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Supplementary files for Silva et al. 2020 "Reptiles on the wrong track?": R Code, data and figures
<p>Datasets, R code and figures pertaining to the manuscript: Silva, I., Crane, M., Marshall, B.M., & Strine, C.T. (2020).<em> </em> <em>Reptiles on the wrong track? Moving beyond traditional estimators with dynamic Brownian Bridge Movement Models.</em> Movement Ecology 8, 43 DOI: 10.1186/s40462-020-00229-3</p> <p>Article available at: <a href="https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3">https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3</a></p>
Supplementary files for Crane et al., "On a wing and a prayer": R Code, data and figures
<p>Datasets, R code and figures pertaining to the manuscript: Crane M, Silva I, Grainger MJ, & Gale GA.<em> On a wing and a prayer: limitations and gaps in global bat wing morphology trait data</em></p>
R script for identification and localisation of prophage within bacterial genomes using outward-oriented paired-end reads.
<p>This R script shows an analysis example of using outwards-oriented paired-end reads (OPRs), identified using the OPR finder function in the mVIRs package, to identify p22 in <em>S</em>. Tm LT2 as described in the publication "<strong>High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains" </strong>by Zünd et al. Microbiome (2021)</p>
Collapse and Continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Lawrence, D., Palmisano, A., and de Gruchy, M.W., 2021. <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244871">Collapse and Continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event</a></strong><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244871">.</a> <em><strong>PLoS ONE</strong></em><strong>,</strong> <strong><em>16</em></strong>(1).</p> <p>The dataset included here provides a collection of <strong>920 </strong>radiocarbon dates and <strong>1070</strong> sites from archaeological surveys. In addition, the digital archive related to this paper provides reproducible analyses in the form of three scripts written in R statistical computing language.</p>
Holocene regional population dynamics and climatic trends in the Near East: a first comparison using archaeo-demographic proxies (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Palmisano, A., Lawrence, D., de Gruchy, M.W., Bevan, A., and Shennan, S., 2021. <a href="https://doi.org/10.1016/j.quascirev.2020.106739">Holocene regional population dynamics and climatic trends in the Near East: a first comparison using archaeo-demographic proxies</a>. <em>Quaternary Science Reviews</em>, <em>252</em></strong>.</p> <p>The dataset included here provides a collection of <strong>10,606</strong> radiocarbon dates, <strong>1884</strong> sites from archaeological surveys (1336 from Central Anatolia and 478 from Upper Mesopotamia) and <strong>16</strong> palaeoclimatic records for a period spanning between 14,000 and 2500 BP. In addition, the digital archive related to this paper provides reproducible analyses in the form of four scripts written in R statistical computing language.</p> <p>List of versions:</p> <ul> <li><strong>2.0.</strong> 15 December 2020 — Includes a few minor error corrections (the files 'References.txt' within the folder csv and the script 'radiocarbon.R').</li> <li><strong>1.0</strong> 28 November 2020 — First public release of the dataset on Zenodo.</li> </ul>
Replication R code and data for "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes"
<p>This repository holds various files and R code used in the publication of the manuscript entitled "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes".</p> <p>Data files include: The 3D landmark coordinates of each individual specimen (Fox_data_Morphologika.txt), the linear measurement data associated with those foxes (fox_linear_volume_data.csv), and replication data measurements. </p> <p>The following files include the R code used to perform the analyses contained within the paper:</p> <p>1_Procrustes_analysis - details the Geometric morphometrics analyses performed</p> <p>2_linear_models - details the model specification for the GLS models employed in the paper</p> <p>3_graph_code - contains R script for the creation of the graphs displayed in the paper</p> <p>4_repeatability_script - contains R code that details the statistical calculations made with the repeatability measurements indicated above. </p> <p> </p> <p> </p> <p> </p>
r-process abundances in neutron-rich merger ejecta given different theoretical nuclear physics inputs
<p>This data release contains nucleosynthesis predictions for the r-process abundances presented in Côté, Eichler, Yagüe, Vassh et al. (2021) for compact object merger ejecta based on the publicly available simulation trajectories of Rosswog et al. (2013). All ejecta for the merger scenarios considered here are very neutron-rich (Ye ~ 0.016-0.11). Calculations were performed with the PRISM code (Mumpower et al. 2018) which accounts for nuclear reheating (here with a reheating efficiency of 50%). Results are reported for several different theoretical nuclear physics inputs but all calculations make use of the GEF fission yield prescription (see Vassh et al. 2019). All abundances are given at 1 Myr (10^6 years) post-merger. Please see the README file for more details and references.</p> <p>When using these nucleosynthesis yields, please cite this Zenodo data release (Vassh et al. 2021), and refer to Vassh et al. (2019) and Côté, Eichler, Yagüe, Vassh et al. (2021) for further details on the nuclear data applied as well as Rosswog et al. (2013), Piran et al. (2013), and Korobkin et al. (2012) for further details on the merger ejecta trajectories.</p>
Figs 20–23. Raunolina spp. 20–22 – R in First record of the genus Raunolina (Hemiptera: Fulgoroidea: Caliscelidae) from tropical Africa with description of two new species from Sudan and Saudi Arabia
Figs 20–23. Raunolina spp. 20–22 – R. circularis (Linnavuori, 1952), holotype. 23 – R. arabica (Gnezdilov & Wilson, 2006). 20 – left wing; 21 – right wing; 22, 23 – head, pro- and mesonotum, dorsal view.
Figs 1–4. Raunolina species, dorsal view. 1–2 – R in First record of the genus Raunolina (Hemiptera: Fulgoroidea: Caliscelidae) from tropical Africa with description of two new species from Sudan and Saudi Arabia
Figs 1–4. Raunolina species, dorsal view. 1–2 – R. remanei sp. nov., paratypes (1 – female; 2 – male); 3 – R. jeddahica sp. nov., holotype; 4 – R. circularis (Linnavuori, 1952), holotype (dissected).
Figs 5–12. Raunolina spp. 5–11 – R in First record of the genus Raunolina (Hemiptera: Fulgoroidea: Caliscelidae) from tropical Africa with description of two new species from Sudan and Saudi Arabia
Figs 5–12. Raunolina spp. 5–11 – R. remanei sp. nov., paratypes (5–8 – male; 9–11 – female). 12 – R. arabica (Gnezdilov & Wilson, 2006). 5 – head, pro- and mesonotum, dorsal view; 6 – head and pronotum, lateral view; 7 – head, frontal view; 8 – fore wing; 9 – female anal tube and pygofer, dorsal view; 10, 12 – female genital block, lateral view; 11 – median part of hind margin of female sternite VII, ventral view.
Phyloseq R object accompanying the paper Temporal Dynamics Cloacal Microbiota 16S metataxonomics
<p>This ready to load <strong>phyloseq</strong> R S4 object contains the ASV table, taxonomy table and sample metadata. This data was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA673103.</p> <p>The accompanying (peer-reviewed) scientific article can be found here: </p> <ul> <li>https://www.frontiersin.org/articles/10.3389/fmicb.2020.626713/abstract </li> <li>DOI: 10.3389/fmicb.2020.626713</li> </ul> <p> </p> <p><strong>Study/paper</strong> </p> <p>J. Schreuder, F.C. Velkers, A. Bossers, R.J. Bouwstra, W.F. de Boer, P. van Hooft, J.A. Stegeman, S.D. Jurburg.</p> <p>Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing.<br> The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 % and 4.4 % of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.</p>
aquila (Whalen & Carter in Carter, Whalen & Guex, 1998), Orbuk-32; R, Pseudoeucyrtis busuangaensis (Yeh & Cheng, 1998), Orbuk-32; S, Farcus graylockensis Pessagno, Whalen & Yeh, 1986, Orbuk-32; T-U, Farcus sp. A, Orbuk-26; V, Farcus sp. B, Orbuk-27; W-X, Anaticapitula anatiformis (De Wever, 1982); W, Orbuk-32; X, Orbuk-38; Y, Saitoum sp. aff. S. triumphense Whalen & Carter in Carter, Whalen & Guex, 1998, Orbuk-32. Scale bar: A-C, K-L, T-U, W-Y, 100 µm; D-J, M-O, 120 µm; P-S, V, 150 µm. in Late Triassic to Early Jurassic radiolarian, conodont and ammonite assemblages from the Tavuscayiri block, Mersin Mélange, southern Turkey: Time constraints for the T/J boundary and sedimentary evolution of the southern margin of the northern Neotethys
aquila (Whalen & Carter in Carter, Whalen & Guex, 1998), Orbuk-32; R, Pseudoeucyrtis busuangaensis (Yeh & Cheng, 1998), Orbuk-32; S, Farcus graylockensis Pessagno, Whalen & Yeh, 1986, Orbuk-32; T-U, Farcus sp. A, Orbuk-26; V, Farcus sp. B, Orbuk-27; W-X, Anaticapitula anatiformis (De Wever, 1982); W, Orbuk-32; X, Orbuk-38; Y, Saitoum sp. aff. S. triumphense Whalen & Carter in Carter, Whalen & Guex, 1998, Orbuk-32. Scale bar: A-C, K-L, T-U, W-Y, 100 µm; D-J, M-O, 120 µm; P-S, V, 150 µm.
Really a nontraded commodity? A look at the international potato trade network (dataset and R code)
<p>This archive contains code and data for a social network analysis of international potato trade that was published at https://perspectivesandforesight.wordpress.com/2012/11/08/really-a-nontraded-commodity-a-look-at-the-international-potato-trade-network/ on 08 November, 2012.</p> <p>It can serve as a reference for understanding the analysis, and as a basis for replication of the results as well as for carrying out more detailed analyses of international potato trade.</p> <p>The following information and data is included:</p> <p>- The R code used for the social network analysis of international potato trade.</p> <p>- Data files with bilateral matrices of global trade in fresh, frozen and seed potatoes.</p> <p>- Data files with supplementary data used for the analysis.</p> <p>- A copy of the original blog post that was written using the data and code provided herewith.</p>
Anthropoid morphometric and phylogenetic data, with R replication code.
<p>This repository contains four files: 1) a NEXUS phylogeny of 100 anthropoid primates; 2) a CSV text file of anthropoid primate lower molar areas, body mass, and primary dietary category; 3) a CSV text file of modern human lower molar area proportions; and, 4) an R script containing replication code for fitting Bayesian phylogenetic generalized linear mixed models to the morphometric data. These files are associated with the paper "The Evolution of Anthropoid Molar Proportions" in BMC Evolutionary Biology (2016).</p>
FIGURE 5. Rivulus amanapira, UFRJ 5930 in Rivulus uakti sp. n. and R. amanapira sp. n. (Teleostei: Cyprinodontiformes: Rivulidae): two new species from the upper Rio Negro, Brazilian Amazon
FIGURE 5. Rivulus amanapira, UFRJ 5930, female, paratype, 32.6 mm SL (two days after collection); Brazil: Amazonas: São Gabriel da Cachoeira: upper rio Negro basin.
FIGURE 6 in Rivulus uakti sp. n. and R. amanapira sp. n. (Teleostei: Cyprinodontiformes: Rivulidae): two new species from the upper Rio Negro, Brazilian Amazon
FIGURE 6. Brazil: Amazonas: São Gabriel da Cachoeira; type locality of Rivulus amanapira: upper rio Negro basin.
FIGURE 4. Rivulus amanapira, UFRJ 5929 in Rivulus uakti sp. n. and R. amanapira sp. n. (Teleostei: Cyprinodontiformes: Rivulidae): two new species from the upper Rio Negro, Brazilian Amazon
FIGURE 4. Rivulus amanapira, UFRJ 5929, male, holotype, 38.6 mm SL (one day after collection); Brazil: Amazonas: São Gabriel da Cachoeira: upper rio Negro basin.
FIGURE 2. Rivulus uakti, UFRJ 5926 in Rivulus uakti sp. n. and R. amanapira sp. n. (Teleostei: Cyprinodontiformes: Rivulidae): two new species from the upper Rio Negro, Brazilian Amazon
FIGURE 2. Rivulus uakti, UFRJ 5926, female, paratype, 27.9 mm SL (two days after collection); Brazil: Amazonas: São Gabriel da Cachoeira: upper rio Negro basin.
FIGURE 3 in Rivulus uakti sp. n. and R. amanapira sp. n. (Teleostei: Cyprinodontiformes: Rivulidae): two new species from the upper Rio Negro, Brazilian Amazon
FIGURE 3. Brazil: Amazonas: São Gabriel da Cachoeira: upper rio Negro basin; type locality of Rivulus uakti.
FIGURE 1. Rivulus uakti, UFRJ 5925 in Rivulus uakti sp. n. and R. amanapira sp. n. (Teleostei: Cyprinodontiformes: Rivulidae): two new species from the upper Rio Negro, Brazilian Amazon
FIGURE 1. Rivulus uakti, UFRJ 5925, male, holotype, 24.0 mm SL (two days after collection); Brazil: Amazonas: São Gabriel da Cachoeira: upper rio Negro basin.
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.