Find research datasets worth reusing

opencc-zeroAug 2020View details →

Data from: Use of web-based species occurrence information systems by academics and government professionals

Web-based information systems designed to increase access to species occurrence data for use in research and natural resource decision-making have become more prevalent over the past few decades. The effectiveness of these systems depends on their usability and extent of use by their intended audiences. We conducted an online survey of academics and government professionals in the United States to compare their species occurrence data needs and their perceptions and use of web-based species occurrence information systems. Our results indicate that although views and perceptions held by academics and government professionals about the importance, usefulness, and ease of use of these information systems tend to be similar, there were differences in their use of species occurrence data and web-based species occurrence information systems. The baseline information obtained in this study will help inform future directions for improvements in species occurrence information systems.

opencc-zeroDec 2017View details →

Data from: Co-occurrence among three divergent plant-castrating fungi in the same silene host species

The competitive exclusion principle postulates that different species can only coexist in sympatry if they occupy distinct ecological niches. The goal of this study was to understand the geographical distribution of three species of Microbotryum anther-smut fungi that are distantly related but infect the same host plants, the sister species Silene vulgaris and S. uniflora, in western Europe. We used microsatellite markers to investigate pathogen distribution in relation to host specialization and ecological factors. Microbotryum violaceo-irregulare was only found on S. vulgaris at high elevations in the Alps. Microbotryum lagerheimii could be subdivided into two genetically differentiated clusters, one on S. uniflora in the UK and the second on S. vulgaris in the Alps and Pyrenees. The most abundant pathogen species, M. silenes-inflatae, could be subdivided into four genetic clusters, co-occurring in the Alps, the UK and the Pyrenees, and was found on both S. vulgaris and S. uniflora. All three fungal species had high levels of homozygosity, in agreement with the selfing mating system generally observed in anther-smut fungi. The three pathogen species and genetic clusters had large range overlaps, but occurred at sites with different elevations, temperatures and precipitation levels. The three Microbotryum species thus do not appear to be maintained by host specialization or geographic allopatry, but instead may occupy different ecological niches in terms of environmental conditions.

opencc-zeroDec 2018View details →

Data from: The role of spore size in the global pattern of co-occurrence among Selaginella species

Aim: Separation of regeneration niches may promote coexistence among closely related plant species, but there is little evidence that regeneration traits affect species ranges at large geographic scales. Here we address patterns of co-occurrence within the genus Selaginella, an ancient lineage of free-sporing, heterosporous, vascular plants. Specifically, we ask whether differences between species in spore size are associated with the extent of overlap in their geographic ranges, a measure of opportunity for ecological interaction. Taxon: Selaginella (Selaginellaceae: Lycopodiales) Methods: We used quantile regression to examine the relationship of spore size ratios (pairwise ratios for megaspores and microspores of co-occurring species) to the area of range overlap and to latitude for a worldwide sample of 112 Selaginella species. Phylogenetically informed tests of statistical significance were used for each percentile relationship examined in the quantile regressions. Results: Large pairwise disparities in megaspore sizes were significantly associated with large range overlap. Disparities also tended to be larger at low latitudes. Microspore size differences, in contrast, were unrelated to shared range area or latitude. Main conclusion: Megaspore size appears to affect coexistence at a broad regional scale among Selaginella species, in at least some cases. The pattern is consistent with some degree of competitive structuring of size-related aspects of dispersal and establishment of propagules among some co-occurring species. Habitat complexity, such as open microsites within otherwise closed and shaded vegetation, seems likely to promote reproductive niche separation and may account for the latitudinal structure in Selaginella spore sizes.

opencc-zeroDec 2017View details →

Data from: A trait-based framework for discerning drivers of species co-occurrence across heterogeneous landscapes

Null model analysis of species co-occurrence patterns has long been used to gain insight into community assembly but is often limited to identifying non-random patterns without providing clarity about underlying ecological mechanisms. This challenge is especially apparent when sampling units are spread across a heterogeneous landscape or along an environmental gradient because multiple mechanisms can produce similar co-occurrence patterns. We developed a trait-based approach for discriminating between environmental filtering and biotic interactions as the probable driver of co-occurrence patterns across environmentally heterogeneous sites. We demonstrate our framework by analyzing the co-occurrence of small mammals over elevation in three independent mountain ranges in the Great Basin of the western United States. Our sampling design accounts for landscape scale environmental variability and within-site habitat heterogeneity. We identified 52 non-random species pairs, of which 36 were aggregated and 16 were segregated. For each pair, we determined which mechanism was the likely ecological explanation using a hypothesis-testing framework based on functional trait similarity. Expectations of biotic interactions were based on similarity of diet and body size whereas habitat affinity and geographic range were used for environmental filtering. Only four pairs were consistent with expectations under biotic interactions, including pairs for which competitive exclusion has previously been documented. In addition to analyzing individual pairs, we used binomial tests of observed versus expected totals of intra- and inter-guild pairs to determine assemblage-wide deviations from random community structure. Signatures of environmental filtering were consistent across mountain ranges and scales. Despite differences in species composition and significant pairs among data sets, our approach revealed consistent mechanistic conclusions, emphasizing the value of trait-based methods to co-occurrence and community assembly.

opencc-by-4.0Dec 2023View details →

Data from "Elevation affects both the occurrence of ungulate browsing and its effect on tree seedling growth for four major tree species in European mountain forests"

This repository contains the field data used in the paper from Bernard et al. on the interactive effect of elevation and ungulate browsing on tree regeneration. This dataset is associated with a github repository containing the code to run the analyses of the paper, publicly available at https://github.com/jbarrere3/BaccaraPaper.  Data were collected for the Baccara project, by Elena Granda, Raquel Benavides, Sonia Rabasa, Georges Kunstler, and Marco Heurich.

opencc-zeroJan 2024View details →

Occurrence data of small rodent species from the Yamal peninsula (1958–2022)

Range shifts and changes in dominance of species in communities are among the major predicted impacts of climate change on ecosystems, supported by numerous modeling studies. While climate is changing particularly rapidly in the Arctic, little observational data is available to document predicted changes in the composition of communities, in particular from the large Russian tundra areas. Small rodents are a key component of tundra ecosystems implementing important ecological functions both as herbivores and as main prey for a whole guild of predators. Here we document changes over 60 years in occurrence of nine species of small rodents along a latitudinal gradient spanning from the forest-tundra ecotone to the high Arctic tundra on the Yamal Peninsula. All data were obtained using a single method: snap-trapping. In general, the occurrence of lemmings, specialized arctic endemics, decreased in the southern parts of the peninsula, whereas the occurrence of voles, representing boreal or wide-spread species, increased and expanded northwards. The occurrence of Siberian lemmings (Lemmus sibiricus) in particular declined over the whole latitudinal gradient and possibly disappeared from the southernmost zones, whereas collared lemmings (Dicrostonyx torquatus) declined significantly only in the forest tundra. The strongest increase was observed in the tundra zones for narrow-headed voles (Lasiopodomys gregalis), a wide-spread species inhabiting meadows and riparian habitats, and Middendorff's voles (Alexandromys middendorffii), a primarily low Arctic species inhabiting waterlogged tundra. Both species also expanded their distribution range northwards during the last two decades. The observed changes might be due to the effect of several drivers of environmental change occurring in concert: climate warming both in winter and in summer, and increased human activity notably related to intensive reindeer herding and industrial development.

opencc-by-4.0Dec 2022View details →

The global distribution of plants used by humans datasets: list of utilised species, occurrence data and model outputs at 10 arc-minutes spatial resolution

Datasets and model outputs used to map the global distribution of utilised plants by humans. The folder is composed of two subfolders raw_data and processed_data containing respectively the list of utilised plant species modelled -utilised_plants_species_list.csv-, and their occurrence data -occurrence_data.zip- and predicted distribution -species_proba_per_cell.rds-.   <ul> <li>The file utilised_plants_species_list.csv in the raw_data folder contains a list of 35687 plant species (and hybrids) used by humans and 10 plant use categories with the following 14 fields:</li> </ul> plant_ID: plant identifier number ranging from between 1-35687 binomial_acc_name: binomial accepted name of the plant species author_acc_name:  name of the author(s) is_hybrid: logical TRUE or FALSE indicating whether the species is an hybrid or not. AnimalFood: forage and fodder for vertebrate animals only. EnvironmentalUses: examples include intercrops and nurse crops, ornamentals, barrier hedges, shade plants, windbreaks, soil improvers, plants for revegetation and erosion control, wastewater purifiers, indicators of the presence of metals, pollution, or underground water. Fuels: charcoal, petroleum substitutes, fuel alcohols, etc. Given the importance of energy plants for people, those were distinguished from Materials. GeneSources: wild relatives of major crops which may possess traits associated with biotic or abiotic resistance and may be valuable for breeding programs. HumanFood: food for humans only, including beverages and food additives. InvertebrateFood: plants consumed by invertebrates used by humans, such as bees, silkworms, lac insects and edible grubs. Materials: woods, fibers, cork, cane, tannins, latex, resins, gums, waxes, oils, lipids, etc. and their derived products. Medicines: both human and veterinary. Poisons: plants which are poisonous to both vertebrates and invertebrates, both accidentally and intentionally, e.g., for hunting and fishing, molluscicides, herbicides, insecticides. SocialsUses: plants used for social purposes, which cannot be defined as food or medicine, for instance, masticatories, smoking materials, narcotics, hallucinogens and psychoactive drugs, and plants with ritual or religious significance. Totals: total number of uses recorded for a species   <ul> <li>The zipfile occurrence_data.zip in the processed_data folder contains 35687 Comma Separated Values (CSV) files, one for each species, containing curated geographic occurrence records used to  build species distribution models with the following 14 fields:</li> </ul> Species: the binomial accepted name of the species Fullname:  same as species decimalLongitude: the geographic longitude of the occurrence records of the species in decimal degrees decimalLatitude: the geographic latitude of the occurrence records of the species in decimal degrees countryCode: a three-letter standard abbreviation for the country of the occurrence locality coordinateUncertaintyinMeters: indicator for the accuracy of the coordinate location, described as the radius of a circle around the stated point location year: year of the observation of the occurrence record of the species individualCount: the number of individuals present at the time of the observation gbifID: unique identifier number for the occurrence from the original database basisOfRecords: the type of the individual record, e.g. observation, physical specimen, fossil, living ex-situ, culture collection specimen institutionCode: the name of the institution or organization listed as the data publisher on GBIF establishmentMeans: statement about whether an organism has been introduced to a given place and time through the direct or indirect activity of modern humans is_cultivated_observation: whether or not an organism is cultivated sourceID: name of the source database   <ul> <li>The file species_proba_per_cell.rds in the processed_data folder is a R Data Serialization (RDS) file containing a data.table object with the following 3 fields:</li> </ul> plant_ID: plant identifier number ranging from between 1-35687 proba: species occurrence probability cell: raster grid cell number between 1-2251762 This object can be used in combination with a raster layer to reconstruct the modelled distribution of each species or retrieve species richness and endemism.

opencc-by-nd-4.0Sep 2011View details →

FIGURE 4 in Occurrence Of A Mediterranean Species In Central Europe And Asia, With Notes On The Generic Status And Biogeography Of Simkinia And Hemileius (Acari: Oribatida)

FIGURE 4: Scheloribates (Hemileius) humeralis PØrez-Iaeigo jr., 1990. A – Leg II; B – Leg III; C – Leg IV (right, antiaxial views).

opencc-by-nd-4.0Sep 2011View details →

FIGURE 2 in Occurrence Of A Mediterranean Species In Central Europe And Asia, With Notes On The Generic Status And Biogeography Of Simkinia And Hemileius (Acari: Oribatida)

FIGURE 2: Scheloribates (Hemileius) humeralis PØrez-Iaeigo jr., 1990 (figure is based on a specimen from Italy). A – Dorsal view of idiosoma; B – Sensillus, bothridium and exobothridial setae; C – Ventral view of idiosoma; D – Posterior view of opisthosoma (legs removed).

opencc-zeroMar 2022View details →

Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest

1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition). 2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence. 3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages. 4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.

Fig. 2 in The Northernmost Record Of The Loggerhead Sea Turtle, Caretta Caretta (Testudines, Cheloniidae), In The Black Sea, With The Review Of The Species Occurrence In The Region

Fig. 2. Frequency of records of the loggerhead sea turtle in the Black Sea by decade.

Fig. 1 in The Northernmost Record Of The Loggerhead Sea Turtle, Caretta Caretta (Testudines, Cheloniidae), In The Black Sea, With The Review Of The Species Occurrence In The Region

Fig. 1. Records of the loggerhead sea turtle in the Black Sea.

opencc-zeroApr 2022View details →

Publication release: How well do species distribution models predict occurrences in exotic ranges?

<div class="record-description"> Species distribution models (SDMs) are widely used predictive tools to forecast potential biological invasions. However, the reliability of SDMs extrapolated to exotic ranges remains understudied, with most analyses restricted to few species and equivocal results. We examined the spatial transferability of SDMs for 647 non-indigenous species extrapolated across 1,867 invaded ranges, and identify what factors may help differentiate predictive success from failure. We performed a large-scale assessment of the transferability of SDMs using two modelling approaches: generalized additive models (GAMs) and MaxEnt. We fitted SDMs on the native ranges of species and extrapolated them to exotic ranges. We examined the influence of general factors and factors related to biological invasions on spatial transferability. Here, we provide the code and data for publication in Global Ecology and Biogeography as part of Nguyen and Leung 2022 "How well do species distribution models predict occurrences in exotic ranges?". Provided are the files and scripts necessary to fit and validate the SDMs using distirbutional data from their native and exotic ranges, respectively, formulated as generalized additive models (GAMs) or MaxEnt models. Additionally, provided is a script to validate the SDMs on their native fitting range using 10-fold cross-validation, and to fit the transferability model, as a linear mixed model (LMM), with a provided cleaned data.frame. The dataset provided includes a full species list with GBIF occurrence records, target-group background (TGB) records to use with model fitting and validation, as well as environmental data associated with the sightings. </div>

opencc-zeroJul 2022View details →

Occurrence datasets, model outputs, and R script for 12 termite species used for niche modeling

The advent of citizen-science databases in conjunction with museum specimen locality information has exponentially increased the power and accuracy of ecological niche modeling (ENM). Increased occurrence data has provided colossal potential to understand the distributions of lesser known or endangered species, including arthropods. Although niche modeling of termites has been conducted in the context of invasive and pest species, few studies have been performed to understand the distribution of basal termite genera. Using specimen records from the American Museum of Natural History (AMNH) as well as locality databases, we generated ecological niche models for 12 basal termite species belonging to six genera and three families. We extracted environmental data from the Worldclim 19 bioclimatic dataset v2, along with SoilGrids datasets and generated models using MaxEnt. We chose Optimal models based on partial Receiving Operating characteristic (pROC) and omission rate criterion and determined variable importance using permutation analysis. We also calculated response curves to understand changes in suitability with changes in environmental variables. Optimal models for our 12 termite species ranged in complexity, but no discernible pattern was noted among genera, families, or geographic range. Permutation analysis revealed that habitat suitability is affected predominantly by seasonal or monthly temperature and precipitation variation. Our findings not only highlight the efficacy of largely citizen-science and museum-based datasets, but our models provide a baseline for predictions of future abundance of lesser-known arthropod species in the face of habitat destruction and climate change.

opencc-by-4.0Sep 2022View details →

Species occurrence data for Colorado restoration project (derived dataset from GBIF)

GBIF species occurrence data downloaded for 53 species included a restoration project. The data have been cleaned to remove incorrect and imprecise coordinates, as well as records older than 1950.

opencc-zeroMay 2024View details →

Species occurrence locations and environmental parameters used for predicting the potential planting regions of Pterocarpus santalinus

This study explores the habitat distribution of Pterocarpus santalinus, a valuable rosewood species, across China, focusing on its response to current and future climate changes. Utilizing the MaxEnt model, we assess its suitable habitat under present conditions and future climate scenarios (SSPs126, SSPs245, and SSPs585). Our findings reveal that the current suitable habitat, spanning approximately 409,600 km², is primarily located in the central and southern parts of Guangdong, Guangxi, Fujian, Yunnan, as well as in the Hainan provinces, along with the coastal regions of Taiwan, and the Sichuan-Chongqing border. The habitat's distribution is significantly influenced by climatic factors such as temperature seasonality (bio4), mean temperature of the wettest quarter (bio8), annual mean temperature (bio1), and annual precipitation (bio12), while terrain and soil factors play a lesser role. Under future climate scenarios, the suitable habitat for P. santalinus is projected to expand, with a northeastward shift in its distribution center. This research not only sheds light on the geoecological characteristics and geographical distribution of P. santalinus in China but also offers a scientific basis for planning its cultivation areas and enhancing cultivation efficiency under changing climate conditions.

opencc-by-4.0Jun 2020View details →

Figure 3 in Occurrence of microplastics in the gastrointestinal tracts of some edible fish species along the Turkish coast

Figure 3. MP particles extracted from edible fish species present in Turkish seas.

Fig. 8 in The occurrence of known Myxobolus and Thelohanellus species (Myxozoa, Myxosporea) from Indian major carps with the description of Myxobolus bandyopadhyayi n. sp. in West Bengal

Fig. 8. Myxobolus dermiscalis plasmodia (P) in the scale of a rohu. Mount picture. Bar = 500 μm.

Fig. 3 in The occurrence of known Myxobolus and Thelohanellus species (Myxozoa, Myxosporea) from Indian major carps with the description of Myxobolus bandyopadhyayi n. sp. in West Bengal

Fig. 3. Spores of T. caudatus. Mount picture. Bar = 10 μm.

Fig. 4 in The occurrence of known Myxobolus and Thelohanellus species (Myxozoa, Myxosporea) from Indian major carps with the description of Myxobolus bandyopadhyayi n. sp. in West Bengal

Fig. 4. Schematic drawing of spore of T. caudatus, a: frontal view, b: sutural view. Bar = 10 μm.