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2,327 results for “Placement”
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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Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
<p>Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the <i>rootstrap</i>, which provides information on the statistical support for any given root position.</p> <p>Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a></p>
Acoustic transfer function data for source and sensor placement
<p>Acoustic transfer function (ATF) data for the codes of source and sensor placement in sound field control. </p> <p>https://github.com/sh01k/SourceSensorPlacementSFC</p> <p>The ATF data in the 2D acoustic field was generated by the finite element method using FreeFem++ (<a href="https://freefem.org/">https://freefem.org/</a>).</p>
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.
Figure 3 in Revisiting the morphology and systematic placement of the enigmatic Cretaceous ommatid beetle Bukhkalius lindae (Coleoptera: Archostemata: Ommatidae)
Figure 3. Details of Bukhkalius lindae, holotype, NIGP166152, ventral view, under confocal microscopy. (A) Head, showing the possibly incomplete antennal groove (arrowhead). (B) Prothorax. Abbreviations: an1 = antennomere 1; ey = compound eye; lbp = labial palp; md = mandible; msv = mesoventrite; mt = mentum; mxp = maxillary palp; pf = profemur; pm = prementum; pp = propleuron; ps = prosternum; ptb = protibia. Scale bars: 200 μm.
Figure 2 in Revisiting the morphology and systematic placement of the enigmatic Cretaceous ommatid beetle Bukhkalius lindae (Coleoptera: Archostemata: Ommatidae)
Figure 2. General habitus of Bukhkalius lindae, holotype, NIGP166152, under widefield fluorescence. (A) Dorsal view. (B) Ventral view. Scale bars: 1 mm.
Figure 4 in Revisiting the morphology and systematic placement of the enigmatic Cretaceous ommatid beetle Bukhkalius lindae (Coleoptera: Archostemata: Ommatidae)
Figure 4. Head of fossil Omma species from Burmese amber, showing the well-defined neck region. (A) Omma lii, holotype, NIGP164898. (B) Omma sp. 1. (C) Omma sp. 2. Scale bars: 500 μm.
Figure 1 in Revisiting the morphology and systematic placement of the enigmatic Cretaceous ommatid beetle Bukhkalius lindae (Coleoptera: Archostemata: Ommatidae)
Figure 1. General habitus of Bukhkalius lindae, holotype, NIGP166152, under incident light. (A) Dorsal view. (B) Ventral view. Scale bars: 1 mm.
Coalhouse Fort Gun Placement
A battery near Coalhouse Fort (on the Thames estuary) that contained 4 x 6-pdr guns. Date: 1893 https://en.wikipedia.org/wiki/Coalhouse_Fort 252 photos taken in July 2014 with a gopro Hero 3 and processed in Agisoft Metashape. Source: Objaverse 1.0 / Sketchfab
Product Placement Bibliometric
<p>Data set of published paper in the Web of Science (WoS) using the query "product placement." from 1992 to 2021 </p>
Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)
<p>Here, we present the Ion Torrent® next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include <em>Galeorhinus galeus</em> (17,487 bp; GenBank accession number ON652874), <em>Mustelus asterias</em> (16,708; ON652873), <em>Mustelus mosis</em> (16,755; ON075077), <em>Mustelus palumbes</em> (16,708; ON075076), and <em>Triakis megalopterus</em> (16,746 bp; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (<em>tRNA<sup>Leu</sup></em><sup> </sup>and <em>tRNA<sup>Ser</sup> </em>are duplicated), except for <em>G</em>. <em>galeus</em> which contains 23 tRNA genes where <em>tRNA<sup>Thr</sup> </em>is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.</p>
Placement Aware Grasp Planning for Efficient Sequential Manipulation
<p>This is a summary and real-world experimental video of Placement Aware Grasp Planning for Efficient Sequential Manipulation. </p> <p>This work accepted in ECAI 2024. </p> <p>Paper link : <a href="https://ebooks.iospress.nl/doi/10.3233/FAIA241020">IOS Press Ebooks - Placement Aware Grasp Planning for Efficient Sequential Manipulation</a></p>
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>
JCSP: Joint Caching and Service Placement for Edge Computing Systems
<p>The archives include the research data associated with the paper <strong><em>JCSP: Joint Caching and Service Placement for Edge Computing Systems</em></strong>. The paper is accepted in IEEE IWQoS 2022.</p> <p>The research data includes the validation dataset for the generalized LQN model that corresponds to section V of the paper. The validation model contains two layers. In the upper layer, the underlying processor adopts the processor sharing strategy. While in the lower layer, the capacity of the cache-task is set as 1 with a total number of 3 items. All the items obey discrete uniform distribution and take the random replacement strategy. </p> <p> </p>
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>
Molecular phylogeny of Dermestidae (Coleoptera) reveals the polyphyletic nature of Trogoderma Latreille, and the taxonomic placement of the Khapra Beetle Trogoderma granarium Everts
<p>The hide, larder and carpet beetles (Coleoptera: Dermestidae) are a family of mainly scavenger beetles, with numerous species such as the khapra beetle (<em>Trogoderma</em> <em>granarium</em> Everts, 1898), the black carpet beetle (<em>Attagenus</em> <em>unicolor</em> (Brahm, 1791)) and the hide beetle (<em>Dermestes</em> <em>maculatus</em> De Geer, 1774) being widely recognised as serious economic pests of stored products and museum collections (Fig. 1). A stable classification and reliable identification of genera and species of these pests and their 1,700 relatives are of great relevance for trade restrictions, biosecurity, pest management, forensics and biodiversity surveys.</p> <p>In this study, we examined and sequenced mitochondrial genomes of 477 dermestid specimens, representing all subfamilies and 90% of the globally recognised tribes and subtribes. Our study provides the most comprehensive, taxonomically verified and vouchered resource of mitochondrial reference sequences linked to specimen images and occurrence records of pests and their relatives, enabling eDNA surveys, metabarcoding and molecular species identification. It also reconstructs the phylogeny of Dermestidae based on molecular and morphological data for the first time, thereby providing robust phylogenetic hypotheses for a stable classification system from family to genus-level.</p> <p>Accordingly, a revised classification of Dermestidae with formal nomenclatural changes is proposed, recognising six subfamilies: Orphilinae, Trinodinae, Trogoparvinae subfam. nov. (type genus <em>Trogoparvus</em> Háva, 2001), Dermestinae, Attageninae and Megatominae. Trinodinae is recovered towards the base of Dermestidae with three tribes: Trinodini (=Trinoparvini syn. nov.), Thylodriini and Trichelodini. Dermestinae is the only subfamily with adults lacking a median ocellus, and it includes the tribes Thorictini stat. nov. (that is downgraded from Thorictinae), Marioutini and Dermestini. The endemic Australian genus <em>Derbyana</em> Lawrence and Ślipiński, was recovered within Holarctic <em>Dermestes</em> Linnaeus. Attageninae is strongly supported and includes the monogeneric Adelaidiini and polygenic Attagenini. Former subgenera of <em>Attagenus</em> Latreille, i.e., <em>Lanorus</em> Mulsant and Rey (= Paranovelsis Casey syn. nov.), <em>Telopes</em> Redtenbacher, and <em>Aethriostoma</em> Motschulsky, are elevated to generic level. The largest clade, Megatominae, is confirmed as monophyletic and is divided into three tribes: Anthrenini, Ctesiini and Megatomini. Megatomini is divided into three subtribes: Megatomina, Orphinina subtribe nov. (type genus <em>Orphinus</em> Motschulsky) and Trogodermina. Within the economically important lineage Trogodermina, <em>Trogoderma</em> Latreille, is delimited to contain only Holarctic species including the Khapra beetle <em>T</em>. <em>granarium</em> Everts, while a Southern Hemisphere clade is here recognised as <em>Eurhopalus</em> Solier in Gay, 1849 (= <em>Anthrenocerus</em> Arrow, 1915; <em>Myrmeanthrenus</em> Armstrong, 1945; <em>Neoanthrenus</em> Armstrong, 1941; <em>Sodaliatoma</em> Háva, 2013; <em>Reesa</em> Beal, 1967 syn. nov.). A revised classification of the extant genera of Dermestidae is also provided.</p>
Ultraconserved element data for phylogenomic placement of the jumping spider genus Iranattus Prószyński, 1992 (Salticidae, Plexippini, Plexippina)
<p>The jumping spider genus <em>Iranattus</em> Prószyński, 1992 has been placed in the Harmochirina based on morphology. We use phylogenomic evidence based on ultraconserved element (UCE) data to show that it belongs instead in the subtribe Plexippina.</p>
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