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133 results for “Molecular phylogenetic analyses”
Fig. 3. Phylogenetic trees obtained from a concatenated dataset with a in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 3. Phylogenetic trees obtained from a concatenated dataset with a total length of 1,277 bp, consisting of seven mitochondrial genes (16S, tRNA-Ala, tRNA-Leu, tRNA-Asn, tRNA-Gln, tRNA-Pro, and COI). The trees were built based on maximum likelihood (ML, left) and Bayesian inference (BI, right). Values at nodes indicate bootstrap scores from ML and posterior probabilities from BI. Outgroups are only shown in the ML tree with both the support values. Scale bars indicate the number of nucleotide substitutions per site. OTUs sequenced in this study are in bold face. Each letter in parentheses after non-bold OTUs denotes the source: C, Chichvarkhin (2017b); F, Foltz and Rocha- Olivares (unpublished); K, Knott et al. (2018); L, Lopes et al. (2016); M, Matsubara et al. (2004); W, Wada et al. (1996). Circles indicate species listed as Setihenricia in Chichvarkhin and Chichvarkhina (2017). Triangles indicate species morphologically identified as Setihenricia in this study (see Fig. 4A).
Fig. 4. Phylogenetic analysis. Molecular analyses identified the specimens collected from CBW2 and CBW3 in Crassicaudiasis in three geographically and chronologically distant Cuvier's beaked whales (Ziphius cavirostris) stranded off Brazil
Fig. 4. Phylogenetic analysis. Molecular analyses identified the specimens collected from CBW2 and CBW3 as Crassicauda anthonyi, based on the ITS2 region, and supported by phylogenetic analysis. Analysis was performed by MEGA X 10.1 using the maximum likelihood method (1,000 bootstrap replicates) and included Habronema muscae as outgroup. GenBank accession numbers are listed along the species names. Branches with bootstrap support lower than 50% were collapsed. *Sequences obtained in this study.
Fig. 4 in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 4. Haplotype network of G1/G3 haplotypes identified on the basis of partial nad5 gene (628 bp). The G1 isolates obtained in this study (Hap01-Hap04), G3 isolates (Hap05, Hap06). Hatch marks represent the number of mutations between the haplotypes and the size of circle corresponds to the frequency of each haplotype in the population. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
Fig. 3. Haplotype network for E in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 3. Haplotype network for E. canadensis (G6/G7) using cox1 gene (616 bp) sequences of different countries. The E. canadensis (G6/G7) isolate obtained in this investigation (Hap_01) and the sequences identified as G7 in the Genbank database were utilized. Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
Fig. 1 in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 1. Hydatid cyst image obtained from the lung (A) and liver (B) and C. tenuicollis (C,D) image obtained from its mesentery of wild boar.
Fig. 2. Haplotype network constructed using cox1 in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 2. Haplotype network constructed using cox1 (744 bp) gene sequences of T. hydatigena. Seven haplotypes formed by the T. hydatigena isolates obtained in this study: (Hap 1-Hap 7). Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
FIG. 3 in A new species and a new record of the genus Phaeophyscia Moberg (Lecanorales, Physciaceae) from Pakistan supported by phenotypic and molecular phylogenetic analyses
FIG. 3. — Phaeophyscia microspora Aptroot & Schumm: A, foliose thallus of type specimen (holo-, LAH[LAH37622]); B, apothecia; C, lobe with rhizines; D, section of an apothecium; E, ascus; F, ascospores. Scale bars: A, 1 cm; B, 3 mm; C, 1.5 mm; D, 80 μm; E, 13 μm; F, 8 μm.
FIG. 2 in A new species and a new record of the genus Phaeophyscia Moberg (Lecanorales, Physciaceae) from Pakistan supported by phenotypic and molecular phylogenetic analyses
FIG. 2. — Phaeophyscia kaghanensis Niazi, Nadeem, Afshan & Khalid, sp. nov.: A, foliose thallus of type specimen (holo-, LAH[LAH37615]); B, apothecia; C, section of an apothecium; D, E, ascus; F, ascospores. Scale bars: A, 1 cm; B, 3 mm; C, 100 μm; D, 28 μm; E, 24 μm; F, 14 μm.
FIG. 1 in A new species and a new record of the genus Phaeophyscia Moberg (Lecanorales, Physciaceae) from Pakistan supported by phenotypic and molecular phylogenetic analyses
FIG. 1. — Phylogeny of Phaeophyscia Moberg and related species based on a maximum likelihood (ML) analysis of the ITS region. Phaeophyscia kaghanensis Niazi, Nadeem, Afshan & Khalid, sp. nov. and P. microspora Aptroot & Schumm are shown in bold.
Figure 4 in Verifying Australian Nilotanypus Kieffer (Chironomidae) In A Global Perspective: Molecular Phylogenetic And Temporal Analyses, New Species And Emended Generic Diagnoses
Figure 4. Phylogenetic tree from Bayesian inference for Nilotanypus Kieffer and outgroups (Table 1) based on concatenated gene fragments. Posterior probabilities (PP) and Bootstrap support (BS from Maximum Likelihood analysis) are indicated above branches only for nodes with PP> 0.95 or BS> 70. Maximal supported nodes are indicated with an asterisk. A dash (–) for either PP or BS indicates a value below the threshold for support; unlabelled nodes lack support under both criteria.
Figure 2. Nilotanypus Kieffer. Pupa. A, B in Verifying Australian Nilotanypus Kieffer (Chironomidae) In A Global Perspective: Molecular Phylogenetic And Temporal Analyses, New Species And Emended Generic Diagnoses
Figure 2. Nilotanypus Kieffer. Pupa. A, B. Thoracic horn; C. Wing sheath; D–F. Abdomen, male); D. dorsal, E. ventral. Larva. F. Head capsule, left side ventral, right side dorsal; G. Dorsal head capsule; H. Antenna; I. Antennal apex, detail; J. Mandible; K. Ligula, paraligula; l. Maxilla; M. Submentum; N. Anterior parapod small comb claw; O. Posterior body; P. Posterior parapod comb claw. A, D–F, H–O. N. haplochelus sp. n.; B, C, G, P. N. ctenochelus sp. n. Abbreviations: S5 – S10 – cephalic setae, DP – dorsal pit, VP – ventral pit.
Figure 1. Nilotanypus Kieffer. Adult. A–D in Verifying Australian Nilotanypus Kieffer (Chironomidae) In A Global Perspective: Molecular Phylogenetic And Temporal Analyses, New Species And Emended Generic Diagnoses
Figure 1. Nilotanypus Kieffer. Adult. A–D. Head, anterior view, right side, ♂, A, C. ♀, B, D.; E–F. Thorax, E. dor- sal, F. lateral; G. Mid-dorsal sensory pit; H. Wing (male); I, J. Tibial apices, I. P1, J. P3; K. Male hypopygium; L. Gonostylus; M. Female genitalia left side only; N. Anterior vaginal cavity, detail. A–B, E–K, M–N. N. haplochelus sp. n.; C–D, L. N. ctenochelus sp.n. Abbreviations: fr–frontal setae, iv–inner vertical setae, ped–pedestal setae, ov– outer vertical setae, sc-scape setae. Fig. 1G after Roback, 1986.
Figure 5. BEAST chronogram from a data set corresponding with Table 1 in Verifying Australian Nilotanypus Kieffer (Chironomidae) In A Global Perspective: Molecular Phylogenetic And Temporal Analyses, New Species And Emended Generic Diagnoses
Figure 5. BEAST chronogram from a data set corresponding with Table 1. Values at nodes are time to most recent common ancestor (tmrca) with HPD (95% Highest Posterior Density) intervals in parentheses. The time scale is in millions of years before present.
Figure 3 in Verifying Australian Nilotanypus Kieffer (Chironomidae) In A Global Perspective: Molecular Phylogenetic And Temporal Analyses, New Species And Emended Generic Diagnoses
Figure 3. Nilotanypus ctenochelus sp. n. A. Wing sheath, tubercle row; B. Larval posterior parapod, comb claw.
Molecular phylogenetic analyses reveal multiple long-distance dispersal events and extensive cryptic speciation in Nervilia (Orchidaceae), an isolated basal Epidendroid genus
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Files for phylogenetic analyses and molecular diagnosis between Diplomystidae catfish species
<p>Diplomystidae is an early-diverged family of freshwater catfish endemic to southern South America. We have recently collected five juvenile specimens belonging to this family from the Bueno River Basin, a basin which the only previous record was a single juvenile specimen collected in 1996. This finding confirms the distribution of the family further South in northern Patagonia, but poses new questions about the origin of this population in an area with a strong glacial history. We used phylogenetic analyses to evaluate three different hypotheses that could explain the origin of this population in the basin. First, the population could have originated in Atlantic basins (East of the Andes) and dispersed to the Bueno Basin after the Last Glacial Maximum (LGM) via river reversals, as it has been proposed for other population of <em>Diplomystes </em>as well as for other freshwater species from Patagonia. Second, the population could have originated in the geographically close Valdivia Basin (West of the Andes) and dispersed south to its current location in the Bueno Basin. Third, regardless of its geographic origin (West or East of the Andes), the Bueno Basin population could have a longer history in the basin, surviving in situ through the LGM. In addition, we conducted species delimitation analyses using a recently developed method that uses a protracted model of speciation. Our goal was to test the species status of the Bueno Basin population along with another controversial population in Central Chile (Biobío Basin), which appeared highly divergent in previous studies with mtDNA. The phylogenetic analyses showed that the population from the Bueno Basin is more related to Atlantic than to Pacific lineages, although with a deep divergence that predated the LGM, supporting in situ survival rather than postglacial dispersal. In addition, these analyses also showed that the species <em>D. nahuelbutaensis</em> is polyphyletic, supporting the need for a taxonomic reevaluation. The species delimitation analyses supported two new species which are described using molecular diagnostic characters: <em>Diplomystes arratiae</em> sp. nov. from the Biobío, Carampangue, and Laraquete basins, maintaining <em>D. nahuelbutaensis</em> valid only for the Imperial Basin, and <em>Diplomystes habitae</em> sp. nov. from the Bueno Basin. This study greatly increases the number of species within both the family Diplomystidae and Patagonia, and contributes substantially to the knowledge of the evolution of southern South American freshwater biodiversity during its glacial history. Given the important contribution to the phylogenetic diversity of the family, we recommend a high conservation priority for both new species. Finally, this study highlights an exemplary scenario where species descriptions based only on DNA data are particularly valuable, bringing additional elements to the ongoing debate on DNAbased taxonomy.</p>
Files for phylogenetic analyses and molecular diagnosis between Diplomystidae catfish species
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FIGURE 2. Optimal phylogenetic tree from Maximum Likelihood analyses for the nrITS1–5.8S–ITS2 in Morphology and molecular data of the species of Suillus (Suillaceae, Boletales) associated with Pinus sibirica at the European northeast of Russia
FIGURE 2. Optimal phylogenetic tree from Maximum Likelihood analyses for the nrITS1–5.8S–ITS2 Suillus data. Bootstrap values (BS ≥ 70%) is added to the left of a node as follows: nearest neighbour method / maximum likelihood method. Scale bar indicates expected changes per site. New sequences from the Komi Republic are marked with red blocks. The specimen GenBank accession numbers in parentheses follows the names.
FIGURE 4. Phylogenetic tree for 56 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 4. Phylogenetic tree for 56 Eligmodontia sequences and two outgroups resulting from the maximum-likelihood analysis of 1140 bp of the cytochrome b gene. Model of sequence evolution was HKY+G+I. Numbers above branches show the percentage values from 500 bootstrap iterations, and Bayesian posterior probabilities (>50 values).
FIGURE 9 in A taxonomic review of Sueus Murayama, 1951 ambrosia beetles (Coleoptera: Curculionidae: Scolytinae: Hyorrhynchini) aided by molecular phylogenetic analyses
FIGURE 9. Sueus pilosus female paratype (USNMENT01595294), 1.6 mm A) dorsal view; B) lateral view; C) frons; D) posterolateral 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)
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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.