Find research datasets worth reusing

opencc-by-4.0Jun 2023View details →

The Long-term, High-accuracy and Seamless Soil Moisture (LHS-SM) dataset over the Qinghai-Tibet Plateau: part 2 (2011-2020)

Soil moisture (SM) is a vital variable in the water-energy cycle and characterizing its spatiotemporal dynamics is crucial for understanding the impacts of climate change. Although substantial efforts have been devoted to derive SM data at fine scale, there is still a research gap in obtaining the long-term, high-accuracy and high-resolution SM data over the Qinghai-Tibet Plateau (QTP) due to its complex topography. Therefore, this study generated the long-term, high-accuracy and seamless soil moisture (LHS-SM) dataset over the QTP during 2001-2020 using a two-step downscaling method. First the daily SM data from the Climate Change Initiative program of the European Space Agency (ESA CCI) was downscaled to 1km utilizing five machine learning approaches. Then a dynamic data merging method that considers the spatiotemporal nonstationary error was applied to derive the final LHS-SM data. Results indicated that LHS-SM data exhibited satisfying accuracy (mean R = 0.55, ubRMSE = 0.049 m³/m³) and certain improvement to the ESA CCI SM data both at station and network scales. The dataset can be used for various regional hydrology, meteorology, ecological analysis and modeling.

Figures 27–29 in A review of Australian long-horned caddisflies in the Oecetis pechana-group (Trichoptera: Leptoceridae), with descriptions of thirteen new species

Figures 27–29, Oecetis litua sp. nov., male genitalia in ventral, lateral and dorsal views.

Figures 43–45 in A review of Australian long-horned caddisflies in the Oecetis pechana-group (Trichoptera: Leptoceridae), with descriptions of thirteen new species

Figures 43–45, Oecetis buitenzorgensis Ulmer, male genitalia in ventral, dorsal and lateral views.

Figures 51–53 in A review of Australian long-horned caddisflies in the Oecetis pechana-group (Trichoptera: Leptoceridae), with descriptions of thirteen new species

Figures 51–53, Oecetis ada sp. nov., male genitalia in ventral, dorsal and lateral views.

opencc-by-4.0Apr 2023View details →

Data of "Inferring the Basal Friction Law from long term observations of Glacier Length, Thickness and Velocity changes on an Alpine Glacier"

This dataset contains the surface velocity and elevation of Argentière Glacier in 2003 and 2018 used in: Gilbert, A., Gimbert, F., Gagliardini, O., & Vincent, C. (2023). Inferring the Basal Friction Law From Long Term Changes of Glacier Length, Thickness and Velocity on an Alpine Glacier. Geophysical Research Letters, 50(16), e2023GL104503. <a href="https://doi.org/10.1029/2023GL104503">https://doi.org/10.1029/2023GL104503</a> Surface DEM files contain elevation Z on a 20X20 meter grid (geotif files, coordinnate are in Lambert 2E ( EPSG:27572 ) ) Horizontal Velocity files contain measured horizontal velocities Vh in m/yr on a 20X20 meter grid (geotif files, coordinnate are in Lambert 2E ( EPSG:27572 ) )

opencc-zeroJun 2023View details →

Genomic data resolve long-standing uncertainty by distinguishing white marlin (Kajikia albida) and striped marlin (K. audax) as separate species

Large pelagic fishes are often broadly and continuously distributed and capable of long-distance movements. These factors can promote gene flow that makes it difficult to disentangle intra- vs. inter-specific levels of genetic differentiation. Here, we assess the relationship of two istiophorid billfishes, white marlin (Kajikia albida) and striped marlin (K. audax), presently considered sister species inhabiting separate ocean basins. Previous studies report levels of genetic differentiation between white marlin and striped marlin that are <a>smaller</a> than those observed among populations of other istiophorid species. To determine whether white marlin and striped marlin comprise separate species or populations of a single globally distributed species, we surveyed 2<a>520</a> single nucleotide polymorphisms (SNPs) in 62 white marlin and 242 striped marlin sampled across the Atlantic, Pacific, and Indian oceans. Multivariate analyses resolved white marlin and striped marlin as distinct groups, and a species tree composed of separate lineages was strongly supported over a single lineage tree. Genetic differentiation between white marlin and striped marlin (FST = 0.5384) was also substantially larger than between populations of striped marlin (FST = 0.0192–0.0840), and we identified SNPs that allow unambiguous species identification. Our findings indicate that white marlin and striped marlin comprise separate species, which we estimate diverged at approximately 2.38 Mya.

Figures 54, 55 in A review of Australian long-horned caddisflies in the Oecetis pechana-group (Trichoptera: Leptoceridae), with descriptions of thirteen new species

Figures 54, 55, Oecetis gilva Neboiss, male genitalia in ventral and lateral views.

opencc-zeroJun 2023View details →

Long-term seedling and small sapling census data from the Barro Colorado Island 50 ha Forest Dynamics Plot, Panama

Tropical forests are well known for their high woody plant diversity. Processes occurring at early life stages are thought to play a critical role in maintaining this high diversity and shaping the composition of tropical tree communities. To evaluate hypothesized mechanisms promoting tropical tree species coexistence and influencing composition, we initiated a census of woody seedlings and small saplings in the permanent 50-ha Forest Dynamics Plot (FDP) on Barro Colorado Island (BCI), Panama. Situated in old-growth, lowland tropical moist forest, the BCI FDP was originally established in 1980 to monitor trees and shrubs ≥1 cm diameter at 1.3 m above ground (dbh) at ca. 5-yr intervals. However, critical data on the dynamics occurring at earlier life stages were initially lacking. Therefore, in 2001 we established a 1-m2 seedling plot in the center of every 5 x 5 m section of the BCI FDP. All freestanding woody individuals ≥20 cm tall and <1 cm dbh (hereafter referred to as seedlings) were tagged, mapped, measured, and identified to species in 19,313 1-m2 seedling plots. Because seedling dynamics are rapid, we censused these seedling plots every 1–2 years. Here we present data from the 14 censuses of these seedling plots conducted between the initial census in 2001 to the most recent census, in 2018. This data set includes nearly 1M observations of ~185,000 individuals of >400 tree, shrub, and liana species. These data will permit spatially-explicit analyses of seedling distributions, recruitment, growth, and survival for hundreds of woody plant species. In addition, the data presented here can be linked to openly-available, long-term data on the dynamics of trees and shrubs ≥1cm dbh in the BCI FDP, as well as existing data sets from the site on climate, canopy structure, phylogenetic relatedness, functional traits, soil nutrients, and topography.

Evidence that long-distance dispersal of aquatic invertebrates by ducks increases with propagule size

<ol> <li> Migratory ducks are key dispersal agents for aquatic organisms, yet differences in their potential for short- and long-distance dispersal are still poorly understood, particularly differences among aquatic invertebrate taxa. </li> <li> Using seven species of aquatic invertebrates and a duck species known to feed on them in the wild (the northern shoveler) as a model system, we evaluated whether their potential for endozoochorous dispersal varies among 5 of the species and scales with propagule size for the 7 species. We also tested the expectation of a lower dispersal potential for invertebrate propagules, as compared to plant seeds; and evaluated whether intra-specific variation (in particular, sexual dimorphism) influences the potential of waterbirds as dispersal vectors. </li> <li>An experiment with 5 invertebrate species demonstrated that most resting eggs (68–95%) were retrieved by 4 h after ingestion, with maximum gut passage times ranging from 16 h for Daphnia magna to 36 h for Artemia salina and Thamnocephalus platyurus. Using models that combine migratory duck movements with gut passage times, we show that aquatic invertebrates may disperse frequently over distances of 15–16 km (median dispersal distance) and regularly over distances up to 110–166 km (Q99 distance). </li> <li> Increasing propagule size resulted in increasing gut passage times, decreasing survival of gut passage and decreasing hatching success. While propagule size had no effects on 'regular' dispersal distances (mean, median, Q95 and Q99), the frequency of long-distance dispersal (LDD) increased with it. </li> <li>Increasing propagule size therefore had two contrasting effects on invertebrate dispersal potential, decreasing the frequency of dispersal (less seeds dispersed) but increasing the potential for long-distance dispersal. </li> <li>Conclusions: We provide evidence that endozoochory of invertebrate propagules by waterbirds results in frequent dispersal among wetlands (tens of km) and regular dispersal at regional scale (over a hundred km).</li> </ol>

Genetic erosion in an endangered desert fish during a multi-decadal megadrought despite long-term supportive breeding

Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande Silvery Minnow. This species experiences 'boom-and-bust' population dynamics where large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We leveraged demographic and genetic data from wild and hatchery individuals to understand the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d=1.34) and remains low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size (NeD) were positively associated (r=0.53) with wild/total abundance, but as the proportion of hatchery-origin spawners increased, NeD was reduced (NeD r= -0.55). Megadrought limits wild spawner abundance and precludes refreshment of hatchery brood stocks with wild fish, hence we predict an increasingly hatchery-dominated population, and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

openJun 2023View details →

A 12-years long (2010-2021) hydrological and biogeochemical dataset in the Sicily Channel (Mediterranean Sea)

The data set presented here consists of 273 CTD-nutrient stations and 2034 data points collected in 12 summer oceanographic cruises, called BANSIC, carried out in the Strait of Sicily, Mediterranean Sea (11.304-15.3203°W; 35.50383-37.732°N) between 2010 and 2021. At all stations, pressure, salinity, and temperature were measured with a CTD (conductivity, temperature, and depth) probe consisting of a CTD SBE 911plus and a General Oceanics rosette with 24 Niskin bottles of 12 L capacity. Seawater samples for dissolved inorganic nutrient analysis were collected from the surface to the bottom by means of Niskin bottles. In particular, during the CTD upcast, a variable number of fixed depths has been considered (surface–25m–50m–75m–100m–150m-200m–300m–400m–500m–600m–700m–800m–900m–1000m–bottom) with slight modifications in the upper layer where significative hydrological variability was detected. An appropriate quality check has been carried out in order to ensure the reliability of the data made available to the scientific community. Data are described in the description paper Placenti et al., 2024, https://doi.org/10.5194/essd-16-743-2024.

opencc-by-4.0Jun 2023View details →

Long-term variations of ambient volatile organic compounds (VOCs) from 2016 to 2020 in Beijing, China

Ambient volatile organic compounds (VOCs) are crucial precursors for the formation of secondary organic aerosol (SOA) and ozone (O3). We have conducted in-situ observations and compiled a comprehensive dataset of ambient volatile organic compound (VOC) compositions and concentrations in Beijing, China, spanning the period from 2016 to 2020. The dataset covers a wide range of VOC species including 29 alkanes, 11 alkenes, 1 alkyne, 16 aromatics, 28 halohydrocarbons, 13 oxygenated VOCs (OVOCs), and 1 nitrogenous VOC (acetonitrile). The presentation and analysis of this dataset is available in a paper submitted to Earth System Science Data (Simon et al, in prep). The findings and analysis of this dataset have been documented in a paper that has been submitted to Earth System Science Data (Liu et al., in prep). If you use the dataset for related scientific research, please cite the corresponding reference:  Liu et al (in prep); Long-term variations of ambient volatile organic compounds (VOCs) from 2016 to 2020 in Beijing, China; Earth System Science Data.

opencc-by-4.0Jul 2023View details →

Fig. 35 in Short-legged daddy-long-leg spiders in North America: the genera Pholcophora and Tolteca (Araneae, Pholcidae)

Fig. 35. Known distribution of Tolteca Huber, 2000.

Long-term livestock exclusion increases plant richness and reproductive capacity in arid woodlands

Aim Herbivore exclusion is implemented globally to recover ecosystems from grazing by introduced and native herbivores, but evidence for large-scale biodiversity benefits is inconsistent in arid ecosystems. We examined the effects of livestock exclusion on dryland plant richness and reproductive capacity. Location Central Australia. Methods We collected data on plant species richness and seeding (reproductive capacity), rainfall, vegetation productivity and cover, soil health, and herbivore grazing intensity from 68 sites across 6500 km2 of arid Georgina gidgee (Acacia georginae) woodlands between 2017 and 2020. Sites were on an actively grazed cattle station and two destocked conservation reserves. We used structural equation modelling to examine indirect (via soil or vegetation modification) versus direct (herbivory) effects of grazing intensity by two introduced herbivores (cattle, camels) and a native herbivore (red kangaroo), on seasonal plant species richness and seeding. Results Soil health and rainfall were the strongest drivers of variation in richness and seeding. Cattle and camel grazing indirectly led to lower seasonal richness and seeding by reducing soil health. Kangaroos had a small but negative direct impact on richness, but no impact on soil health. Both introduced and native herbivores reduced annual chenopod shrub richness and seeding, whereas only cattle directly reduced perennial shrub richness and seeding. Camels indirectly reduced perennial shrub richness by impacting shrub abundance. Introduced herbivores reduced native grass richness and seeding indirectly via impacts on soil health, whereas forbs responded positively to cattle and camel activity. Main conclusion Considering indirect impacts improves evaluations of the effects of disturbances on biodiversity, as focusing only on direct effects can mask critical mechanisms of change. Our results indicate substantial biodiversity benefits from excluding livestock and controlling camels in drylands. Reducing introduced herbivore impacts will improve soil and vegetation condition, ensure reproduction and seasonal persistence of species, and protect native plant diversity.

Data for: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly-interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc finger-based TFs. We show that circuits 'wired' using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-termcontinuous culture. Our naturally-inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.

opencc-by-4.0Aug 2023View details →

Project BioDyn: compilation of long-term (>20yrs) community timeseries data from terrestrial and freshwater realms

The given dataset was compiled for n=2668 communities (242 study IDs in total, see the metadata file) across terrestrial and freshwater realms (terrestrial birds: n=1259, invertebrates: n=124, plants: n=435, and mammals: n=136, freshwater fish: n=587, invertebrates: n=112, and phytoplankton: n=15). Community timeseries include species-level abundance (or biomass in 15% of cases) and a minimum of 20 years sampled. We have compiled this data and used it for the first time to analyze how community stability and its drivers (species richness, overall synchrony, and tail-dependent synchrony) would differ across realms.

opencc-zeroAug 2023View details →

Data from: Differential early-life survival underlies the adaptive significance of temperature-dependent sex determination in a long-lived reptile

Many ectotherms rely on temperature cues experienced during development to determine offspring sex. The first descriptions of temperature-dependent sex determination (TSD) were made over 50 years ago, yet an understanding of its adaptive significance remains elusive, especially in long-lived taxa. One novel hypothesis predicts that TSD should be evolutionarily favored when two criteria are met – (a) incubation temperature influences annual juvenile survival and (b) sexes mature at different ages. Under these conditions, a sex-dependent effect of incubation temperature on offspring fitness arises through differences in age at sexual maturity, with the sex that matures later benefiting disproportionately from temperatures that promote juvenile survival. The American alligator (Alligator mississippiensis) serves as an insightful model in which to test this hypothesis, as males begin reproducing nearly a decade after females. Here, through a combination of artificial incubation experiments and mark-recapture approaches, we test the specific predictions of the survival-to-maturity hypothesis for the adaptive value of TSD by disentangling the effects of incubation temperature and sex on annual survival of alligator hatchlings across two geographically distinct sites. Hatchlings incubated at male-promoting temperatures consistently exhibited higher survival compared to those incubated at female-promoting temperatures. This pattern appears independent of hatchling sex, as females produced from hormone manipulation at male-promoting temperatures exhibit similar survival to their male counterparts. Additional experiments show that incubation temperature may affect early-life survival primarily by affecting the efficiency with which maternally transferred energy resources are used during development. Results from this study provide the first explicit empirical support for the adaptive value of TSD in a crocodilian and point to developmental energetics as a potential unifying mechanism underlying persistent survival consequences of incubation temperature.

opencc-byAug 2023View details →

Corn field management for wintering waterfowl on eastern Long Island, New York

The study took place in corn fields in Suffolk County, Long Island, New York, 7 February – 4 April 2018 and 7 February – 10 April 2019 (Fig.1). Fields were planted for typical production corn with 15.2 cm (6 inch) spacing among plants in rows 30.5 cm (12 inch) apart. Suffolk County contains coastal wetlands, freshwater ponds, and rural landscapes where corn fields are available to wintering waterfowl. Seasonal corn yield and wildlife abundance were determined at two corn fields in 2018 and 2019 (Cutchogue [41.023 ° N, -72.511° W] and Orient Point [41.141° N, -72.278° W]) and included another corn field in 2019 (Brookhaven [40.798° N, -72.891° W]). Corn fields were divided into three sections and marked them with flagging to identify them from a distance. The mean (± SE) corn field size was 4.08 ± 0.20 ha (Cutchogue = 3.99 ha, [0.87 ha, 1.33 ha, and 1.79 ha sections]; Orient = 4.47 ha, [1.46 ha, 1.46 ha, and 1.55 ha sections]; Brookhaven = 3.78 ha, [1.26 ha, 1.26 ha, and 1.26 ha sections]). Corn field samples were taken to obtain an index of corn availability and corn depletion rates following Barney [8]. One section in each field was chopped with a brush-hog every 2 weeks until all three sections in a field were chopped. Section of standing corn were sampled once the day before chopping and after chopping once every two weeks in 2018 and weekly in 2019. Sampling was adjusted to weekly in 2019 because some sections were depleted to zero or near zero kg/ha in < 2 weeks during 2018. A random sampling design was used to distribute samples throughout the field. Main transects (n = 3) were established perpendicular to the field edge in each section of a field (evenly spaced 20 − 26 m apart). Each sampling period, a random number generator was used to select sampling points along each main transect. The same number of samples were taken along each main transect (n = 4; n = 12 per section). A random number generator was used to determine the left or right direction of samples to be taken off of the main transect along a perpendicular transect. A random number generator was used to determine the distance of the sampling point along the perpendicular transect (between 1 – 10 m). Corn was sampled using a 1 m × 1 m quadrat at each sampling point and all corn within each quadrat was collected and placed in marked plastic bags. All individual kernels, cobs full of kernels, and cobs partial covered in kernels were included in the sample and frozen within 4 hrs of sampling. In the lab, corn was thawed, kernels were removed from cobs, and samples were dried at 60℃ until a constant mass at 48 hrs and weighed to ± 0.1 g, and reported as kg/ha. Wildlife surveys were conducted at each field 8 February – 3 April 2018 and 8 February – 9 April 2019. Morning and evening surveys were conducted, switching the time of survey at each field weekly. Morning surveys occurred 30 min before to 2 h after sunrise and evening surveys were 2 h before to 30 mins after sunset. To survey two fields on the same day, one field was surveyed in the morning and another field in the evening following weekly protocol for switching survey times. Each field was surveyed 3 times per week. Observation points were adjusted accordingly to maximize clear line of site when each section was chopped. Waterfowl flew into and landed in fields during sunrise and sunset surveys. Canada geese that were in fields at the start counts were included. This scenario reduced error in counting and identifying waterfowl to species, so 100% detection was assumed. For each field, total number of waterfowl, species composition, and other wildlife were recorded. Other wildlife included blackbirds (Icteridae), white-tailed deer (Odocoileus virginianus), and wild turkeys (Meleagris gallopavo).

opencc-by-4.0Aug 2023View details →

Hemostatic system in Takotsubo patients at long-term follow-up: A hidden activation?

This record contains raw data related to the article “Hemostatic system in Takotsubo patients at long-term follow-up: A hidden activation?” Background: Takotsubo cardiomyopathy (TTS) has long been considered a benign condition, despite recurrent events and long-term adverse outcomes are often reported. Endothelial damage, blood hyperviscosity, and platelet activation described in acute phase persist in long-term follow-up; however, TTS pathophysiology is still not fully understood. Here, we explored the hemostatic system at a median of 3.1 years after TTS to uncover additional long-lasting changes in these patients. Methods: We assessed hemostatic parameters in women with TTS (n = 23) or coronary artery disease (CAD; n = 31) and in control women (n = 26) age-matched, by thromboelastographic analysis, prothrombin time (PT) and partial thromboplastin time (aPTT) coagulation assays and microparticle exposing Tissue Factor (MP-TF). Functional fibrinogen and fibrin polymerization were analyzed by Clauss method and spectrophotometry, respectively. Platelet reactivity was evaluated by light transmission aggregometry, whereas plasminogen activator inhibitor-1 (PAI-1) and brain-derived neurotrophic factor (BDNF) were measured by ELISA kit. Results: Compared with control subjects, TTS patients exhibit an accelerated clot formation, higher percentage of fibrin polymerization and higher PAI-1 levels. Compared with CAD, TTS patients showed sustained residual platelet activation but decreased functional fibrinogen, fibrin polymerization and MP-TF levels, prolonged aPTT and a marked BDNF increase. Conclusions: The long-term activation of hemostatic system observed in TTS patients compared to control subjects suggests a persistent humoral abnormality that may be related to the propensity for TTS recurrence. The higher residual platelet activity observed in TTS than in CAD patients invites investigation on TTS-tailored antiplatelet therapy potentially needed to prevent TTS adverse outcomes.