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opencc-by-4.0Jun 2018View details →

Figure 4 in Occurrence and distribution of tetraodontiform fishes of the Andaman and Nicobar Islands, India

Figure 4. Non-randomized cumulative species accumulation curves with sites ordered from southern Nicobar to northern Andaman Islands. The reported number of species was highest at sites located at Nicobar and South Andaman regions, where they contribute to 17 out of the 25 species reported. Among islands towards higher latitudes, the curve shows an increase at the Japanese bunker site after which only 3 species were added to the curve for 39 sampled islands in middle and North Andaman regions.

opencc-by-4.0Jun 2018View details →

Figure 3 in Occurrence and distribution of tetraodontiform fishes of the Andaman and Nicobar Islands, India

Figure 3. Some species of fish belonging to the order Tetraodontiformes from the Andaman and Nicobar Islands. A. Oxymonacanthus longirostris. B. Ostracion cubicus. C. Ostracion melegris.D. Arothron nigropunctatus. E. Arothron stellatus. F. Canthigaster petersii.

Fig. 6 in Spatio-temporal segregation and size distribution of fish assemblages as related to non-native species occurrence in the middle rio Doce Valley, MG, Brazil

Fig. 6. Least-square means and 95% confidence intervals from ANCOVA of the first three environmental factors from PCA. Different markers represent significantly different means as detected by planned contrasts with 5% significance level, first comparing lakes with any non-native species with those without them, and then comparing the two categories of lakes with non-natives (non-piscivores vs. piscivores).

Fig. 4 in Spatio-temporal segregation and size distribution of fish assemblages as related to non-native species occurrence in the middle rio Doce Valley, MG, Brazil

Fig. 4. Scatterplot of species body size (mean standard length) vs. a relative index of native affinity to lakes containing piscivorous invaders (the proportion of biomass of a given native species in lakes with piscivorous invaders). The estimated regression line is also presented (Y = 0.044*X - 0.279; R2 = 0.443; p = 0.007). Species codes: ast = Astyanax sp.; aus = Australoheros facetus; cyp = Cyphocharax gilbert; cre = Crenicichla lacustris; geo = Geophagus brasiliensis; gym = Gymnotus gr. carapo; hop = Hoplias malabaricus; lep = Leporinus steindachneri; lor = Loricariidae (unidentified species); lyc = Lycengraulis sp.; moe = Moenkhausia doceana; oli = Oligosarcus solitarius; pac = Pachyurus adspersus; pro = Prochilodus vimboides; tra = Trachelyopterus striatulus.

Fig. 5 in Spatio-temporal segregation and size distribution of fish assemblages as related to non-native species occurrence in the middle rio Doce Valley, MG, Brazil

Fig. 5. Least-square means and 95% confidence intervals from ANCOVA of mean individual size and temporal turnover as related to the three lake categories. Different markers represent significantly different means as detected by planned contrasts with 5% significance level, first comparing lakes with any non-native species with those without them, and then comparing the two categories of lakes with non-natives (non-piscivores vs. piscivores).

Fig. 2 in Spatio-temporal segregation and size distribution of fish assemblages as related to non-native species occurrence in the middle rio Doce Valley, MG, Brazil

Fig. 2. Alpha (mean) and beta richness. a) Comparison among the temporal and spatial components of richness. b) Species richness for each lake. The alpha (mean) and beta richness were taken along the temporal component. Lake codes: No = Nova; Ca = Capim; Fe = Ferrugem; Cr = Crentes; Po = Poço Redondo; Ro = Romoalda; Ti = Timburé; Ag = Águas Claras; Pa = Palmeirinha; Ar = Ariranha. "Natives" represents lakes without non-native species; "Non-piscivores" represents lakes with non-piscivorous non-native species; "Piscivores" represents lakes with invasive piscivorous species.

opencc-by-4.0Sep 2021View details →

Global Flash Drought Data for the article "Global Distribution, Trends, and Drivers of Flash Drought Occurrence"

Data is provided (in netcdf format) to reproduce Figures 1-4 in the article entitled "Global Distribution, Trends, and Drivers of Flash Drought Occurrence."

dryad40/100

Data from: Traits mediate niches and co-occurrences of forest beetles in ways that differ among bioclimatic regions

Aim To investigate the role of traits in beetle community assembly and test for consistency in these effects among several bioclimatic regions. We asked (1) whether traits predicted species' responses to environmental gradients (i.e., their niches), (2) whether these same traits could predict co-occurrence patterns, and (3) how consistent were niches and the role of traits among study regions. Location Boreal forests in Norway and Finland, temperate forests in Germany. Methods We complied capture records of 468 wood-living beetle species from the three regions, along with nine morphological and ecological traits. Eight climatic and forest covariates were also collected. We used Bayesian hierarchical joint species distribution models to estimate the influence of traits and phylogeny on species' niches. We also tested for correlations between species associations and trait similarity. Finally, we compared species niches and the effects of traits among study regions. Results Traits explained some of the variability in species' niches, but their effects differed among study regions. However, substantial phylogenetic signal in species niches implies that unmeasured but phylogenetically structured traits have a stronger effect. Degree of trait similarity was correlated with species associations but depended idiosyncratically on the trait and region. Species niches were much more consistent – widespread taxa often responded similarly to an environmental gradient among regions. Main conclusions The inconsistent effects of traits among regions limits their current use in understanding beetle community assembly. Phylogenetic signal in niches, however, implies that better predictive traits can eventually be identified. Consistency of species niches among regions means niches may remain relatively stable under future climate and land use changes; this lends credibility to predictive distribution models based on future climate projections but may imply that species' scope for short-term adaptation is limited.

opencc-zeroSep 2021View details →

opencc-by-4.0Nov 2022View details →

Puma concolor occurrence points (filtered data)

Puma concolor occurrence points (duplicates removed) in Canada until December 2021.  Used in Maxent habitat suitability model (performed in R).

opencc-by-4.0Jan 2023View details →

Literature review of occurrence and transmission dynamics of SARS-CoV2 in mammal animals

A literature review has been conducted, focusing on susceptibility of wild and domestic animal species reported under field and laboratory conditions, considering different diagnostic tests (e.g., virus isolation, RNA and antibody detection), infection dynamic, pathogenesis, immunity and further transmission of the virus. Review protocol and data extraction tables are available. The following review questions were considered: <ul> <li>Which mammal species have been reported positive to SARS CoV 2 in the field (either at RNA, isolated virus, antibodies), and their geographical distribution?</li> </ul> <ul> <li>Which wild and domestic mammal species are susceptible to SARS CoV 2 in laboratory conditions</li> <li>Dynamic of infection and pathogenesis: <ul> <li>What are confirmed infection routes for these species?</li> <li>What is the length of the incubation period in these species</li> <li>What are the clinical signs, if any, their severity, duration, etc.</li> <li>Which species are able to shed the virus (even in absence of clinical signs)</li> <li>Do these species develop protective immunity</li> </ul> </li> <li>Which of these species can further transmit the disease to same/other species ?</li> <li>What are the genetic virus variants in each species where it is isolated?</li> <li>In which animals vaccines against SARS CoV 2 have been tested, and what are the results in terms of immunogenicity, protection to challenge, or safety?</li> </ul> <ul> <li>Which diagnostic tests are used in animals to detect SARS CoV <ul> <li>Type of test</li> <li>Test performance (Se, Sp)</li> <li>Sample matrix used</li> </ul> </li> </ul>

opencc-by-4.0Dec 2022View details →

Occurrence data on N-nitrosamines provided to EFSA

The file contains the raw occurrence dataset on nitrosamines in food as extracted from EFSA DWH on 3 July 2021 and presented in the EFSA opinion on Risk assessment of N-nitrosamines in food available at https://doi.org/10.2903/j.efsa.2023.7884. The data is provided in csv format. This dataset is compliant with EFSA SSD2 data model and contains two additional columns documenting issues identified in the cleaning process (column: issue) and the action taken (column: action) to address the issue (e.g. delete record or update values in specific fields). The link to the catalogues of controlled terminologies for the updated textual description of fields values can be found under "Related identifiers”.

opencc-by-4.0Feb 2023View details →

Filtered GBIF dataset of occurrences for food species in the brown bear (Ursus arctos) trophic database

We reviewed 47 studies of brown bear diet in Europe by searching in SCI Journals, master’s and PhD theses, and grey literature. We obtained a list of 276 species in the brown bear diet in Europe and Turkey. We used the R package rgbif to download occurrences of each food species from the Global Biodiversity Information Facility (GBIF). We selected occurrences of food species, with an uncertainty of <1 km2, in Europe, North Africa and the Middle East for the period 1989–2018.

opencc-by-4.0Feb 2023View details →

Rename Chains: An Exploratory Study on the Occurrence and Characteristics of Identifiers Undergoing Multiple Renamings

This is the dataset that accompanies the study: "Rename Chains: An Exploratory Study on the Occurrence and Characteristics of Identifiers Undergoing Multiple Renamings." This study has been accepted for publication at the 2022 International Workshop on Refactoring. Following is the abstract of the study: Identifier names play a significant role in program comprehension activities, with high-quality names improving developer productivity and system quality. To correct poor-quality names, developers rename identifiers to reflect their intended purpose better. However, renames do not always result in high-quality, long-lasting names; in many cases, developers perform multiple rename operations on the same identifier throughout the system's lifetime. In this paper, we report on a large-scale empirical study that examines the occurrence of identifiers undergoing multiple renames (i.e., rename chains). Our findings show the presence of rename chains in almost every project, with methods typically having more rename chains than other identifier types. Furthermore, it is usually the same developer responsible for creating all renames within a chain, with most names maintaining the same grammatical structure. Understanding rename chains can help us provide stronger advice, and targeted research, on how to craft high-quality, long-lasting identifiers.

FIG. 5. — Phylogenetic hypotheses including Podocnemis tatacoensis n in A new fossil turtle ends the controversy on the occurrence of the extant genus Podocnemis Wagler, 1830 at the Miocene fauna of La Venta, Colombia

FIG. 5. — Phylogenetic hypotheses including Podocnemis tatacoensis n. sp.: A, strict consensus of 192 most parsimonious trees (MPTs), obtained from the first analysis (all taxa, all morphological characters), tree length (TL) = 1318, consistency index (CI) = 0.275, retention index (RI) = 0.741, see the full tree in Supplementary Data S3 (Appendix 3); B, close up of the Podocnemis clade shown in (A). C, close up of the Podocnemis clade obtained in the strict consensus from the second analysis excluding all fossil Podocnemis except P. tatacoensis n. sp., see the full tree in Supplementary Data S4 (Appendix 4), MPTs = 48, TL = 1310, CI = 0.277, and RI = 0.744. Bootstrap (upper) and Bremer support (lower) indices are shown for some clades in (B) and (C); D, close up of the Podocnemis clade obtained from the total evidence analysis that produced a single MPT, TL = 4225, CI = 0.699, and RI = 0.794, as in the morphology only analyses, P. tatacoensis n. sp. is found to be part of Podocnemis and closer to the extant P. unifilis and the fossil P. negrii. Symbol: *, fossil taxa.

FIG. 4 in A new fossil turtle ends the controversy on the occurrence of the extant genus Podocnemis Wagler, 1830 at the Miocene fauna of La Venta, Colombia

FIG. 4. — Left hyoplastron-peripherals region in extant and some fossil podocnemidids: A, B, Podocnemis tatacoensis n. sp., specimen VPPLT-1727; C, D, P. vogli UF- 39060; E, F, P. unifilis MTKD-45847; G, P. unifilis CRI-2778; H, P. unifilis ICN-6455; I, J, P. erythrocephala CRI-6023; K, P. erythrocephala CRI-8207; L, P. erythrocephala CRI-1194; M, N, P. expansa USNM-29476; O, P. expansa NMW-35550; P, P. expansa AMNH-62947; Q, R, P. sextuberculata CRI-6543; S, P. sextuberculata CRI-2830; T, P. sextuberculata CRI-5500; U, V, P. lewyana ICN-7653; W, P. lewyana MNHN-286; X, P. lewyana ICN-1699; Y, Z, P. pritchardi UCMP-63782; A', B', Erymnochelys madagascariensis NMW-1811; C', E. madagascariensis MNHM-1534; D', E. madagascariensis NMW-139; E', F', Peltocephalus dumerilianus CRI-1344; G', Pe. dumerilianus CRI-3295;H', Pe. dumerilianus CRI-7524.Red circle indicates the close-up region showed in the right images. Green arrows indicate the axillary musk foramen of the hyoplastron (character 222), and red arrows indicate the lateral musk foramen or foramina at the hyoplastron-peripherals contact (character 269). Specimens not to scale.

FIG. 3. — Podocnemis tatacoensis n in A new fossil turtle ends the controversy on the occurrence of the extant genus Podocnemis Wagler, 1830 at the Miocene fauna of La Venta, Colombia

FIG. 3. — Podocnemis tatacoensis n. sp. details of its anatomy: A, B, close-up of the keeled neurals 2-4; C, D, left costal 1 in ventral view, sowing the shape of the axillary scar; E, left posterior margin of the carapace showing the bone predation trauma occurred to the peripherals; F, left peripherals 10-11 where the bone healed from the injury increasing the thickness and smoothing the surface; G, H, view of the right pelvic girdle; I, J, close-up of the three lateral musk foramina of the left hyoplastron-peripherals region. Abbreviations: axs, axillary scar; co, costal; hyo, hyoplastron; ili, ilium; isc, ischium; ker, keel rigde; M, marginal scute; mfo, musk foramina; ne, neural; sp, suprapygal; P, pleural scute; pe, peripheral; pub, pubis; py, pygal; res, resin; V, vertebral scute; xip, xiphiplastron. Scale bars: A, B, E, G, H, 2 cm; C, D, 1 cm; F, I, J, 5 mm.

FIG. 2 in A new fossil turtle ends the controversy on the occurrence of the extant genus Podocnemis Wagler, 1830 at the Miocene fauna of La Venta, Colombia

FIG. 2. — Stratigraphic context and temporal frame for Podocnemididae: A, chronostratigraphic context for the Honda Group (La Victoria and Villavieja formations), including the magnetostratigraphy, cartographic units, horizons and radiometric ages, as well as where the fossil podocnemidids occur including Podocnemis tatacoensis n. sp. Redrawn and modified from Montes et al. (2021); B, time of origination for the genera and some species of Podocnemididae based on the molecular hypothesis of Vargas-Ramírez et al. (2008) and fossil record (this study) for the clades that they represent. Abbreviations: Fm, formation; Gr, group; H, Holocene; L, Langhian; M, magnetostratigraphic chrons; Ma, million of years; Pleistoc., Pleistocene; Qut, Quaternary. Dotted lines indicate ghost lineage duration.

FIG. 1. — Podocnemis tatacoensis n in A new fossil turtle ends the controversy on the occurrence of the extant genus Podocnemis Wagler, 1830 at the Miocene fauna of La Venta, Colombia

FIG. 1. — Podocnemis tatacoensis n. sp. from the Middle Miocene (Serravallian), La Tatacoa Desert, Colombia: A, B, carapace in dorsal view; C, D, shell in left lateral view; D, shell in anterior view; F, G, plastron in ventral view. Abbreviations: Abd, abdominal scute; Ana, anal scute; co, costal; ent, entoplastron; epi, epiplastron; Ext, extragular scute; Fem, femoral scute; Hum, humeral scute; hyo, hyoplastron; hyp, hypoplastron; Int, intergular scute; M, marginal scute; mes, mesoplastron; mfo, musk foramina; ne, neural; nu, nuchal; P, pleural scute; pe, peripheral; Pec, pectoral scute; sp, suprapygal; py, pygal; V, vertebral scute; xip, xiphiplastron. Reconstructed bones showed in yellow shading. Scale bar: 10 cm.

opencc-by-4.0Mar 2023View details →

Supplementary Material 7 including Salamandra salamandra occurrence data, topographic, geological and land cover data and node-based resistances

Supplementary material for the article "Habitat connectivity supports the local abundance of fire salamanders (Salamandra salamandra) but also the spread of Batrachochytrium salamandrivorans" by Bolte et al. (2023) published in Landscape Ecology (DOI: 10.1007/s10980-023-01636-8) This folder comprises a .shp file with fire salamander occurrences, topographic and land cover data (GeoTiff) from the northern Eifel region as well as the R Code used for the statistical analysis of salamander habitat suitability and connectivity.