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Annual plant competition experiment results and associated mycobiome ASV tables
<p>Major theories regarding microbe-mediated plant community dynamics assume that plant species cultivate distinct microbial communities. However, few studies empirically assess the role of species-associated microbial community dissimilarity in plant competitive dynamics. In this study, we paired a competition experiment between eight annual forbs with a characterization of species-associated fungal communities to assess whether mycobiome dissimilarity is associated with pairwise competitive dynamics. Using a quantitative approach informed by modern coexistence theory, we found that fungal dissimilarity was correlated with both increased stabilizing niche differences and fitness inequalities. Additionally, we found that the probability of coexistence increased with mycobiome dissimilarity. When subsetting the community into different fungal functional groups (pathotrophs, saprotrophs, symbiotrophs), overall relationships between dissimilarity and competitive dynamics were independent of these functional groups. </p> <p>Synthesis: These results suggest that fungal community divergence may play an important role in mediating plant competitive dynamics. Although fungal community dissimilarity is associated with both niche and fitness differences, complex biotic and/or abiotic interactions belowground may result in an observed correlation between fungal community dissimilarity and plant coexistence. Ultimately, this study suggests a novel approach to better understanding how microbiome dissimilarity may impact host community dynamics.</p>
Figure 2. Dendrogram resulting from a in Host specificity and the structure of helminth parasite communities of fishes in a Neotropical river in Mexico
Figure 2. Dendrogram resulting from a similarity matrix based on the Sørensen measure for component communities of adult autogenic helminth parasites of 10 fish species from Apazapan, Río La Antigua, Veracruz, Mexico. Host species are: Amex, A. mexicanus; Rgua, R. guatemalensis; Smar, S. marmoratus; Hbim, P. bimaculata; Pmex, Poecilia mexicana; Pgra, Poeciliosis gracilis; Psph, Poecilia sphenops; Xell, X. helleri; Tell, T. ellioti; Vfen, V. fenestrata.
Fig. 1 in Response of Sphagnum Testate Amoebae to Drainage, Subsequent Re-wetting and Associated Changes in the Moss Carpet - Results from a Three Year Mesocosm Experiment
Fig. 1. Left: schematic cross-section through a mesocosm showing the peat and Sphagnum layer. Right: expected evolution of community structure or traits over the stress and recovery phases. At the onset of the experiment (T0) the community included the whole range of species living in pool, lawn and hummock, taken in a natural Sphagnum peatland. D1 is the point of maximum disturbance effect and R1 and R2 are sampling points during the recovery phase. Dotted lines represented the possible evolution of both species community structure and community weighted mean of functional traits in response to disturbance. Full recovery depended on the survival potential of species. The new equilibrium represents the situation when the local conditions or present species pool do not allow a fully recovery of original state. In our case this is due to the fact that some species are likely to be lost during the disturbance phase.
Fig. 3 in Response of Sphagnum Testate Amoebae to Drainage, Subsequent Re-wetting and Associated Changes in the Moss Carpet - Results from a Three Year Mesocosm Experiment
Fig. 3. Evolution of standardized effect size of mean pairwise distance between sampling plots relatively to a null model (random species matrix with respect to observed species richness, see text for details) of testate amoeba community weighted mean (CWM) of functional trait data from a Sphagnum fallax mesocosm experiment simulating water table changes. The mean pairwise distance represents the distance separating communities based on the pool of functional traits. Horizontal grey dotted line represents p-value of 0.05, points below the line are significantly different from the null model. Each replicate was represented separately, with a grey scale.
Fig. 2 in Response of Sphagnum Testate Amoebae to Drainage, Subsequent Re-wetting and Associated Changes in the Moss Carpet - Results from a Three Year Mesocosm Experiment
Fig. 2. Principal component analyses (PCA) of a) testate amoeba species and b) community weighted mean (CWM) of functional traits in Sphagnum fallax from a mesocosm experiment simulating water table changes. The species dataset was Hellinger transformed and the CWM data were scaled. Projection of descriptors (left) and samples (right), scaling 2. On the right plots, arrows represent the time line for each treatment (mean coordinates of the five sampling plots of each treatment and time). In both PCAs, axes 1 and 2 were the only significant axes and accounted respectively for 60.4% (species based) and 80.2% (CWM based) of the variance. Characteristic plots for wet and intermediate treatments were labelled. Taxa abbreviations: Amp_wri: Amphitrema wrightianum, Pse_gra: Pseudodifflugia gracilis, Arc_fla: Archerella flavum, Cyc_arc: Cyclopyxis arcelloides, Phy_gri: Physochila griseola, Hya_pap: Hyalosphenia papilio, Cen_acu: Centropyxis aculeata, Hel_syl: Heleopera sylvatica, Cry_ovi: Cryptodifflugia oviformis, Eug_cil: Euglypha ciliata, Phr_acr: Phryganella acropodia, Hel_ros: Heleopera rosea, Cor_dub: Corythion dubium, Neb_tin: Nebela tincta s.l., Arc_cat: Arcella catinus, Ass_mus: Assulina muscorum.
Fig. 1 in Occurrence Of Phytophthora Spp. In Deciduous Trees In Lithuania: First Results
Fig. 1. The number of Phytophthora spp. disturbed trees in different districts and climate regions of Lithuania, 2010–2014. I – Western, II – Northern, III – Southern, and IV – Eastern. The white colour indicates the districts, which were not surveyed.
Fig. 1 in Callicultureinducingfromredclover(Trifolium Pratense L.) Wild Accessions And Results Of Dna Extraction
Fig. 1. Results of flow cytometry: a) 2n ploidy control, b) the typical result for leaves, c) the typical result for stems, d) the typical result for roots.
Fig. 5. Emys orbicularis habitat 3 in P R O J E C T S O N E M Y S O R B I C U L A R I S (R E P T I L I A: Testudines: Emydidae) In Latvia For Thirty Years (1984 - 2014): Biological Aspects, Results And Effect On Population And Ecosystems
Fig. 5. Emys orbicularis habitat 3 in Silene Nature Park before restoration (Google Earth service, SAS services).
Fig. 4. Emys orbicularis habitats 1 and 2 in P R O J E C T S O N E M Y S O R B I C U L A R I S (R E P T I L I A: Testudines: Emydidae) In Latvia For Thirty Years (1984 - 2014): Biological Aspects, Results And Effect On Population And Ecosystems
Fig. 4. Emys orbicularis habitats 1 and 2 in Silene Nature Park before (a) and after (b) restoration (Google Earth service, SAS services).
Fig. 2 in P R O J E C T S O N E M Y S O R B I C U L A R I S (R E P T I L I A: Testudines: Emydidae) In Latvia For Thirty Years (1984 - 2014): Biological Aspects, Results And Effect On Population And Ecosystems
Fig. 2. Old Emys orbicularis female, found in 1984 in Daugavpils living for 20 years in a zooculture (Photo: 2005).
Fig. 6. Emys orbicularis habitat 3 in P R O J E C T S O N E M Y S O R B I C U L A R I S (R E P T I L I A: Testudines: Emydidae) In Latvia For Thirty Years (1984 - 2014): Biological Aspects, Results And Effect On Population And Ecosystems
Fig. 6. Emys orbicularis habitat 3 in Silene Nature Park after restoration (Google Earth service, SAS services).
Fig.1. Funnel trap for gathering living RESULTS AND DISCUSSION D.latissimus a in Conceptual Application Of Dytiscus Latissimus Linnaeus, 1758 (Dytiscidae, Coleoptera) Gathering Methods In Natural Habitat
Fig.1. Funnel trap for gathering living RESULTS AND DISCUSSION D.latissimus a result of the individual (from Jan G.M. Cuppen and other): As many years application of the material gathering methods was 1 – float; 2- rubber; 3 – aeration net; a possibility to catch on regular and predictable 4 – entrance Ø 30 mm. basis a required number of animals for our laboratory research. itself. This can be identified from locating specific cuts on it. (Vahrusevs 2009) The key to a successful egg collection is a search of the plants used by beetles during their Below is an example from field notes of catching reproduction period, as well as the correct beetles during the autumn season: locating of clutches. Such plants in our reservoir "The research on the reservoir was done during under study are Carex acuta, Carex rostrata, 11.10.2009 - 28.10.2009. Caltha palustris. One has to identify suitable plants in the locations of beetles' clutches The weather conditions were favourable. It was (usually located on the sunny side along the quite warm and windless all this time in order to coast of a water reservoir). The person gathering work comfortably. Water temperature was +7-8 ŗ the material has to grasp with fingers the C. We worked as usual on the proven location. underwater part of the identified plant stem Coordinates in Google Earth (latitude 55 ° 52'33 reaching almost to its base, and slowly palpate it.95 "C; longitude 26 ° 35'18.78" H). by letting it through the fingers in the upwards direction. The upwards direction is imperative, We prepared the traps in advance (they had to as stems of many sedge plants have microscopic be repaired and mended, and modernized a little. thorns which are rooting upwards. If this method (Fig.2.). is not followed, an injury of a palm can occur. A stem of the plant which has protruding bumps We took along 21 trap to the water reservoir. The on it guarantees the presence of a clutch. A stem bait was pieces of beef heart. The traps were in its normal condition is usually smooth and placed along the coastline. The first "throw" was often flat. Such plants as Caltha palustris which kept in the water for almost a week with regular have fleshy stem are to be studied in addition check ups made every day or every second day. visually as eggs can be located inside the stem Traps were installed partly dipped under water.
Рис. 1. Вероятность обнаружения меченых животных (среΑнее ± ошибка) при пяти- и Αесятиметровых интерваΛах межΑу прикормочными станциями в Αвух экспериментах. По второму эксперименту расчеты сΑеΛаны ΑΛя резуΛьтатов отΛова в течение первых трех и поΛных Αесяти Αней. Значение «p» отражает уровень статистической значимости разΛичий межΑу ΑоΛями животных с меткой при Αвух интерваΛах Fig. 1. Probability of finding marked animals (average±standard error) between feeding stations placed at intervals of five and ten meters in the two experiments. In the second experiment, calculations were made for the results of trapping during the first three days and during the whole period of ten days. The p value reflects the statistical significance of differences between the fractions of animals with a mark for two types of intervals in Verification of the bottle-based method for estimating abundance of small mammals using biomarkers
Рис. 1. Вероятность обнаружения меченых животных (среΑнее ± ошибка) при пяти- и Αесятиметровых интерваΛах межΑу прикормочными станциями в Αвух экспериментах. По второму эксперименту расчеты сΑеΛаны ΑΛя резуΛьтатов отΛова в течение первых трех и поΛных Αесяти Αней. Значение «p» отражает уровень статистической значимости разΛичий межΑу ΑоΛями животных с меткой при Αвух интерваΛах Fig. 1. Probability of finding marked animals (average±standard error) between feeding stations placed at intervals of five and ten meters in the two experiments. In the second experiment, calculations were made for the results of trapping during the first three days and during the whole period of ten days. The p value reflects the statistical significance of differences between the fractions of animals with a mark for two types of intervals
FIGURE 37. Phylogenetic results from parsimony analysis using the cranial dataset. A in A reappraisal of the cranial and mandibular osteology of the spinosaurid Irritator challengeri (Dinosauria: Theropoda)
FIGURE 37. Phylogenetic results from parsimony analysis using the cranial dataset. A, strict consensus tree of 153 MPTs retained from an equal weighting analysis (see Methods for details); B, reduced consensus tree, pruning wild card taxa from the strict consensus. Wild card taxa are highlighted with coloured boxes in A, and their possible topological positions are shown with same coloured squares in B. Important clades are labelled.
FIGURE 36. Phylogenetic results from parsimony analysis using the full dataset. A in A reappraisal of the cranial and mandibular osteology of the spinosaurid Irritator challengeri (Dinosauria: Theropoda)
FIGURE 36. Phylogenetic results from parsimony analysis using the full dataset. A, strict consensus tree of 8184 MPTs retained from an equal weighting analysis (see methods for details); B, partial reduced consensus tree, showing the clade Spinosauridae after removal of the taxon Vallibonavenatrix; C, strict consensus tree of 406 MPTs retained from an implied weighting analysis using a concavity constant of k=10 (see Methods for details). Important clades are labelled. Irritator as the main focus of our study is highlighted in bold face within the clade Spinosauridae.
Sharpness metric results and Instron method script for 'Raw Material Sharpness and Lithic Patterns: An Analysis of Holocene Susitna River Basin, Central Alaska' MPhil dissertation
<p>Data for appendix B in 'Raw Material Sharpness and Lithic Patterns: An Analysis of Holocene Susitna River Basin, Central Alaska' MPhil dissertation. This data set Includes initial and dulled sharpness metric data from the Instron® experiment for each flake. It also includes the Instron® bluehill method program script.</p>
Advanced PySPAM: An Infrastructure to Constrain Underlying Interacting Galaxy Parameters Synthetic Results
<p>This database contains the results for the Chapter 3 of DOR's thesis. For a full description of these results and the way they were built, please see <em>Link to be added on publication</em>.</p> <p>The aim of this Chapter was to use MCMC methods with a fast, efficient simulation algorithm (APySPAM) to constrain the underyling parameters of observed interacting galaxy systems. This algorithm used a Chi-Squared distance minimisation between morphology distributions of observed and simulated images to constrain 13 underlying parameters of galaxy interaction. We applied our algorithm to to 50 of the 62 systems described in <a href="https://ui.adsabs.harvard.edu/abs/2016MNRAS.459..720H/abstract">Holincheck et al. (2016).</a></p> <p>We opted to use the Holincheck et al. sample as the underlying parameters of these systems had already been constrained using a Citizen Science project named <a href="https://mergers.galaxyzoo.org/">Galaxy Zoo: Mergers</a>. This gave us a ground truth to which compare our constraints to. We created synthetic observations of each image, and then ran our MCMC over them, achieving constraint across the sample and parameter space. However, when applied to observational data (we opted to use SDSS images of these systems) we are unable to constrain the full parameter space. This is particularily true of the orientations of the interacting system and their relative sizes.</p> <p>Exploring using velocity information in our constraints find that we improve almost all our constrains considerably. Therefore, adding in spectroscopic information to this method could drastically improve it. The main limitation of this approach, however, is computation time with each system taking approximately 20 hours on a well parallelised HPC to converge. Alternatives to improve performance lie in simulation based inference (SBI, an introduction can be found <a href="https://arxiv.org/pdf/2009.08459">here</a>) or including the use of GPUs (such as done by NVIDEA in fluid dynamics <a href="https://developer.nvidia.com/blog/ai-powered-simulation-tools-for-surrogate-modeling-engineering-workflows-with-siml-ai-and-nvidia-modulus/">here</a>)</p> <p>The results are portrayed as corner plots, with contour plots showing the distribution of likelihoods found in each MCMC run and the histograms on the side showing the marginalised posterior distributions.</p>
Figure 3. – Average STRUCTURE results aggregated using CLUMPAK for populations 2–6 and 9. K in Landscape biogeography and population structuring of a facultatively amphidromous galaxiid fish, Galaxias brevipinnis
Figure 3. – Average STRUCTURE results aggregated using CLUMPAK for populations 2–6 and 9. K = 6 was selected as the most likely population estimate using Evanno's method. STRUCTURE initially separated the lakes draining to the east coast (L. Wānaka and L. Wakatipu) from all other sites at K = 2. The West Coast lakes were split away next (K = 3), with L. Moeraki and L. Paringa splitting at K = 4 and L. Cristabel at K = 5. East coast L. Wānaka and L. Wakatipu were split at K = 6. L. Paringa and L. Moeraki are split form each other at K = 9.
Figure 1 in Results of the research expedition Biaçores 1971. Fishes and list of stations
Figure 1. – Location of the stations of the Biaçores 1971 cruise (stars). Some stars signal several stations (see Appendix I for details).
Figure 1 in Fishes of São Tomé - Results of the expeditions of Fernando Frade (1954) and Fernando Correia da Costa (1955)
Figure 1. – Location of the stations (A to M) at São Tomé Island (between: 0°25'8.91"N-0°01'19.69"N and 6°27'45.54" E- 6°45'30.64"E) (see Appendix I for details).
ScienceDex guides
Understand access before you commit
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.