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opencc-by-4.0Jan 2020View details →

Modelling Avian Habitat Suitability in Boreal Forest using Structural and Spectral Remote Sensing Data

Data used in research regarding avian habitat suitability models in Harry's River Watershed in Newfoundland, Canada

opencc-by-4.0Apr 2020View details →

Improving early estimates of large earthquake's final fault lengths and magnitudes leveraging source fault structural maturity information - supplementary data

Supplementary dataset for Improving early estimates of large earthquake’s final fault lengths and magnitudes leveraging source fault structural maturity information. This contains individual performance test results for the algorithm discussed in this publication for each earthquake included in the study

opencc-zeroDec 2019View details →

Data from: Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning

Objectives: To develop, demonstrate and evaluate an automated deep learning method for multiple cardiovascular structure segmentation. Background: Segmentation of cardiovascular images is resource-intensive. We design an automated deep learning method for the segmentation of multiple structures from Coronary Computed Tomography Angiography (CCTA) images. Methods: Images from a multicenter registry of patients that underwent clinically-indicated CCTA were used. The proximal ascending and descending aorta (PAA, DA), superior and inferior vena cavae (SVC, IVC), pulmonary artery (PA), coronary sinus (CS), right ventricular wall (RVW) and left atrial wall (LAW) were annotated as ground truth. The U-net-derived deep learning model was trained, validated and tested in a 70:20:10 split. Results: The dataset comprised 206 patients, with 5.130 billion pixels. Mean age was 59.9 ± 9.4 yrs., and was 42.7% female. An overall median Dice score of 0.820 (0.782, 0.843) was achieved. Median Dice scores for PAA, DA, SVC, IVC, PA, CS, RVW and LAW were 0.969 (0.979, 0.988), 0.953 (0.955, 0.983), 0.937 (0.934, 0.965), 0.903 (0.897, 0.948), 0.775 (0.724, 0.925), 0.720 (0.642, 0.809), 0.685 (0.631, 0.761) and 0.625 (0.596, 0.749) respectively. Apart from the CS, there were no significant differences in performance between sexes or age groups. Conclusions: An automated deep learning model demonstrated segmentation of multiple cardiovascular structures from CCTA images with reasonable overall accuracy when evaluated on a pixel level.

opencc-zeroMay 2020View details →

Data from: From structure to function in mutualistic interaction networks: topologically important frugivores have greater potential as seed dispersers

1. Networks of mutualistic interactions between animals and plants are considered a pivotal part of ecological communities. However, mutualistic networks are rarely studied from the perspective of species-specific roles, and it remains to be established whether those animal species more relevant for network structure also contribute more to the ecological functions derived from interactions. 2. Here, we relate the contribution to seed dispersal of vertebrate species with their topological role in frugivore-plant interaction networks. For one year in two localities with remnant patches of Colombian tropical dry forest, we sampled abundance, morphology, behavior, and fruit consumption from fleshy-fruited plants of various frugivore species. 3. We assessed the network topological role of each frugivore species by integrating their degree of generalization in interactions with plants with their contributions to network nestedness and modularity. We estimated the potential contribution of each frugivore species to community-wide seed dispersal, on the basis of a set of frugivore ecological, morphological and behavioral characteristics important for seed dispersal, together with frugivore abundance and frugivory degree. 4. The various frugivore species showed strong differences in their network structural roles, with generalist species contributing the most to network modularity and nestedness. Frugivores also showed strong variability in terms of potential contribution to seed dispersal, depending on the specific combinations of frugivore abundance, frugivory degree and the different traits and behaviors. 5. For both localities, the seed dispersal potential of a frugivore species responded positively to its contribution to network structure, evidencing that the most important frugivore species in the network topology were also those making the strongest contribution as seed dispersers. Contribution to network structure was correlated with frugivore abundance, diet, and behavioral characteristics. This suggests that the species-level link between structure and function is due to the fact that the occurrence of frugivore-plant interactions depends largely on the characteristics of the frugivore involved, which also condition its ultimate role in seed dispersal. 22-May-2020

opencc-by-4.0May 2020View details →

Statistical model training data for "Continuous Structural Parameterization: A proposed method for representing different model parameterizations within one structure demonstrated for atmospheric convection"

Gzipped CSV files containing convection scheme inputs and outputs used for training. Column format of each file: THETA_IN_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,Q_IN_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,DTHETA_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,DQ_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28 where THETA_IN are input values of potential temperature [K], Q_IN are input values of specific humidity [kg/kg], DTHETA are changes in potential temperature due to convection [K], DQ are changes in specific humidity due to convection [kg/kg]. Key: "llcs" are simulations with Lambert-Lewis. "gr" are simulations with Gregory-Rowntree. "4xco2" have 4 x pre-industrial atmospheric carbon dioxide concentration. (Others have 1 x pre-industrial atmospheric carbon dioxide concentration.) "rh0.7" and "rh0.9" have LLCS RHCRIT set to 70% and 90% respectively. All are 30 day simulations either for January "jan" or July "jul".

opencc-zeroMar 2020View details →

Data from: Climate and local environment structure asynchrony and the stability of primary production in grasslands

Aim: Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when decreased performance by some species is offset by increased performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species, reducing buffering. Local conditions, such as soil nutrients, can further alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling experiment. Location: Grasslands in North America, Europe and Australia. Time period: Annual surveys over five-year intervals occurring between 2007 and 2014. Major taxa studied: Herbaceous plants. Methods: We annually sampled per-species cover and aboveground community biomass (net primary productivity; NPP), plus soil chemical properties, in twenty-nine grasslands. We tested how soil conditions, combined with precipitation and temperature variability, affect species richness, asynchrony and temporal stability of primary productivity. We used bivariate relationships and structural equation modeling to examine proximate and ultimate relationships. Results: Climate variability strongly predicted asynchrony, whereas NPP stability was more related to soil conditions. Species richness was structured by both climate variability and soils, and in turn increased asynchrony. Temperature and precipitation variability caused a unimodal asynchrony response, with asynchrony lowest at low and high climate variability. Climate impacted stability indirectly through its effect on asynchrony, with stability increasing at higher asynchrony due to lower inter-annual NPP variability. Soil conditions had no detectable effect on asynchrony but increased stability by increasing mean NPP, especially when soil organic matter was high. Main Conclusions: We found globally consistent evidence that climate modulates species asynchrony, but that the direct effect on stability is low relative to local soil conditions. Nonetheless, our observed unimodal responses to temperature and precipitation variability suggest asynchrony thresholds, beyond which there are detectable destabilizing impacts of climate on primary productivity.

opencc-zeroJun 2020View details →

Data from: Fruit traits of pioneer trees structure seed dispersal across distances on tropical deforested landscapes: implications for restoration

<ol> <li>Pioneer trees with fleshy fruits are typically planted in restoration projects to attract frugivores as a mean to increase dispersal and accelerate forest regeneration. However, differences in fruit traits of pioneer trees can potentially influence dispersal and their restoration outcomes.</li> <li>Here we investigated the effects of bird and plant traits, and distance to forest fragments, on the seed rain using a tree-planting experiment replicated in 12 deforested sites in Brazil. Factors were fruit traits of pioneer trees (wind-dispersed, bird-dispersed with lipids or with carbohydrates, and controls) and distance (10, 50, 300 m) from forest fragments.</li> <li>We found that density and richness of birds and seeds decreased exponentially with distance from fragments, yet these effects were minor compared to the effects of fruit traits on the structure of the seed rain.</li> <li>Overall, plots with fleshy-fruited pioneers attracted much greater bird activity and seed dispersal than plots with wind-dispersal pioneers and the controls. For instance, plots with carbohydrate-rich fruits received more than twice the average species richness and density of birds and seeds of plots with lipid-rich pioneer trees, surpassing wind-dispersed pioneers by more than 80%, and controls by over 90%. Furthermore, the fruit trait treatments resulted in morphological shifts in the average traits of visiting birds. Significant differences in bill gape and flight capacities (wing-loading) were associated with the differences in the seed rain associated with each treatments.</li> <li> Synthesis and applications. Understanding how trait-matching processes mediating mutualistic seed dispersal by frugivores interact with distance-dependent dispersal limitation on deforested tropical landscapes is critical for improving forest restoration efforts. This is especially relevant in the context of applied nucleation. As shown here, avian seed dispersal can thus be manipulated in restoration projects in order to increase connectivity and speed up forest recovery and the provision of the multiple ecosystem services that follow forest succession.</li> </ol>

Data from: Forest structure determines spatial changes in avian community along an elevational gradient in tropical Africa

Aim To test if tree species richness and forest structure drive spatial variation in avian communities along a tropical elevation gradient and to present information about the role of detailed forest parameters. Location A 2000-m long elevational gradient of tropical forest on Mt. Cameroon, west-central Africa. Taxon Birds and trees. Methods We performed bird censuses and vegetation mapping at the same plots across six forested sites at elevations of 350, 650, 1,100, 1,500, 1,850, and 2,200 m a.s.l., with 16 plots per elevation. We tested the effects of elevation, forest structure and tree diversity on the species richness, functional diversity and β-diversity of birds (Bray-Curtis dissimilarity). We used conditional inference trees based on random forests (RF) to investigate these relationships across all elevation sites as well as within elevations. Results Both tree and bird species richness declined monotonically with elevation. Vegetation structure correlated with elevation, and all vegetation attributes significantly differed among elevations. The RF explained 70% of the variance in avian species richness, with the most important predictors being elevation, proportion of dead trees, tree species richness and herb layer coverage. We found that elevation (and shrub layerE2) was a particularly important predictor of avian functional diversity. We identified no important predictor of bird species richness after standardization within elevations, and the proportion of dead trees was the sole important predictor of functional diversity. Within-elevation β-diversity in avian community composition was determined by the dissimilarity of the tree community and differences in leaf area index, solar radiation and spatial distance. The functional dissimilarity was best explained by leaf area index. Main conclusions Apart from elevation itself, spatial distance even within elevations correlated with compositional and functional variation among avian assemblages. Forest structural traits can have a significant influence on distribution of birds. Thus, gaps in the spatial distribution of species such as along elevations might be caused by fine-scale recognition of suitable habitats.

Data from: Warming alters plant phylogenetic and functional community structure

<ol> <li>Climate change is known to affect many facets of the Earth's ecosystems. However, little is known about its impacts on phylogenetic and functional properties of ecological communities. </li> <li>Here we studied the responses of plant communities in an alpine grassland on the Tibetan Plateau to environmental warming across taxonomic, phylogenetic, and functional levels in a six-year multiple-level warming experiment. </li> <li>While low-level warming did not alter either plant species richness or phylogenetic/functional community structure, high-level warming significantly decreased species richness. Higher-level warming more strongly reduced soil moisture and caused stronger environmental filtering, consequently changing species composition and community structure. At the plant functional trait level, high-level warming promoted species turnover through altering the effects of traits such as plant height on species extinction and specific leaf area on species colonization. As a result, high-, but not low-level warming drove phylogenetic/functional community structure from overdispersion to randomness, by filtering out species that were functionally dissimilar and distantly related to the resident species. </li> <li>Synthesis. Our study provides evidence that the responses of plant phylogenetic and functional community structure to low warming differ from those in the future scenarios of increasing temperature. Importantly, the extinction of species that were functionally dissimilar and distantly related to the resident species contributed to alterations in plant community structure under high warming. Our study underscores the need to incorporate the phylogenetic and functional perspectives to gain a more complete understanding of community responses to climate warming.</li> </ol>

Data from: Genetic structure at three spatial scales is consistent with limited philopatry in Ricord's Rock Iguanas (Cyclura ricordii)

Cyclura ricordii is an endemic iguana from Hispaniola Island and is threatened on the IUCN Red List. The main threats are predation by introduced mammals, habitat destruction, and hunting pressure. The present study focused on two nesting sites from Pedernales Province in the Dominican Republic. The hypothesis that natal philopatry influences dispersal and nest site selection was tested. Monitoring and sampling took place in 2012 and 2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley's K revealed that nests were significantly clustered at multiple scales, when both nesting sites were considered and within each nesting site. This suggests a patchy, non-random distribution of nests within nest sites. Hierarchical AMOVA revealed that nest site aggregations did not explain a significant portion of genetic variation within nesting sites. However, a small but positive correlation between geographic and genetic distance was detected using a Mantel's test. Hence, the relationship between geographic distance and genetic distance among hatchlings within nest sites, while detectable, was not strong enough to have a marked effect on fine scale genetic structure. Spatial and genetic data combined determined that the nesting sites included nesting females from multiple locations, and the hypothesis of 'natal philopatry', was not supported because females nesting in the same cluster were no more closely related to each other than to other females from the same nesting site. These findings imply that nesting aggregations are more likely associated with cryptic habitat variables contributing to optimal nesting conditions.

opencc-zeroJun 2020View details →

Data from: The geographic mosaic of arms race coevolution is closely matched to prey population structure

Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.

opencc-zeroJun 2020View details →

Data from: Biomass–density relationships of plant communities deviate from the self‐thinning rule due to age structure and abiotic stress

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. 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. 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. 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.

opencc-by-sa-4.0Jul 2020View details →

Data for "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure"

This upload includes the data presented and analyzed in the article "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure" by Tuomas P. Rossi, Paul Erhart, and Mikael Kuisma. The codes for reproducing the data are provided at <a href="http://doi.org/10.5281/zenodo.3964229">doi:10.5281/zenodo.3964229</a>. See README.md in data.zip for a detailed description.

Data from: eDNA concentration, population size structure, and mark-recapture data

Organism abundance is a critical parameter in ecology, but its estimation is often challenging. Approaches utilizing eDNA to indirectly estimate abundance have recently generated substantial interest. However, preliminary correlations observed between eDNA concentration and abundance in nature are typically moderate in strength with significant unexplained variation. Here we apply a novel approach to integrate allometric scaling coefficients into models of eDNA concentration and organism abundance. We hypothesize that eDNA particle production scales non-linearly with mass, with scaling coefficients < 1. Wild populations often exhibit substantial variation in individual body size distributions; we therefore predict that the distribution of mass across individuals within a population will influence population-level eDNA production rates. To test our hypothesis, we collected standardized body size distribution and mark-recapture abundance data using whole-lake experiments involving nine populations of brook trout. We correlated eDNA concentration with three metrics of abundance: density (individuals/ha), biomass (kg/ha), and allometrically scaled mass (ASM) (∑(individual mass0.73)/ha). Density and biomass were both significantly positively correlated with eDNA concentration (adj. r2 = 0.59 and 0.63, respectively), but ASM exhibited improved model fit (adj. r2 = 0.78). We also demonstrate how estimates of ASM derived from eDNA samples in 'unknown' systems can be converted to biomass or density estimates with additional size structure data. Future experiments should empirically validate allometric scaling coefficients for eDNA production, particularly where substantial intraspecific size distribution variation exists. Incorporating allometric scaling may improve predictive models to the extent that eDNA concentration may become a reliable indicator of abundance in nature.

opencc-zeroJan 2020View details →

Data from: Temporal variation in spatial genetic structure during population outbreaks: distinguishing among different potential drivers of spatial synchrony

Spatial synchrony is a common characteristic of spatio-temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, is generally unknown. Distinguishing these mechanisms and their effects on synchrony can help us to better understand spatial population dynamics, design conservation and management strategies, and predict climate change impacts. Population genetic data can be used to tease apart these two processes as the spatio-temporal genetic patterns they create are expected to be different. A challenge, however, is that genetic data are often collected at a single point in time, which may introduce context-specific bias. Spatio-temporal sampling strategies can be used to reduce bias and to improve our characterization of the drivers of spatial synchrony. Using spatio-temporal analyses of genotypic data, our objective was to identify the relative support for these two mechanisms to the spatial synchrony in population dynamics of the irruptive forest insect pest, the spruce budworm (Choristoneura fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by distance and sPCA were used to characterize spatio-temporal genomic variation using 1370 SBW larvae sampled over four years (2012-2015) and genotyped at 3,562 SNP loci. We found evidence of overall weak spatial genetic structure that decreased from 2012 to 2015 and a genetic diversity homogenization among the sites. We also found genetic evidence of a long-distance dispersal event over > 140 km. These results indicate that dispersal is the key mechanism involved in driving population synchrony of the outbreak. Early intervention management strategies that aim to control source populations have the potential to be effective through limiting dispersal. However, the timing of such interventions relative to outbreak progression is likely to influence their probability of success.

opencc-zeroAug 2020View details →

Data from: Genetic population structure and variation at phenology-related loci in anadromous Arctic char (Salvelinus alpinus)

The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology-related loci associated with timing of migration and spawning. We contrasted genetic population structure at 53 SNPs versus four phenology-related loci among 15 anadromous Arctic char populations from Western Greenland and three outgroup populations. Among anadromous populations, the time period available for foraging at sea (> 2oC) ranges from a few weeks to several months, motivating two research questions: 1) Is population structure compatible with possibilities for evolutionary rescue of anadromous populations during climate change? 2) Does selection associated with latitude or SST regimes act on phenology-related loci? In Western Greenland, strong isolation-by-distance at SNPs was observed and spatial autocorrelation analysis showed genetic patch size up to 450 km, documenting contingency and gene flow among populations. Outlier tests provided no evidence for selection at phenology-related loci. However, in Western Greenland, mean allele length at OtsClock1b was positively associated with the time of year when SST first exceeded 2oC and negatively associated with duration of the period where SST exceeded 2oC. This is consistent with local adaptation for making full use of the time period available for foraging in the sea. Current adaptation may become maladaptive under climate change, but long-distance connectivity of anadromous populations could redistribute adaptive variation across populations and lead to evolutionary rescue.

opencc-zeroAug 2020View details →

Data from: Environmental variables associated with Nothophaeocryptopus gaeumannii population structure and Swiss needle cast severity in Western Oregon and Washington

The environment has a strong influence on the abundance and distribution of plant pathogenic organisms, and plays a major role in the causation of plant disease. Climatological factors may also alter the dynamics of the interactions between plant pathogens and their hosts. Nothophaeocryptopus (=Phaeocryptopus) gaeumannii, the causal agent of Swiss needle cast (SNC) of Douglas-fir, is endemic to western North America where it exists as two sympatric, reproductively isolated lineages. The abundance of this fungus and the severity of SNC are strongly influenced by climate. We used statistical and population genetic analyses to examine relationships between environment, pathogen population structure, and SNC severity. Although N. gaeumannii Lineage 2 in western Oregon and Washington was most abundant where SNC symptoms were most severe, we did not detect a significant relationship between Lineage 2 and disease severity. Warmer winter temperatures were inversely correlated with foliage retention (AFR) and positively correlated with the relative abundance of Lineage 2 (PL2). However when distance inland, which was strongly correlated with both AFR and PL2, was included in the model, there was no significant relationship between Lineage 2 and AFR. Spring/early summer dew point temperatures also were positively associated with total N. gaeumannii abundance (colonization index (CI)), and inversely correlated with AFR. Warmer summer mean temperatures were associated with lower CI and higher AFR. Our results suggest that the two lineages have overlapping environmental optima, but slightly different tolerance ranges. Lineage 2 was absent from more inland sites where winters are colder and summers are warm and dry, while Lineage 1 occurred at most sites across an environmental gradient suggesting broader environmental tolerance. These relationships suggest that climate influences the abundance and distribution of this ecologically important plant pathogen, and may have played a role in the evolutionary divergence of these two cryptic fungal lineages.