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15,520 results for “r”
Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations
<p>Plants growing outside their native range may be confronted by new regimes of herbivory, but how this affects plant chemical defense profiles has rarely been studied. Using <em>Plantago lanceolata</em> as a model species, we investigated whether introduced populations show significant differences from native populations in several growth and chemical defense traits. <em>Plantago lanceolata </em>(ribwort plantain) is an herbaceous plant species native to Europe and Western Asia that has been introduced to numerous countries worldwide. We sampled seeds from nine native and ten introduced populations that covered a broad geographic and environmental range and performed a common garden experiment in a greenhouse, in which we infested half of the plants in each population with caterpillars of the generalist herbivore <em>Spodoptera littoralis</em>. We then measured size-related and resource-allocation traits as well as the levels of constitutive and induced chemical defense compounds in roots and shoots of <em>P. lanceolata</em>. When we considered the environmental characteristics of the site of origin, our results revealed that populations from introduced ranges were characterized by an increase of chemical defense compounds without compromising plant biomass. The concentrations of iridoid glycosides and verbascoside, the major anti-herbivore defense compounds of <em>P. lanceolata</em>,<em> </em>were higher in introduced populations than in native populations. In addition, introduced populations exhibited greater rates of herbivore-induced volatile organic compound emission and diversity, and similar chemical diversity based on untargeted analyses of leaf methanol extracts. In general, the geographic origin of the populations had a significant influence on morphological and chemical plant traits, suggesting that <em>P. lanceolata</em> populations are not only adapted to different environments in their native range but also in their introduced range.</p>
Overcoming confusion and stigma in habitat fragmentation research - supplementary data and R code
<p>Data and code necessary to produce results and figures for the manuscript:</p> <p>Riva, Koper and Fahrig (2024). "Overcoming confusion and stigma in habitat fragmentation research". Biol Rev. Accepted conditional on minor revisions. </p>
funspace: an R package to build, analyze and plot functional trait spaces
<p>Functional trait space analyses are pivotal to describe and compare organisms' functional diversity across the tree of life. Yet, there is no single application that streamlines the many sometimes-troublesome steps needed to build and analyze functional trait spaces.</p> <p>To fill this gap, we propose funspace, an R package to easily handle bivariate and multivariate (PCA-based) functional trait space analyses. The six functions that constitute the package can be grouped in three modules: 'Building and exploring', 'Mapping', and 'Plotting'. The building and exploring module defines the main features of a functional trait space (e.g., functional diversity metrics) by leveraging kernel density-based methods. The mapping module uses general additive models to map how a target variable distributes within a trait space. The plotting module provides many options for creating flexible and high-quality figures representing the outputs obtained from previous modules. We provide a worked example to demonstrate a complete funspace workflow.</p> <p>funspace will provide researchers working with functional traits across the tree of life with an indispensable asset to easily explore: (i) the main features of any functional trait space, (ii) the relationship between a functional trait space and any other biological or non-biological factor that might contribute to shaping species' functional diversity.</p>
Sexual dimorphism in subterranean amphipod crustaceans covaries with subterranean habitat type: data and R code
<p>The data and R code used for data analyses in the manuscript titled "Sexual dimorphism in <em>Niphargus </em>amphipods is predicted by surface-subterranean environmental gradient". The collection contains:</p> <ol> <li>A zipped folder "videos", where raw videos used in the study are stored.</li> <li>A zipped folder "tracking_results", where video-tracking results obtained from the raw videos are stored, along with supporting files and R code (Rscript_extract_behavior.Rmd) with custom functions (Behavior_custom_functions.Rmd) needed to analyze tracking results and retrieve final behavioral data.</li> <li>A README file with details on how the data and code is organized.</li> <li>Supplementary Material file including all raw data used in the main data analysis (SupplementaryMaterial.xlsx)</li> <li>A supporting file with data from another study used in the main data analysis (sex_ratio.xlsx, results from https://onlinelibrary.wiley.com/doi/full/10.1111/jeb.13917; https://zenodo.org/records/5175861)</li> <li>Two files containing phylogenetic trees: one complete phylogenetic tree of<em> Niphargus </em>(consensus_tree)<em> </em>and 100 randomly drawn phylogenetic trees from the stationary phase of the Bayesian analysis, pruned to focal species (100_pruned_trees), which were used in the main data analysis.</li> <li>The Rcode containing the code of the main data analysis to reproduce the reported results (RScript_data_analysis.Rmd), as well as some additional analyses not included in the manuscript.</li> </ol>
Alaimus elegans de Man. α, anterior r i end, 1/ 12, ok. 3, x 600. b, tail obj. 7, ok. 3, x 360. c, region of the female organs obj. 7, ok. 3, x 3 6 0. in Terrestrial nematodes from Jan Mayen
Alaimus elegans de Man. α, anterior r i end, 1/ 12, ok. 3, x 600. b, tail obj. 7, ok. 3, x 360. c, region of the female organs obj. 7, ok. 3, x 3 6 0.
Monhystera agilis de Man. a, a n t e r i o r e n d 1 /12, ok. 3,.x.450. b, tail 1/ 12, ok. 3, x 4 5 0. in Terrestrial nematodes from Jan Mayen
Monhystera agilis de Man. a, a n t e r i o r e n d 1 /12, ok. 3,.x.450. b, tail 1/ 12, ok. 3, x 4 5 0.
Dataset and R code used in "Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes"
<p>Dataset and R code used for the manuscript:</p> <p>Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C., & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. <em>Environmental Microbiology</em>, 26(3), e16607.</p> <p>This dataset and code are also available on GitHub (<a href="https://github.com/jvoneggers/WYLakeSedMicrobes">https://github.com/jvoneggers/WYLakeSedMicrobes</a>).</p>
Figure 4. – S i c y o p t e r u s e in A new species of Sicyopterus (Teleostei: Gobioidei: Sicydiinae) from Papua New Guinea
Figure 4. – S i c y o p t e r u s e lo m i onearum, Paratypes, MNHN 2019-0108. A: Female, SL 41.8 mm; B: Male, SL 43.7 mm. Bereme village, Huvenganga River, West New Britain Island, Papua New Guinea, 19 Oct. 2018, Keith et al. coll.
F I G U R E 3 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 3 Comparison of trait-based metrics expressed in relative number of individuals computed from eDNA () and traditional electro-fishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: ns, not significant (P> 0.05)
F I G U R E 4 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 4 Boxplots (, median value;, interquartile range;, full range;, outliers) showing the variability in the eDNAadapted fish index (six metrics) computed at three sites (Brangues, Rhins and Usses) where 10 eDNA water samples were collected once. At each site, the eDNA-based six-metric fish index was computed for each of the 45 possible pairs of samples
F I G U R E 2 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 2 Comparison of trait-based metrics expressed in number of species computed from eDNA () and traditional electrofishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: P <0.05; P <0.01; ns, not significant (P> 0.05)
F I G U R E 7 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 7 Gouania hofrichteri sp. nov., PMR VP4595, holotype, male, 30.35+3.67 mm, Souda Beach, Plakias, Crete, Greece. Lateral view of specimen preserved in 4% formaldehyde (top). Lateral, dorsal and ventral view, alive (below). Photographs by M. Wagner and M. Kovacˇic
F I G U R E 1 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 1 Sampling locations along river stretches (RS) A to E () of the main channel of the Rhône River, France, using both traditional electro-fishing (TEF) and eDNA., Sites sampled every 2 months (September 2015– August 2016);, sites where ten eDNA water samples (filtration capsules) were collected once;, sites located on the tributaries or the Rhône River itself sampled once for eDNA. The 10 metric fish index and the adapted six-metric fish index were computed at all sites with a black filled symbol within natural water bodies
F I G U R E 9 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 9 Gouania willdenowi (Risso 1810), PMR VP4574, neotype, male, 46.11+6.56 mm, Cagnes-sur-mer, Nice, France. Lateral view of specimen preserved in 4% formaldehyde (top). Lateral, dorsal and ventral view, alive (below). Photographs by M. Wagner and M. Kovacˇic
F I G U R E 1 0 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 1 0 Results of DNA-barcoding analyses. (a) Net between-group mean distances (mean and S.E.). The phylogeny shown in this figure is based on Wagner et al. (2019). (b) DNA-barcoding gap represented by boxplots showing maximum intraspecific and minimum interspecific divergences in %
F I G U R E 6 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 6 Gouania orientalis sp. nov., PMR VP4585, holotype, male, 32.8+4.93 mm, Plakias, Crete, Greece. Lateral view of specimen preserved in 4% formaldehyde (top). Lateral, dorsal and ventral view, alive (below). Photographs by M. Wagner and M. Kovacˇic
F I G U R E 8 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 8 Gouania pigra (Nardo, 1827), PMR VP3529, neotype, female, 43.12+5.03 mm, Glavotok, Krk, Croatia. Lateral view of specimen preserved in 4% formaldehyde (top). Lateral, dorsal and ventral view, alive (below). Photographs by M. Wagner and M. Kovacˇic
F I G U R E 5 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 5 Head osteology of Gouania species. (a) G. adriatica sp. nov. (PMR VP4618 – Holotype), (b) G. orientalis sp. nov. (PMR VP4585 – Holotype), (c) G. hofrichteri sp. nov. (ZSM-PIS- 047656 – Paratype), (d) G. pigra (Nardo 1827) (PMR VP3531 – Other material) and (e) G. willdenowi (Risso 1810) (ZSM-PIS-0476654 – Other material). Red, ceratobranchial 5; orange, premaxillary bone; blue, maxillary bone; green, nasal bone
F I G U R E 3 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 3 Gouania adriatica sp. nov., PMR VP4618, holotype, male, 41.41+6.77 mm, Stoja, Pula. Lateral view of specimen preserved in 4% formaldehyde (top). Lateral, dorsal and ventral view, alive (below). Photographs by M. Wagner and M. Kovacˇic
F I G U R E 4 in Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra
F I G U R E 4 Sucking discs and disc-papillae of Gouania species. (a) G. adriatica sp. nov. (PMR VP4618 – Holotype), (b) G. orientalis sp. nov. (PMR VP4585 – Holotype), (c) G. hofrichteri sp. nov. (PMR VP4595 – Holotype), (d) G. pigra (Nardo 1827) (ZSM-PIS-047649 – Other material) and (e) G. willdenowi (Risso 1810) (PMR VP4574 – Neotype). (f) Males of Gouania can have seemingly perfused prominent finger-like extensions on sucking disc edge in region A.A, B and C correspond to disc regions. Photographs by M. Wagner
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.