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Parrot
<p>The netCDF files "SF*.nc" that can be found in the repository "Parrot_experiment" contain the experimental results of intense sediment transport experiments (sheet flow) carried out in the LEGI tilting flume with two sizes of uniformly distributed acrylic particles having median diameters of 1 mm (S1 experiment) and 3 mm (S3 experiment). The data contained in this repository are presented in Fromant et al. (2018). The files contain :</p> <p> 1/ Synchronised and colocated concentration and veclocity (streamwise component) profiles measurements collected with an Acoustic Concentration and Velocity Profiler (ACVP - Hurther et al., 2011). <br> 2/ Concentration profiles time series collected with Conductivity and Concentration Profilers (Lanckriet et al., 2013), with two different vertical resolutions, 1 mm (CCP1mm) and 2mm (CCP2mm).</p> <p>Details about the experimental protocol can be found in Revil-Baudard et al. (2015). More details regarding the experimental protocol and flow conditions can be found in Fromant et al. (2018). </p>
Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
<p>Parrots (Order: Psittaciformes) are a diverse clade that are easily distinguishable from other birds. Despite the clear characters that define the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024; Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus <em>Probosciger</em> and we restrict usage of the recently introduced tribe Touitini to its type-genus <em>Touit</em>. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades and we further reinstate five valid, available generic names not widely used in recent literature if at all (<em>Licmetis</em>, <em>Gymnopsittacus</em>, <em>Clarkona</em>, <em>Suavipsitta</em>, <em>Cardeos</em>). We advocate the retention of <em>Vini</em> Lesson, 1833 over <em>Coriphilus</em> Wagler, 1832 based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., <em>Bolborhynchus</em> parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the <em>Psittacula</em> <em>sensu lato</em> ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields.</p>
Figure 10 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 10. Pl. XLII in Sclater (1882): the bird illustrated was one of two females received by London Zoo in April 1882 from northern Angola, and has the blue rump characteristic of female Rüppell's Parrot Poicephalus rueppellii but which is paler in colour than that of Namibian parrots, a fact Sclater failed to notice (Jonathan Jackson, © Natural History Museum, London)
Figure 6 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 6. Type material of Poicephalus rueppellii mariettae, from left to right (in both A and B): holotype, adult female, NHMUK 1889.1.20.647; paratypes, adult male, NHMUK 1878.12.31.502, and juvenile, NHMUK 1878.12.31.431, all from Otjimbingwe, Damaraland, Namibia (Jonathan Jackson, © Natural History Museum, London)
Figure 3 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 3. Rüppell's Parrot Poicephalus r. rueppellii from north-west and west-central Angola; note the turquoise-blue plumage in females. (A) adult female, near Luanda, 16 September 2019 (© David & Sara Elizalde); (B) adult female, Mirador la Lua, Luanda province, 24 August 2012 (© Tommy P. Pedersen)
Figure 2 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 2. Differences in the blue coloration of females of the two subspecies of Rüppell's Parrot Poicephalus rueppellii. Left-hand bird in both A and B, P. r. rueppellii from northern Angola (NHMUK 1890.4.1.21, died 7 June 1882 at London Zoo, see also Fig. 7) and right P. r. mariettae from Namibia (NHMUK 1852.5.1.16, collected by C. J. Andersson in 1850 in Namibia, see Fig. 6) (Jonathan Jackson, © Natural History Museum, London)
Figure 9 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 9. Three of the four specimens received alive at London Zoo in April 1882 and which died in June 1882, from left to right: male, NHMUK 1890.4.1.19; male, NHMUK 1890.4.1.20; female, NHMUK 1890.4.1.21 (Jonathan Jackson, © Natural History Museum, London)
Figure 8 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 8. Bird specimens collected by C. J. Andersson in 1850 in Damaraland (Namibia) were sold by the dealer A. D Bartlett of London and some were acquired by the British Museum, including this male (NHMUK 1852.5.1.15), on left in A and B, and female (NHMUK 1852.5.1.16) Rüppell's Parrot Poicephalus rueppellii mariettae. These specimens were seen by Strickland & Sclater (1852) and, because Andersson had not sexed the birds during preparation, due to the differences in colour it was assumed that the more colourful individual was the male (Jonathan Jackson, © Natural History Museum, London)
Figure 5 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 5. Specimen of nominate Rüppell's Parrot Poicephalus rueppellii from north Angola, in the Naturalis Biodiversity Center, RMNH.AVES.209654, which is smaller and overall darker but has the blue rump and belly paler than birds from south-west Angola and Namibia (© Naturalis Biodiversity Center, Leiden)
Figure 4 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 4. Female of the recently described Poicephalus rueppellii mariettae, Namibia, 4 March 2018; this taxon, with dark ultramarine-blue plumage in females, is better known and more widespread than the nominate subspecies (© Charles James Sharp)
Figure 1 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 1. Distribution map of Rüppell's Parrot Poicephalus rueppellii based on e-Bird (https://ebird. org/species/ruepar1?siteLanguage=de). P. r. rueppellii (red dots) occurs only in north-west and west-central Angola around Luanda and Benguela, whereas P. r. mariettae (green dots) is widespread in Namibia and south-west Angola (© Thomas Arndt)
Figure 2 in C. H. McLennan ('Mallee Bird') and his Aboriginal informant Jowley: The source of early records of the Night Parrot Pezoporus occidentalis in Victoria?
Figure 2. Participants at a reception held for Gregory Mathews by the 1914 RAOU Council at Melbourne's Royal Botanic Gardens on 10 March 1914. From left to right the participants are: Dr J. Leach, L. Chandler, C. McLennan, C. Barrett, A.J. Campbell, D. Le Souef, T. Tregellas, Z. Grey and G. Mathews.
Data from: Widespread cultural change in declining populations of Amazon parrots
<p>This dataset of parrot call measurements and metadata is associated with the article "Widespread cultural change in declining populations of Amazon parrots" in Proceedings of the Royal Society B. The data was used to address change and stability in regional vocal dialects of yellow-naped amazon (<em>Amazona auropalliata</em>) contact calls recorded in Costa Rica over three sampling periods that spanned 22 years.</p>
FIGURE 3 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 3. Species-level topology of Psittacinae. Support values come from the maximum likelihood tree. Nodes have ultrafast bootstrap values of ≥95% otherwise noted.
FIGURE 8 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 8. Photographs (not to scale) of Calyptomena hosii (left photo: Dubi Shapiro) a suboscine passerine of Borneo (Brunei, Indonesia) and Triclaria malachitacea (right photo: Marcos Eugênio) of southeastern Brazil showing presumably convergent evolution in ventral coloring. See text for discussion. Photographs reproduced with permission from the photographers.
FIGURE 16 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 16. Dorsal view of specimens of Glossopsitta concinna from the Australian National Wildlife Collection (ANWC) showing variation within and between sexes and within and between mainland southeastern Australia versus Tasmania. Note the bluer coronal color in mainland males. Registration numbers from the bird collection at ANWC are shown. Photograph: Gordon Gullock.
Fig. 1 in Morphological and molecular characterization of Eimeria purpureicephali n. sp. (Apicomplexa:Eimeriidae) in a red-capped parrot (Purpureicephalus spurius, Kuhl, 1820) in Western Australia
Fig. 1. Nomarski interference-contrast photomicrographs of E. purpureicephali n. sp. oocysts showing spheroidal to subspheroidal sporocysts (scale bar = 20 Mm) (1—5) and line drawing of the sporulated oocyst of E. purpureicephali n. sp. Scale bar = 20 Mm (6).
Material related to the blog that reports on the parrot LUT
<p><strong>Material related to the blog that reports on the parrot LUT</strong></p> <p>The blog was published at the Node: <a href="http://thenode.biologists.com/parrot-lut/research/">http://thenode.biologists.com/parrot-lut/research/</a></p> <p> </p> <p><strong>-Source</strong></p> <p>The ‘morgenstemning’ LUT was originally described in:</p> <p>M. Geissbuehler and T. Lasser - "How to display data by color schemes compatible with red-green color perception deficiencies”, Optics Express, 2013</p> <p>The ‘inferno’ LUT was originally created by Stéfan van der Walt and Nathaniel Smith (<a href="http://bids.github.io/colormap/">http://bids.github.io/colormap/</a>).</p> <p>The ‘pseudocolorMM’ LUT was derived from MetaMorph software (version 7.6).</p> <p>The ‘royal’ and ‘Fire’ LUT are available in ImageJ (version 1.49j)</p> <p>The ‘parrot’ LUT was designed by Joachim Goedhart and first described here:<br> <a href="http://thenode.biologists.com/parrot-lut/research/">http://thenode.biologists.com/parrot-lut/research/</a></p> <p><br> <strong>-Distribution</strong></p> <p>The colormaps Magma, Inferno, Plasma and Viridis are available under a CC0 "no rights reserved" license (<a href="https://creativecommons.org/share-your-work/public-domain/cc0">https://creativecommons.org/share-your-work/public-domain/cc0</a>) and are present in FIJI.</p> <p><br> The colormaps Mongenstemning & Parrot are free software: you can redistribute them and/or modify<br> it under the terms of the GNU General Public License as published by<br> the Free Software Foundation, either version 3 of the License, or<br> (at your option) any later version.</p> <p>These colormaps are distributed in the hope that they will be useful,<br> but WITHOUT ANY WARRANTY; without even the implied warranty of<br> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br> GNU General Public License for more details: <<a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>>.</p>
Review of Recent Trends in Measuring the Computing Systems Intelligence-Figure 3. Intelligence of different living creature (accessed 01.11.2017). 3.1. A painting elephant (http://www.wittyfacts.com/suda-the-painting-elephant/); 3.2. A common octopus (https://en.wikipedia.org/wiki/Octopus). 3.3. An African grey parrot (https://en.wikipedia.org/wiki/Grey_parrot)
<p>Many observations proved that octopus species have an impressive spatial learning capacity, advanced navigational abilities, and advanced predatory techniques. The dexterity is important for using and manipulating tools. Zullo, Sumbre, Agnisola, Flash, & Hochner, (2009) studied the successful dexterity of octopuses. They have highly sensitive suction cups and prehensile arms, squid, and cuttlefish. This allows them to hold and manipulate objects. The motor skills of octopuses (Figure 3.2) do not seem to depend upon mapping their body. Some species of parrots are able to mimic very well the human speech. There were performed many studies with parrots that shown that some individuals are able to associate words with their meanings. Another observed ability is to form simple sentences. It has been shown that some grey parrots perform at the cognitive level of a 3-year-old child in some tasks. Pepperberg (2006) proved that some parrots can count up to 6. Figure 3.3 presents a frequently studied species of parrots, called African grey parrot.</p>
Fig. 5 in A critically co-endangered feather louse Forficuloecus pezopori n. sp. (Phthiraptera: Philopteridae) detected through conservation intervention for the western ground parrot Pezoporus flaviventris (Psittaculidae)
Fig. 5. Forficuloecus pezopori Martin, Keatley & Ash n. sp., dorsal (left) and ventral perspective, A. female allotype posterior terminus with egg, B. female alloptype anterior dorsal plate, C. male holotype posterior terminus, D. male holotype terminal genitalia. Tergopleurites and sternopleurites labelled with Roman numerals. Abbreviations: a, basal apodeme; e, endomere; m, mesosomal plate; p, paramere; sgp, subgenital plate; svs, subvulvular sclerite; t, telomere. Scale bars: 200 μm.
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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.