechanism of the beneficiary species and the phylogenetic distance between interacting species were crucial factors affecting the co-occurrence between Q. coccifera and its neighbours, while climatic conditions (irradiance) played a secondary role. Values of phylogenetic distance between 207–272.8 Myr led to competition, while values outside this range or fleshy-fruitness in the beneficiary species led to positive interactions. The low importance of environmental conditions as a general driver of pairwise interactions was caused by the species-specific response to changes in either rainfall or radiation. This result suggests that factors other than climatic conditions must be included in theoretical models aimed to generally predict the outcome of plant–plant interactions. Our study helps to improve current theory on plant–plant interactions and to understand how these interactions can respond to expected modifications in species composition and climate associated to ongoing global environmental change.
Data from: Comparison of the abiotic preferences of macroinvertebrates in tropical river basins
We assessed and compared abiotic preferences of aquatic macroinvertebrates in three river basins located in Ecuador, Ethiopia and Vietnam. Upon using logistic regression models we analyzed the relationship between the probability of occurrence of five macroinvertebrate families, ranging from pollution tolerant to pollution sensitive, (Chironomidae, Baetidae, Hydroptilidae, Libellulidae and Leptophlebiidae) and physical-chemical water quality conditions. Within the investigated physical-chemical ranges, nine out of twenty-five interaction effects were significant. Our analyses suggested river basin dependent associations between the macroinvertebrate families and the corresponding physical-chemical conditions. It was found that pollution tolerant families showed no clear abiotic preference and occurred at most sampling locations, i.e. Chironomidae were present in 91%, 84% and 93% of the samples taken in Ecuador, Ethiopia and Vietnam. Pollution sensitive families were strongly associated with dissolved oxygen and stream velocity, e.g. Leptophlebiidae were only present in 48%, 2% and 18% of the samples in Ecuador, Ethiopia and Vietnam. Despite some limitations in the study design, we concluded that associations between macroinvertebrates and abiotic conditions can be river basin-specific and hence are not automatically transferable across river basins in the tropics.
Data from: Trait-mediated community assembly: distinguishing the signatures of biotic and abiotic filters
Conflicting hypotheses predict how traits mediate species establishment and community assembly. Traits of newly establishing individuals are predicted to converge, or be more similar to the resident, preexisting community, when the biotic or abiotic environment favors a single best phenotype, but are predicted to diverge when trait differences reduce competitive interactions. We tested these competing hypotheses using transplant seedlings in an old-field environment, and assessed the contribution of inter- and intra-specific transplant trait variation to community-level patterns. Using a soil moisture gradient and resident plant removals, we determined when traits of newly-establishing plants converge or diverge from the resident community by calculating community weighted mean traits for transplant and resident communities. We saw evidence of environmentally- and competitively-driven trait shifts that resulted in both trait convergence and divergence from the resident community, whose traits reflect the combined effects of both drivers. Leaf dry matter content (LDMC) of transplants diverged in the presence of competition, whereas plant height and stem-specific density (SSD) showed the opposite pattern, converging with the resident community in their presence. Specific leaf area (SLA) shifted with competition but did not reflect resident community SLA. All transplant traits were influenced by soil moisture, often in an interaction with competition, indicating that the strength of convergence or divergence is contingent on the abiotic environment. Intraspecific differences in transplant traits among treatments were evident in three of four traits; intraspecific height and SLA trends mirrored transplant community-level trends, whereas intraspecific shifts in SSD were distinct from community-level trends. Our study shows competition between plant species may cause traits of newly establishing plants to converge with the resident community, as frequently as it selects for trait divergence. These opposing effects of competition suggest that it plays a pervasive role in both intraspecific and species-level trait differences among communities.
Data from: Spatio-temporal variation of biotic and abiotic stress agents determines seedling survival in assisted oak regeneration
1. Mediterranean oak woodlands are currently undergoing considerable anthropogenic changes that globally threaten their long-term persistence. Restoration efforts via assisted regeneration depend on species traits and type of stress. However, how different sources of stress vary across space (microsites) and time (intra and inter-annual variation) for co-occurring oak species remains largely unknown. 2. We examined spatio-temporal variation of biotic (herbivory, seed predation) and abiotic (drought) stress agents to evaluate seedling survival across different regeneration microsites, and considering two climatically contrasting years. We used two co-occurring species of contrasting ecology and leaf traits in California oak woodlands: the deciduous Quercus lobata and the evergreen Q. agrifolia. 3. Most oak seedlings (98.8%) suffered from some type of stress. For both species, summer drought was the main cause of mortality, followed by rodent damage, ungulate browsing and insect damage. Rodents represented the predominant biotic stress, as all rodent-affected seedlings eventually died. Interactions among stress factors were nuanced: insect and ungulate-browsing stresses were greater during dry year, whereas rodent damage was similar in dry and average years. Intra-annually, rodent damage was the main stress agent in early spring, whereas water stress and ungulate-browsing were greater in late spring-early fall. Plant species traits were also determinant: overall, the evergreen species had greater survival probability than the deciduous one. 4. Across microsites, water stress showed higher occurrence in open grassland habitats, while rodent damage was prevalent under palatable shrubs and ungulate browsing under conspecific trees. Shrub and tree cover reduced damage attributed to water stress but increased rodent and ungulate damage, respectively. Interestingly, lower water stress but higher rodent damage was found further inside the shrub cover. 5. Synthesis and applications. Intra and inter-annual variation are critical determinants of stress type and intensity on oak recruitment. Spatial variation (microsite identity) is also informative to manipulate stress agent impact. We conclude that assisted regeneration should consider not only the predominance and lethality of each stress type and microsite, but also the interactions thereof and thus manipulate protective microsites accordingly.
Data from: Abiotic and habitat drivers of tick vector abundance, diversity, phenology and human encounter risk in southern California
The distribution, abundance and seasonal activity of vector species, such as ticks and mosquitoes, are key determinants of vector-borne disease risk, and are strongly influenced by abiotic and habitat conditions. Despite the numerous species of tick vectors in the heavily populated North American West Coast, all but Ixodes pacificus, the primary vector of the Lyme disease spirochete, is poorly characterized with regard to seasonal activity patterns and fine scale drivers of distribution and abundance, particularly in heavily populated regions of southern California. This lack of knowledge inhibits both scientific understanding and public health efforts to minimize vector exposure and risk of pathogen transmission to humans. Here we address this gap by characterizing the abiotic and habitat drivers of the distribution, abundance, and diversity of the vector tick community using fine scale temporal surveys over two seasons (2014 and 2015) across coastal and inland regions of Santa Barbara County, CA. We also characterize patterns of seasonal activity of the more common vector species to understand seasonality in risk of vector exposure, and specifically focus on human encounter risk using standardized tick drags as our method of collection. Leveraging plot-level habitat and abiotic variables in partial least squares regression analysis, we find the seven different vector species collected in this study have divergent drivers of activity and abundance. For example, I. pacificus is strongly associated with dense forest habitats and cool and moist microclimates, while Dermacentor occidentalis and Dermacentor variabilis, competent vectors of Rocky Mountain Spotted Fever, were found to be more tolerant of higher average temperatures and more open habitats. These results suggest that I. pacificus may be expected to experience reductions in geographic distribution and seasonal activity under projected land cover and climate change in coastal southern California, while D. occidentalis may experience more limited effects. We discuss implications for changing tick-borne disease risk associated with pathogens transmitted by Ixodes as well as Dermacentor species ticks in the western US, and contrast these predictions with eastern North America.
Data from: Impacts of microplastic versus natural abiotic particles on the clearance rate of a marine mussel
In coastal habitats, mussels are exposed to microplastic (MP; plastic <5mm) and silt, two abiotic particles that are similarly sized and lack nutrition. The addition of MP or silt may change the functional response of mussels. We measured clearance rate of Mytilus trossulus in three particle treatments (algae, MP + algae, and silt + algae) across four concentrations to 1) determine if the effects of MP and silt are similar and 2) disentangle the effects of particle type, particle concentration, and proportion of abiotic particles. Clearance rate decreased by 62% at high MP concentrations (>1,250 particles/ml) but was not affected at equivalent silt concentrations. These findings suggest high MP concentrations inhibit mussel clearance rate, more than expected by changes in particle concentration or the proportion of abiotic particles. As plastic production increases, mussel exposure to MP will increase, potentially reducing energy transfer, benthic-pelagic coupling, and water clarity.
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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.