Find research datasets worth reusing

Data from: A case for the "Competitive exclusion – tolerance rule" as a general cause of species turnover along environmental gradients

Closely-related, ecologically-similar species often segregate their distributions along environmental gradients of time, space, and resources, but previous research suggests diverse underlying causes. Here, we review reciprocal removal studies in nature that experimentally test the role of interactions among species in determining their turnover along environmental gradients. We find consistent evidence for asymmetric exclusion coupled with differences in environmental tolerance causing the segregation of species pairs, where a dominant species excludes a subordinate from benign regions of the gradient, but is unable to tolerate challenging regions to which the subordinate species is adapted. Subordinate species were consistently smaller and performed better in regions of the gradient typically occupied by the dominant species compared to their native distribution. These results extend previous ideas contrasting competitive ability with adaptation to abiotic stress to include a broader diversity of species interactions (intraguild predation, reproductive interference) and environmental gradients, including gradients of biotic challenge. Collectively, these findings suggest that adaptation to environmental challenge compromises performance in antagonistic interactions with ecologically-similar species. The consistency of this pattern across diverse organisms, environments, and biomes suggests generalizable processes structuring the segregation of ecologically-similar species along disparate environmental gradients, a phenomenon that we propose should be named the Competitive exclusion – tolerance rule.

Herbivory selects for tolerance and constitutive defence across stages of community succession

Plants defend themselves from herbivory by either reducing damage (resistance) or minimizing its negative fitness effects with compensatory growth (tolerance). Factors mediating the selection for defenses such as herbivory and competition are in constant flux in an early secondary successional community, which can create temporal variation in selection for these traits. We manipulated successional age of the community and insect herbivory in a genotypic selection experiment with the perennial herb Solidago altissima. We found selection for investment in aboveground biomass in early succession but not in mid-succession, suggesting that the importance of competition is highest in the very first years of succession. Herbivory selected for smaller and better defended plants in both successional ages but decreased plant survival and probability of flowering only in mid-succession. Despite dramatic differences in herbivory between early and mid-succession, selection on defense traits did not change. These results demonstrate that changes in the community that affect key life-history traits in an individual species can occur over very short timescales in a dynamic secondary successional environment. Such temporal variation may be an important, yet overlooked, contributor to adaptive mosaics across populations.

Invasion tolerance varies along a topographic gradient irrespective of invader presence

Invasive exotic plants often impact native plant species through strong competition, yet their effects can vary across different native populations. Previous exposure to invasive species but also differentiation along abiotic gradients may determine to what extent native populations are competitively suppressed by plant invasive species. Here, we experimentally investigated whether competitive effects of the invasive exotic jewelweed Impatiens parviflora on its native congener Impatiens noli-tangere are related to previous exposure to the invader or rather to topography of the source populations, i.e., to terrain features such as elevation, aspect, or slope. We also asked whether, in return, topographic settings of invasive I. parviflora populations may explain competitive effects of the native jewelweed. In a common garden competition experiment we found that populations of native jewelweed from colder, higher altitude sites and from drier sites were on average seven and six times, respectively, more tolerant to interspecific competition than populations from warmer and wetter sites. In contrast, previous exposure of native jewelweed populations to the invader was not a significant predictor of invader's competitive effects. Further, topographic settings of populations of invasive jewelweed were not significantly related to the native's competitive effects. Our study suggests that the native jewelweed's population differentiation along topographic gradients is more important in determining competitive interactions with an invasive congener than invasion-induced selection. As fine-scale environmental variation can shape adaptation of native species to the effects of invasive species, such variation should be considered when predicting invasive species' impact on native plant communities.

Arbuscular mycorrhizal fungi improve the growth and drought tolerance of Cinnamomum migao by enhancing physio-biochemical responses

Drought is the main limiting factor for plant growth in karst areas with a fragile ecological environment. Cinnamomum migao H. W. Li is an endemic medicinal woody plant present in the karst areas of southwestern China, and it is endangered due to poor drought tolerance. Arbuscular mycorrhizal fungi (AMF) are known to enhance the drought tolerance of plants. However, few studies have examined the contribution of AMF in improving the drought tolerance of Cinnamomum migao seedlings. Therefore, we conducted a series of experiments to determine whether a single inoculation and coinoculation of AMF (Claroideoglomus lamellosum and Claroideoglomus etunicatum) enhanced the drought tolerance of Cinnamomum migao. Further, we compared the effects of single inoculation and coinoculation with different inoculum sizes (20, 40, 60, and 100 g; four replicates per treatment) on mycorrhizal colonization rate, plant growth, photosynthetic parameters, antioxidant enzyme activity, and malondialdehyde (MDA) and osmoregulatory substance contents. The results showed that compared with nonmycorrhizal plants, AMF colonization significantly improved plant growing status; net photosynthetic rate; superoxide dismutase, catalase, and peroxidase activities; and soluble sugar, soluble protein, and proline contents. Further, AMF colonization increased relative water content and reduced MDA content in cells. These combined cumulative effects of AMF symbiosis ultimately enhanced the drought tolerance of seedlings and were closely related to the inoculum size. With an increase in inoculum size, the growth rate and drought tolerance of plants first increased and then decreased. The damage caused by drought stress could be reduced by inoculating 40–60 g of AMF, and the effect of co-inoculation was significantly better than that of single inoculation at 60 g of AMF, while the effect was opposite at 40 g of AMF. Additionally, the interaction between AMF and inoculum sizes had a significant effect on drought tolerance. In conclusion, the inoculation of the AMF Claroideoglomus lamellosum and Claroideoglomus etunicatum improved photosynthesis, activated antioxidant enzymes, regulated cell osmotic state, and enhanced the drought tolerance of Cinnamomum migao, enabling its growth in fragile ecological environments.

opencc-by-4.0Jan 2023View details →

Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation

The unprocessed and processed benchmarking data used in the paper of "Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation"

opencc-by-4.0Jan 2023View details →

Climate-related adaptation of metabolic rate across the distribution of a broadly tolerant invasive forest pest

Metabolic rate is a widely-studied physiological species trait related to energetics, climate, and geographic distributions. Hypotheses have been proposed to explain variation in metabolic rate, but evidence has been mixed due to the limited sampling scope of intraspecific studies. Successful biological invasions offer a unique opportunity to examine the development of intraspecific physiological variation and how it relates to climate, invasive spread, and species range limits. Here we conducted a macro-scale study of routine metabolic rate variation across the Spongy moth (Lymantria dispar) invasive range in North America. We found a positive latitudinal cline with population-specific metabolic rates increasing from the southern range to the north that was significantly related to climate. Our comprehensive macrophysiological analyses provide further evidence that local adaptation of physiological and life history traits to climate has played a significant role in the spread of L. dipsar across the landscape in the past 150 years.

opencc-zeroFeb 2023View details →

Data from: Glutaredoxin regulation of primary root growth confers early drought stress tolerance in pearl millet

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat- and drought-tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet's early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modelling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including GWAS and QTL approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.

opencc-zeroFeb 2023View details →

Taurine depletion impairs cardiac function and affects tolerance to hypoxia and high temperatures in brook char (Salvelinus fontinalis)

Physiological and environmental stressors can cause osmotic stress in fish hearts, leading to a reduction in intracellular taurine concentration. Taurine is a beta amino acid known to regulate cardiac function in other animal models but its role in fish has not been fully elucidated. We generated a model of cardiac taurine-deficiency (TD) by feeding brook char (Salvelinus fontinalis) a diet enriched in β-alanine, which inhibits cardiomyocyte taurine uptake. Cardiac taurine levels were reduced by 21%, and stress-induced changes in normal taurine handling were observed in TD brook char. Responses to exhaustive exercise and acute thermal and hypoxia tolerance were then assessed using a combination of in vivo, in vitro, and biochemical approaches. Critical thermal maximum was higher in TD brook char despite significant reductions in maximum heart rate. In vivo, TD brook char exhibited a lower resting heart rate, blunted hypoxic bradycardia, and a severe reduction in time to loss of equilibrium under hypoxia. In vitro function was similar between control and TD hearts under oxygenated conditions, but stroke volume and cardiac output were severely compromised in TD hearts under anoxia. Aspects of mitochondrial structure and function were also impacted in TD permeabilized cardiomyocytes, but overall effects were modest. High levels of intracellular taurine are required to achieve maximum cardiac function in brook char and cardiac taurine efflux may be necessary to support heart function under stress. Taurine appears to play a vital, previously unrecognized role in supporting cardiovascular function and stress tolerance in fish.

opencc-zeroMar 2023View details →

Data from: The Competitive exclusion – tolerance rule explains habitat partitioning among co-occurring species of burying beetles

Habitat partitioning among co-occurring, ecologically similar species is widespread in nature and thought to be an important mechanism for coexistence. The factors that cause habitat partitioning, however, are unknown for most species. We experimentally tested among three alternative hypotheses to explain habitat partitioning among two species of co-occurring burying beetle (Nicrophorus) that occupy forest (N. orbicollis) and wetland (N. hebes) habitats. Captive experiments revealed that the larger N. orbicollis (forest) was consistently dominant to N. hebes (wetland) in competitive interactions for carcasses that they require for reproduction. Transplant enclosure experiments in nature revealed that N. hebes had poor reproductive success whenever the dominant N. orbicollis was present. In the absence of N. orbicollis, N. hebes performed as well, or better, in forest versus its typical wetland habitat. In contrast, N. orbicollis performed poorly in wetlands regardless of the presence of N. hebes. These results support the Competitive exclusion – tolerance rule where the competitively dominant N. orbicollis excludes the subordinate N. hebes from otherwise suitable or preferable forest habitat, while the subordinate N. hebes is uniquely able to tolerate the challenges of breeding in wetlands. Transplant experiments further showed that carcass burial depth – an important trait thought to enhance the competitive ability of the dominant N. orbicollis – is costly in wetland habitats. When in the presence of N. hebes, N. orbicollis buried carcasses deeper; deeper burial is thought to provide a competitive advantage in forests, but further compromised the reproductive success of N. orbicollis in wetlands. Overall, results provide evidence that the Competitive exclusion – tolerance rule underlies habitat partitioning among ecologically similar species, and that the traits important for competitive dominance in relatively benign environments are costly in more challenging environments, consistent with a trade-off.

opencc-by-4.0Sep 2021View details →

Developmental Temperature Affects Life-History Traits and Heat Tolerance in the Aphid Parasitoid Aphidius colemani

Dataset associated to the paper "Developmental Temperature Affects Life-History Traits and Heat Tolerance in the Aphid Parasitoid Aphidius colemani". In this study, we exposed the aphid parasitoid Aphidius colemani to different temperature regimes (10, 20, or 28 °C) throughout larval development and measured morphological and physiological traits indicator of fitness and heat tolerance in the adult.

opencc-by-4.0May 2023View details →

Supplementary data for "Fault-tolerant quantum algorithm for symmetry-adapted perturbation theory"

Supplementary data belonging to "Fault-tolerant quantum algorithm for symmetry-adapted perturbation theory". The data includes geometries for the molecules in the paper as well as the Hamiltonian matrix elements, orbital coefficients and overlap matrices to reproduce the data in the paper.

opencc-zeroMay 2023View details →

Light-demanding tree species are more susceptible to lianas than shade-tolerant tree species in a subtropical secondary forest

<ol> <li> Tree-tree competition has been widely studied as a mechanism responsible for maintaining forest plant species diversity. Other common plant types, such as lianas, may influence tree species competition. Previous studies reported the negative effects of lianas on trees; however, variation in susceptibility to lianas among tree species and the species-specificity of liana species for tree hosts remain unclear. If lianas have species-specific interactions with trees, based either on tree or liana species identity, then lianas may influence tree-tree interactions by altering tree species-specific competitiveness. </li> <li> We surveyed 5,676 lianas (DBH ≥ 0.5 cm) and 61,538 trees (DBH ≥ 1 cm) in a 12-ha subtropical secondary forest plot to assess liana-tree interactions. We tested variation among the 20 most common tree species in their susceptibility to lianas, including whether light-demanding and shade-tolerant tree species differed. We quantified liana-tree network structure and evaluated the specificity between the 20 most common tree species and the 15 most common liana species. We expected that: (1) tree species would vary in their susceptibility to lianas, and the extent of this variation would be predicted by tree shade-tolerance; and (2) liana species would have distinct species-specific interactions with host trees. </li> <li> Tree species differed greatly in their susceptibility to lianas, with some tree species accumulating many more lianas than others. Light-demanding tree species particularly had greater susceptibility to lianas than shade-tolerant tree species. Both the liana-tree network structure and the interaction intensity between the 15 liana species and 20 tree species showed distinct specialization of liana-tree interactions. </li> <li>Synthesis. Variation in tree species' susceptibility to lianas implies that lianas may alter tree species-specific competitive abilities by disproportionately affecting some tree species more than others. In contrast to studies in neotropical forests, light-demanding tree species were more susceptible to lianas than shade-tolerant tree species, suggesting that lianas could reduce light-demanding tree performance in this forest. The distinct species specialization between liana and tree species suggests that increases in the relative abundance of liana species, which is occurring in many forests, may alter the tree community by reducing the relative abundance of preferred host tree species. </li> </ol>

opencc-zeroJun 2023View details →

Data for: Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird

Animal hosts can adapt to emerging infectious disease through both disease resistance, which decreases pathogen numbers, and disease tolerance, which limits damage during infection without limiting pathogen replication. Both resistance and tolerance mechanisms can drive pathogen transmission dynamics. However, it is not well understood how quickly host tolerance evolves in response to novel pathogens or what physiological mechanisms underlie this defense. Using natural populations of house finches (Haemorhous mexicanus) across the temporal invasion gradient of a recently emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid evolution of tolerance (<25 years). In particular, populations with a longer history of MG endemism have less pathology but similar pathogen loads compared with populations with a shorter history of MG endemism. Further, gene expression data reveal that more targeted immune responses early in infection are associated with tolerance. These results suggest an important role for tolerance in host adaptation to emerging infectious diseases, a phenomenon with broad implications for pathogen spread and evolution.

opencc-by-4.0Jul 2023View details →

Dataset: Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions

This repository contains the files associated with the following article: Johanna Croce, Ernesto I. Badano, Andrés Tálamo. Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions Submitted to Land Degradation & Development. The first Microsoft Excel file (Dataset 01 - Microclimate.xlsx) contains two sheets with the microclimatic data (average, maximum and minimum soil temperatures, and volumetric soil water content) measured in Cerro Chachapoyas and Cerro Fachacano. These measurements were performed on three plots of each trearment, including shrub-protected treatment with high shade, shrub-protected treatment with medium shade, sunny treatment with high herbaceous cover, sunny treatment with medium herbaceous cover and controls. The second Microsoft Excel file (Dataset 02 -Plant responses.xlsx Dataset 02 - Plant responses.xlsx) contains three sheets with the data used to estimate the seedling emergence rates, plant survival rates and net aboveground growth rates of the tree species, including Anadenanthera colubrina and Ceiba chodatii in Cerro Chachapoyas, and Jacaranda mimosifolia in Cerro Fachacano.

opencc-by-4.0Dec 2022View details →

Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance

Processed datasets for publication at BMC Genomics. We exposed human primary monocytes from healthy donors (n=6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2hr LPS; LPS2) and two models of endotoxin tolerance: repeated stimulations (6+6hr; LPS6:6) and prolonged exposure to endotoxin (24hr LPS; LPS24). Another subset of monocytes was left untreated (naïve; UT). We performed total RNA-seq and ATAC-seq for monocytes across these treatment conditions. The following processed datasets include the raw and normalised count data for each gene or ATAC peak, and the bedGraph and bigWig format for genome-wide signal data. [ bigWig files for RNA-seq (monocytes_*_mean.bw); bigWig files for ATAC-seq (Monocyte_ATAC_*_mean_normalised.by.1/size.factor.bw); bedgraph files for eRNA visualization (*RPKM_FR.bedgraph.gz); raw and normalised count files for ATAC-seq and RNA-seq data (Monocyte.featureCounts_RNAseq.txt.gz; Monocyte_filtered_log2.normalized_RNAseq_counts.txt.gz; Meta.file.txt.gz; Monocyte_raw.counts_ATACseq.txt.gz.).] Data curator: Ping Zhang

Data for: The effects of embryonic incubation temperature on subsequent growth and thermal tolerance in white sturgeon throughout onset of exogenous feeding to early juveniles

An organism's phenotypic characteristics can be altered by environmental variation experienced during embryonic development, potentially leading to changes that persist into adulthood. Increasing global temperatures are a current concern that may be particularly acute for species already threatened or endangered, such as the white sturgeon, Acipenser transmontanus. Given the limited information on the effects of embryonic temperatures on subsequent physiological parameters such as thermal tolerance and growth in this species, the effects of global climate change on the future of white sturgeon populations are uncertain. To investigate carryover effects resulting from early rearing temperatures, white sturgeon embryos were incubated at different environmental temperatures (Te) of 12, 15, and 18 °C until hatch, after which fish were reared at a common 15 °C for 80 days post-hatch (dph). Individuals from each temperature treatment were tested for thermal tolerance using the critical thermal maximum method (CTmax) at regular intervals from 13 to 80 dph, which bridged the time from the start of exogenous feeding through the transition into early juveniles. In addition, body length measures were taken to determine the effects of embryonic Te on growth through these life stages. We found that embryonic Te affected both thermal tolerance and growth; fish that developed at 18 °C had the lowest thermal tolerance, while those that developed at 12 °C grew largest over the observation period. This research represents a window into a critical period of development during which organisms are particularly vulnerable to climatic variation. The results can inform environmental managers on the best strategies to help conserve current white sturgeon populations across their range.

opencc-zeroJul 2023View details →

High physiological function for corals with thermally tolerant, host-adapted symbionts

The flexibility to associate with more than one symbiont may considerably expand a host's niche breadth. Coral animals and dinoflagellate micro-algae represent one of the most functionally integrated and widespread mutualisms between two eukaryotic partners. Symbiont identity greatly affects a coral's ability to cope with extremes in temperature and light. Over its broad distribution across the Eastern Pacific, the ecologically dominant branching coral, Pocillopora grandis, depends on mutualisms with the dinoflagellates Durusdinium glynnii and Cladocopium latusorum. Measurements of skeletal growth, calcification rates, total mass increase, calyx dimensions, reproductive output and response to thermal stress were used to assess the functional performance of these partner combinations. The results show both host–symbiont combinations displayed similar phenotypes; however, significant functional differences emerged when exposed to increased temperatures. Negligible physiological differences in colonies hosting the more thermally tolerant D. glynnii refute the prevailing view that these mutualisms have considerable growth tradeoffs. Well beyond the Eastern Pacific, pocilloporid colonies with D. glynnii are found across the Pacific in warm, environmentally variable, near-shore lagoonal habitats. While rising ocean temperatures threaten the persistence of contemporary coral reefs, lessons from the Eastern Pacific indicate that co-evolved thermally tolerant host–symbiont combinations are likely to expand ecologically and spread geographically to dominate reef ecosystems in the future.

opencc-by-4.0Jul 2023View details →

Effect of thermal acclimation on the tolerance of the peach fruit fly (Bactrocera zonata: Tephritidae) to heat and cold stress

The effect of thermal acclimation on cold and heat tolerance of the peach fruit fly (Bactrocera zonata) was studied. Males and females were acclimated at 20, 25 and 30°C for up to 19 days following adult emergence. The critical thermal minimum (CTmin) and maximum (CTmax) were subsequently recorded as well adult survival following acute exposure to chilling (0 or -3°C for 2 hours). Additionally, the survival of pupae subjected for two hours to temperatures ranging from -12°C to 5°C was determined. The raw data collected during this study is available in the provided data file.

opencc-by-4.0Aug 2023View details →

Dataset and R-script for Article: Increased heat tolerance of geothermal plants comes at the cost of reduced performance under cooler conditions

Dataset and R-script for Article "Increased heat tolerance of geothermal plants comes at the cost of reduced performance under cooler conditions" to be published in the Journal "Ecology and Evolution"