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684 results for “phylogenetic placement”
FIG. 2 in A new small Acanthogonatus Karsch, 1880 (Mygalomorphae, Pycnothelidae) species from Argentinean Patagonia: description of A. messii Signorotto & Ferretti n. sp. and its phylogenetic placement
FIG. 2. — Acanthogonatus messii Signorotto & Ferretti n. sp., habitus: A, female molted in laboratory; B, female collected and photographed from field; C, male molted in laboratory; D, male collected walking in the field. Scale bars: 1 cm.
FIG. 6. — A in A new small Acanthogonatus Karsch, 1880 (Mygalomorphae, Pycnothelidae) species from Argentinean Patagonia: description of A. messii Signorotto & Ferretti n. sp. and its phylogenetic placement
FIG. 6. — A, habitat at type locality of Acanthogonatus messii Signorotto & Ferretti n. sp.; B, C, female burrows opened at night at type locality.
FIG. 7 in A new small Acanthogonatus Karsch, 1880 (Mygalomorphae, Pycnothelidae) species from Argentinean Patagonia: description of A. messii Signorotto & Ferretti n. sp. and its phylogenetic placement
FIG. 7. — Most parsimonious cladogram using IW. Symbols: black squares: exclusive synapomorphies; white squares: homoplasies. Numbers above the circles: characters; below: states. Species group notations follows Goloboff (1995).
Data and scripts for: Read length dominates phylogenetic placement accuracy of ancient DNA reads
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Data from: PlaceMyFossils: An integrative approach to analyse and visualize the phylogenetic placement of fossils using backbone trees
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Interrogating genomic data in the phylogenetic placement of treeshrews reveals potential sources of conflict
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Fast and accurate distance‐based phylogenetic placement using divide and conquer
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Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions
<p><span><span><span><span><span><span><span><span><span><span><span>Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (<b>new definition</b>), as the sister group of scorpions. Panscorpiones (<b>new name</b>) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Micromphale sect. Perforantia (Agaricales, Basidiomycetes); expansion and phylogenetic placement
DNA sequences show that the traditional genus Micromphale appears to be polyphyletic. Nuclear ribosomal LSU and ITS DNA sequences place Micromphale sect. Perforantia Singer (typus sect. M. perforans) within Gymnopus, comprising a clade sister to a mixture of traditional Gymnopus taxa including G. fusipes (typus generis) plus traditional Marasmius sect. Androsacei. This study enlarges sect. Perforantia and shows that sect. Perforantia is a clade separate from those including Micromphale sect. Micromphale and sect. Rhizomorphigena. A new subsection Pinophili is proposed to include new species G. pinophilus and G. ponderosae. Eleven taxa are accepted at species rank, of which nine are proposed as new, mostly morpho-taxa.
Phylogenetic placement of Pseudoneobacillus sp. JJ-79 within Bacillaceae family
<p>This repository contains phylogenetic trees (and associated sequence data) inferred to assess the phylogenetic placement of <em>Pseudoneobacillus</em> sp. JJ-79 (tax id: 2880968) within 512 type strains representative of the <em>Bacillaceae</em> family.</p> <p> </p> <p>Three phylogenetic trees were inferred, each from a multi-gene dataset (as described at <a href="http://giphy.pasteur.fr/PhyloM/Bacillaceae">http://giphy.pasteur.fr/PhyloM/Bacillaceae</a>):</p> <ul> <li><strong>BM1</strong>: 87 conserved genes (<a href="https://doi.org/10.1371/journal.pone.0077033">Wu et al. 2013</a>, <a href="https://doi.org/10.1099/ijsem.0.004475">Gupta et al. 2020</a>, <a href="https://doi.org/10.1099/ijsem.0.003775">Patel and Gupta 2020</a>),</li> <li><strong>BM2</strong>: major subunits of the DNA Gyrase (<em>GyrA</em> and <em>GyrB</em>) and RNA polymerase (<em>RpoB</em> and <em>RpoC</em>; <a href="https://doi.org/10.1099/ijsem.0.003775">Patel and Gupta 2020</a>),</li> <li><strong>BM3</strong>: DNA helicase II and DNA polymerase I (<em>UvrD</em> and <em>PolA</em>; <a href="https://doi.org/10.1099/ijsem.0.003775">Patel and Gupta 2020</a>).</li> </ul> <p> </p> <p>For each dataset <strong>BM<em>i</em></strong> (<em>i</em> = 1, 2, 3), four files are available:</p> <ul> <li><code>BM<em>i</em>.faa </code> the concatenation of the filtered multiple sequence alignments (FASTA format);</li> <li><code>BM<em>i</em>.nwk </code> a maximum likelihood phylogenetic tree inferred from <code>BM<em>i</em>.faa</code> (NEWICK format);</li> <li><code>BM<em>i</em>.pdf </code> a graphical representation of the phylogenetic tree (PDF format);</li> <li><code>BM<em>i</em>.seq.tar.gz </code> for each gene name, three FASTA files are available in this tar.gz archive: <ul> <li>initial sequences (*.faa),</li> <li>multiple sequence alignment (*.afa),</li> <li>filtered multiple sequence alignment (*.ffa).</li> </ul> </li> </ul> <p> </p> <p>In complement, the multiple sequence alignments of 11 loci are available in the archive <code>CSI.tar.gz</code>. Each of these loci shares a conservative signature indel (CSI) that is indicative of the closely related <em>Neobacillus</em> genus (see Table 4 —Niacini clade— in <a href="https://doi.org/10.1099/ijsem.0.003775">Patel and Gupta 2020</a>):</p> <ul> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_066086220">fliF</a></em>, flagellar M-ring protein FliF;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_066094713">rplX</a></em>, 50S ribosomal protein L24;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_007087611">prmA</a></em>, 50S ribosomal protein L11 methyltransferase;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_066065587">hisH</a></em>, imidazole glycerol phosphate synthase subunit HisH;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_040344893">hisZ</a></em>, ATP phosphoribosyltransferase regulatory subunit;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_007086698">mdoB</a></em>, LTA synthase family protein;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_066365003">topA</a></em>, type I DNA topoisomerase;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_042455853">pncB</a></em>, nicotinate phosphoribosyltransferase;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_007085202">thiD</a></em>, phosphomethylpyrimidine kinase;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_034672618">recJ</a></em>, single-stranded-DNA-specific exonuclease RecJ;</li> <li><em><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?FULL&SEQUENCE=WP_066089666">dxs</a></em>, 1-deoxy-D-xylulose-5-phosphate synthase.</li> </ul>
Fig 17 in Phylogenetic placement of Carrhotus Thorell, 1891 with three new species from Sri Lanka (Araneae: Salticidae)
Fig 17. Distribution of Carrhotus spp. of Sri Lanka.
Description of two new species and phylogenetic placement of recent taxonomic novelties in the Chilean endemic genus Miersia (Gilliesieae, Allioideae, Amaryllidaceae)
<p>Abstract: Two new species in the Chilean endemic genus <em>Miersia</em> (Gilliesieae, Allioideae, Amaryllidaceae) are introduced: <em>M. stellata</em> and <em>M. raucoana</em>. A morphological description, distribution map, illustration, and the assessment of their conservation status are provided for each new taxon, along with an updated key to all species in <em>Miersia</em>. Additionally, analyses of DNA sequences were performed to inquire the evolutionary affinities of both new species and the recently described, <em>M. putaendensis</em>, within Gilliesieae phylogenetic framework. Data from multiple single-copy nuclear genes, as well as the inclusion of <em>Trichlora</em> and <em>Schickendantziella</em>, are necessary to corroborate the tribe’s phylogeny and reassess its generic classification.</p> <p>Dataset description: Two phylip alignment files were uploaded: 1) Miersia_nov_ITS_3.0.phy, includes sequences of nrDNA ITS (nrITS) region, and 2) Miersia_nov_cpDNA_3.0.phy, includes concatenated sequences of two chloroplast (cpDNA) markers, <em>trnL-F</em> and <em>rbcL</em>. Sequences were aligned using MAFFT v.1.4.0.</p> <p>Three *.bestTree.tre files for 1) nrITS, 2) cpDNA, and 3) concatenated dataset of all loci (nrITS, <em>trnL-F</em>, <em>rbcL</em>). All were inferred using RAxML-NG v.1.1.0 (Kozlov et al. 2019), GTR+Γ as the model of molecular evolution (--model GTR+G), and partitioned by locus. nrITS and cpDNA analyses were performed conducting 50 tree searches using 25 random and 25 parsimony-based starting trees to pick the best-scoring topology (--tree pars{25},rand{25}), and the concatenated analysis included 100 tree searches using 50 random and 50 parsimony-based starting trees (--tree pars{50},rand{50}). </p> <p>Also, the respective boostrap trees (*.bootstraps.tre) were uploaded for each analysis. Likelihood bootstrap analyses were conducted in RAxML-NG v.1.1.0 with 1,000 pseudoreplicates (--bs-trees 1000).</p> <p>We also uploaded two Nexus files which correspond to sequence data from Escobar et al. (2020, Bot. J. Linn. Soc. 194: 84–99), considering that these are currently not available in TreeBase.</p>
Fig. 3 in Phylogenetic placement of a new paleoendemic pill scarab from the Udzungwa Mountains, Tanzania, triggers biogeographic interpretations (Coleoptera: Hybosoridae, Ceratocanthinae)
Fig. 3 – Habitus of select ingroup and outgroup pill scarabs, dorsal view; images are to scale.
Data from: APPLES: Scalable distance-based phylogenetic placement with or without alignments
<p>Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They also rely on assembled sequences for the reference set and aligned sequences for the query. Thus, ML methods cannot analyze datasets where the reference consists of unassembled reads, a scenario relevant to emerging applications of genome-skimming for sample identification. We introduce APPLES, a distance-based method for phylogenetic placement. Compared to ML, APPLES is an order of magnitude faster and more memory efficient, and unlike ML, it is able to place on large backbone trees (tested for up to 200,000 leaves). We show that using dense references improves accuracy substantially so that APPLES on dense trees is more accurate than ML on sparser trees, where it can run. Finally, APPLES can accurately identify samples without assembled reference or aligned queries using kmer-based distances, a scenario that ML cannot handle. APPLES is available publically at github.com/balabanmetin/apples.</p>
FIGURE 3 in Redescription, phylogenetic placement, and taxonomic reassignment of Mesobdella lineata (Sciacchitano, 1959) (Hirudinida: Arhynchobdellida)
FIGURE 3 (below). Parapraobdella lineata, n. gen. A. Dorsal surface of body
FIGURE 4 in Redescription, phylogenetic placement, and taxonomic reassignment of Mesobdella lineata (Sciacchitano, 1959) (Hirudinida: Arhynchobdellida)
FIGURE 4. Strict consensus of 12 equally parsimonious trees obtained from 32 morpho-
Figure 13 in An overview of labeonin relationships and the phylogenetic placement of the Afro-Asian genus Garra Hamilton, 1922 (Teleostei: Cyprinidae), with the description of five new species of Garra from Ethiopia, and a key to all African species
Figure 13. Garra geba, holotype, AMNH 228485, 86.4 mm standard length.
Figure 12 in An overview of labeonin relationships and the phylogenetic placement of the Afro-Asian genus Garra Hamilton, 1922 (Teleostei: Cyprinidae), with the description of five new species of Garra from Ethiopia, and a key to all African species
Figure 12. Garra duobarbis, holotype, AMNH 228484, 66.8 mm standard length.
Figure 11 in An overview of labeonin relationships and the phylogenetic placement of the Afro-Asian genus Garra Hamilton, 1922 (Teleostei: Cyprinidae), with the description of five new species of Garra from Ethiopia, and a key to all African species
Figure 11. Garra regressus, holotype, AMNH 228487, 121.8 mm standard length.
Figure 15 in An overview of labeonin relationships and the phylogenetic placement of the Afro-Asian genus Garra Hamilton, 1922 (Teleostei: Cyprinidae), with the description of five new species of Garra from Ethiopia, and a key to all African species
Figure 15. Garra dembecha, holotype, AMNH 228483, 78.8 mm standard length.
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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)
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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.