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3,339 results for “heterogeneities”
Supplementary Information for Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS
<p>Supplementary information for<br> Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B, & Lindahl, E.. (2020). Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. The Journal of Chemical Physics, 2020</p> <p>Contains benchmark methodology description as well as all inputs used in the application performance benchmarks included the paper.</p>
Data from: The evolution of parasite host range in heterogeneous host populations
<p>Theory on the evolution of niche width argues that resource heterogeneity selects for niche breadth. For parasites, this theory predicts that parasite populations will evolve, or maintain, broader host ranges when selected in genetically diverse host populations relative to homogeneous host populations. To test this prediction, we selected the bacterial parasite Serratia marcescens to kill Caenorhabditis elegans in populations that were genetically heterogeneous (50% mix of two experimental genotypes) or homogeneous (100% of either genotype). After 20 rounds of selection, we compared the host range of selected parasites by measuring parasite fitness (i.e. virulence, the selected fitness trait) on the two focal host genotypes and on a novel host genotype. As predicted, heterogeneous host populations selected for parasites with a broader host range: these parasite populations gained or maintained virulence on all host genotypes. This result contrasted with selection in homogeneous populations of one host genotype. Here, host range contracted, with parasite populations gaining virulence on the focal host genotype and losing virulence on the novel host genotype. This pattern was not, however, repeated with selection in homogeneous populations of the second host genotype: these parasite populations did not gain virulence on the focal host genotype, nor did they lose virulence on the novel host genotype. Our results indicate that host heterogeneity can maintain broader host ranges in parasite populations. Individual host genotypes, however, vary in the degree to which they select for specialization in parasite populations.</p>
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
Fine-scale habitat heterogeneity influences browsing damage by elephant and giraffe
Effects of large mammalian herbivores on woody vegetation tend to be heterogeneous in space and time, but the factors that drive such heterogeneity are poorly understood. We examined the influence of fine-scale habitat heterogeneity on the distribution and browsing effects of two of the largest African terrestrial mammals, the elephant and giraffe. We conducted this study within a 120-ha (500 x 2400 m) ForestGEO long-term vegetation monitoring plot located at Mpala Research Center, Kenya. The plot traverses three distinct topographic habitats ('plateau', 'steep slopes', and 'valley') with contrasting elevation, slope, soil properties, and vegetation composition. To quantify browsing damage, we focused on Acacia mellifera, a palatable tree species that occurs across the three habitat categories. Overall tree density, species richness, and diversity was highest on the steep slopes and lowest on the plateau. Acacia mellifera trees were tallest and had the lowest number of stems per tree on the steep slopes. Both elephant and giraffe avoided the steep slopes and their activity was higher during the wet season than during the dry season. Browsing damage on Acacia mellifera was lowest on the steep slopes. Elephant browsing damage was highest in the valley whereas giraffe browsing damage was highest on the plateau. Our findings suggest that fine-scale habitat heterogeneity is an important factor in predicting the distribution of large herbivores and their effects on vegetation and may interact with other drivers such as edaphic variations to influence local variation in vegetation structure and composition.
Host heterogeneity mitigates virulence evolution
<p>Parasites often infect genetically diverse host populations, and the evolutionary trajectories of parasite populations may be shaped by levels of host heterogeneity. Mixed genotype host populations, compared to homogeneous host populations, can reduce parasite prevalence and potentially reduce rates of parasite adaptation due to tradeoffs associated with adapting to specific host genotypes. Here, we used experimental evolution to select for increased virulence in populations of the bacterial parasite <em>Serratia marcescens</em> exposed to either heterogenous or homogenous populations of<em> Caenorhabditis elegans</em>. We found that parasites exposed to heterogenous host populations evolved significantly less virulence than parasites exposed to homogeneous host populations over several hundred bacterial generations. Thus, host heterogeneity impeded parasite adaptation to host populations. While we detected tradeoffs in virulence evolution, parasite adaptation to two specific host genotypes also resulted in modestly increased virulence against the reciprocal host genotypes. These results suggest that parasite adaptation to heterogenous host populations may be impeded by both tradeoffs and a reduction in the efficacy of selection as different host genotypes exert different selective pressures on a parasite population.</p>
Root trait responses to drought are more heterogeneous than leaf trait responses
<p>Drought can strongly modify plant diversity and ecosystem processes. As droughts are expected to intensify in the future, it is important to better understand plant responses to this global driver. Root traits are an overlooked but powerful predictor of plant responses to drought because they are in direct contact with the soil environment and are responsible for taking up nutrients and water.</p> <p>Here, we determine which root traits are sensitive to drought and the magnitude of that response. We also tested whether root trait relationships with shoot biomass are affected by drought and to what extent all these responses depend on plant species identity. To do so, we conducted a glasshouse experiment with 24 plant species grown in pots (10 replicates per species), which included grasses, forbs and legumes. All replicates were well watered during the first month and then half of them were kept under drought (30 % water holding capacity (WHC)), with the other half serving as control (70 % WHC). After two months of treatment, leaf and root traits were measured.</p> <p>Leaf traits had a strong and more uniform response to drought compared to root traits. Root trait responses were variable and differed among plant species. Overall, grasses and several forbs had increased root diameter with drought while forbs had decreased specific root surface area (SRSA) and specific root length (SRL). Increase of root diameter and reduction of root elongation or sacrificing fine roots are different strategies that may promote nutrient and water acquisition, depending on plant species identity.</p> <p>Our results identify changes in root morphological traits as mechanisms to likely tolerate drought and highlight that, although such drought responses are species-specific, they are phylogenetically clustered.</p>
On the causes of geographically heterogeneous parallel evolution in sticklebacks
<p>The three-spined stickleback (<i>Gasterosteus aculeatus</i>) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern Pacific and trans-oceanic marine–freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine–freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine–freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.</p>
Thermophysical properties and surface heterogeneity of landing sites on Mars from overlapping THEMIS observations-Data
<p>Files, scripts/functions, observed temperature data, and modeled results used in the Ahern et al. paper entitled: Thermophysical properties and surface heterogeneity of landing sites on Mars from overlapping THEMIS observations.</p>
Landscape heterogeneity shapes bird phylogenetic responses at forest-matrix interfaces in Atlantic Forest, Brazil
<p>Agricultural intensification is one of the major factors driving biodiversity loss. However, most studies in human-dominated landscapes have used taxonomic diversity in their analysis, ignoring evolutionary relationships. Consequently, the relationship between landscape structure and phylogenetic diversity is not well understood. Here, we tested the hypothesis that landscape heterogeneity is positively related to bird phylogenetic indexes of diversity and structure, leading to over-dispersed phylogenies in very heterogeneous landscapes. We analyzed phylogenetic responses in interfaces between forest edges and anthropogenic matrices (forest-pasture and forest-eucalyptus) using generalized linear mixed models. We also compared these indexes between land covers to assess which one best preserves the phylogenetic history of communities. We used both traditional phylogenetic indexes and those corrected for species richness. Our results showed that phylogenetic diversity varied significantly between land cover types, but this did not occur when we removed effects associated with species richness, suggesting that all land covers preserve similar levels of evolutionary history. Additionally, our best models showed a positive relationship between landscape heterogeneity and bird phylogenetic indexes of diversity and structure, but the strength of these relationships may be land-cover dependent. In summary, our work highlights the influence of landscape heterogeneity on the phylogenetic diversity and structure of bird communities, reinforcing the need for its incorporation into conservation-based studies.</p>
Foraging in nature: contrasting responses to resource heterogeneity at small and large spatial scales.
<p>A key problem faced by foragers is how to forage when resources are distributed heterogeneously in space. This heterogeneity and associated trade-offs may change with spatial scale. Furthermore, foragers may also have to optimize acquiring multiple resources. Such complexity of decision-making while foraging is poorly understood. We studied the butterfly <i>Ypthima huebneri</i> to examine how foraging decisions of adults are influenced by spatial scale and multiple resources. We predicted that, at a small-spatial scale, the time spent foraging in a patch should be proportional to resources in the patch, but at large-spatial scales, due to limitations arising from large travel costs, this relationship should turn negative. We also predicted that both adult and larval resources should jointly affect foraging butterflies. To test these predictions, we laid eleven plots, and sub-divided them into patches. We mapped nectar and larval resources and measured butterfly behavior in these patches and plots. We found that adult foraging behavior showed contrasting relationships with adult resource density at small versus large-spatial scales. At the smaller-spatial scale, butterflies spent more time feeding in resource-rich patches, whereas at the large-scale, butterflies spent more time feeding in resource-poor plots. Furthermore, both adult and larval resources appeared to affect foraging decisions, suggesting that individuals may optimize search costs for different resources. Overall, our findings suggest that the variation in foraging behavior seen in foragers might result from animals responding to complex ecological conditions, such as, resource heterogeneity at multiple spatial scales and the challenges of tracking multiple resources.</p>
Data accompanying "Drone data reveal heterogeneity in tundra greenness and phenology not captured by satellites"
<p>This dataset contains the spatial data underlying the statistical analysis in:</p> <p><em>Assmann et al. (in press) - Drone data reveal heterogeneity in tundra greenness and phenology not captured by satellites</em></p> <p>Together with the code and tabular data contained in <a href="https://github.com/jakobjassmann/qhi_phen_ts/">https://github.com/jakobjassmann/qhi_phen_ts/</a> the data in this repository are required to reproduce the figures, tables and statistics reported in the manuscript.</p> <p>This dataset consists of two components:</p> <ol> <li> <p>Multispectral drone observations from the growing seasons 2016 and 2017 for 8 study plots on Qikiqtaruk - Herschel Island in Canada collected with Parrot Sequioa sensors (62 sets of multispectral orhomosaics in total).</p> </li> <li> <p>Post-porcessed Sentinel-2 MSI L2A scenes covering the same 8 study plots, including all scenes for which the area of the plots and their immediate surroundings were cloud free between May and September in 2016 and 2017.</p> </li> </ol> <p>-----------------------------------------------------------------------------------------------------------------</p> <p><strong>Citation</strong>: Jakob J. Assmann, Isla H. Myers-Smith, Jeffrey T. Kerby, Andrew M. Cunliffe and Gergana N. Daskalova.<em> <strong>In press</strong>.</em> Drone data reveal heterogeneity in tundra greenness and phenology not captured by satellites. <a href="https://doi.org/10.32942/osf.io/tqekn">https://doi.org/10.32942/osf.io/tqekn</a></p> <p><strong>Legal notice:</strong> This dataset contains modified Copernicus Sentinel [2016, 2017] data.</p> <p><strong>Acknowledgements (from the manuscript):</strong></p> <p>We would like to thank the Team Shrub field crews of the 2016 and 2017 field seasons for their hard work and effort invested in collecting the data presented in this research, this includes Will Palmer, Santeri Lehtonen, Callum Tyler, Sandra Angers-Blondin and Haydn Thomas. Furthermore, we would like to thank Tom Wade and Simon Gibson-Poole from the University of Edinburgh Airborne GeoSciences Facility, as well as Chris McLellan and Andrew Gray from the NERC Field Spectroscopy Facility for their support in our drone endeavours. We also want to express our gratitude to Ally Phillimore, Ed Midchard, Toke Høye and two anonymous reviewers for providing feedback on earlier versions of this manuscript. Lastly, JJA would like to thank IMS, Ally Phillimore and Richard Ennos for academic mentorship throughout his PhD.</p> <p>We thank the Herschel Island—Qikiqtaruk Territorial Park Team and Yukon Government for providing logistical support for our field research on Qikiqtaruk including: Richard Gordon, Cameron Eckert and the park rangers Edward McLeod, Sam McLeod, Ricky Joe, Paden Lennie and Shane Goosen. We thank the research group of Hugues Lantuit at the Alfred Wegener Institute and the Aurora Research Institute for logistical support. Research permits include Yukon Researcher and Explorer permits (16-48S&E and 17-42S&E) and Yukon Parks Research permits (RE-Inu-02-16 and 17-RE-HI-02). All airborne activities were licensed under the Transport Canada special flight operations certificates ATS 16-17-00008441 RDIMS 11956834 (2016) and ATS 16-17-00072213 RDIMS 12929481 (2017).</p> <p>Funding for this research was provided by NERC through the ShrubTundra standard grant (NE/M016323/1), a NERC E3 Doctoral Training Partnership PhD studentship for Jakob Assmann (NE/L002558/1), a research grant from the National Geographic Society (CP-061R-17), a Parrot Climate Innovation Grant, the Aarhus University Research Foundation, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (754513) for Jeffrey Kerby, a NERC support case for use of the NERC Field Spectroscopy Facility (738.1115), equipment loans from the University of Edinburgh Airborne GeoSciences Facility and the NERC Geophysical Equipment Facility (GEF 1063 and 1069).</p> <p>Finally, we would like to thank the Inuvialuit people for the opportunity to conduct research in the Inuvialuit Settlement Region.</p>
Data from: Integration and harmonization of trait data from plant individuals across heterogeneous sources
<p>Trait data represent the basis for ecological and evolutionary research and have relevance for biodiversity conservation, ecosystem management and earth system modelling. The collection and mobilization of trait data has strongly increased over the last decade, but many trait databases still provide only species-level, aggregated trait values (e.g. ranges, means) and lack the direct observations on which those data are based. Thus, the vast majority of trait data measured directly from individuals remains hidden and highly heterogeneous, impeding their discoverability, semantic interoperability, digital accessibility and (re-)use. Here, we integrate quantitative measurements of verbatim trait information from plant individuals (e.g. lengths, widths, counts and angles of stems, leaves, fruits and inflorescence parts) from multiple sources such as field observations and herbarium collections. We develop a workflow to harmonize heterogeneous trait measurements (e.g. trait names and their values and units) as well as additional information related to taxonomy, measurement or fact and occurrence. This data integration and harmonization builds on vocabularies and terminology from existing metadata standards and ontologies such as the Ecological Trait-data Standard (ETS), the Darwin Core (DwC), the Thesaurus Of Plant characteristics (TOP) and the Plant Trait Ontology (TO). A metadata form filled out by data providers enables the automated integration of trait information from heterogeneous datasets. We illustrate our tools with data from palms (family Arecaceae), a globally distributed (pantropical), diverse plant family that is considered a good model system for understanding the ecology and evolution of tropical rainforests. We mobilize nearly 140,000 individual palm trait measurements in an interoperable format, identify semantic gaps in existing plant trait terminology and provide suggestions for the future development of a thesaurus of plant characteristics. Our work thereby promotes the semantic integration of plant trait data in a machine-readable way and shows how large amounts of small trait data sets and their metadata can be integrated into standardized data products.</p>
Spatial heterogeneity in soil pyrogenic carbon mediates tree growth and physiology following wildfire
<table> <tbody> <tr> <td>Pyrogenic carbon (PyC) is a ubiquitous legacy of wildfire in terrestrial soils, yet how it affects the growth and function of regenerating plants has received little research attention.<br> <br> We examined responses to a natural gradient of PyC deposition five years following a severe fire in a northern boreal forest, based on measurements of growth (height, basal area increment, and leader extension), physiological performance (Fv/Fm), and foliar nutrition (foliar C, N, P, K, Mg) of Pinus banksiana Lamb. We determined the concentration of PyC, expressed as a dosage (t·ha-1), in mineral soils collected from the rhizospheres of each sapling and used it as an independent factor to model trait responses to increasing PyC levels, in conjunction with measurements of soil physio-chemical properties (pH, EC, VOC, Ash, N, P, K, Ca, and Mg).<br> <br> Quantification and spatial analysis of PyC reveals heterogeneous deposition across the landscape with fine-grained patchiness at scales <0.5 m. In response to this heterogeneity, phenotypic and nutritional adjustments followed dose-dependent response patterns. Beneficial effects of PyC on sapling growth occurred to an optimum point of ~30-60 t·ha-1, while declining patterns were found for trees in dosages exceeding 100 t·ha-1. Some traits were positively and negatively related to soil K and N, respectively, and shared strong negative associations with soil pH and volatile matter.<br> <br> Synthesis. This study supports the longstanding hypothesis that soil PyC enhances growth and physiological function of fire-adapted plants, but indicates that responses are highly dosage-dependent, with natural levels of PyC deposition commonly exceeding an optimum point. These results also suggest that the main mechanisms for observed responses to PyC include: i) enhanced supply of base cations, ii) immobilization of N, and iii) pronounced liming. Future changes in climate are expected to increase fire frequency, particularly in circumpolar boreal forests. We predict shifts in PyC to frequently exceed the threshold resulting in reduced plant growth and ultimately ecosystem productivity.</td> <td> </td> <td> </td> </tr> </tbody> </table>
Automated classification of avian vocal activity using acoustic indices in regional and heterogeneous datasets
<p>Acoustic indices combined with clustering and classification approaches have been increasingly used to automate identification of the presence of vocalizing taxa or acoustic events of interest. While most studies using this approach standardize data collection and study design parameters at the project or study level, recent trends in ecological research are to investigate patterns at regional or continental scales. Large-scale studies often require collaboration between research groups and integration of data from multiple sources to fulfill objectives, which can lead to variation in recording equipment and data collection protocols.</p> <p>Our objectives were to determine how analytical approaches and variation in data collection and processing that is typical of regional acoustic monitoring programs influences accuracy when identifying vocal activity in migratory breeding birds. We used data from three regional datasets in Northern Alberta, Northern British Columbia, and Southern and Central Yukon, Canada to investigate the effect of analytical framework, sample size, local species richness, and data collection variables on classification accuracy.</p> <p>We found supervised classification approaches to be the most effective, with boosted regression trees identifying vocal activity with a 92.0% accuracy and easily able to accommodate variation in data collection and processing parameters. We also provide recommendations on effectively processing large and heterogeneous datasets including sufficient sample size, accommodating nuisance variables, and selecting suitable model training data.</p> <p>The results presented in this study can help inform decisions in data collection, data processing, and study design and analysis, maximize performance and accuracy during analysis, and efficiently process large, heterogeneous datasets to answer questions at scales previously difficult to investigate.</p>
Heterogeneous genetic basis of age at maturity in salmonid fishes
<p>Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus <i>Oncorhynchus</i>) that exhibit intra- and interspecific variation in this trait – Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, <i>six6 </i>and <i>vgll3</i>, that are strongly associated with the same trait in Atlantic Salmon (<i>Salmo salar</i>). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between <i>six6 </i>and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46x10<sup>-9</sup> after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the <i>vgll3 </i>genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.</p>
Fine-scale habitat heterogeneity favours the coexistence of supergene-controlled social forms in Formica selysi
<p><b>Background:</b> Social insects vary widely in social organization, yet the genetical and ecological factors influencing this variation remain poorly known. In particular, whether spatially varying selection influences the maintenance of social polymorphisms in ants has been rarely investigated. To fill this gap, we examined whether fine-scale habitat heterogeneity contributes to the co-existence of alternative forms of social organization within populations. Single-queen colonies (monogyne social form) are generally associated with better colonization abilities, whereas multiple-queen colonies (polygyne social form) are predicted to be better competitors and monopolize saturated habitats. We hypothesize that each social form colonizes and thrives in distinct local habitats, as a result of their alternative dispersal and colony founding strategies. Here, we test this hypothesis in the Alpine silver ant, in which a supergene controls polymorphic social organization.</p> <p><b>Results:</b> Monogyne and polygyne colonies predominate in distinct habitats of the same population. The analysis of 59 sampling plots distributed across six habitats revealed that single-queen colonies mostly occupy unconnected habitats that were most likely reached by flight. This includes young habitats isolated by water and old habitats isolated by vegetation. In contrast, multiple-queen colonies were abundant in young, continuous and saturated habitats. Hence, alternative social forms colonize and monopolize distinct niches at a very local scale.</p> <p><b>Conclusions:</b> Alternative social forms colonized and monopolized different local habitats, in accordance with differences in colonization and competition abilities. The monogyne social form displays a colonizer phenotype, by efficiently occupying empty habitats, while the polygyne social form exhibits a competitor phenotype, thriving in saturated habitats. The combination of the two phenotypes, coupled with fine-scale habitat heterogeneity, may allow the coexistence of alternative social forms within populations. Overall, these results suggest that spatially varying selection may be one of the mechanisms contributing to the maintenance of genetic polymorphisms in social organization.</p>
Data from: Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug
<p>Cancer cell populations consist of phenotypically heterogeneous cells. Growing evidence suggests that pre-existing phenotypic differences among cancer cells correlate with differential susceptibility to anticancer drugs and eventually lead to a relapse. Such phenotypic differences can arise not only externally driven by the environmental heterogeneity around individual cells but also internally by the intrinsic fluctuation of cells. However, the quantitative characteristics of intrinsic phenotypic heterogeneity emerging even under constant environments and their relevance to drug susceptibility remain elusive. Here we employed a microfluidic device, mammalian mother machine, for studying the intrinsic heterogeneity of growth dynamics of mouse lymphocytic leukemia cells (L1210) across tens of generations. The generation time of this cancer cell line had a distribution with a long tail and a heritability across generations. We determined that a minority of cell lineages exist in a slow-cycling state for multiple generations. These slow-cycling cell lineages had a higher chance of survival than the fast-cycling lineages under continuous exposure to the anticancer drug Mitomycin C. This result suggests that heritable heterogeneity in cancer cells' growth in a population influences their susceptibility to anticancer drugs.</p>
Propagule composition regulates the success of an invasive seaweed across a heterogeneous seascape
<p>1. Propagule pressure is acknowledged as a key determinant of invasion success. Nonetheless, the role of morphological or physiological attributes of propagules (i.e., their quality) in regulating invader establishment has been little explored. In particular, no study has investigated how the presence of propagules differing in quality within an inoculum influences establishment across heterogeneous landscapes.</p> <p>2. We experimentally tested the hypothesis that the quality (+Fronds+Rhizoids; +Fronds–Rhizoids; –Fronds+Rhizoids) and the diversity (1, 2, 3 fragment types) of vegetative fragments of the seaweed <i>Caulerpa taxifolia</i> determine their establishment success across seascapes consisting of bare sediments and patches of the seagrass <i>Zostera muelleri</i> exposed to different disturbance intensities (control, seagrass canopy clipping and total removal).</p> <p>3. After 6 weeks, seaweed biomass, stolon and frond length, frond and rhizoid number were generally greater in unvegetated habitats (bare sediments and total seagrass removal) than full or reduced seagrass canopies. The type and the diversity of types of fragments inoculated had significant effects on the final biomass and morphological features of <i>C. taxifolia</i> only in vegetated habitats. In control plots, inocula of fragments retaining both fronds and rhizoids achieved higher biomass, developed longer stolons and more fronds. In canopy clipping plots, mixed inocula of +Fronds+Rhizoids and –Fronds+Rhizoids fragments had the greatest biomass and stolon length.</p> <p>4. Synthesis. Assessing how propagules differing in quality perform in different habitats might be not sufficient to draw a comprehensive picture of invasion risk, as their establishment can be modulated by both negative and positive interactions among them. Propagule composition should be, therefore, considered as a further dimension of propagule pressure. Our results also suggest that the relevance of specific propagule traits for invader establishment decreases from intact to degraded habitats. Considering propagule size in terms of amount of competent propagules, rather than an absolute measure, would refine our ability of predicting invasion risk across habitats differing in biotic or abiotic conditions.</p>
Data from: Soil heterogeneity increases plant diversity after twenty years of manipulation during grassland restoration
The 'environmental heterogeneity hypothesis' predicts that variability in resources promotes species coexistence, but few experiments support this hypothesis in plant communities. A previous 15-y test of this hypothesis in a prairie restoration experiment demonstrated a weak effect of manipulated soil resource heterogeneity on plant diversity. This response was attributed to a transient increase in richness following a post-restoration supplemental propagule addition, occasionally higher diversity under nutrient enrichment, and reduced cover of a dominant species in a subset of soil treatments. Here, we report community dynamics under continuous propagule addition in the same experiment, corresponding to 16-20 y of restoration, in response to altered availability and heterogeneity of soil resources. We also quantified traits of newly added species to determine if heterogeneity increases the amount and variety of niches available for new species to exploit. The heterogeneous treatment contained a factorial combination of altered nutrient availability and soil depth; control plots had no manipulations. Total diversity and richness were higher in the heterogeneous treatment during this 5 y study due to higher cover, diversity, and richness of previously established forbs, particularly in the N-enriched subplots. All new species added to the experiment exhibited unique trait spaces, but there was no evidence that heterogeneous plots contained a greater variety of new species representing a wider range of trait spaces relative to the control treatment. The richness and cover of new species was higher in N-enriched soil, but the magnitude of this response was small. Communities assembling under long-term N addition were dominated by different species among subplots receiving added N, leading to greater dispersion of communities among the heterogeneous relative to control plots. Contrary to the deterministic mechanism by which heterogeneity was expected to increase diversity (greater variability in resources for new species to exploit), higher diversity in the heterogeneous plots resulted from destabilization of formerly grass-dominated communities in N-enriched subplots. While we do not advocate increasing available soil N at large scales, we conclude that the positive effect of environmental heterogeneity on diversity can take decades to materialize and depend on development of stochastic processes in communities with strong establishment limitation.
Configurational crop heterogeneity increases within-field plant diversity
<p>1. Increasing landscape heterogeneity by restoring semi-natural elements to reverse farmland biodiversity declines is not always economically feasible or acceptable to farmers due to competition for land. We hypothesized that increasing the heterogeneity of the crop mosaic itself, hereafter referred to as crop heterogeneity, can have beneficial effects on within-field plant diversity.</p> <p>2. Using a unique multi-country dataset from a cross-continent collaborative project covering 1451 agricultural fields within 432 landscapes in Europe and Canada, we assessed the relative effects of compositional and configurational crop heterogeneity on within-field plant diversity components. We also examined how these relationships were modulated by the position within the field.</p> <p>3. We found strong positive effects of configurational crop heterogeneity on within-field plant alpha and gamma diversity in field interiors. These effects were as high as the effect of semi-natural cover. In field borders, effects of crop heterogeneity were limited to alpha diversity. We suggest that a heterogeneous crop mosaic may overcome the high negative impact of management practices on plant diversity in field interiors, whereas in field borders, where plant diversity is already high, landscape effects are more limited.</p> <p>4. <em>Synthesis and applications</em>. Our study shows that increasing configurational crop heterogeneity is beneficial to within-field plant diversity. It opens up a new effective and complementary way to promote farmland biodiversity without taking land out of agricultural production. We therefore recommend adopting manipulation of crop heterogeneity as a specific, effective management option in future policy measures, perhaps adding to agri-environment schemes, to contribute to the conservation of farmland plant diversity.</p>
ScienceDex guides
Understand access before you commit
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.