Find research datasets worth reusing

opencc-zeroDec 2020View details →

Eighty-four per cent of all Amazonian arboreal plant individuals are useful to humans

Plants have been used in Amazonian forests for millennia and some of these plants are disproportionally abundant (hyperdominant). At local scales, people generally use the most abundant plants, which may be abundant as the result of management of indigenous peoples and local communities. However, it is unknown whether plant use is also associated with abundance at larger scales. We used the population sizes of 4,454 arboreal species (trees and palms) estimated from 1946 forest plots and compiled information about uses from 29 Amazonian ethnobotany books and articles published between 1926 and 2013 to investigate the relationship between species usefulness and their population sizes, and how this relationship is influenced by the degree of domestication of arboreal species across Amazonia. We found that half of the arboreal species (2,253) are useful to humans, which represents 84% of the estimated individuals in Amazonian forests. Useful species have mean populations sizes six times larger than non-useful species, and their abundance is related with the probability of usefulness. Incipiently domesticated species are the most abundant. Population size was weakly related to specific uses, but strongly related with the multiplicity of uses. This study highlights the enormous usefulness of Amazonian arboreal species for local peoples. Our findings support the hypothesis that the most abundant plant species have a greater chance to be useful at both local and larger scales, and suggest that although people use the most abundant plants, indigenous people and local communities have contributed to plant abundance through long-term management.

opencc-by-4.0Jul 2021View details →

Peakhood: individual site context extraction for CLIP-seq peak regions

Peakhood Supplementary Data Archive, see content.txt for file content descriptions.

Time scales of ecosystem impacts and recovery under individual and serial invasions

Introductions of keystone or engineering species have complex and long-term impacts on multiple ecosystem features. Anticipating these consequences requires knowledge of the magnitude and pace of a species' impacts and whether they subside as resident species and communities adapt. Managing for the effects of invasive species is particularly complicated by a paucity of long-term ecosystem studies, the fact that invaders can represent novel ecological types, and as serial invasions by new species mediate the impacts of an original invader. We resolve the impacts of quagga (Dreissena rostriformis bugensis) and zebra mussels (D. polymorpha), two of the most widespread species that increasingly co-invade and re-engineer energy flows in freshwater ecosystems. Following many-decade time series and seven ecosystem features, we find remarkably similar ecosystem responses to mussel invasion across seven lakes in Europe and North America. Lakes invaded by zebra mussels only experienced the most severe changes within 5-10 years of invasion, followed by a partial recovery of several key ecosystem features. However, recovery disappeared, and initial impacts amplified in lakes where subsequent, serial invasions by quagga mussels competitively displaced zebra mussels. Our results suggest that the impact of quagga is stronger per unit biomass due to their greater effects on phytoplankton during spring and fall. Thus, we show that the effects of species introductions on many lake ecosystem features can manifest quickly and partially subside, except when multiple species invade a system.

Data for "Boosting propagule transport models with individual-specific data from mobile apps"

<ol> <li>Management of invasive species and pathogens requires information about the traffic of potential vectors. Such information is often taken from vector traffic models fitted to survey data. Here, user-specific data collected via mobile apps offer new opportunities to obtain more accurate estimates and to analyze how vectors' individual preferences affect propagule flows. However, data voluntarily reported via apps may lack some trip records, adding a significant layer of uncertainty. We show how the benefits of app-based data can be exploited despite this drawback.</li> <li>Based on data collected via an angler app, we built a stochastic model for angler traffic in the Canadian province of Alberta. There, anglers facilitate the spread of whirling disease, a parasite-induced fish disease. The model is temporally and spatially explicit and accounts for individual preferences and repeating behaviour of anglers, helping to address the problem of missing trip records.</li> <li>We obtained estimates of angler traffic between all subbasins in Alberta. The model's accuracy exceeds that of direct empirical estimates even when fewer data were used to fit the model. The results indicate that anglers' local preferences and their tendency to revisit previous destinations reduce the number of long inter-waterbody trips potentially dispersing whirling disease. According to our model, anglers revisit their previous destination in 64% of their trips, making these trips irrelevant for the spread of whirling disease. Furthermore, 54% of fishing trips end in individual-specific spatially contained areas with mean radius of 54.7 km. Finally, although the fraction of trips that anglers report was unknown, we were able to estimate the total yearly number of fishing trips in Alberta, matching an independent empirical estimate.</li> <li>We make two major contributions: (1) we provide a model that uses mobile app data to boost the mechanistic accuracy of classic propagule transport models, and (2) we demonstrate the importance of individual-specific behaviour of vectors for propagule transport. Ignoring vectors' local preferences and their tendency to revisit previous destinations can lead to significant overestimates of vector traffic and biased estimates of propagule flows. This has clear implications for the management of invasive species and animal diseases.</li> </ol>

Productivity, niche availability, species richness and extinction risk: Untangling relationships using individual-based simulations

It has been widely hypothesised that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species size. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems where niches are not already saturated with species, and where partitioning is therefore still possible. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favour of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH. --

The risk faced by the early bat: individual plasticity and mortality costs of the timing of spring departure after hibernation

Hibernation is a widespread adaptation in animals to seasonally changing environmental conditions. In the face of global anthropogenic change, information about plastic adjustments to environmental conditions and associated mortality costs are urgently needed to assess population persistence of hibernating species. Here, we used a five-year data set of 1,047 RFID-tagged individuals from two bat species, Myotis nattereri and Myotis daubentonii that were automatically recorded each time they entered or left a hibernaculum. Because the two species differ in foraging strategy and activity pattern during winter, we expected species–specific responses in the timing of hibernation relative to environmental conditions, as well as different mortality costs of early departure from the hibernaculum in spring. Applying mixed-effects modelling, we were able to disentangle population-level and individual-level plasticity in the timing of departure. To estimate mortality costs of early departure, we used both a capture mark recapture analysis and a novel approach that takes into account individual exposure times to mortality outside the hibernaculum. We found that the timing of departure varied between species as well as among and within individuals, and was plastically adjusted to large-scale weather conditions as measured by the NAO (North Atlantic Oscillation) index. Individuals of M. nattereri, which can exploit milder temperatures for foraging during winter, tuned departure more closely to the NAO index than individuals of M. daubentoniid which do not hunt during winter. Both analytical approaches used to estimate mortality costs showed that early departing individuals were less likely to survive until the subsequent hibernation period than individuals that departed later. Overall, our study demonstrates that individuals of long-lived hibernating bat species have the potential to plastically adjust to changing climatic conditions, although the potential for adjustment differs between species.

opencc-zeroDec 2022View details →

Wild kangaroos become more social when caring for young and may maintain long-term affiliations with popular individuals

Kangaroos are an iconic group of Australian fauna. Despite considerable research on kangaroo behaviour, key gaps remain in our understanding of their social organization in the wild. In particular, it remains largely unknown whether kangaroos form long-term social bonds and what factors might prompt individuals to associate or dissociate from one another. Over 6 years, we monitored the social affiliations of individually identified eastern grey kangaroos, Macropus giganteus, in a large wild population. We investigated the short-term and long-term relationships of kangaroos and the extent those relationships varied with age, sex and reproductive state. We found evidence that long-term relationships among eastern grey kangaroos are possible, especially between adult females. Those individuals that were more sociable within years were also more likely to establish affiliations across years. Contrary to previous studies, we observed females actively associating with other mothers in the years in which they had young. These data suggest that the fission-fusion dynamics of eastern grey kangaroo social behaviour allow females to modulate their social position with conspecifics according to their current reproductive state. We highlight the adaptive implications of the formation of long-term bonds and the changes in social behaviour observed in females.

opencc-by-4.0Dec 2022View details →

Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals: GWAS summary statistics

Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories as well as complex trait architectures remain hidden due to the lack of Big Data. To fill this gap, the Mexican Biobank project genotyped 1.8 million markers in 6,057 individuals from 32 states and 898 sampling localities across Mexico with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Through a suite of state-of-the-art methods for ancestry deconvolution and inference of identity-by-descent (IBD) segments, we inferred detailed ancestral histories for the last 200 generations in different Mesoamerican regions, unravelling native and colonial/post-colonial demographic dynamics. We observed large variations in runs of homozygosity (ROH) among genomic regions with different ancestral origins reflecting their demographic histories, which also affect the distribution of rare deleterious variants across Mexico. We analysed a range of biomedical complex traits and identified significant genetic and environmental factors explaining their variation, such as ROH found to be significant predictors for trait variation in BMI and triglycerides. ====================================== This dataset contains GWAS summary statistics for the Mexico Biobank Project. Summary statistics for 22 binary and quantitative traits are provided from the full cohort of 5721 individuals from across Mexico, and a subset of 1061 individuals inferred to have more than 90% Native American ancestry.

opencc-zeroDec 2022View details →

STR genotypes of 195 black grouse individuals

The data file contains the individual genotypes of 195 black grouse (Lyrurus tetrix) individuals, genotyped at 9 STR (microsatellite) loci. The data is curated into 10 subpopulations as decribed in the accompanied publication. The data is uploaded in the commonly used genepop file format.

opencc-by-4.0Dec 2021View details →

Data for: Neural correlates of individual odor preference in Drosophila

Data associated with: Neural correlates of individual odor preference in Drosophila Abstract: Behavior varies even among genetically identical animals raised in the same environment. However, little is known about the circuit or anatomical origins of this individuality. We show individual Drosophila odor preferences (odor-vs-air and odor-vs-odor) are predicted by idiosyncratic calcium dynamics in olfactory receptor neurons (ORNs) and projection neurons (PNs), respectively. Variation in ORN presynaptic density also predicts odor-vs-odor preference. The ORN-PN synapse appears to be a locus of individuality where microscale variation gives rise to idiosyncratic behavior. Finally, simulating microscale stochasticity in ORN-PN synapses of a 3,062-neuron model of the antennal lobe recapitulates patterns of variation in PN calcium responses matching experiments. Our results demonstrate how physiological and microscale structural circuit variations can give rise to individual behavior, even when genetics and environment are held constant.

opencc-by-4.0Dec 2022View details →

Prosocial Behavior and the Individual Normative Standard of Fairness within a Dynamic Context: Experimental Evidence

The data is of the economic experiment conducted in Georgia in summer 2022. The experiment was conducted online via LIONESS web-based software. The experiment was conducted in Georgian Language. The instructions and PC screen information translated from Georgian language into English language. The participants were mostly students of different major, average age of 20, about 16% were non-students. 63% was female. The data consist of two treatments: (1) Control treatment - two round standard double blind dictator game, dictators' roles were kept constant in both rounds (2) Treatment T1 - consisted from three parts, in part 1 subjects play standard double blind Dictator Game, in part 2 subjects play tend rounds of Public Goods Game with peer punishment, and in part 3 subjects play same standard double blind Dictator Game; dictators' stay in same role in part 1 and part 3. In part 2 , in Public Goods Game was partner treatment with constant group composition.

opencc-by-4.0Nov 2022View details →

DATA FOR NON-INVASIVE (PHOTO) INDIVIDUAL FISH IDENTIFICATION OF MULTIPLE SPECIES

This paper describes data from five studies focused on the individual fish identification of the same species. The lateral images of five fish species are present in the dataset. The dataset's primary purpose is to provide a data to develop a non-invasive and remote method of individual fish identification using fish skin patterns, which can serve as a substitute for the common invasive fish tagging. The lateral images of the whole fish body on the homogenous background for Sumatra barb, Atlantic salmon, Sea bass, Common carp and Rainbow trout are available with automatically extracted parts of the fish with skin patterns. A different number of individuals (Sumatra barb – 43, Atlantic salmon – 330, Sea bass – 300, Common carp – 32, Rainbow trout   - 1849) were photographed by the digital camera Nikon D60 under controlled conditions. The photographs of only one side of the fish with several (from 3 to 20) repetitions were taken. Common carp, Rainbow trout and Sea bass were photographed out of the water. Atlantic salmon was photographed underwater, out of the water, and the eye of the fish was photographed by the microscope camera. Sumatra barb was photographed under the water only. For all species, except Rainbow trout, the data collection was repeated after a different period (Sumatra barb – four months, Atlantic salmon – six months, Sea bass – one month, Common carp – four months) to collect the data for a study of skin patter changes (aging). The development of the method for photo-based individual fish identification was performed on all datasets. The identification accuracy for all species for all periods was 100% using the nearest neighbour classification. Different methods for skin pattern parametrization were used.  The dataset can be used to develop remote and non-invasive individual fish identification methods. The studies focused on the discrimination power of the skin pattern can benefit from it. The changes of skin patterns due to fish aging can be explored from the dataset.

opencc-zeroDec 2022View details →

Transition from transperitoneal to retroperitoneal approach in laparoscopic living donor nephrectomy: Team-based and individual learning curve: A cross-sectional study

Background: Laparoscopic living donor nephrectomy (LLDN) is a standard practice for kidney donor transplantation due to fewer complications associated with the treatment. Retroperitoneal approach to LLDN is thought to be more advantageous in preventing injuries to various abdominal organs. However, the transition process from transperitoneal to retroperitoneal LLDN is important to ensure the best outcome for the patients. The aim of this study was to investigate the learning curve for the retroperitoneal approach in LLDN among urologists in an individual and team-based approach Methods: A retrospective analysis of retroperitoneal LLDN was performed on procedures performed by a kidney donor team consisting of four (4) urologists from January 2019 to January 2022 at Cipto Mangunkusumo National General Hospital, Indonesia. The data were taken from pre-existing medical records. The learning curve for the operation time, warm ischemic time, and estimated blood loss were analyzed using cumulative sum (CUSUM) analysis. Phase 1 represents the initial learning curve, the phase 2 plateau represents the period of proficiency, and phase 3 represents the mastery period. Results: A total of 127 retroperitoneal LLDN procedures were done during the study period by four operators with various experience. The average procedure needed to achieve proficiency was 16.5 procedures. Meanwhile, the average procedure needed to achieve mastery was 28 procedures. A shorter learning curve was achieved by operators with more experience in other laparoscopic procedures. Conclusions: The learning curve for transition from transperitoneal to retroperitoneal approach to LLDN is relatively short and feasible for both individuals and teams of urologists. Therefore, the transition to a retroperitoneal approach is a feasible option to reduce the complication rate of LLDN.

opencc-zeroJan 2023View details →

A novel camera trapping method for individually identifying pumas by facial features

Camera traps (CTs), used in conjunction with capture-mark-recapture analyses (CMR; photo-CMR), are a valuable tool for estimating abundances of rare and elusive wildlife. However, a critical requirement of photo-CMR is that individuals are identifiable in CT images (photo-ID). Thus, photo-CMR is generally limited to species with conspicuous pelage patterns (e.g., stripes or spots) using lateral-view images from CTs stationed along travel paths. Pumas (Puma concolor) are an elusive species for which CTs are highly effective at collecting image data, but their suitability to photo-ID is controversial due to their lack of pelage markings. For a wide range of taxa, facial features are useful for photo-ID, but this method has generally been limited to images collected with traditional handheld cameras. Here we evaluate the feasibility of using puma facial features for photo-ID in a CT framework. We consider two issues: 1) the ability to capture puma facial images using CTs, and 2) whether facial images improve human ability to photo-ID pumas. We tested a novel CT accessory that used light and sound to attract the attention of pumas, thereby collecting face images for use in photo-ID. Face captures rates increased at CTs that included the accessory (n = 208, χ2 = 43.23, P ≤ 0.001). To evaluate if puma faces improve photo-ID, we measured the inter-rater agreement of 5 independent assessments of photo-ID for 16 of our puma face capture events. Agreement was moderate to good (Fleiss' kappa = 0.54, 95% CI = 0.48–0.60), and was 92.90% greater than a previously published kappa using conventional CT methods. This study is the first time such a technique has been used for photo-ID, and we believe a promising demonstration of how photo-ID may be feasible for an elusive but unmarked species.

opencc-by-4.0Jan 2023View details →

Non - invasive identification of individuals of Sumatra barb Puntigrus tetrazona

Non-invasive fish identification of individuals can provide new possibilities for the monitoring of fish cultivation, improve and make fish production technologies less demanding for farmers, and increase fish welfare. The aim of this research is to confirm the idea of automatic non-invasive image-based fish identification of individuals using visible features on a fish body and prove the pattern stability during the fish cultivation period. Visible patterns, such as black stripes along the body of a Sumatra barb (Puntigrus tetrazona), were used for machine identification of individual fish. Two experiments were completed: A short-term experiment (43 fish) to show the uniqueness of the stripe patterns for identification, and a long-term experiment (25 fish) to test the stability of patterns during the cultivation period. The overall accuracy of classification was 100% for data collection in one day and 88% between two data collection times. This study shows that visible patterns and image processing methods can be used to automatically identify individual fish of the same species.

opencc-by-4.0Jan 2023View details →

IDSL.CSA grouping of individual peaks and adduct annotation

IDSL.CSA grouping and adduction annotation of individual peaks for test file a test file pool_P1_A1-A12.mzML from the  ftp://massive.ucsd.edu/MSV000088661/  ( IROA metabolite standards )

opencc-zeroJan 2023View details →

Data: Large old trees increase growth under shifting climatic constraints: Aligning tree longevity and individual growth dynamics in primary mountain spruce forests

In a world of accelerating changes in environmental conditions driving tree growth, tradeoffs between tree growth rate and longevity could curtail the abundance of large, old trees (LOTs), with potentially dire consequences for biodiversity and carbon storage. However, the influence of tree-level tradeoffs on forest structure at landscape scales will also depend on disturbances, which shape tree size and age distribution, and on whether LOTs can benefit from improved growing conditions due to climate warming. We analyzed temporal and spatial variation in radial growth patterns from ~5000 Norway spruce (Picea abies (L.) H. Karst) live and dead trees from the Western Carpathian primary spruce forest stands. We applied mixed-linear modeling to quantify the importance of LOT growth histories and stand dynamics (i.e. competition and disturbance factors) on lifespan. Finally, we assessed regional synchronization in radial growth variability over the 20th century, and modelled the effects of stand dynamics and climate on LOTs recent growth trends. Tree age varied considerably among forest stands, implying an important role of disturbance as an age constraint. Slow juvenile growth and longer period of suppressed growth prolonged tree lifespan, while increasing disturbance severity and shorter time since last disturbance decreased it. The highest age was not achieved only by trees with continuous slow growth, but those with slow juvenile growth followed by subsequent growth releases. Growth trend analysis demonstrated an increase in absolute growth rates in response to climate warming, with late summer temperatures driving the recent growth trend. Contrary to our expectation that LOTs would eventually exhibit declining growth rates, the oldest LOTs (>400 years) continuously increase growth throughout their lives, indicating a high phenotypic plasticity of LOTs for increasing biomass, and a strong carbon sink role of primary spruce forests under rising temperatures, intensifying droughts, and increasing bark beetle outbreaks.

opencc-by-4.0Jan 2023View details →

Intra and Inter-Individual Variability in Functional Connectomes of Patients with First Episode of Psychosis

Test-retest functional connectomes for 32 Healthy Controls and 30 First Episode of Psychosis patients. This dataset was originally used in the following article: (Preprint) Tepper, Ángeles and Núñez, Javiera Vásquez and Ramirez-Mahaluf, Juan Pablo and Aguirre, Juan Manuel and Barbagelata, Daniella and Maldonado, Elisa and Dellarossa, Camila Díaz and Nachar, Ruben and Gonzalez-Valderrama, Alfonso and Undurraga, Juan and Goñi, Joaquín and Crossley, Nicolas, Intra and Inter-Individual Variability in Functional Connectomes of Patients with First Episode of Psychosis. Available at SSRN: <a href="https://ssrn.com/abstract=4241607">https://ssrn.com/abstract=4241607</a> or <a href="http://dx.doi.org/10.2139/ssrn.4241607">http://dx.doi.org/10.2139/ssrn.4241607</a> More details and python code used for analyses can be found in this <a href="https://github.com/angietep/Inter-and-Intra-Indiv-Variability">GitHub repository</a>

opencc-zeroFeb 2023View details →

Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal vs. sexual reproduction affected Ne. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on Ne confidence intervals. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence Ne. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.