Find research datasets worth reusing

opencc-zeroDec 2001View details →

FIG. 3. — A in Redescription and range extension of the sea anemone Exocoelactis actinostoloides (Wassilieff, 1908), with revision of genus Exocoelactis (Cnidaria, Anthozoa, Actiniaria)

FIG. 3. — A, longitudinal section at margin of Exocoelactis actinostoloides (Wassilieff, 1908) (KUNHM 01267) illustrating the location and length of the sphincter muscle and texture of the mesoglea; note strands of mesoglea extending across sphincter muscle; B, close-up of sphincter muscle. Magnification is 3.9 times that of A (KUNHM 01266); C, proximal terminus of the sphincter. Magnification is 3.75 times that of A (KUNHM 01267). Scale bar: A, 1 mm.

opencc-by-4.0May 2021View details →

Fig. 2 in Arganiella Giusti & Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?

Fig. 2. Shells, operculum and radulae of Docleiana tabanensis (Boeters, Glöer & Pešić, 2014) (UGSB 18847). A–C. Shells. D–E. Operculum (D = inner side; E = outer side). F. Protoconch. G–I. Radulae. G. Portion of radula ribbon. H. Central radular teeth. I. Inner and outer marginal teeth.

opencc-by-4.0May 2021View details →

Fig. 1 in Arganiella Giusti & Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?

Fig. 1. Maximum likelihood tree based on the combined (COI, 18S) dataset. Statistical support of the nodes is indicated when Bayesian posterior probabilities ≥ 0.95 and bootstrap supports ≥ 75% (black dots). On the right, the morphology of shell, penis and distal female genitalia is presented for: a) Arganiella wolfi Boeters & Glöer, b) A. pescei Giusti & Pezzoli, 1980 and c) A. tabanensis Boeters, Glöer & Pešić, 2014. Reproductive organs were re-drawn from Arconada & Ramos (2007a), Bodon et al. (2001) and Boeters et al. (2014) for the three species, respectively. Scale bar below topology: substitutions per site.

opencc-zeroSep 2021View details →

Home range use in the West Australian seahorse Hippocampus subelongatus is influenced by sex and partner's home range but not by body size or paired status

These data and scripts form the basis for Kvarnemo C, Andersson SE, Elisson J, Moore GI and Jones AG (2021). Home range use in the West Australian seahorse Hippocampus subelongatus is influenced by sex and partner's home range but not by body size or paired status. Journal of Ethology 39: 235–248. https://doi.org/10.1007/s10164-021-00698-y. The abstract below is from this paper: Genetic monogamy is the rule for many species of seahorse, including the West Australian seahorse Hippocampus subelongatus. In this paper, we revisit mark-recapture and genetic data of H. subelongatus, allowing a detailed characterization of movement distances, home range sizes and home range overlaps for each individual of known sex, paired status (paired or unpaired) and body size. As predicted, we find that females have larger home ranges and move greater distances compared to males. We also confirm our prediction that the home ranges of pair-bonded individuals (members of a pair known to reproduce together) overlap more on average than home ranges of randomly chosen individuals of the opposite or same sex. Both sexes, regardless of paired status, had home ranges that overlapped with, on average, 6–10 opposite-sex individuals. The average overlap area among female home ranges was significantly larger than the overlap among male home ranges, probably reflecting females having larger home ranges combined with a female biased adult sex ratio. Despite a prediction that unpaired individuals would need to move around to find a mate, we find no evidence that unpaired members of either sex moved more than paired individuals of the same sex. We also find no effect of body size on home range size, distance moved or number of other individuals with which a home range overlapped. These patterns of movement and overlap in home ranges among individuals of both sexes suggest that low mate availability is not a likely explanation for the maintenance of monogamy in the West Australian seahorse.

opencc-zeroOct 2021View details →

Data from: Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila

1. Populations that expand their range can undergo rapid evolutionary adaptation of life-history traits, dispersal behaviour, and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context. 2. However, few empirical and experimental studies have investigated the genetic basis of adaptive evolution during range expansions. Even less attention has been given to the question how sexual reproduction may modulate such adaptive evolution during range expansions. 3. We here studied genomic adaptation during experimental range expansions of the protist Tetrahymena thermophilain landscapes with a uniform environment or a pH-gradient. Specifically, we investigated two aspects of genomic adaptation during range expansion. Firstly, we investigated adaptive genetic change in terms of the underlying numbers of allele frequency changes from standing genetic variation and de novo variants. We focused on how sexual reproduction may alter this adaptive genetic change. Secondly, we identified genes subject to selection caused by the expanding range itself, and directional selection due to the presence or absence of the pH-gradient. We focused this analysis on alleles with large frequency changes that occurred in parallel in more than one population to identify the most likely candidate targets of selection. 4. We found that sexual reproduction altered adaptive genetic change both in terms of de novo variants and standing genetic variation. However, sexual reproduction affected allele frequency changes in standing genetic variation only in the absence of long-distance gene flow. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH-gradient additionally affected genes involved in ion balance, and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH. 5. In the absence of gene flow, sexual reproduction may have aided genetic adaptation. Gene flow may have swamped expanding populations with maladapted alleles, thus reducing the extent of evolutionary adaptation during range expansion. Sexual reproduction also altered the genetic basis of adaptation in our evolving populations via de novo variants, possibly by purging deleterious mutations or by revealing fitness benefits of rare genetic variants.

opencc-zeroOct 2021View details →

Data & R code for: Paquette & Hargreaves 'Biotic interactions are more often important at species' warm vs. cool range edges'

Predicting which ecological factors constrain species distributions is a fundamental ecological question and critical to forecasting geographic responses to global change. Darwin hypothesized that abiotic factors generally impose species' high-latitude and high-elevation (typically cool) range limits, whereas biotic interactions more often impose species' low-latitude/low-elevation (typically warm) limits, but empirical support has been mixed. Here, we clarify three predictions arising from Darwin's hypothesis, and show that previously mixed support is partially due to researchers testing different predictions. Using a comprehensive literature review (885 range limits), we find that biotic interactions, including competition, predation, and parasitism, contributed to >60% of range limits, and influenced species' warm limits more often than cool limits. Abiotic factors contributed more often than biotic interactions to cool range limits, but temperature contributed frequently to both cool and warm limits. Our results suggest that most range limits will be sensitive to climate warming, but warm-limit responses will depend strongly on biotic interactions.

opencc-by-4.0Nov 2022View details →

Electronic correlations and universal long-range scaling in kagome metals

Dataset for the constrained Random Phase Approximation calculations shown in the manuscript. The VASP OUTCAR (ascii plain texy file) contains the whole cRPA U_iijj, U_ijij and U_ijji tensors, from which the numbers in the table of the paper (Supplementary Material) are extracted. Input files necessary to reproduce the results are also in the repository.

opencc-by-4.0Nov 2022View details →

Data from: "Influence of natal habitat preference on habitat selection during extra-home range movements in a large ungulate"

Secondary dataset used for analysis in "Influence of natal habitat preference on habitat selection during extra-home range movements in a large ungulate". Raw GPS relocation data are not publicly available due to potential ethical implications but are available from the corresponding author (Nathan Hooven, nathan.d.hooven@gmail.com) upon reasonable request. Files include: deer_data_6.csv: Sampled covariate values for each used and available location used in SSF analysis Metadata: Metadata information for deer_data_6.csv

opencc-zeroNov 2022View details →

Identification of free-ranging mugger crocodiles by applying deep learning methods on UAV imagery

Individual identification contributes significantly towards investigating behavioral mechanisms of animals and understanding underlying ecological principles. Most studies employ invasive procedures for individually identifying organisms. In recent times, computer-vision techniques have served as an alternative to invasive methods. However, these studies primarily rely on user input data collected from captivity or from individuals under partially restrained conditions. Challenges in collecting data from free-ranging individuals are higher when compared to captive populations. However, the former is a far more important priority for real-world applications. In this paper, we used UAV to collect data from free-ranging mugger crocodiles Crocodylus palustris. We applied convolutional neural networks (CNNs) to individually identify muggers based on their dorsal scute patterns. The CNN model was trained on a data set of 88,000 images focusing on the mugger's dorsal body. The data was collected from 143 individuals across 19 different locations along the western part of India. We trained two CNN models, one with an annotated bounding box approach, the YOLO-v5l, and another without annotations, the Inception-v3. We used two parameters, True Positive Rate (TPR) and True Negative Rate (TNR), to validate the efficiency of the trained models. Using YOLO-v5l, TPR (re-identification of trained muggers) and TNR (differentiating untrained muggers as 'unknown') values at 0.84 threshold were 88.8% and 89.6%, respectively. The trained model showed 100% TNR for the non-mugger species, the Gharial Gavialis gangeticus, and the Saltwater crocodile Crocodylus porosus. The performance of the CNN model was reliable and accurate while using only 125 images per individual for training purposes. Inception-v3 underperformed for both the parameters, thus, showing that a bounding box approach (YOLO-v5l model) with background elimination is a promising method to individually identify free-ranging mugger crocodiles. Our manuscript demonstrates that UAV imagery appears to be a promising tool for non-invasive collection of data from free-ranging populations. It can be used to train open-source algorithms for individual identification. Further, the identification method is entirely based upon dorsal scute patterns, which can be applied to different crocodilian species, as well.

Data from: A well-studied parasitoid fly of field crickets uses multiple alternative hosts in its introduced range

Organisms and their natural enemies can have dynamic coevolutionary trajectories, but anthropogenic effects like species introductions interrupt existing coevolutionary relationships. For parasites in particular, if they are introduced to a location without their hosts, they can only persist in the new environment if alternative hosts are 1) present, 2) detectable to parasites, and 3) capable of sustaining parasites. The circumstances surrounding the addition of alternative hosts to a parasite's repertoire are rarely observed. The parasitoid fly Ormia ochracea locates its field cricket hosts by orienting acoustically to their conspicuous mating songs. In Hawaii, O. ochracea is only known to parasitize one species, Teleogryllus oceanicus, but rapid evolution of T. oceanicus mating song over the past 20 years has led to several prevalent morphs of the cricket that produce no song or novel songs that the flies cannot detect. Yet flies persist in populations that lack ancestral singing T. oceanicus, prompting us to investigate the possibility of alternative hosts in Hawaii. We demonstrate first that three potential alternative hosts (Gryllodes sigillatus, Gryllus bimaculatus, and Modicogryllus pacificus) are present. Second, O. ochracea exhibits a positive phonotactic response to all three species' songs in the field and in the lab. And third, O. ochracea can successfully develop to pupae and emerge as adults in all three species. Our discovery of alternative hosts for O. ochracea in Hawaii infuses the system with intriguing complexity and offers extensive opportunities for future work.

WRF Geographic Files for Cordillera Mountain Range Precipitation Experiments

These WRF geographic files (in netcdf format) were used as input for experiments to evaluate the sensitivity of Tropical Cyclone precipitation to the height of the Cordillera Mountain Range in Luzon, Philippines. A total of six files are included, for two domains (d01 and d02) and three different orographic experiments (orig, redu, enha). These are provided to allow reproduction of the said sensitivity experiments.

HomeRange: A global database of mammalian home ranges

Motivation: Home range is a common measure of animal space use as it provides ecological information that is useful for conservation applications. In macroecological studies, values are typically aggregated to species means to examine general patterns of animal space use. However, this ignores the environmental context in which the home range was estimated and does not account for intraspecific variation in home range size. In addition, the focus of macroecological studies on home ranges has been historically biased toward terrestrial mammals. The use of aggregated numbers and terrestrial focus limits our ability to examine home range patterns across different environments, variation in time and between different levels of organisation. Here we introduce HomeRange, a global database with 75,611 home-range values across 960 different mammal species, including terrestrial, as well as aquatic and aerial species. Main types of variable contained: The dataset contains mammal home-range estimates, species names, methodological information on data collection, home-range estimation method, period of data collection, study coordinates and name of location, as well as species traits derived from the studies, such as body mass, life stage, reproductive status and locomotor habit. Spatial location and grain: The collected data is distributed globally. Across studies, the spatial accuracy varies, with the coarsest resolution being 1 degree. Time period and grain: The data represent information published between 1939 and 2022. Across studies, the temporal accuracy varies, some studies report start and end dates specific to the day. For other studies, only the month or year is reported. Major taxa and level of measurement: Mammal species from 24 of the 27 different taxonomic orders. Home-range estimates range from individual-level values to population-level averages.

Zebras of all stripes repel biting flies at close range

The best-supported hypothesis for why zebras have stripes is that stripes repel biting flies. While this effect is well-established, the mechanism behind it remains elusive. Myriad hypotheses have been suggested, but few experiments have helped narrow the field of possible explanations. In addition, the complex visual features of real zebra pelage and the natural range of stripe widths have been largely left out of experimental designs. In paired-choice field experiments in a Kenyan savannah, we found that hungry Stomoxys flies released in an enclosure strongly preferred to land on uniform tan impala pelts over striped zebra pelts but exhibited no preference between the pelts of the zebra species with the widest stripes and the narrowest stripes. Our findings confirm that zebra stripes repel biting flies under naturalistic conditions and do so at close range (suggesting that several of the mechanisms hypothesized to operate at a distance are unnecessary for the fly-repulsion effect) but indicate that interspecific variation in stripe width is associated with selection pressures other than biting flies.

Dataset for "Narrow range of early habitable Venus scenarios permitted by modelling of oxygen loss and radiogenic argon degassing"

Code and datasets required to reproduce figures in main text of Warren & Kite 2023 "Narrow range of early habitable Venus scenarios permitted by modelling of oxygen loss and radiogenic argon degassing." https://www.pnas.org/doi/full/10.1073/pnas.2209751120 Code and usage instructions are also available at: github.com/aowarren/Venus_O2 After downloading, code will need to be modified to find files in chosen directories for running the full model (also requires installation of VolcGases from github.com/Nicholaswogan/VolcGases) and files for re-creating plots. All .zip files contain data used to create figures in paper. Instructions to reproduce figures below:   1. To reproduce full dataset, download all files excluding .zip files and install VolcGases. Modify "modular_functions_clean_redox.py" to match VolcGases installation. For runaway greenhouse runs: Ensure "modular_functions_clean_redox.py" line 512 is commented out. Run "adding_dissolution_clean.py" followed by "ext1line.py" to pre-run runaway greenhouse model and save output to read into full model (this speeds up running the entire suite of "melting" models, but is not strictly necessary). Next, use "gridsearch_all_redox.csv" to set model parameters, then run "input_clean_redox.py" to initiate model.  For runs without runaway greenhouse melting: uncomment "modular_functions_clean_redox.py" line 512. Use "gridsearch_all_redox.csv" to set model parameters, then run "input_clean_redox.py" to initiate model.  2. To reproduce Figures 2, 3, S1, and S2, either download all zip files beginning with "Fig2_" and "Fig3_", extract all files to single location, or save all new model output into a single directory and use "plot_together.py" to generate figures (instructions contained within script). Use same script to reproduce Figures S9 and S10 with data in "t_atm_sensitivity.zip" and "bH_sensitivity.zip".  3. To reproduce Figures 4 and 5, If using new model runs to generate plots, first run "gen_data_forplots.py". Alternatively, download: <ul> <li>e_statistics_nomelt_CO_FMQ0.npz </li> <li>e_wd_statistics_melt_CO_FMQ0.npz</li> <li>40_Ar_hab_dlith_KU_mix_52522.csv</li> <li>40_Ar_hab_dlith_KU_nomix_52522.csv</li> </ul> Then, run maintext_plotting_new.py. 4. To reproduce Figures S5 to S8, run "Ar_plots.py". Requires: "serpent_dehyd2.csv" and "eclogite_transition.csv".

opencc-by-4.0Sep 2022View details →

Data and Code for figures of "Long-range transport and fate of DMS-oxidation products in the free troposphere derived from observations at the high-altitude research station Chacaltaya (5240 m a.s.l.) in the Bolivian Andes"

This database includes the material to create the figures in "Measurement Report: Long-range transport and fate of DMS-oxidation products in the free troposphere derived from observations at the high-altitude research station Chacaltaya (5240 m a.s.l.) in the Bolivian Andes" and the analyzed time series of all atmospheric variables presented.

Fig. 3 in Further And Further East: Steppe Land Snail, Xerolenta Obvia (Gastropoda, Geomitridae), Expands Its Range In Ukraine

Fig. 3. Shells of X. obvia with an atypically dark colored upper part from Western Ukraine: A — Sosulivka, Ternopil Region; B — Romaniv, Lviv Region; C — Lviv. Scale bars 5 mm.

Fig. 1 in Further And Further East: Steppe Land Snail, Xerolenta Obvia (Gastropoda, Geomitridae), Expands Its Range In Ukraine

Fig. 1. Xeropicta derbentina (A, B) and Xerolenta obvia (C–E) from the Slovianskyi Kurort Regional Landscape Park, Donetsk Region: 1 — stylophores, 2 — swollen basal part of stylophore. Scale bars 5 mm for A–D, 1 mm for E.

opencc-zeroDec 2021View details →

Are trapping data suited for home-range estimation?

Modern home-range estimation typically relies on data derived from expensive radio- or GPS-tracking. Although trapping represents a low-cost alternative to telemetry, there lacks an evaluation of the performance of home-range estimators on trap-derived data. Using simulated data, we evaluate three variables reflecting the key trade-offs ecologists face when designing a trapping study: 1) the number of observations obtained per individual, 2) the trap density, and 3) the proportion of the home range falling inside the trapping area. We compare the performance of five home-range estimators (MCP, LoCoH, KDE, AKDE, bicubic interpolation). We further explore the potential benefits of combining these estimators with asymptotic models, which leverage the saturating behavior of changes in the estimated home-range area as the number of observations increases to improve accuracy, as well as different data ordering procedures. We then quantified the bias in home-range size under the different scenarios investigated. The number of observations and the proportion of the home range within the trapping grid were the most important predictors of the accuracy and the precision of home-range estimates. The use of asymptotic models helped obtain accurate estimates at smaller sample sizes, while distance-ordering improved the precision and asymptotic consistency of estimates. While AKDE was the best-performing estimator under most conditions evaluated, bicubic interpolation was a viable alternative under common real-world conditions of low trap density and area covered. A case study using empirical data from white-tailed deer in Florida and another from jaguars in Belize demonstrated support for the findings of our simulation results. Although researchers with trap data often overlook home-range estimation, our results indicate that these data have the capacity to yield accurate estimates of home-range size. Trapping data can therefore lower the economic costs of home-range analysis, potentially enlarging the span of species, researchers and questions studied in ecology and conservation.

Spatial distribution of Mesozoic deposits and their temperature ranges within the Weser-Wiehengebirge Syncline of the inverted Lower Saxony Basin, Minden area, Germany

This repository contains the supplementary material for the publication "Spatial distribution of Mesozoic deposits and their temperature ranges within the Weser-Wiehengebirge Syncline of the inverted Lower Saxony Basin, Minden area, Germany" by Alexander Jüstel, Olga Knaub, Frank Strozyk, Gregor Bussmann, Florian Wellmann, Peter Kukla.

Data from: Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures

Data used for the study entitled "Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures". These are the distribution data collected from literature and personal communications to complete the GBIF and OBIS distributional records of the Atlantic European coast, the weekly growth data taken from the study individuals as well as the binomial survival data used for the graphs of the last week of the experiment.