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2,620 results for “Molecular Phylogeny”
Figure 2. Male abdominal terminal. A in Molecular phylogeny of Chinese raspy crickets (Orthoptera: Gryllacrididae) reveals incongruences in current classification
Figure 2. Male abdominal terminal. A, Diaphanogryllacris sp.; B, Mi. dicrana; C, D, Ho. gladiate; E, F, Ho. obtusitubera; G, F. wufengensis (from: Liu et al. 2022b); H, W. lianhua; I, Metriogryllacris sp.; J, Ni. testaceus; K, Si. quadrateprocera; L, Dial. zhoui (from: Shi et al. 2016) (arrows in A and B indicate a pair of dilated and strongly upwards extending whiskers at male abdominal tergite, arrow in G indicates short spines extending at male terminal tergite, arrow in H indicates longer spines extending at male abdominal tergite).
Figure 1 in Molecular phylogeny of Chinese raspy crickets (Orthoptera: Gryllacrididae) reveals incongruences in current classification
Figure 1. ML tree based on COI, COII, Cytb, 18S, and 28S gene sequence, the nodes are bootstrap values/Bayesian posterior probabilities/ SH-aLRT, respectively, and the first column on the right is the taxonomy system by Cadena-Castañeda (2019), the second by Ingrisch (2018), white colour for new genera and species erected in this study, or species not mentioned by Ingrisch (2018).
Figure 9. Living Gryllacrididae. A in Molecular phylogeny of Chinese raspy crickets (Orthoptera: Gryllacrididae) reveals incongruences in current classification
Figure 9. Living Gryllacrididae. A, Mar. sequestris; B, Dr. spinose; C, Capnogryllacris sp.; D, Mag. hainanensis; E, Ocellarnaca sp.; F, E. ruficeps; G, R. xiei; H, Prosopogryllacris sp..
Figure 2 in Morphology and molecular phylogeny of a Chinese population of Rubrioxytricha guamensis Kumar et al., 2018 (Ciliophora: Hypotrichia)
Figure 2. Maximum likelihood (ML) phylogenetic tree inferred from the 18S rRNA gene sequences. Numbers near nodes represent the ML bootstrap values and Bayesian posterior probabilities. For both trees, the scale bar corresponds to 0.01 expected substitutions per site. The red box (arrow) indicates the clade of genus Rubrioxytricha.
FIGURE 7 in A phylogeny and evolutionary natural history of mesoamerican toads (Anura: Bufonidae: Incilius) based on morphology, life history, and molecular data
FIGURE 7. Generalized distributional patterns of the species of Incilius, organized by clade. This figure highlights the varying geographic scales over which evolution in each clade has proceeded.
FIGURE 3. A in Molecular phylogeny of pimoid spiders and the limits of Linyphiidae, with a reassessment of male palpal homologies (Araneae, Pimoidae)
FIGURE 3. A maximum likelihood phylogeny of Pimoidae using five molecular markers (matrix M2). Support metrics at nodes indicate Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT)/ultrafast bootstrap (UFBoot).
Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria
<p>A phylogenetic framework provides the necessary evolutionary context for studies of comparative anatomy, life history, behavior, biogeography, systematics, and conservation. Time-scaled phylogenetic analyses require researchers to include calibration ages which are used to fit a model that transforms tree branch lengths into units of time. The inclusion of multiple calibration ages (if they are available) is a best practice that brings all the available evidence to bear on the temporal model. While selecting the appropriate ages of calibrating fossil taxa is obviously important, perhaps more relevant is where those calibrations are applied in the tree. A misattributed fossil calibrator (e.g., using a stem-taxon to set a minimum age on a tipward crown-node) can severely distort the results. Our aim is to provide a summary of fossil calibrators that can be used in molecular phylogenetic assessments of Afrotheria. The literature that documents these fossils, and discusses their ages and affiliations, is somewhat scattered. Included in this contribution are the oldest extinct species that are (in our opinion) securely attributable to stem lineages of afrotherian clades. Each informs a minimum age for the adjacent rootward tree node. We then assemble a large DNA supermatrix that includes 32 genes and 39 afrotherian genera – including recently extinct elephants and sea-cows. A time-scaled phylogenetic estimate is derived from this dataset with explicit inclusion of fossil taxa in the analysis.</p>
Figure 6 in Phylogeny and taxonomy of European funnel-web spiders of the Tegenaria-Malthonica complex (Araneae: Agelenidae) based upon morphological and molecular data
Figure 6. Bayesian tree of single analysis of 28S. Posterior probabilities of clades are expressed in percentages and given above branches. Clade support (> 50) from the resampling method (jack-knife, 1000 replications) based on parsimony analysis with implied weighting (K = 6) is given below the branches. Abbreviations: GR, Greece; IT, Italy.
FIGURE 1. Clustering diagram showing overall similarity among 15 in A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes
FIGURE 1. Clustering diagram showing overall similarity among 15 data blocks of the full data set (5 genes × 3 codon positions) using SAS. Each block is indicated at the tip of terminal branches by gene name and codon position. Each node shows clustering terminal branches (data set) based on hierarchical clustering algorithm using a Bayesian approach.
FIG. 2 in Molecular phylogeny of the Aplodactylidae (Perciformes: Cirrhitoidea), a group of Southern Hemisphere marine ®shes
FIG. 2. The pattern of observed transition and transversion nucleotide substitution accumulation at third codon positions for mitochondrial DNA partial cytochrome c oxidase subunit I and cytochrome b sequences when combined. Squares represent pairwise comparisons among aplodactylids. Diamonds, circles and triangles represent comparisons of Chironemus marmoratus (Chironemidae), Cheilodactylus fasciatus (Cheilodactylidae) and Cirrhitus splendens (Cirrhitidae) against the aplodactylids, respectively. The mean observed transition±transversion nucleotide substitution ratio and its standard deviation are listed for each set of comparisons.
Figure 4 in Morphological and molecular phylogeny of Epiperipatus (Onychophora: Peripatidae): a combined approach
Figure 4. BEAST chronogram showing divergence time estimates for Peripatidae. Error bars at nodes show 95% highest probability densities of estimated divergence times.
FIGURE 3 in Molecular phylogeny of long-tailed shrews (genus Sorex) from México and Guatemala
FIGURE 3. Major mountain ranges of México (Conabio 2003) and geographical location of the collecting localities for Mexican samples of long-tailed shrew species of the genus Sorex. Durango: 1= S. monticolus, 2= S. emarginatus; Coahuila: 3= S. milleri; Nuevo León: 4= S. milleri, 5= S. veraecrucis; Jalisco: 6= S. saussurei; Michoacán: 7= S. veraecrucis; Distrito Federal: 8= Sorex oreopolus; Puebla: 9 = S. ventralis; Guerrero: 10= S. veraepacis; Oaxaca: 11= S. veraecrucis, 12 = S. macrodon, 13= S. ixtlanensis; Chiapas: 14= S. veraecrucis; Guatemala: 15= S. saussurei; 16 = S. veraepacis.
FIGURE 4 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 4. ML tree based on ITS1 sequences. Sequence data for the ITS1 was aligned from a total of 23 individuals from nine species. The outgroups Neoseiulus swirskii and Typhlodromus pyri (GenBank nos. EU310505 and FM179376, respectively) were used to root the ITS1 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).
FIGURE 3 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 3. Neighbor-joining (NJ) tree (a) and maximum likelihood (ML) tree (b) based on COI sequences. Twentythree of the COI sequences were obtained from the nine Chinese tetranychid species analyzed in this study. In addition, thirteen acarine COI sequences were obtained from the GenBank: the COI sequence (GenBank nos. DQ789590 and AY320029) from Brevipalpus obovatus and Cenopalpus pulcher were used as outgroups; the other COI sequences Tetranychus truncatus, T. turkestani, T. piercei, T. neocaledonicus, Panonychus citri, Pa. ulmi, Pa. mori, Amphitetranychus viennensis, A. quercivorus, Petrobia harti and P. tunisiae (GenBank nos. AB257317, AJ316604, AB257314, X80859, AB041252, AB041253, AB041256, X99875, X99873, EU487121 and EU487119 respectively) from GenBank also included into our phylogenetic analysis. Numbers adjacent to branches show the bootstrap values (> 50%) of 1000 replicates.
Figure 28 in Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species
Figure 28. Scanning electron micrographs of male soft parts of Parapolycope miurensis sp. nov. A, male paratype (SUM-CO-2240); B, male paratype (SUM-CO-2241); C, D, male paratype (SUM-CO-2242). A, left lateral view of upper lip; B, right lateral view of upper lip; C, right lateral view of uropod and uropodal projection; D, right lateral view of uropodal projection with numerous small spines.
Figure 16 in Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species
Figure 16. Parapolycope setouchiensis sp. nov., female paratype (SUM-CO-2210). A, right lateral view of upper lip; B, antennula; C, antenna except part of exopodite. Arrowhead indicates inward bulge. Abbreviations: ba, basis; en, endopodite; ex, exopodite. Scale bar = 50 μm.
Figure 9 in Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species
Figure 9. Scanning electron micrographs of male soft parts of Kliecope oligohalina comb. nov. A, right lateral view of distal part of antennula, male paratype (SUM-CO-2199); B, left lateral view of antenna, male paratype (SUM-CO-2200). Arrows and arrowheads indicate small and large disc-shaped suckers, respectively. Abbreviations: en, endopodite; ex, exopodite.
Figure 6 in Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species
Figure 6. Scanning electron micrographs of male soft parts of Kliecope mihoensis gen. et sp. nov. A, paratype (SUM- CO-2182); B, E paratype (SUM-CO-2183); C, paratype (SUM-CO-2184); D, F, paratype (SUM-CO-2185). A, left lateral view of upper lip; B, right lateral view of second and third podomeres of antennula (A1); C, left lateral view of third and four podomeres of A1; D, right lateral view of setae with sucker of A1; E, right lateral view of endopodite and hookshaped claw of antenna; F, left lateral view of posterior trunk segment, uropod, and copulatory organ. Arrows and arrowheads indicate small and large disc-shaped suckers, respectively. Abbreviation: en, endopodite.
Figure 6 in Molecular phylogeny of hinge-beak shrimps (Decapoda: Caridea: Rhynchocinetes and Cinetorhynchus) and allies: a formal test of familiar and generic monophyly using a multilocus phylogeny
Figure 6. Two-phase (above) and three-phase (below) phylogenetic analyses of maximum likelihood (ML) and Bayesian inference (BI) for representatives of the family Rhynchocinetidae using three genes. The software MAFFT was used for sequence alignment The two phylogenetic trees resulted from the combined analysis of 12S, Histone (H3), and Enolase gene fragments of Rhynchocinetes (seven taxa and eight terminals), Cinetorhynchus (five taxa and 12 terminals), Lipkius (one taxon and two terminals), Eugonatonotus (one taxon) and outgroups. The general topology of the trees obtained from two-phase and three-phase ML and BI analyses was the same. The numbers above or below the branches represent the posterior probabilities from the BI analysis in MrBayes and bootstrap values obtained from ML analyses in TREEFINDER (ML/BI).
Figure 15 in Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species
Figure 15. Parapolycope setouchiensis sp. nov. A, male holotype (SUM-CO-2201), left lateral view of posterior trunk segment, uropod, and copulatory organ; B, female paratype (SUM-CO-2210), right lateral view of posterior trunk segment, uropod, and copulatory organ. Abbreviations: fs, female spermatheca; urp, uropodal projection. Scale bar = 50 μm.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.