Find research datasets worth reusing

Data from: Microenvironment and functional-trait context dependence predict alpine plant community dynamics

Predicting the structure and dynamics of communities is difficult. Approaches linking functional traits to niche boundaries, species co‐occurrence and demography are promising, but have so far had limited success. We hypothesized that predictability in community ecology could be improved by incorporating more accurate measures of fine‐scale environmental heterogeneity and the context‐dependent function of traits. We tested these hypotheses using long term whole‐community demography data from an alpine plant community in Colorado. Species distributions along microenvironmental gradients covaried with traits important for below‐ground processes. Positive associations between species distributions across life stages could not be explained by abiotic microenvironment alone, consistent with facilitative processes. Rates of growth, survival, fecundity and recruitment were predicted by the direct and interactive effects of trait, microenvironment, macroenvironment and neighbourhood axes. Synthesis. Context‐dependent interactions between multiple traits and microenvironmental axes are needed to predict fine‐scale community structure and dynamics.

Data from: Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which substantial mortality occurs in both field and laboratory settings. Previous pair-crossing experiments with the Pacific oyster Crassostrea gigas have revealed significant selective or genotype-dependent mortality around the metamorphic transition, but the fine-scale nature and timing of this mortality is not known, particularly whether it occurs before, during or after metamorphosis. In this laboratory study, microsatellite marker segregation ratios were followed daily throughout the settlement and metamorphosis of an F2 cross of the Pacific oyster to examine the fine-scale patterns of genotype dependent mortality at this transition and whether settlement timing (early vs. late) might be under genetic control and affect inference of genotype dependent mortality. Settlement occurred over nine days (day 18 to day 27 post-fertilization) with 68% of individuals settling either early (day 19) or late (day 24). Tracking the survival of spat for 40 days after initial settlement revealed almost no mortality and thus no appreciable genetic mortality. Temporal genetic analysis revealed that 3/11 loci exhibited genotype dependent mortality around the metamorphic transition, one of which (Cg205) was followed throughout settlement and metamorphosis. Alternative temporal patterns of strong selection against each homozygous genotype at Cg205 revealed possible defects in both the competency pathway (inability to initiate metamorphosis) and the morphogenesis pathway (mortality during the metamorphic transition). Quantitative trait locus (QTL) mapping of settlement timing identified three individual and one epistatic QTL with significant genetic effects on this trait (29% of the variance explained in total); however, two of these loci were linked to markers exhibiting selective mortality at metamorphosis, potentially confounding their apparent association with settlement timing. Overall, the results of this study highlight the complex nature of mortality and behavior during settlement and metamorphosis in oysters and suggest that endogenous sources of mortality at settlement may play an important role in the recruitment dynamics of oysters and possibly other broadcast spawning marine invertebrates.

opencc-zeroJul 2019View details →

Data from: Benefits of increased colonist quantity and genetic diversity for colonization depend on colonist identity

Larger numbers of colonists can be more likely to establish and spread due to the benefits provided by either more individuals (quantity) or a greater diversity of genotypes or phenotypes (genetic diversity). However, the value of higher colonist quantity or genetic diversity varies widely across studies, leaving a great deal of uncertainty in how these respective mechanisms affect colonization success. This variability is potentially driven by differences in which traits are present in respective colonist pools ('colonist identity'). Studies with high-performing colonizers (e.g. genotypes pre-adapted to the colonizing environment) may find increasing quantity or diversity to be beneficial because it increases the chance high-performers are sampled, while studies with no high-performers may find no effects of quantity or diversity. Alternatively, quantity and genetic diversity may play little to no role if the smallest populations already contain high-performing colonists because there is no scope for a sampling effect to operate. We conducted a field mesocosm experiment to determine if variability in the benefits provided by increased quantity or genetic diversity relates to colonist traits. Nine distinct genotypes of Daphnia pulex, characterized also by phenotype, were introduced in 'single' (one individual) or 'many' (nine individuals) introduction quantities and at 'low' (monoclonal) and 'high' (mixed genotypes) genetic diversities. We found that larger-bodied D. pulex genotypes benefited less from increased colonist quantity, while increasing genetic diversity tended to have a lower effect on higher growth rate genotypes. Our results show that the trait values of the colonists can determine the benefits gained when colonist quantity or genetic diversity are increased, with potential applications to future research and practical efforts to promote, or prevent, population establishment.

opencc-zeroDec 2018View details →

Data from: Protocol dependence and state variables in the force-moment ensemble

Stress-based ensembles incorporating temperature-like variables have been proposed as a route to an equation of state for granular materials. To test the efficacy of this approach, we perform experiments on a two-dimensional photoelastic granular system under three loading conditions: uniaxial compression, biaxial compression, and simple shear. From the interparticle forces, we find that the distributions of the normal component of the coarse-grained force-moment tensor are exponential-tailed, while the deviatoric component is Gaussian-distributed. This implies that the correct stress-based statistical mechanics conserves both the force-moment tensor and the Maxwell-Cremona force-tiling area. As such, two variables of state arise: the tensorial angoricity and a new temperature-like quantity associated with the force-tile area which we name keramicity. Each quantity is observed to be inversely proportional to the global confining pressure; however only keramicity exhibits the protocol-independence expected of a state variable, while tensorial angoricity behaves as a variable of process.

opencc-zeroDec 2018View details →

Data from: The species richness pattern of vascular plants along a tropical elevational gradient and the test of elevational Rapoport's rule depend on different life‐forms and phytogeographic affinities

The research about species richness pattern and elevational Rapoport's rule (ERR) have been carried out mostly in the temperate regions in the recent years and scarcely in the tropical mountains; meanwhile, it is unclear whether the ERR is consistent among different life‐forms and phytogeographic affinities. Here, we compiled a database of plant species of Mount Kenya, a tropical mountain of East Africa, and divided these species into twelve groups depending on the life‐form and phytogeographic affinity of each species. We inspected the species richness pattern of each group along the elevation gradient and also tested ERR of each group using Stevens' method. Our results showed that species richness of the total species showed a positively skewed (hump‐shaped) pattern along the elevation gradient and different life‐forms and phytogeographic affinities showed similar hump‐shaped patterns as the total species. The average elevation range size of the total species and herbaceous species showed increasing patterns along the elevation gradient, while lycophytes and ferns, and woody species showed an obvious downward trend after peaking in the high elevation regions. We concluded that the widely distributed herbaceous species which also have broad elevation range sizes are more applicable to ERR, while the narrowly distributed woody species with small elevation range sizes occurring in the higher elevations could reverse ERR. Therefore, we concluded that the ERR is not consistent among different organisms in the same region.

opencc-zeroDec 2012View details →

Data from: Maternal and paternal contributions to pathogen resistance dependent on development stage in a whitefish (Salmonidae)

1. It is often assumed that maternal and paternal contributions to offspring phenotype change over the lifetime of an individual. However, studies on parental effects typically suffer from the problems that heritabilities and maternal environmental effects are difficult to separate, and that both may depend on environmental factors and developmental stage 2. In order to experimentally disentangle maternal from paternal contributions and the likely effects of developmental stage from ecological effects, we sampled a natural population of the whitefish Coregonus palaea, used gametes for full-factorial in vitro fertilizations, raised over 10,000 of the resulting offspring singly at controlled conditions, and exposed them at different points during embryonic development to one of two strains of Pseudomonas fluorescens that differed in their virulence characteristics (only one caused mortality, while both delayed hatching and reduced growth) 3. Vulnerability to infection increased markedly over embryo development. This change coincided with a distinct shift in the importance of maternal to additive genetic effects on survival. Timing of exposure also affected the variance components for hatching time and larval length, but in a less consistent direction than the variance components for mortality. No significant genetic variation was found for any reaction norms across time points of exposure, indicating a uniformity among genotypes in how susceptibility changed over development. Phenotypes were also typically correlated across time points, which could constrain the evolution of the reaction norms 4. Our experiment demonstrates that the relative maternal and paternal contributions to susceptibility to an infection, and hence the evolutionary potential to respond to pathogen-induced selection, depends not only on the kind of pathogenic stress but also on the timing of the challenge.

opencc-zeroAug 2019View details →

Data from: Scale-dependent strategies for coexistence of mesocarnivores in human-dominated landscapes

Identifying factors influencing the distribution of, and interactions within carnivore communities is important for understanding how they are affected by human activities. Species differ in their ability to adapt to humans depending on their degree of specialization in habitat use and feeding habits. This results in asymmetric changes in the ecology of co-occurring species that can influence their interactions. We investigated whether human infrastructures and free-ranging domestic dogs (a species typically associated with humans) influenced the co-occurrence and habitat use of mesocarnivores in a landscape of high human population density in Maharashtra, India. We used 40 camera trap locations during 233 trapping nights and used Bayesian co-occurrence occupancy models to investigate the habitat use and coexistence of species at different spatial scales. Additionally, we investigated their temporal overlap in space use. Indian foxes altered their habitat use both spatially and temporally in order to avoid free-ranging domestic dogs and other larger competitors. The use of human infrastructure by jackals and jungle cats was limited by the presence of dogs. Our results illustrate how habitat use of smaller carnivore species change both spatially and temporally in order to avoid larger competitors. We also show that the presence of species associated with humans mediates the influence of human infrastructures on the habitat use of mesocarnivores. We highlight the importance of acknowledging the potential impact of urbanization not only on single species, but also on the interactions within the community.

opencc-zeroDec 2018View details →

Data from: Size‐dependent stress response in juvenile Arctic charr (Salvelinus alpinus) under prolonged predator conditioning

Predator conditioning can be used to improve post-release antipredator recognition of hatchery-reared salmonids. However, possible negative stress-related effects of prolonged predator conditioning on juvenile fish physiology are poorly understood. We studied the effects of prolonged (91 days) predator odour exposure on whole-body cortisol level and spleen size in six full-sib families of juvenile hatchery-bred Arctic charr (Salvelinus alpinus). Chemical cues from water containing charr-fed pikeperch (Sander lucioperca) were used as the predator exposure stimuli, and lakewater was used as a chemical control. Our study revealed that juvenile body cortisol levels post-predator conditioning were affected by treatment, fish size and their interaction. Importantly, among the smaller (i.e. slowest growing) charr, the predator-exposed fish had higher cortisol levels than control fish, while the opposite pattern was true for the larger fish. These results suggest that chemical cues from charr-fed predators induce a prolonged stress response in juvenile charr. As prolonged predation exposure seems to elevate stress levels in a size-dependent manner, the larger, faster growing fish could possibly have intrinsically lower stress responses to predation threats than smaller, slower growing fish. Possible coupling between stress sensitivity and growth requires further attention due to the likely implications for the management of unintended domestication among captive-reared salmonids.

Data from: Survival estimates strongly depend on capture-recapture designs in a disturbed environment inducing dispersal

Capture‐Recapture (CR) approaches are extensively used to estimate demographic parameters. Their robustness relies on the selection of suitable statistical models, but also on the sampling design and effort deployed in the field. In colonial or territorial species showing breeding site fidelity, recurrent local perturbations, such as predation‐induced breeding failure, may lead individuals to disperse locally or regionally. This might induce heterogeneity in individual CR histories and biases in demographic parameter estimates. Here, we assessed the effect of buffer areas and multi‐site designs on annual survival estimate accuracy and precision. First, using simulated data with and without a multi‐site design, we compared survival estimates for different scenarios involving contrasted local and regional dispersal. Then, using data from a local multi‐site long‐term monitoring survey carried out in a colony of black‐legged kittiwakes, we tested the homogeneity of individual CR histories and compared survival estimates from three datasets including one or several breeding cliffs with or without buffer areas. Results from simulations highlighted that a single‐site design consistently led to underestimated or less precise survival values compared to a multi‐site design. Similarly, a multi‐site design allowed detecting significant temporal trends while a single‐site one did not. In the field‐based study, adding buffer areas reduced individual heterogeneity, but all three datasets suffered from strong trap‐dependence possibly due to individual breeding success affecting nest‐site fidelity. Implementing a multi‐site design significantly improved the accuracy and precision of annual survival estimates, regardless of CR models applied. Adapting the spatial scale of sampling design to the local environment and species behaviour is essential to provide robust parameters of key relevance for population monitoring and management. We show that implementing buffer areas and/or multi‐site designs may be especially beneficial for long‐lived species facing regular local perturbation events leading to local dispersal.

opencc-zeroDec 2014View details →

Data from: Unraveling conflicting density- and distance-dependent effects on plant reproduction using a spatially-explicit approach

1. Density- and distance-dependent (DDD) mechanisms are important determinants of plant reproductive success (PRS). Different components of sequential PRS can operate either in the same or in different directions and thus reinforce or neutralize each other, and they may also operate at different spatial scales. Thus, spatially-explicit approaches are needed to detect such complex DDD effects across multiple PRS components and spatial scales. 2. To reveal DDD effects of different components of early PRS of the Iberian pear (Pyrus bourgaeana) sampled over three consecutive years, we used marked point pattern analysis. Our special interest is to identify conflicting processes that regulate populations at different spatial scales, e.g. whether DDD on fruit initiation and on fruit development acted in opposite directions. To evaluate the significance of observed mark correlation functions based on empirical data (e.g. fruiting success) we compared them to expectations given by spatially-explicit null models. 3. Diverse DDD processes affected several aspects of PRS in a variable extent over the three seasons. First, early fruit set was higher for individuals with more neighbors at small distances (i.e. up to 40m). However, late P. bourgaeana fruit set decreased with increasing number of nearby neighbors, but these effects canceled for overall fruit set that did not show DDD effects. Second, the absolute number of fruits produced (crop sizes) by trees showed positive density dependence in 2011 and 2012 but not in 2013. Finally, the total number of seeds produced did not show DDD effects, indicating that conflicting demographic processes can disrupt the initial spatial pattern of tree investment in reproduction. 4. Synthesis: Understanding complex spatial effects of density- and distance-dependent (DDD) processes requires dissection of component processes to attain the complete picture since contrasting DDD processes may be hidden behind a single cumulative measure of reproductive success. The combination of novel and classic mark correlation functions used here constitute a powerful spatially-explicit tool that can be broadly applied to unravel conflicting mechanisms of DDD regulating the persistence of sessile organisms at a range of spatial scales. Our findings help to explain why some authors failed to find expected DDD of PRS and highlight the importance of detailed multi-year field studies on plant reproductive success.

opencc-zeroDec 2015View details →

Data from: Fungal disease incidence along tree diversity gradients depends on latitude in European forests

European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured the foliar fungal disease incidence on 16 different tree species in 209 plots in six European countries, representing a forest-type gradient from the Mediterranean to boreal forests. Forest plots of single species (monoculture plots) and those with different combinations of two to five tree species (mixed species plots) were compared. Specifically, we analyzed the influence of tree species richness, functional type (conifer vs. broadleaved) and phylogenetic diversity on overall fungal disease incidence. The effect of tree species richness on disease incidence varied with latitude and functional type. Disease incidence tended to increase with tree diversity, in particular in northern latitudes. Disease incidence decreased with tree species richness in conifers, but not in broadleaved trees. However, for specific damage symptoms, no tree species richness effects were observed. Although the patterns were weak, susceptibility of forests to disease appears to depend on the forest site and tree type.

Data from: Context-dependent colonisation of terrestrial habitat 'islands' by a long-distance migrant bird

Landscape context can affect how individuals perceive patch quality during colonisation. However, although context-dependent colonisation has been observed in aquatic environments it has rarely been studied in terrestrial environments or at large spatial scales. Here, we assessed how landscape context influenced colonisation rates in a large-scale (c.7000 km2) terrestrial system where colonisers (Willow Warbler Phylloscopus trochilus) are capable of rapid, long-distance movements. Bioacoustic recorders were used to detect first song dates (an indicator of colonisation or re-colonisation) and settlement in 23 naturally replicated habitat patches. We compared support for three competing hypotheses describing colonisation patterns that depend on landscape context ('redirection', 'landscape-selection' and 'relative patch size') with two patch-level hypotheses (patch 'quality' and 'heterospecific attraction'). First song was earlier when habitat availability in the landscape was low, supporting the 'redirection' hypothesis. Settlement probability was best predicted by patch 'quality' and was lower in woodlands with a dense understorey. Results suggest that colonisation of habitat patches by male P. trochilus after spring migration is spatially hierarchical. First, initial colonisation depends on landscape context, and settlement is then determined by fine-scale vegetation characteristics. More broadly, we suggest that patterns observed in fragmented aquatic environments (e.g. 'redirection') can, in some circumstances, be extended to large-scale terrestrial environments.

opencc-zeroDec 2014View details →

Data from: Pest control of aphids depends on landscape complexity and natural enemy interactions

Aphids are a major concern in agricultural crops worldwide, and control by natural enemies is an essential component of the ecological intensification of agriculture. Although the complexity of agricultural landscapes is known to influence natural enemies of pests, few studies have measured the degree of pest control by different enemy guilds across gradients in landscape complexity. Here, we use multiple natural-enemy exclosures replicated in 18 fields across a gradient in landscape complexity to investigate (1) the strength of natural pest control across landscapes, measured as the difference between pest pressure in the presence and in the absence of natural enemies; (2) the differential contributions of natural enemy guilds to pest control, and the nature of their interactions across landscapes. We show that natural pest control of aphids increased up to six-fold from simple to complex landscapes. In the absence of pest control, aphid population growth was higher in complex than simple landscapes, but was reduced by natural enemies to similar growth rates across all landscapes. The effects of enemy guilds were landscape-dependent. Particularly in complex landscapes, total pest control was supplied by the combined contribution of flying insects and ground-dwellers. Birds had little overall impact on aphid control. Despite evidence for intraguild predation of flying insects by ground-dwellers and birds, the overall effect of enemy guilds on aphid control was complementary. Understanding pest control services at large spatial scales is critical to increase the success of ecological intensification schemes. Our results suggest that, where aphids are the main pest of concern, interactions between natural enemies are largely complementary and lead to a strongly positive effect of landscape complexity on pest control. Increasing the availability of seminatural habitats in agricultural landscapes may thus benefit not only natural enemies, but also the effectiveness of aphid natural pest control.

Figure 2 in Climatic dependence in the daily and seasonal calling activity of anurans from coastal wetlands of southernmost Brazil

Figure 2. Rose-diagram of the circular analysis and mean vector length (r), indicated by the arrow vector, of the number of anuran species exhibiting calling activity (a; r = 0.36) and frequency of the calling activity records throughout the day (b; r = 0.46). The arrow vector indicates the concentration of species exhibiting calling activities throughout the months (a) and the recording frequency of these species throughout the hours of the day (b).

Figure 1 in Climatic dependence in the daily and seasonal calling activity of anurans from coastal wetlands of southernmost Brazil

Figure 1. Map of the study area. (a) The North and South America continent. (b) The Rio Grande do Sul state, Brazil. (c) The area of the TAIM Ecological Station.

Figure 3 in Climatic dependence in the daily and seasonal calling activity of anurans from coastal wetlands of southernmost Brazil

Figure 3. (a) Monthly variation of the maximum (continuous line) and minimum (dashed line) water temperature (°C), minimum absolute air relative humidity (dotted line; %), and hours of rainfall from December 2012 to April 2014. (b) Monthly calling activity of the anuran amphibians community in a wetland area from southernmost Brazil from December 2012 to April 2014. The number of species that exhibited calling activities in each month is shown at the top of the graph and the following categories were used: white – no records; dotted area – between 0.1 and 3.99 hours of daily activity; horizontal bar – between 4 and 7.99 hours of daily activity; dark grey – between 8 and 11.99 hours of daily activity; black – between 12 and 17 hours of daily activity; and plus symbol – activity peak indicated by the mean vector (µ) of the circular analysis.

Figure 4 in Climatic dependence in the daily and seasonal calling activity of anurans from coastal wetlands of southernmost Brazil

Figure 4. Calling activity frequency of the species of anuran amphibians found in wetlands from southernmost Brazil, highlighting the seasons with greatest activity: spring 2013 (September– November 2013); summer 2013 (December 2012–February 2013) and summer 2014 (December 2013–February 2014). The number of records per hour is represented by: white – no records; dotted area – 1-7 records; horizontal bar – 8-14 records; dark grey – 15-21 records; black – 22- 36 records; and plus symbol – activity peak indicated by the mean vector (µ) of the circular analysis.

opencc-zeroJun 2021View details →

Scale-dependent shifts in functional and phylogenetic structure of Mediterranean island plant communities over two centuries

1. Since the Industrial Revolution, the rapid global population and economic expansion has had tremendous impacts on biodiversity across spatial scales, especially for islands. While changes in species richness are easily inferred, the impact of human activity on the underlying community assembly processes has been difficult to ascertain because of lack of long-term community data. 2. Here, we document how the manifestations of plant community assembly have changed over time and space in a Mediterranean archipelago, using a long-term dataset of plant species composition on 16 Tuscan islands sampled across two centuries. The community structure of Mediterranean island plant communities was assessed by integrating species' trait and evolutionary distances. 3. We found that, with increasing island area, the functional and phylogenetic structure of plant communities shifted from clustered early (1830–1950) to overdispersed more recently (1951–2015). On large islands, extirpated species were generally more phylogenetically or functionally similar to remaining residents than expected by chance, while colonists were generally more distantly related to residents. The extinction of similar species and the colonization of dissimilar species drove plant communities towards overdispersion. 4. Synthesis. We provide evidence that plant community assembly on islands has dramatically changed following increased human impacts during the last two centuries, and that this change is shaped by the scale dependency of species extinctions and colonizations. Our results reveal accelerated species replacements of closely related residents by distant colonists on large islands over time, reflecting changes in community assembly and which could alter the functioning of island ecosystems in the future.

opencc-by-4.0Jun 2021View details →

Back to the Past - Analysing Backporting Practices in Package Dependency Networks

This is the replication package of our paper on the practice of backporting in package distributions. Please refer to the instructions in the README file.