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32 results for “novel taxa”
Data and Scripts from: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa
<p>Morphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Futhermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa, but yields new insights about the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet, but serves as a general framework for predicting multivariate ecology from phenotypic traits.</p>
APPENDIX 3. — Maximum likelihood phylogram inferred from 47 taxa and 3314 in Mucoralean fungi in Thailand: novel species of Absidia from tropical forest soil
APPENDIX 3. — Maximum likelihood phylogram inferred from 47 taxa and 3314 characters based on LSU, SSU and ACT-1 matrix using GTR+G model. ML bootstrap support (≥ 70%) are indicated above the branches or near the nodes. Tree is artificially rooted using Cunninghamella homothallica (CBS 168.53), C. phaeospora (CBS 692.68), and C. bainieri (FSU319). The new species are in black bold and the type species in the dataset are indicated using T. (-) represent bootstrap support lower than 70%. (*) indicates unrecovered branching.
Novel metagenome assembled genomes (MAGs) that best represent novel species level taxa within the phylum Chloroflexota
<p>1280 Chloroflexita MAGs from the study "Taxonomic re-classification and expansion of the phylum Chloroflexota based on over 5000 genomes and metagenome-assembled genomes". Only MAGs that improved the representation of a species-level genome cluster within the phylum <em>Chloroflexota</em> were included in this deposition.</p> <p>Most of these MAGs were assembled from publicly availabe metagenome sequence data obtained from the NCBI sra database.</p> <p>An overview of the here deposited MAGs can be found in <a href="https://zenodo.org/api/files/2a6a7fa1-489c-426d-8e05-ada23038dfdf/Zenodo_deposited_MAGS_overview.xlsx?versionId=9cde1488-8388-4fdb-a45e-2d48dc066f9a"> Zenodo_deposited_MAGS_overview.xlsx</a>, for more details please refer to the abive mentioned publication.</p> <p>MAG assemblies are deposited as gzip compressed tar.archive. Three tar.gz archives have been deposited, containing the same MAG assemblies but sorted by different criteria:</p> <ol> <li>All MAGs sorted by category of the source environment</li> <li>All MAGs sorted by class designation</li> <li>All MAGs sorted by MIMAG quality (high or moderate)</li> </ol>
Data and Scripts from: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa
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Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree
<p>Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being the most elusive. Ploeotids make up most of this backbone diversity—yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show they are non-monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships between these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single-cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place <em>Decastava</em> in Alistosa; while <em>Hemiolia</em> branches with <em>Liburna</em>, establishing the novel clade Karavia. We describe <em>Hemiolia limna</em>, a freshwater-dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: <em>Chelandium granulatum</em> nov. gen. nov. sp. branches as sister to <em>Olkasia</em>, and <em>Gaulosia striata</em> nov. gen. nov. sp. remains an orphan taxon.</p>
Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree
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FIGURE 10. A–E. Reteporella ilala n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 10. A–E. Reteporella ilala n. sp. A. View of the colony (SAMC-A029168) (scale bar = 10 mm). B. Autozooids surrounding the fenestrula with avicularia along the margins (SAMC-A029107) (scale bar = 0.4 mm, magnified x50). C. Abfrontal view (SAMC-A028899) (scale bar = 0.4 mm, magnified x35). D. Group of autozooids at the growing edge (SAMC-A029107) (scale bar = 0.2 mm, magnified x100). E. Autozooids and avicularia (SAMC-A029107) (scale bar = 0.2 mm, magnified x75).
FIGURE 8. A–E. Hippomonavella lingulata n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 8. A–E. Hippomonavella lingulata n. sp. (SAMC-A029050) A. Group of autozooids (scale bar = 0.4 mm, magnified x35). B. Close-up of autozooids (scale bar = 0.2 mm, magnified x75). C. Close-up of the orifice, showing condyles and two oral spine bases (scale bar = 0.1 mm, magnified x200). D. Developing ooecium (scale bar = 0.2 mm, magnified x100). E. Ovicelled zooid (scale bar = 0.1 mm, magnified x150).
FIGURE 7. A–E. Adeonella assegai n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 7. A–E. Adeonella assegai n. sp. (SAMC-A028960) A. Autozooids at the growing edge (scale bar = 0.2 mm, magnified x75). B. Frontal view of autozooids near the margin (scale bar = 0.2 mm, magnified x75). C. Close-up of two zooids (scale bar = 0.2 mm, magnified x100). D. Close-up of the secondary orifice, paired frontal avicularia and spiramen (scale bar = 0.1 mm, magnified x200). E. Dimorphic brooding zooids at the branch margin (scale bar = 0.4 mm, magnified x50).
FIGURE 5. A–F. Trypostega richardi n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 5. A–F. Trypostega richardi n. sp. A. Group of ovicelled and non-ovicelled autozooids and zooeciules (SAMCA026788) (scale bar = 0.2 mm, magnified x250). B. Close-up of two zooids, one ovicelled. Note the dimorphic orifice in the ovicelled zooid (SAMC-A026788) (scale bar = 0.2 mm, magnified x400). C. Close-up of an ovicell with circular opening of the associated zooeciule (SAMC-A026788) (scale bar = 0.1 mm, magnified x1.0K). D. Cleithridiate orifice with operculum (SAMC-A026788) (scale bar = 0.05 mm, magnified x1.8K). E. Cleithridiate orifice from an angle showing detail of condyles (SAMC-A028976) (scale bar = 0.05 mm, magnified x350). F. Close-up of two zooeciules (SAMC-A028976) (scale bar = 0.1 mm, magnified x200).
FIGURE 4. A–F in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 4. A–F.?Micropora erecta n. sp. A. Group of autozooids (SAMC-A029102) (scale bar = 0.4 mm, magnified x35). B. Autozooids and interzooidal avicularia (SAMC-A029102) (scale bar = 0.2 mm, magnified x75). C. Close-up of the orifice, showing proximal indentations and thickened suboral margin (SAMC-A029102) (scale bar = 0.05 mm, magnified x500). D. Interzooidal avicularia (SAMC-A029102) (scale bar = 0.1 mm, magnified x150). E. Group of ovicelled and non-ovicelled zooids (SAMC-A028821) (scale bar = 0.4 mm, magnified x50). F. Ovicelled zooid (SAMC-A028821) (scale bar = 0.2 mm, magnified x150).
FIGURE 3. A–B. Chaperiopsis familiaris n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 3. A–B. Chaperiopsis familiaris n. comb. (SAMC-A026415) A. Group of zooids, some with ovicells (scale bar = 0.4 mm, magnified x120). B. Closer view of some ovicelled zooids (scale bar = 0.2 mm, magnified x250). C–F. Aspidostoma sarcophagus n. sp. (SAMC-A029067). C. Zooids and kenozooids with cryptocystal pits (scale bar = 0.5 mm, magnified x35). D. Close-up of the orifice (scale bar = 0.2 mm, magnified x150). E. Developing antler-like processes (scale bar = 0.2 mm, magnified x100). F. Ovicelled zooid with well-developed antler-like processes (zooid on the left) (scale bar = 0.4 mm, magnified x50).
FIGURE 2. A–E. Biflustra adenticulata n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 2. A–E. Biflustra adenticulata n. sp. A. View of autozooids around the fenestrula (SAMC-A028915) (scale bar = 0.5 mm, magnified x50). B. Smaller, irregular shaped zooids (kenozooids) (SAMC-A028915) (scale bar = 0.1 mm, magnified x200). C. Frontal view of young zooids (SAMC-A028915) (scale bar = 0.2 mm, magnified x100). D. View of zooids near the fenestrula margin (SAMC-A029105) (scale bar = 0.2 mm, magnified x75). E. Multiporous distal mural septula (arrow) and kenozooids on the outer margin (SAMC-A029105) (scale bar = 0.2 mm, magnified x75).
FIGURE 6. A–F. Khulisa carolinae n. gen. et n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 6. A–F. Khulisa carolinae n. gen. et n. sp. (SAMC-A029002) A. Group of autozooids and interzooidal avicularia (scale bar = 0.4 mm, magnified x50). B. Close-up of the interzooidal avicularium (scale bar = 0.2 mm, magnified x75). C. Autozooids and enlarged dimorphic zooid (scale bar = 0.4 mm, magnified x50). D. View of the apertural bar and detail of the distal pore plates (scale bar = 0.2 mm, magnified x100). E. Close-up of the apertural bar (scale bar = 0.1 mm, magnified x200). F. Orificial rim of an enlarged, dimorphic zooid (scale bar = 0.1 mm, magnified x200).
FIGURE 1 in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 1. Map of the southern African sub-region showing the subdivision of the ocean into the Exclusive Economic Zone (EEZ), as a dashed line, indicating four a priori marine bioregions (West, South, Southeast and East Coasts) with some localities mentioned in-text. False Bay in the Western Cape Province and East London in the Eastern Cape Province are considered marine transition zones (i.e. zones lying between two regions).
FIGURE 11. A–D. Reteporella ilala n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 11. A–D. Reteporella ilala n. sp. A. Close-up of the orifice with beaded anter and suboral avicularium forming a pseudosinus (SAMC-A028986) (scale bar = 0.1 mm, magnified x200). B. Developing ooecium and different types of avicularia (SAMC-A029107) (scale bar = 0.2 mm, magnified x100). C. View of ovicelled zooid with ooecium covered by secondary calcification (SAMC-A029107) (scale bar = 0.2 mm, magnified x75). D. Close-up of ooecia covered by secondary calcification, except frontal fissure (SAMC-A029107) (scale bar = 0.1 mm, magnified x150). E–F. Triphyllozoon sp. (SAMC-A028905) E. View of trabeculae and autozooids (scale bar = 0.4 mm, magnified x35). F. Orifice and adventitious avicularia (scale bar = 0.2 mm, magnified x75).
FIGURE 9. A–F. Phidolopora chakra n in Novel taxa of Cheilostomata Bryozoa discovered in the historical backlogs of the Iziko South African Museum
FIGURE 9. A–F. Phidolopora chakra n. sp. (SAMC-A029097) A. Partial view of a colony fragment showing ovicelled zooids and fenestrulae (scale bar = 0.4 mm, magnified x50). B. Abfrontal view of a colony fragment showing conspicuous vibices and two types of adventitious avicularia (scale bar = 0.2 mm, magnified x75). C. Close-up of an ovicell and avicularia (scale bar = 0.1 mm, magnified x200). D. Close-up of the orifice with beaded anter and shallow sinus (scale bar = 0.05 mm, magnified x500). E. Developing ooecium (scale bar = 0.1 mm, magnified x200). F. Close-up of ovicells with median convexity and secondary calcification (scale bar = 0.1 mm, magnified x200).
FIGURE 1. Dorsal habitus photos Spanagonicus Berg species. A. male S in A review of the genus Spanagonicus Berg (Hemiptera: Miridae: Phylinae: Nasocorini) with the description of novel antennal characters, the description of a new species from Central America, and a key to currently known taxa
FIGURE 1. Dorsal habitus photos Spanagonicus Berg species. A. male S. albofasciatus (Reuter) B. female S. albofasciatus, macropterous C. female S. albofasciatus, brachypterous D. male S. argentinus E. female S. argentinus F. male S. aricanus G. female S. aricanus H. male S. schusterus I. female S. schusterus. J. female S. tiquensis (Image from the Museo de La Plata online holotype database). Images not to scale; see Table 2 for measurements.
FIGURE 4 in A review of the genus Spanagonicus Berg (Hemiptera: Miridae: Phylinae: Nasocorini) with the description of novel antennal characters, the description of a new species from Central America, and a key to currently known taxa
FIGURE 4. Scanning electron microscopy images of Spanagonicus albofasciatus. A. Lateral head and thorax view of male S. albofasciatus, B. Lateral view of second antennal segment of male S. albofasciatus, C. spatulate setae on ventral surface of second antennal segment in male S. albofasciatus, D. lateral view of female S. albofasciatus. Magnifications at base of images.
FIGURE 6 in A review of the genus Spanagonicus Berg (Hemiptera: Miridae: Phylinae: Nasocorini) with the description of novel antennal characters, the description of a new species from Central America, and a key to currently known taxa
FIGURE 6. Transmission electron microscopy images of a cross-section of the second antennal segment in Spanagonicus albofasciatus. A. Male S. albofasciatus dorsal cuticular surface, highlighting the basicornis setae and associated structures. B. Male S. albofasciatus ventral cuticular surface, highlighting the layers of cuticle and spatulate setae internal morphology. cucuticle p—pores, tr—trichogen cells, to—tormogen cells. Scale bars are equivalent to 1 micron.
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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.