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58 results for “taxonomic inference”
Figure 1. Bayesian phylogenetic tree inferred from the 640 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach
Figure 1. Bayesian phylogenetic tree inferred from the 640-bp of cytochrome c oxidase subunit I gene under GTR + I + G model of sequence evolution. The two new species are highlighted in light grey (Cratera ochra sp. nov.) and dark grey (Obama maculipunctata sp. nov.). Values indicate support for each node according to the maximum posterior probabilities>70% and bootstrap support values> 70%, respectively.
Fig. 2. Tree inferred from COI-5P in Molecular phylogenies support taxonomic revision of three species of Laurencia (Rhodomelaceae, Rhodophyta), with the description of a new genus
Fig. 2. Tree inferred from COI-5P + rbcL + LSU using Bayesian analysis (BI) and including 30 specimens of the Laurencia complex and two outgroup taxa. The numbers above branches indicate Bayesian posterior probabilities (pp) and below branches indicate bootstrap values (bp) inferred from 1 000 ML bootstrap replicates (ML); pp <0.95 and bp <75% are not shown.
FIGURE 3. Haplotype network inferred from A in On the taxonomic identity of Pteronotus davyi incae Smith, 1972 (Chiroptera: Mormoopidae)
FIGURE 3. Haplotype network inferred from A, cyt-b and B, CO1 datasets, highlighting the clusters corresponding to Pteronotus davyi, P. fulvus, and P. gymnonotus. Each circle represents one distinct haplotype (H), whose size is proportional to its frequency in the sample (1 to 6 individuals).
Text-fig. 2. Species of Masillamys considered on the phylogenetic tree of theridomorphs (Vianey-Liaud and Marivaux 2017: fig. 7), within the basal Theridomorpha, before the polyphyletic genus Protadelomys. Position inferred from their dental features (see text). in A Reevaluation Of The Taxonomic Status Of The Rodent Masillamys Tobien, 1954 From Messel (Germany, Late Early To Early Middle Eocene, 48-47 M.Y.)
Text-fig. 2. Species of Masillamys considered on the phylogenetic tree of theridomorphs (Vianey-Liaud and Marivaux 2017: fig. 7), within the basal Theridomorpha, before the polyphyletic genus Protadelomys. Position inferred from their dental features (see text).
Figure 5 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 5. Lateral, dorsal, and ventral views of a tadpole of Scaphiophryne brevis (ZSM 632/2004) showing the typical morphology of the relatively small tadpoles of the Scaphiophryne (Pseudohemisus) type.
Figure 1 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 1. Dorsal and lateral views of tadpoles of Scaphiophryne madagascariensis (stage 35, ZSM 595/2004) (A, B), S. menabensis (stage 35, ZSM 413/2004) (C, D), S. spinosa (stage 29, ZSM 604/2004) (E, F), S. brevis (stage 31, ZSM 618/ 2004) (G, H) and S. calcarata (stage 31, ZSM 410/2004) (I, J). Scale bars represent 5 mm.
Figure 2 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 2. Oral disc (OD), buccal floor (BF) and buccal roof (BR) of tadpoles of Scaphiophryne madagascariensis (OD: ZSM 600/2004; BF, BR: stage 38, ZSM 599/2004) (A–C), S. menabensis (OD: stage 36 BF, BR: stage 36); all from specimens in batch ZSM 413/2004) (D–F), S. spinosa (OD: stage 28, ZSM 616/2004; BF, BR: stage 29, ZSM 612/2004) (G–I), S. brevis (OD: stage 34; BF, BR: stage 31, ZSM 619/2004) (J–L) and S. calcarata (OD: stage 34; BF, BR: stage 32; both from specimens in batch ZSM 410/2004) (M–O). Scale bars are indicated on the images.
Figure 3 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 3. Dorsal and lateral views of tadpoles of Dyscophus insularis (A, B) (stage 34, ZSM 402/2004) and Paradoxophyla palmata (C, D) (stage 37, ZSM 647/2004). Oral disc of D. insularis (E) (stage 36, specimen from batch ZSM 402/2004) and P. palmata (H) (stage 35, ZSM 645/2004). Buccal floor (BF) and buccal roof (BR) of tadpoles of D. insularis (F, G) (stage 38, specimen from batch ZSM 402/2004) and P. palmata (I, J) (stage 37, ZSM 645/2004). Scale bars in A–D represent 5 mm, scale bars for E–J are indicated on the images.
Figure 4 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 4. Dorsal, lateral, and ventral views of a tadpole of Scaphiophryne spinosa (ZSM 606/2004) showing the typical morphology of the relatively large tadpoles of the Scaphiophryne (Scaphiophryne) type.
Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
<p>How insect communities are assembled in nature remains largely unknown. In particular, whether habitat filtering or competition serves as the main mechanism in forming insect communities is rarely subject to an in-depth investigation. One bottleneck lies in the difficulty of species identification when dealing with a large number of diverse insects. However, High-Throughput Sequencing (HTS) technology coupled with classic DNA barcoding offers a great opportunity to infer community assembly for this speciose group. In this study, using 13,909 full-length barcodes obtained by Sanger sequencing or the SOAPBarcode metabarcoding method, we showed that competition was the main assembly mechanism for the moth communities studied in temperate forests of China. The two sequencing methods showed highly consistent results with regards to both diversity composition and community assembly mechanism. Significant phylogenetic signals and structure suggested that the focal moth communities were the result of the non-neutral assembly process, which was further confirmed by results of neutral assembly test that accounted for immigration and speciation rates. In conclusion, HTS coupled with a well-curated DNA barcode library can facilitate community assembly inferences, especially for speciose taxonomic groups.</p>
Table of hsp65 OTUs (cutoff 99%), their inferred taxonomic allocations according to the hsp65 database and, for selected OTUs, closest species obtained from GenBank (BLAST) with percent identity.
<p>This table is part of the paper intitled "Comparison of Actinobacteria communities from human-impacted and pristine karst caves"</p>
Data and Files for Zito, Rigon and Dunson (2022): "Inferring taxonomic affiliation from DNA barcoding aiding in discovery of new taxa"
<p>This folder contains the data and the R code to reproduce the figures and tables in the paper Zito, Rigon and Dunson (2022) - "Inferring Taxonomic placement from DNA barcoding aiding in discovery of new taxa", accepted as open access publication in Methods in Ecology and Evolution.</p> <p>The file "main_FinBOL.R" reproduces the tables in the main document and in the Supporting information available online for the analysis of the FinBOL data, while "main_Simulation_Section4_SI.R" reproduces the simulation in Section 4 of the Supporting information. </p> <p>All data are saved in the folder "data". For replicability purposes, we added version 2.13 of the RDP classifier to the repository, in the folder "RDP/java". This has been downloaded from https://sourceforge.net/projects/rdp-classifier/. </p> <p>For questions, contact the author at alessandro.zito@duke.edu<br> </p>
Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
Open the record for dataset details and reuse information.
Fig. 2. 95 in Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-loop Gene
Fig. 2. 95% minimum spanning haplotype network of D-loop haplotypes of the greater horseshoe bat, Rhinolophus ferrumequinum, in Iran. The size of the shape is proportional to the frequency of that haplotype. Gray and white circles correspond to the clade 1- sub- clade A and clade 1-subclade B in Fig. 4 respectively.
Fig. 4 in Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-loop Gene
Fig. 4. Maximum likelihood (ML) tree of D-loop sequences of the greater horseshoe bat, Rhinolophus ferrumequinum from Iran, Turkey, and Europe. Numbers above branches represent bootstrap support for NJ (3000 replicates)/ML (1000) inherence, and numbers below branches indicate Bayesian posterior probabilities. Values below 50% are not shown.
Data from: Taxonomic reassessment of Clevosaurus latidens Fraser, 1993 (Lepidosauria, Rhynchocephalia) and rhynchocephalian phylogeny based on parsimony and Bayesian inference
The Late Triassic rhynchocephalian Clevosaurus latidens Fraser, 1993 is known from the fissure deposits of Cromhall Quarry, England. Many studies have questioned its referral to the genus Clevosaurus and some phylogenetic analyses suggest a close relationship with herbivorous rhynchocephalians. We reexamine the type specimens and referred material of C. latidens to elucidate its taxonomic identity. Additionally, we provide new phylogenetic analyses of the Rhynchocephalia using both parsimony and Bayesian approaches. Our taxonomic review and both phylogenetic analyses reveal that C. latidens is not referable to Clevosaurus, but represents a new genus. We reassess C. latidens and provide an amended diagnosis for the new genus Fraserosphenodon gen. nov. Both parsimony and Bayesian analyses recover similar topologies and we propose formal names for two higher clades within Rhynchocephalia: Eusphenodontia and Neosphenodontia.
FIGURE 4. Bayesian inference tree derived from cyt b in Molecular evidence for taxonomic status of the gudgeon genus Huigobio Fang, 1938 (Teleostei: Cypriniformes), with a description of a new species from Guangdong Province, South China
FIGURE 4. Bayesian inference tree derived from cyt b gene for the Armatogobionina of the subfamily Gobioninae. Nodal numbers are posterior probability values. Only values above 50% are given.
Fig. 3. Phylogenetic inferences and uncorrected p in More than meets no eyes: Taxonomic status of a Liotyphlops Peters, 1881 (Serpentes: Anomalepididae) blindsnake from the Atlantic Rainforest
Fig. 3. Phylogenetic inferences and uncorrected p-distances for Scolecophidia terminals, based on the small subunit ribosomal RNA (16S rRNA) gene fragment. A) Maximum likelihood (RAxML) phylogenetic tree inference and geographic distribution of evaluated samples (white circles = L. beui literature records; black and white circles = L. beui examined records); B) Pairwise uncorrected p-distances for Scolecophidia terminals.
Figs. 27–37 in Taxonomic Review of Pseudips Cognato (Coleoptera: Curculionidae: Scolytinae: Ipini) Inferred from Morphology and a DNA-Based Phylogeny
Figs. 27–37. Pseudips yak, new species. Male holotype: 27) Habitus, dorsal view; 28) Habitus, lateral view; 29) Frontal view; 30) Declivital view. Paratype male: 31) Genitalia, ventral view; 32) Genitalia, dorsal view. Female allotype: 33) Habitus, dorsal view; 34) Habitus, lateral view; 35) Frontal view; 36) Declivital view. 37) Exposed arcuate egg galleries made in Picea crassifolia, MaiXiu Forest Park, Qinghai Province, China.
Figs. 11–18 in Taxonomic Review of Pseudips Cognato (Coleoptera: Curculionidae: Scolytinae: Ipini) Inferred from Morphology and a DNA-Based Phylogeny
Figs. 11–18. Pseudips mexicanus. Male: 11) Habitus, dorsal view; 12) Habitus, lateral view; 13) Frontal view;
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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.