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727 results for “molecular taxonomy”
A molecular taxonomy of tumors independent of tissue-of-origin
<p>This tarball contains the pre-processed data in .Rda files required to compile our manuscript entitled "A molecular taxonomy of tumors independent of tissue-of-origin"</p>
Fig. 2 in Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea), with implications for taxonomy and evolutionary scenarios
Fig. 2. Conflicting results among different molecular markers. The phylogenetic relationships of four species are detailed for separate and combined analyses performed in Maximum Likelihood (ML) and Bayesian Inference (BI). Boxes colored as 'Untested or unresolved' refer to missing data and multifurcation, respectively.
Fig. 1 in Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea), with implications for taxonomy and evolutionary scenarios
Fig. 1. [part 2 on next page] Optimal phylogenetic tree reconstructed in Maximum Likelihood with the combined dataset. Bootstrap values and posterior probabilities are reported for each node (bootstrap values below 25% are not displayed). The color of internal branches is proportional to bootstrap values. Geographic origin of the specimens sequenced is provided in brackets after the species names. In purple, monophyletic group congruent with morphological hypotheses; in blue, monophyletic group with geographic consistency at the continental level; in brown, incertae sedis species; in green, four species with conflicting and supported positions (Thanatophyllum akinetum Grandcolas, 1991 and Phoetalia pallida (Brunner von Wattenwyl, 1865) or congruent, but weakly supported positions (Laxta sp. and Pronauphoeta cf. viridula (Palisot de Beauvois, 1805)). The four latter species are discussed in the text (see also Fig. 2). The subfamilies indicated on the right of the tree are derived from traditional morphology-based classifications. Units for the branch length scale at the bottom right: number of expected substitutions per site.
Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon
<p>This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus <em>Calandrella</em>, with the description of a range-restricted African relic taxon" by Stervander <em>et al</em>. </p> <p>For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript. </p> <p><strong>Phylogenetic analyses</strong></p> <ol> <li>Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa</li> <li>BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml</li> <li>BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log</li> <li>BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees</li> <li>TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk</li> </ol> <p><strong>Species delimitation</strong></p> <ol> <li>Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk</li> <li>mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt</li> <li>mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt</li> <li>mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg</li> </ol>
FIGURE 17. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 17. Hungarosoma bokori Verhoeff, 1928, female, vulvae (Driny Cave). Vulvae in posterior-ventral view (o = opercula) Not scaled.
FIGURE 19 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 19. Distribution of the genus Hungarosoma Verhoeff, 1928. Empty dot: H. inexpectatum, solid dots: H. bokori. Distribution of H. bokori in Slovak-Aggtelek Karst drawn in higher scale.
FIGURE 18. A in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 18. A Maximum-Likelihood tree (GTR + G + I model) based on the COI gene and rooted with Polyxenus lagurus. All data—except from H. bokori — were obtained from Genbank. Numbers refer to bootstrap values (1000 replicates). Scale bar = 0.02 substitutions / site. For origin of the H. bokori material, see Table 1.
FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928, male (Abaliget Cave). 12: Antenna. 13: Gonopod complex, anterior view. The right side of pair structures is slightly turned laterally. 14: Gonopods in right lateral view. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta. Not scaled. Photos: Andrej Mock.
FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928, specimens from the Abaliget Cave, preserved in alcohol (not scaled). 6: Habitus of adult male in lateral view; the cheirites of anterior gonopods are visible. 7: Details of the dorsal part of the male trunk. 8: Ventral side of mid-body segments in detail. 9: Dorsal side of a juvenile of stadium III with the shape of the pleurotergites typical for the genus (all material from the Abaliget Cave, Hungary). Photos: Andrej Mock.
FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928, female from the Driny Cave, scanning electronic microscopy of details of the shape and surface of mid-body segments. 10: Dorsolateral view (left side). 11: A pleurotergite, dorsolateral view in detail. Photos: Andrej Mock & Karel Tajovský.
FIGURE 16. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 16. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Right lateral view. Letters a – h signal equivalent structures in both views. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.
FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928, female, holotype (Abaliget Cave). 2: Head end of the body, right lateral view. 3: Tergite 15, dorsal view. 4: Antenna, lateral view. 5: Discernable vulvae in situ (v), right lateral view. Photos: Jörg Spelda.
FIGURE 15. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 15. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Anterior view (right side of pair structures is slightly turned laterally). Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.
FIGURE 1. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 1. Hungarosoma bokori Verhoeff, 1928, female, sampled at the entrance of the Baradla Cave, Hungary, 21. iii. 2013. Photo: Ľubomír Kováč & Andrej Mock.
FIGURE 3 in Molecular phylogeny, morphology and taxonomy of Moroccan Triops granarius (Lucas, 1864) (Crustacea: Notostraca), with the description of two new species
FIGURE 3. Phylogenetic relationships of A, Triops samples obtained in a combined analysis of three molecular markers (12 S, 16 S, 28 S) and B, western Moroccan Triops granarius samples as inferred from 12 S sequences (best scoring trees obtained in RAxML are shown). ML bootstrap support / Bayesian posterior probabilities are given for selected nodes. Provisional taxon labels of previously discovered lineages correspond to those used in Korn et al. (2013). Symbols correspond to those used in Fig. 1.
FIGURE 2 in Molecular phylogeny, morphology and taxonomy of Moroccan Triops granarius (Lucas, 1864) (Crustacea: Notostraca), with the description of two new species
FIGURE 2. Schematic drawing of A, a detail of the right lateral margin of the telson of a Triops granarius specimen in dorsal view, showing how the length of the largest furcal spine was measured (dotted line), and B, the endopodite of the second trunk limb in anterior view, demonstrating how the length of the endopodite was measured (dotted line). C, a detail of the row of digging spines positioned at the margin of the endopodite showing three examples of length measurements (dotted lines; note that in the present example the largest spine cannot be identified easily so that several rather large spines have to be measured in order to obtain a value for the length of the largest spine) and the position of subsidiary lines used for measurements of spine lengths (dashed lines). D, the distal part of the endopodite showing the distal claw and three of the digging spines. The point where the dashed line (drawn from the base of the distal claw) meets the dotted line (median line of the distal claw) was used as the starting point for length measurements of the endopodite (in the present study the base of the distal claw was defined as the point where the distalmost digging spine diverges from the endopodite). Grey bars (directed approx. in a right angle to measured lines) indicate where measured lines start and end. Abbreviations: C, distal claw; DS, digging spines; SP, largest furcal spine; SPL, length of largest furcal spine; TE, telson; F, furcal ramus.
FIGURE 1. A in Molecular phylogeny, morphology and taxonomy of Moroccan Triops granarius (Lucas, 1864) (Crustacea: Notostraca), with the description of two new species
FIGURE 1. A, map indicating the geographical position of the study area (marked in black). B, map showing the geographical distribution of studied populations of Triops granarius. Symbols used to mark study sites refer to phylogenetic lineages (see Table 1, Fig. 3; population no. 6 was determined morphologically by DFA in this study). Open square: ‘ Triops granarius 8 ’; filled asterisk: ‘ Triops granarius 10 ’.
FIGURES 188 – 190 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURES 188 – 190. Coloration in life of Indosticta deccanensis — (188) teneral male; (189) male; (190) female [Photo: M. Bedjanič].
FIGURES 180 – 187 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURES 180 – 187. Indosticta deccanensis — (180) thorax and head, lateral view [male]; (181) prothorax, lateral view [male]; (182) anal appendages, dorsolateral view [male]; (183) anal appendages, lateral view [male]; (184) thorax and head, lateral view [female]; (185) prothorax, dorsolateral view [female]; (186) ovipositor, lateral view [female]; (187) wings [male]. [Material origin: male and female—Ponmudi, Kerala, India]
FIGURES 171 – 173 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURES 171 – 173. Coloration in life: Platysticta secreta sp. nov. — (171) female; Platysticta serendibica sp. nov. — (172) male; (173) female [photos: M. Bedjanič, fig. 171 photo: G. de Silva Wijeyeratne].
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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
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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.