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10 results for “Phylo”
Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective
<p>The supplemental dataset for "Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective."</p>
FIGURE 23. Phylo fimbriatus, A in Review of Orbiniidae (Annelida, Sedentaria) from Australia
FIGURE 23. Phylo fimbriatus, A. AM W.7444, B–L: AM W.7445. A–G: stereomicroscope, methylene blue staining; H–L: compound microscope, chaetigers 30–31. A. Anterior end, dorsal view; B. Thorax-abdomen transition, lateral view; C. Anterior end, lateral view; D. Thorax-abdomen transition, dorsal view; E. Neuropodia of chaetigers 5–7; F. Neuropodia of chaetigers 15–16; G. Abdomen, latero-posterior view; H, I. Abdominal parapodia; J. Abdominal neuropodia; K. Notopodial forked chaeta; L. Neuropodial flail chaeta. a, acicula; br, branchia; cc, crenulated capillaries; fc, forked chaeta; flc, flail chaeta; ic, interramal cirrus; ne, neuropodium; no, notopodium; s, spines; u, uncini.
FIGURE 21. Phylo felix. A–D in Review of Orbiniidae (Annelida, Sedentaria) from Australia
FIGURE 21. Phylo felix. A–D: AM W.30718, stereomicroscope. A. General view; B. Thorax-abdomen transition, lateral view; C. Anterior end, dorsal view; D. Posterior thoracic chaetigers, lateral view; E–H, AM W.24306, compound microscope. E. Parapodium of chaetiger 17; F. Neuropodium of chaetiger 17; G. Parapodium of chaetiger 23; H. Posterior parapodium. a, acicula; br, branchia; cc, crenulated capillaries; fc, forked chaeta; flc, flail chaeta; ic, interramal cirrus; ne, neuropodium; no, notopodium; ss, spear-like spines; u, uncini.
Data from: Phylo-allometric analyses showcase the interplay between life history patterns and phenotypic convergence in cleaner wrasses
Phenotypic convergence is a macroevolutionary pattern that need not be consistent across life history. Ontogenetic transitions in dietary specialization clearly illustrate the dynamics of ecological selection as organisms grow. The extent of phenotypic convergence among taxa that share a similar ecological niche may therefore vary ontogenetically. Because ontogenetic processes have been shown to evolve, phylogenetic comparative methods can be useful in examining how the scaling of traits relates to ecology. Cleaning, a behavior in which taxa consume ectoparasites off clientele, is well-represented among wrasses (Labridae). Nearly three-fourths of labrids that clean do so predominately as juveniles, transitioning away as adults. We examine the scaling patterns of 33 labrid species to understand how life history patterns of cleaning relate to ontogenetic patterns of phenotypic convergence. We find that as juveniles, cleaners exhibit convergence in body and cranial traits that enhance ectoparasitivory. We then find that taxa that transition away from cleaning exhibit ontogenetic trajectories that are distinct from those of other wrasses. Obligate and facultative species that continue to clean over ontogeny, however, maintain characteristics that are conducive to cleaning. Collectively, we find that life history patterns of cleaning behavior are concordant with ontogenetic patterns in phenotype in wrasses.
FIGURE 43. Phylo felix Kinberg, 1866 in Polychaeta Orbiniidae from Antarctica, the Southern Ocean, the Abyssal Pacific Ocean, and off South America
FIGURE 43. Phylo felix Kinberg, 1866. (LUCE, Sta. M60, SMNH 154435). A, anterior end, dorsolateral view; B, another specimen, right lateral view; C–D, thoracic neuropodial uncini; E, posterior thoracic parapodium, ventral view, with thoracic neuropodial spear; F, posterior thoracic and anterior abdominal segments showing stomach papillae.
FIGURE 42. Phylo felix Kinberg, 1866. A in Polychaeta Orbiniidae from Antarctica, the Southern Ocean, the Abyssal Pacific Ocean, and off South America
FIGURE 42. Phylo felix Kinberg, 1866. A, Anterior end, left lateral view; B, posterior thoracic parapodium, anterior view; C, abdominal parapodium, anterior view; D, heavy thoracic neuropodial uncinus; E, thin thoracic neuropodial uncinus; F, spearlike neuroseta from posterior thoracic setiger; G, furcate seta; H pygidium. (A, C, G, after Hartman, 1957; A, D–H, originals from LUCE, Sta. M60, SMNH 154435).
Phylo-k-mers databases for SHERPAS
<p>SHERPAS is a new program to identify novel recombinant sequences in a large collection of viral sequences, and to provide a first estimate of their recombinant structure. SHERPAS is much faster than other softwares for recombination detection; its main feature is the use of a pre-computed database of "phylogenetically-informed k-mers" (or phylo-k-mers). The computation of this phylo-k-mer database is a heavy computational step, but it only needs to be executed once for a given reference alignment.</p> <p>A phylo-k-mer database can be built from any reference alignment, and a phylogenetic tree built from that alignment, using RAPPAS2 (<a href="https://github.com/phylo42/rappas2">https://github.com/phylo42/rappas2</a>). We propose here three ready-to-use databases, for three reference alignments:<br> -An alignment of 167 sequences of the pol region of the HIV genome, provided with the program SCUEAL, accessible at <a href="https://github.com/spond/SCUEAL/blob/master/data/pol2009.nex">https://github.com/spond/SCUEAL/blob/master/data/pol2009.nex</a><br> -An alignment of 339 sequence of the whole HBV genome, provided with the programm jpHMM, accessible at <a href="http://jphmm.gobics.de/download.html">http://jphmm.gobics.de/download.html</a>.<br> -An alignment of 881 sequences of the whole HIV genome, also provided with jpHMM, accessible at <a href="http://jphmm.gobics.de/download.html">http://jphmm.gobics.de/download.html</a>.</p> <p>For each of these alignments, we provide a .zip file containing three files: The phylo-k-mer database (.rps file), the reference phylogenetic tree used to build the database (.tree file), and a table associating each reference sequence to a strain of the virus (.csv file). The details of the construction of the database, the construction of the tree, as well as the origin of the information reported in the table, can be found in the Supplementary Materials associated with the original Bioinformatics publication.</p>
Data from: Phylo-allometric analyses showcase the interplay between life history patterns and phenotypic convergence in cleaner wrasses
Open the record for dataset details and reuse information.
Phylo-k-mers databases for SHERPAS
Open the record for dataset details and reuse information.
Comparing 3D genome organization in multiple species using Phylo-HMRF
GEO Series GSE128800. Pan troglodytes; Gorilla gorilla; Pan paniscus. 3 samples. Type: Other.
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)
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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.