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Supplementary material 2 from: Grunewald K, Schweppe-Kraft B, Syrbe R-U, Meier S, Krüger T, Schorcht M, Walz U (2020) Hierarchical classification system of Germany's ecosystems as basis for an ecosystem accounting – methods and first results. One Ecosystem 5: e50648. https://doi.org/10.3897/oneeco.5.e50648
Supplementation of ecosystem types (ETs) by more differentiated spatially and non-spatially explicit data (system of assignment of biotope and habitat types relevant for nature conservation to ETs
Supplementary material 1 from: Short G, Claassens L, Smith R, De Brauwer M, Hamilton H, Stat M, Harasti D (2020) Hippocampus nalu, a new species of pygmy seahorse from South Africa, and the first record of a pygmy seahorse from the Indian Ocean (Teleostei, Syngnathidae). ZooKeys 934: 141-156. https://doi.org/10.3897/zookeys.934.50924
Genetic distance analysis (uncorrected p distances) of COI sequence data from H. nalu, H. bargibanti, H. denise, H. japapigu, and H. pontohi
Supplementary material 3 from: Petersen M, Pramann B, Toepfer R, Neumann J, Enke H, Hoffmann J, Mauer R (2020) Research Data Management - Current status and future challenges for German non-university research institutions. Research Ideas and Outcomes 6: e55141. https://doi.org/10.3897/rio.6.e55141
Praxisbericht: Entwicklung eines Maßnahmenkatalogs zur Verbesserung des Forschungsdatenmanagements am Herder-Institut für historische Ostmitteleuropaforschung
FIG. 7 in Comparative chromosomal studies in Rhinolophus formosae and R. luctus from China and Vietnam: elevation of R. l. lanosus to species rank
FIG. 7. Metaphase spreads of R. formosae after CBG-banding (A, B) and silver-staining (C). A — Centromeric heterochromatin is clearly visible at acrocentric chromosomes but only faintly stained at the metacentric ones. The arrows point to the smallest autosomal pair no. 25 which is presumably bi-armed. B — The C-banded X chromosomes of the female R. formosae showed the usual appearance for the family without a large hetero-chromatic block. The arrows indicate pair 25. C — Silver-stained metaphase plate with arrows indicating the NORs
FIG. 3 in Comparative chromosomal studies in Rhinolophus formosae and R. luctus from China and Vietnam: elevation of R. l. lanosus to species rank
FIG. 3. FISH examples showing the hybridization patterns of A. stoliczkanus (AST) chromosome-specific painting probes onto metaphase spreads of R. cf. luctoides (A, D), R. lanosus (B, E) and R. formosae (C, F). A–C — hybridization signals of AST1 (red) and AST8 (green) meet in chromosome 5 in R. cf. luctoides (A) and R. lanosus (B) but not in R. formosae (C). In B and C AST X (yellow) was applied in addition. D, E — hybridization signals of AST2 (green) and AST5 (red) meet in chromosome 3 of R. cf. luctoides (D), but not in R. lanosus (E), where AST2 (green) is found in combination with AST1 (red) on chromosome 4 instead.
Supplementary material 1 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Summary of GenBank accession numbers, Taxon names, Project numbers, Herbarium Accession numbers, voucher collectors and collection numbers, phylogenetic position and taxonomy and classification according to Shepherd et al.
R script: Species coexist more easily if reinforcement is based on habitat preferences than on species recognition
<p><b>1.</b> Maladaptive hybridization selects for prezygotic isolation, a process known as reinforcement. Reinforcement reduces gene flow and contributes to the final stage of speciation. Ecologically, however, coexistence of the incipient species is difficult if they initially use identical resources.</p> <p><b>2. </b>Habitat segregation offers an alternative to species discrimination as a way to reduce gene flow: production of unfit hybrids is reduced if mate encounters become rare due to differing habitat choice. Using a modelling approach, we show that hybridization avoidance alone can select for habitat specialization, even if neither of the species is intrinsically better at using a specific niche.</p> <p><b>3. </b>While habitat segregation and species discrimination both reduce the risk of producing unfit hybrids, these two isolation mechanisms differ from each other with respect to their effects on resource competition. Our model shows that, as a consequence of such differences, reinforcement evolves much more easily if hybridization is avoided based on habitat segregation than if the mechanism involves species recognition (mate choice traits).</p> <p><b>4.</b> We also examine the outcomes when both isolation mechanisms evolve jointly. The establishment of one isolation mechanism <i>a priori</i> weakens selection for the other. However, an asymmetry persists here too. The net effect of habitat segregation on species discrimination was typically facilitative, but not vice versa. This asymmetry arises because habitat segregation, by enhancing coexistence, secures time for the subsequent evolution of species discrimination in a mate choice context (still relevant if habitat use is not perfectly segregated). Species discrimination does not have such a stabilizing effect on coexistence.</p> <p><b>5.</b> Our results emphasize the importance of habitat segregation in reinforcement, and offer a way to interpret findings where closely related taxa show similar performance on different resources or in different habitats. Studies of ecological generalization and specialization should therefore take into account that niche differences can be initiated and/or maintained by hybridization avoidance.</p>
FIGURES 38−40 in New species of Rivudiva Lugo-Ortiz & McCafferty (Ephemeroptera: Baetidae) with comments on R. minantenna Lugo-Ortiz & McCafferty and R. trichobasis Lugo-Ortiz & McCafferty
FIGURES 38−40. Habitus of living nymphs of Rivudiva spp. (38) Male of Rivudiva inma, sp. nov.; (39) Female of Rivudiva inma, sp. nov.; (40) Female of R. trichobasis.
FIGURES 11−16 in New species of Rivudiva Lugo-Ortiz & McCafferty (Ephemeroptera: Baetidae) with comments on R. minantenna Lugo-Ortiz & McCafferty and R. trichobasis Lugo-Ortiz & McCafferty
FIGURES 11−16. Rivudiva oonirikoperi, sp. nov., nymph. (11) Labrum; (12) Left mandible; (13) Right mandible; (14) Hypopharynx; (15) Maxilla; (16) Labium (left = dorsal surface, right = ventral surface).
FIGURES 17−21 in New species of Rivudiva Lugo-Ortiz & McCafferty (Ephemeroptera: Baetidae) with comments on R. minantenna Lugo-Ortiz & McCafferty and R. trichobasis Lugo-Ortiz & McCafferty
FIGURES 17−21. Rivudiva oonirikoperi, sp. nov., nymph. (17) Fore leg (anterior surface); (18) detail of foreclaw; (19) mid leg (anterior surface); (20) Paraproct; (21) Dorsal view of body.
FIGURES 7−10 in New species of Rivudiva Lugo-Ortiz & McCafferty (Ephemeroptera: Baetidae) with comments on R. minantenna Lugo-Ortiz & McCafferty and R. trichobasis Lugo-Ortiz & McCafferty
FIGURES 7−10. Rivudiva inma, sp. nov., nymph. (7) Fore leg; (8) Tarsal claw; (9) Posterior margin of tergum IV; (10) Paraproct.
ClinePlotR: Visualizing genomic clines and detecting outliers in R
<p class="Normal1">Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize 'genomic clines' are limited.</p> <p>Here, we introduce the <span class="MsoSubtleReference">ClinePlotR R</span>-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, <span class="MsoSubtleReference">bgc </span>and <span class="MsoSubtleReference">Introgress.</span></p> <p><span class="MsoSubtleReference">ClinePlotR </span>bundles both input generation (i.e, filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as <span class="MsoSubtleReference">ENMeval </span>and <span class="MsoSubtleReference">RIdeogram</span></p> <p>Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms.</p>
Data and R code used in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants
<p>This repository contains the data and R markdown files supporting the findings presented in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants.</p>
Finland COVID-19 R-value estimate March - August
<p>This dataset contains the time-dependent effective reproduction number R<sub>t</sub> of the COVID-19 epidemic in Finland for the period Feb 27th 2020 - August 14th 2020. The reproduction number was estimated using the daily new coronavirus cases in <a href="https://thl.fi/en/web/thlfi-en/statistics/statistical-databases/open-data/confirmed-corona-cases-in-finland-covid-19-">the infectious diseases registry of Finland</a> with an unscented RTS smoother and the SEIR epidemic model.</p> <p>The SEIR model was defined as<br> <span class="math-tex">\(S(t+1) = S(t) - \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} + \omega_{S}\\ E(t+1) = E(t) + \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} - \frac{E(t)}{T_e} + \omega_{E}\\ I(t+1) = I(t) + \frac{E(t)}{T_e}-\frac{I(t)}{T_i} + \omega_{I} \\ R_t(t+1) = R_t(t) + \omega_{R_t}\)</span></p> <p>with S, E, and I being the susceptible, exposed, and infective populations, R<sub>t</sub> the time-dependent effective reproduction number, and ωs are normally distributed random numbers with zero mean and small (1e-8) variance except for ω<sub>Rt</sub> whose variance was set to 0.00025. The exposed state duration was set to T<sub>e</sub>=3 days and infective state duration T<sub>i</sub>=5 days.</p> <p>The measurement model (from the SEIR state to observed daily new cases) was defined as<br> <span class="math-tex">\(P_\text{new cases}(k) \propto \mathcal{N}\left[ \alpha \frac{R_t(t-5 days)}{T_i}I(t-5\text{days}) \frac{S(t-5\text{days})}{N}, \sigma_\text{new cases}^2(t) \right]\)</span>, i.e., via a time-delayed gaussian process whose variance was computed by the observed daily new cases with a 7-day rolling mean. Here the detection rate α is set to 10%, but has no significant affect on the computed R-values.</p> <p> </p> <p>The data is a CSV-format file with the columns</p> <ul> <li>date = ISO 8601 date string</li> <li>Rt = maximum a posteriori estimate of R<sub>t</sub></li> <li>Rt_lower50 = lower limit of the 50% credible interval for R<sub>t</sub></li> <li>Rt_upper50 = upper limit of the 50% credible interval for R<sub>t</sub></li> <li>Rt_lower90 = lower limit of the 90% credible interval for R<sub>t</sub></li> <li>Rt_upper90 = upper limit of the 90% credible interval for R<sub>t</sub></li> </ul>
Supplementary material 1 from: Abram PK, McPherson AE, Kula R, Hueppelsheuser T, Thiessen J, Perlman SJ, Curtis CI, Fraser JL, Tam J, Carrillo J, Gates M, Scheffer S, Lewis M, Buffington M (2020) New records of Leptopilina, Ganaspis, and Asobara species associated with Drosophila suzukii in North America, including detections of L. japonica and G. brasiliensis. Journal of Hymenoptera Research 78: 1-17. https://doi.org/10.3897/jhr.78.55026
Collection information for specimens reported in: New records of Leptopilina, Ganaspis, and Asobara species associated with Drosophila suzukii in North America, including detections of L. japonica and G. brasiliensis
Fig. 17-18 in Notes on taxonomy and distribution of Cryptophagus jakowlewi R , 1888 (Coleoptera: Cryptophagidae) with remarks on further species
Fig. 17-18: (17) Cryptophagus freyi BRUCE, 1941, holotype, (18) Cryptophagus archangelicus J.R. SAHLBERG. 1929, Siberia. Fig. 19-20: Habitus of (19) Cryptophagus quadridentatus MANNER- HEİM, 1843, (20) Cryptophagus dentaus (HERBST, 1793).
The role of boundary length and adjacent patch contrast in guppy mate choice: Dataset, Matlab and R codes
<p>The presence of various combinations of adjacent colours within polymorphic species' colour pattern could have a major impact on mate choice. We studied the role of pattern geometry in predicting mate choice in guppies using boundary strength analysis (BSA). BSA estimates the visual contrast intensity between two adjacent colour patches (<i>ΔS</i>) weighted by the lengths of the boundaries between these adjacent colour patches. We measured both the chromatic (hue and saturation) and achromatic (luminance) <i>ΔS</i> for each pair of adjacent patches. For each male's colour pattern, we measured BSA as both mean (<i>mΔS</i>)<i> </i>and coefficient of variation (<i>cvΔS</i>) of all <i>ΔS</i> weighted by their corresponding boundary lengths. We also determined if specific colour patch boundaries had an impact on female preferences and whether these predicted overall male contrast (<i>mΔS</i>). We found that males with a higher <i>mΔS</i> were more attractive to females and that six boundaries containing either fuzzy black or black as one of the pair colours significantly affected female preferences, indicating that (1) females favoured highly conspicuous males and (2) melanin-based patches could be used as a signal amplifier, not only for orange but for other colours.</p>
Dataset (.esg files) of a multiphase aggregate representative of a lower mantle composition compressed at High P/T in an R rDAC
<p>A collection of .esg files for use in the software package Materials Analysis Using Diffraction (MAUD; Lutterotti et al., 1997). Seven files are included, spanning the range used in data analysis. All are post-conversion from San Carlos olivine. Files are named in the following format:</p> <p>MPBrgFp: Stands for Multiphase, primary phases bridgmanite and ferropericlase<br> ###: Number of the diffraction pattern taken during the experiment<br> ##GPa: Approximate temperature, rounded to the nearest whole number. This is to cross-correlate .esg files with experimental Pt pressures cited within the paper.</p>
Supplementary material 1 from: Huang J, Guo Z, Tang S, Ren W, Chu G, Wang L, Zhao L, Yu R, Xu Y, Ding Y, Zang R (2020) Floristic composition and plant diversity in distribution areas of native species congeneric with Betula halophila in Xinjiang, northwest China. Nature Conservation 42: 1-17. https://doi.org/10.3897/natureconservation.42.54735
Figure S1. The correlation between environmental variables in distribution areas of five congeneric species with Betula halophila
Supplementary material 4 from: Smart AS, Tingley R, Phillips BL (2020) Estimating the benefit of quarantine: eradicating invasive cane toads from islands. NeoBiota 60: 117-136. https://doi.org/10.3897/neobiota.60.34941
Figure S3. Posterior distributions of the detection probabilities of cane toads on Horan and Indian Islands
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.