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opencc-zeroDec 2018View details →

Data from: 18S rRNA metabarcoding diet analysis of the predatory fish community across seasonal changes in prey availability

Predator-prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts of predatory fishes. Predator GI samples were taken from the Black River, Cheboygan Co., MI, USA (n=367 samples, 12 predator species) during periods of high prey availability, including the larval stage of regionally threatened lake sturgeon (Acipenser fulvescens Rafinesque 1817) in late May/early June of 2015 and of relatively lower prey availability in early July of 2015. DNA was extracted and sequenced from 355 samples (96.7%), and prey DNA was identified in 286 of the 355 samples (80.6%). Prey were grouped into 33 ecologically significant taxonomic groups based on the lowest taxonomic level sequences that could be identified using sequences available on GenBank. Changes in the makeup of diet composition, dietary overlap, and predator preference were analyzed comparing the periods of high and low prey abundance. Some predator species exhibited compositional changes in diet. Dietary overlap was slightly but significantly higher during the period of high prey abundance. There was little evidence for large changes in predator preference between the two periods. This study demonstrates the utility of molecular diet analysis in understanding predator-prey interactions in complex freshwater communities.

opencc-zeroDec 2016View details →

Data from: Does soil moisture availability explain liana seedling distribution across a tropical rainfall gradient?

Liana density tends to increase with decreasing rainfall and increasing seasonality. However, the pattern of liana distribution may be due to differences in soil water retention capacity, not rainfall and seasonality per se. We tested the effect of rainfall and soil substrate with respect to the distribution of liana seedlings in six sites across a rainfall gradient from the wet Atlantic to the dry Pacific in central Panama. Soils were either limestone, with low water-holding capacity, or laterite, with higher water-holding capacity. We sampled liana seedlings at each site using three 1 × 100 m transect. We found that relative liana seedling density was higher on limestone soils compared to laterite soils regardless of the amount of rainfall. Furthermore, liana community composition on limestone soils was more similar to dry forest sites than to adjacent wet and moist forest sites. Liana seedling species diversity relative to trees was significantly higher in a low-fertility dry forest site compared to a high-fertility forest, but did not differ from the other sites. Thus, liana seedling density and community structure may be driven more by soil type and thus by soil moisture availability than strictly by mean annual rainfall and the seasonality of rainfall.

Data from: Time-integrated habitat availability is a resource attribute that informs patterns of use in intertidal areas

In dynamic environments, resource availability may change by several orders of magnitude, over hours to months, but the duration of resource availability is not often included as a characteristic attribute of resources even though temporal resource dynamics might limit patterns of use. In our study of wading birds foraging in intertidal areas, tides cause large changes in the areal extent of shallow-water foraging habitat (i.e., the resource), but tides also constrain the duration of availability, which is often overlooked. We hypothesized that temporal constraints on habitat availability from tides would be reflected in patterns of habitat use by foraging birds. We estimated the time-integrated habitat availability and compared it to traditional habitat attributes (seagrass cover, substrate type, instantaneous water depth, and proximity to mangrove islands or deep water) that have strong evidential support for influencing patterns of use. To evaluate our hypotheses, we quantified habitat attributes at intertidal areas in the Florida Keys, U.S.A, where wading birds were observed foraging (Little Blue Heron, Egretta caerulea: N=183; Great White Heron, Ardea herodias occidentalis: N=162). We tested for non-random use by sampling habitat attributes at two spatial scales around the observed feeding locations and we analyzed the data using a conditional logistic regression model. There was no evidence that seagrass cover or substrate explained patterns of use. The proximity of foraging locations relative to mangroves and to deep water were important at both spatial scales but had lower effect sizes (odds-ratios) than time-integrated habitat availability and water depth, and the latter may only serve as a physical constraint on access. We found support that time-integrated habitat availability was a distinct resource attribute, had the greatest effect size (4-8-fold change in relative probability of use), and best explained patterns of habitat use at the largest spatial scale. In studies of resource use where changes in resource availability are non-linear or when strong constraints on access are imposed by behavior, incorporating time-integrated estimates of resource availability into analyses can improve insights into spatiotemporal patterns of resource use.

opencc-zeroMar 2020View details →

Data from: Switchgrass rhizosphere metabolite chemistry driven by nitrogen availability

Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. Plants were grown with the inoculum Azotobacter vinelandii DJ for three days before harvest. We found switchgrass root exudate chemistry to be driven by N availability. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment. However, we found little evidence of N treatment and inoculation interaction effects which suggests this response is not directly mediated by N availability.

Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity

Aim: The International Tree-Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: i) quantify its biases, ii) assess how well it represents global forests, iii) develop tools to identify priority areas to improve its representativity, and iv) make available the corrected database. Location: Worldwide. Time period: Contributed datasets between 1974 and 2017. Major taxa studied: Trees. Methods: We identified and corrected formatting issues in all individual datasets of the ITRDB. We then calculated the representativity of the ITRDB with respect to species, spatial coverage, climatic regions, elevations, need for data update, climatic limitations on growth, vascular plant diversity, and associated animal diversity. We combined these metrics into a global Priority Sampling Index (PSI) to highlight ways to improve ITRDB representativity. Results: Our refined dataset provides access to a network of >52 million growth data points worldwide. We found, however, that the database is dominated by trees from forests with low diversity, in semi-arid climates, coniferous species, and in western North America. Conifers represented 81% of the ITRDB and even in well sampled areas, broadleaves were poorly represented. Our PSI stressed the need to increase the database diversity in terms of broadleaf species and identified poorly represented regions that require scientific attention. Great gains will be made by increasing research and data sharing in African, Asian, and South American forests. Main conclusions: The extensive data and coverage of the ITRDB shows great promise to address macroecological questions. To achieve this, however, we have to overcome the significant gaps in the representativity of the ITRDB. A strategic and organized group effort is required, and we hope the tools and data provided here can guide the efforts to improve this invaluable database.

opencc-zeroNov 2019View details →

Data from: Water availability and temperature induce changes in oxidative status during pregnancy in a viviparous lizard

<ol> <li>Reproduction involves considerable reorganization in an organism's physiology that incurs potential toxicity for cells (e.g., oxidative stress) and decrease in fitness. This framework has been the cornerstone of the so-called 'oxidative cost of reproduction', a theory that remains controversial and relatively overlooked in non-model ectotherms.</li> <li>Here, we used two complementary approaches in natural and controlled conditions to test whether altered access to climate conditions (water and temperature resources) alters oxidative status and mediates reproductive trade-offs in viviparous populations of the common lizard (Zootoca vivipara).</li> <li>First, we examined whether access to free standing water and differences in ambient temperature across 12 natural populations could be related with variation in oxidative status, reproductive effort and reproductive success. Second, we determined whether an experimental restriction to water triggers higher oxidative cost of reproduction and correlates with fitness measures (reproductive success, future survival rate and probability of future reproduction).</li> <li>Pregnant females exhibited higher sensitivity than males to natural or experimental limitations in temperature and water access. That is, in restricted environments, pregnant females with higher reproductive effort exhibited stronger oxidative damage despite enhanced non-enzymatic antioxidant capacity.</li> <li>Enhanced antioxidant defensive capacity in pregnant females was positively correlated with higher reproductive success, whereas elevated oxidative damage negatively correlated with offspring annual survival. </li> <li>Altogether, our results revealed a context-dependent oxidative cost of reproduction that was concomitant with a conflict in water demand from offspring. These new insights should be critical for understanding ectotherm responses to heat waves and summer droughts that are increasing in frequency and duration.</li> </ol>

Data from: Water availability drives urban tree growth responses to herbivory and warming

1. Urban forests provide important ecosystem services to city residents, including pollution removal and carbon storage. Climate change and urbanization pose multiple threats to these services. However, how these threats combine to affect urban trees, and thus how to mitigate their effects, remains largely untested because multi-factorial experiments on mature trees are impractical. 2. We used a unique urban warming experiment paired with a laboratory chamber experiment to determine how three of the most potentially damaging factors associated with global change for urban and rural trees—warming, drought, and insect herbivory—affect growth of Quercus phellos (willow oak), the most commonly-planted large shade tree in the southeastern US, which is known for its resilience to these potential stressors. 3. In a previous study, we found that the urban heat island effect was associated with reduced growth of Q. phellos and higher abundance of Parthenolecanium scale insects, key pests of oaks in cities. Here, we tested the hypothesis that tree water stress is the mechanism for these effects of warming. We found evidence that water stress is a major, interactive factor reducing urban tree growth, but found no evidence that water stress is associated with Parthenolecanium survival or abundance. Warming and Parthenolecanium only reduced growth in Q. phellos saplings that were simultaneously water stressed. 4. Synthesis and applications. Across many temperate cities worldwide, urban trees grow less than rural trees. Our results point to water stress as the most likely driver for this pattern. Importantly, we found that water stress both reduces tree growth on its own and exacerbates effects of warming and insect pests on tree growth. Therefore, management strategies targeted at increasing tree hydration in cities may reduce effects of these three key stressors that are expected to intensify with further urbanization and climate change.

opencc-zeroDec 2015View details →

Data from: Sources of (co)variation in alternative siring routes available to male great tits (Parus major)

Males of socially monogamous species can increase their siring success via within-pair and extra-pair fertilizations. In this study, we focused on the different sources of (co)variation between these siring routes, and asked how each contributes to total siring success. We quantified the fertilization routes to siring success, as well as behaviors that have been hypothesized to affect siring success, over a five-year period for a wild population of great tits Parus major. We considered siring success and its fertilization routes as "interactive phenotypes" arising from phenotypic contributions of both members of the social pair. We show that siring success is strongly affected by the fecundity of the social (female) partner. We also demonstrate that a strong positive correlation between extra-pair fertilization success and paternity loss likely constrains the evolution of these two routes. Moreover, we show that more explorative and aggressive males had less extra-pair fertilizations, whereas more explorative females laid larger clutches. This study thus demonstrates that (co)variation in siring routes is caused by multiple factors not necessarily related to characteristics of males. We thereby highlight the importance of acknowledging the multi-level structure of male fertilization routes when studying the evolution of male mating strategies.

opencc-zeroDec 2016View details →

Data from: Mismatch between dietary requirements for lipid by a predator and availability of lipid in prey

Growth is an important factor in predicting an organism's overall success as an adult. Understanding how abiotic and biotic factors influence body size is key to predicting how environmental changes will impact organisms and predicting optimal behaviors under varying conditions. Food items can vary widely in nutrient content and this variation can affect growth. We tested how the quantity and macronutrient content of live prey affected the growth of juvenile jumping spiders, Phiddipus audax, using 420 spiderlings raised on one of 21 diets. In addition, we measured the nutrient content of prey from the field and compared average prey nutrient content with the diet at which spiders maximized growth. Our results show that the quantity and nutrient content of prey have significant and interacting effects on the growth of an actively hunting predator. In particular, spiders grew larger in body size (tibia/patella length and posterior lateral eye width) and were heavier on diets with higher lipid content. Yet, data on the nutrient content of prey from the field shows that most potential prey have high protein and low lipid content in their bodies. This apparent mismatch between spider nutritional requirements and prey nutrient availability likely presents a challenge to spiders seeking to maximize growth in the field. Several hypotheses for how these predators overcome this challenge to reach the large body sizes observed in the field are discussed.

opencc-zeroDec 2015View details →

Data from: Resource availability and roosting ecology shape reproductive phenology of rain forest insectivorous bats

Bats in temperate and subtropical regions typically synchronize birth of a single young with peaks in resource availability driven by local climate patterns. In tropical rain forest, insects are available throughout the year, potentially allowing departures from seasonal monoestry. However, reproductive energy budgets may be constrained by the cost of commuting to foraging grounds from distant roosts. To test these hypotheses, we simultaneously tracked female reproductive activity of 11 insectivorous bat species, insect biomass, and local weather variables for 20 months in a Malaysian rain forest. Five species roost in forest structures and hence have low commuting costs, whereas six species depend on caves, which are limited in the landscape, and are presumed to incur higher commuting costs to foraging sites. Monthly insect biomass was positively correlated with monthly rainfall, and there was a significant relationship between insect biomass and lactation in cave-roosting but not forest-roosting species. Cave-roosting species were seasonally monoestrus, with parturition confined to a two-month period, whereas in forest-roosting species, pregnancy and lactation were recorded throughout the year. Our results suggest that the energetic costs of commuting from roosts to foraging grounds shape annual reproductive patterns in tropical rain forest insectivorous bats. Ongoing changes in forest landscapes are likely to increase these costs for cave-roosting bats, further restricting reproductive opportunities. Climate change is projected to influence the timing of rainfall events in many tropical habitats, which may disrupt relationships between rainfall, insect biomass, and bat reproductive timing, further compromising reproductive success.

opencc-zeroDec 2010View details →

Data from: Diversity of S-alleles and mate availability in 3 populations of self-incompatible wild pear (Pyrus pyraster)

Small populations of self-incompatible plants may be expected to be threatened by limitation of compatible mating partners (i.e. S-Allee effect). However, few empirical studies have explicitly tested the hypothesis of mate limitation in small populations of self-incompatible plants. To do so, we studied wild pear (Pyrus pyraster), which possesses a gametophytic self-incompatibility system. We determined the S-genotypes in complete samplings of all adult trees from three populations using a PCR-RFLP approach. We identified a total of 26 different S-alleles, homologous to S-alleles of other woody Rosaceae. Functionality of S-alleles and their Mendelian inheritance were verified in artificial pollination experiments and investigations of pollen tube growth. The smallest population (N = 8) harboured nine different S-alleles and showed a mate availability of 92.9%, while the two larger populations harboured 18 and 25 S-alleles and exhibited mate availabilities of 98.4% and 99.2%, respectively. Therefore, we conclude that even small populations of gametophytic self-incompatible plants may exhibit high diversity at the S-locus and are not immediately threatened owing to reduced mate availability.

Data from: Decomposition of coarse woody debris in a long-term litter manipulation experiment: a focus on nutrient availability

1.The majority of aboveground carbon in tropical forests is stored in wood, which is returned to the atmosphere during decomposition of coarse woody debris. However, the factors controlling wood decomposition have not been experimentally manipulated over time scales comparable to the length of this process. 2.We hypothesized that wood decomposition is limited by nutrient availability and tested this hypothesis in a long-term litter addition and removal experiment in a lowland tropical forest in Panama. Specifically, we quantified decomposition using a 15 year chronosequence of decaying boles, and measured respiration rates and nutrient limitation of wood decomposer communities. 3.The long-term probability that a dead tree completely decomposed was decreased in plots where litter was removed, but did not differ between litter addition and control treatments. Similarly, respiration rates of wood decomposer communities were greater in control treatments relative to litter removal plots; litter addition treatments did not differ from either of the other treatments. Respiration rates increased in response to nutrient addition (nitrogen, phosphorus, and potassium) in the litter removal and addition treatments, but not in the controls. 4.Established decreases in concentrations of soil nutrients in litter removal plots and increased respiration rates in response to nutrient addition suggest that reduced rates of wood decomposition after litter removal were caused by decreased nutrient availability. The effects of litter manipulations differed directionally from a previous short-term decomposition study in the same plots, and reduced rates of bole decomposition in litter removal plots did not emerge until after more than 6 years of decomposition. These differences suggest that litter-mediated effects on nutrient dynamics have complex interactions with decomposition over time.

Data from: Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or "microbial jungles", where in analogy to forests, diverse and multi-trophic level communities lend stability to ecosystem functioning. This multi-trophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments.

opencc-zeroMay 2020View details →

Data from: An exploratory study of staff perceptions of shift safety in the critical care unit and routinely available data on workforce, patient and organisational factors

Objectives To explore: bedside professional reported (BPR) perceptions of safety in intensive care staff; and the relationships between BPR safety, staffing, patient and work environment characteristics. Design An exploratory study of self-recorded staff perceptions of shift safety and routinely collected data. Setting A large teaching hospital comprising 70 critical care beds. Participants All clinical staff working in adult critical care. Interventions Staff recorded whether their shift felt "safe, unsafe or very unsafe" for 29 consecutive days. We explored these perceptions and relationships between these and routine data on staffing, patient and environmental characteristics. Outcome measures Relationships between BPR safety and staffing, patient and work environment characteristics. Results 2836 BPR scores were recorded over 29 consecutive days (response rate 57.7%). Perceptions of safety varied between staff, including within the same shift. There was no correlation between perceptions of safety and two measures of staffing; care hours per patient day (r= 0.13 p=0.108) and Safecare Allocate (r= -0.19 p=0.013). We found a significant, positive relationship between perceptions of safety and the percentage of Level 3 (most severely ill) patients (r=0.32, p=0.0001). There was a significant inverse relationship between perceptions of safety and the percentage of Level 1 patients on a shift (r= -0.42, p=<0.0001). Perceptions of safety correlated negatively with increased numbers of patients (r= -0.44, p=0.0006) and higher percentage of patients located side rooms (r=0.63, p<0.0001). We found a significant relationship between perceptions of safety and the percentage of staff with a specialist critical care course (r=0.42. p=0.0001). Conclusion Existing staffing models, which are primarily influenced by staff:patient ratios may not be sensitive to patient need. Other factors may be important drivers of staff perceptions of safety and should be explored further. Trial registration- UK Health Research Authority approval was obtained (ID249248).

opencc-zeroDec 2014View details →

Data from: Feed or fight: testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard

Body size often varies among insular populations relative to continental conspecifics – the 'island rule' – and functional, context-dependent morphological differences tend to track this body size variation on islands. Two hypotheses are often proposed as potential drivers of insular population differences in morphology: one relating to diet and the other involving intraspecific competition and aggression. We directly tested whether differences in morphology and maximum bite capacity were explained by interisland changes in hardness of both available and consumed prey, and levels of lizard-to-lizard aggression among small-island populations. Our study included 11 islands in the Greek Cyclades and made use of a gradient in island area spanning five orders of magnitude. We focused on the widespread lizard Podarcis erhardii. We found that on smaller islands, P. erhardii body size was larger, head height was larger relative to body size, and maximum bite capacity became proportionally stronger. This pattern in morphology and performance was not related to differences in diet, but was highly correlated with proxies of intraspecific aggression – bite scars and missing toes. Our findings suggest that critical functional traits such as body size and bite force in P. erhardii follow the predictions of the island rule and are changing in response to changes in the competitive landscape across islands of different sizes.

Figure 5 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 5. Non-metric multidimensional scaling (nMDS) plots showing infaunal invertebrate community at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by sandy shore site and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.

Figure 6 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 6. Non-metric multidimensional scaling (nMDS) plots of (a) sediment parameters (depth to the aRPD, water content, particle size, penetrability, % macrophyte coverage, % Zostera marina cover, and % wood cover) by site and round and (b) the food availability (chlorophyll a and organic matter content) at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. Vector overlays for sediment and food variables show the correlation between variables and nMDS axes, with each vector showing the direction of increased value. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May 23–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.

Figure 2 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 2. Flow chart demonstrating statistical analysis conducted on the biotic and abiotic variables sampled at intertidal mudflats (n = 3) and intertidal sandy shores (n = 3) on the north coast of British Columbia, Canada during the summer of 2017.

Figure 1 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 1. Map of intertidal mudflats and sandy shore study sties around Prince Rupert, and on Prescott Island, British Columbia, sampled during summer of 2017. Figure 1(a) shows mudflats close to the Skeena River (CC: Cassiar Cannery 54.1747, 130.1721; TB: Tyee Banks 54.2000, 129.9634; WC: Wolfe Cove 54.2424, 130.2730). Figure 1(b) shows sandy shores on Prescott Island (BO: Boulder Beach 54.0871, 130.5970; PI: Prescott Inlet 54.0709, 130.5950; GU: Coast Guard Beach 54.0659, 130.5757).

Figure 3 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 3. Non-metric multidimensional scaling (nMDS) graphs showing infaunal invertebrate community at three intertidal mudflats on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by mudflat and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. CC: Cassiar Cannery. TB: Tyee Banks. WC: Wolfe Cove. Round A: 23 May–June 1. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.