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1,696 results for “DNA sequence”
Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach
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Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
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Raw sequence of: A comparative analysis of spider prey spectra analyzed through the next-generation sequencing of individual and mixed DNA samples
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Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae
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Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods
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Aligned DNA sequence matrix for phylogenetic analyses in the article "Description and phylogenetic relationships of a new trans-Andean species of Elachistocleis Parker 1927 (Amphibia, Anura, Microhylidae)"
<p>Aligned DNA sequence matrix for phylogenetic analyses in the article "Description and phylogenetic relationships of a new trans-Andean species of <em>Elachistocleis</em> Parker 1927 (Amphibia, Anura, Microhylidae)"</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>16S = 1-1165;<br> BDNFcodonPos1 = 1166 - 1874\3;<br> BDNFcodonPos2 = 1167 - 1875\3;<br> BDNFcodonPos3 = 1168 - 1876\3;<br> cmyccodonPos1 = 1878 - 2319\3;<br> cmyccodonPos2 = 1879 - 2320\3;<br> cmyccodonPos3 = 1877 - 2318\3;<br> CO1codonPos1 = 2321 - 2981\3;<br> CO1codonPos2 = 2322 - 2979\3;<br> CO1codonPos3 = 2323 - 2980\3;<br> histcodonPos1 = 2983 - 3307\3;<br> histcodonPos2 = 2984 - 3308\3;<br> histcodonPos3 = 2982 - 3309\3;<br> siacodonPos1 = 3311 - 3704\3;<br> siacodonPos2 = 3312 - 3705\3;<br> siacodonPos3 = 3310 - 3706\3;<br> tyrcodonPos1 = 3708 - 4263\3;<br> tyrcodonPos2 = 3709 - 4264\3;<br> tyrcodonPos3 = 3707 - 4262\3;<br> 28S = 4265-5084;<br> 12S = 5085-6171;</p> <p> </p>
Simulated read data analysed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph"
<p>Simulated read data analyzed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph".</p> <p><strong>1) Human sequence data</strong></p> <p><strong>HO_chr11_50bp_sliding_window*fq.gz:</strong><br> All possible 50 bp reads overlapping chromosome 11 SNPs in the Human Origins dataset. Files with the word "alternate" in their filename carry the alternate allele, otherwise, they carry the reference allele. Deamination has been added into these simulated reads using gargammel (Renaud 2016) based on empirically estimated post-mortem damage in a dataset of 102 ancient genomes (Allentoft et al., 2015).</p> <p><strong>2) microbial data</strong></p> <p><strong>simulation_*_s.fq.gz:</strong><br> Simulated microbial read data from a set of microbial reference genomes identified in the ancient Clovis genome (Rasmussen 2014), using gargammel.</p>
Figure 1 from: Nxele TC, Plisko JD, Mwabvu T, Zishiri OT (2020) Molecular phylogeny of Kazimierzus Plisko, 2006 (Clitellata, Kazimierzidae) from the Western and Northern Cape Province inferred from mitochondrial DNA sequences. African Invertebrates 61(2): 83-92. https://doi.org/10.3897/afrinvertebr.61.53380
Figure 1 COI gene phylogram showing relationships amongst Kazimierzus species. Numbers above nodes are bootstrap support/posterior probabilities from Maximum Likelihood and Bayesian analyses. Letters A–F represents different clades.
Fig. 54 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Fig. 54. One of four trees from total evidence analysis with POY of 92-taxon data set using 1: 2 indel ⁄ transition–transversion cost ratio. (d) Non-homoplasious; (s) homoplasious.
Figs 49–52. 49 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Figs 49–52. 49. Singletreederivedfromanalysisof ~470 bpof 28S rRNAusing 1: 1 indel ⁄ transition–transversioncost ratio. 50. Singletree derivedfromanalysis of ~1100 bp of COImtDNAusing 1: 1 indel ⁄ transition–transversioncost ratio. 51. Totalevidenceanalysiswith POYof 52- taxondatasetusing 1: 1 indel ⁄ transition–transversioncostratio. 52. Totalevidenceanalysiswith POYof 52-taxondatasetusing 2: 2 indel ⁄ transition–transversioncostratio.
Fig. 42 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Fig. 42. Strict consensus of 96 most parsimonious trees for full-taxon morphological data set, with unsupported nodes supressed. Length = 207; consistency index = 42; retention index = 86. (d) Non-homoplasious; (s) homoplasious.
Fig. 44 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Fig. 44. Strict consensus of 12 trees derived from implied weighting analysis of morphological data using PIWE. (d) Non-homoplasious; (s) homoplasious.
Figs 35–41. 35 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Figs 35–41. 35. Garsauria usambarica (Cydnidae), female. Gonapophyses 9 moderately sclerotized, second rami thinly sclerotized; gonangulum membraneous. 36. Aphylum syntheticum (Aphylidae), female. Gonapophyses 9 reduced, second rami lost; gonangulum absent. 37. Serbana borneensis (Phloeidae). (a) Female genital plates, right gonocoxite 8 removed; (b) gonapophyses 8 with intergonocoxal membrane and first rami. 38. Dichelops sp. (Pentatomidae), female. Ductus receptaculi with three distinct walls, distal aperture of vesicular area open; thickenings of vaginal intima present. 39. Cyrtocoris sp. (Cyrtocoridae), female. Ductus receptaculi dilated and invaginated, distal aperture of vesicular area closed. 40. Serbana borneensis (Phloeidae), female. Ductus receptaculi dilated and invaginated, distal aperture of vesicular area closed. 41. Eurygaster sinica (Scutelleridae), female. Elongate grooved sclerite present on pars comunis. aaf, anterior annular flange; ch, chitinelipsen; cs, capsula seminalis; da, distal aperture; dr, ductus receptaculi; g8, gonapophyses 8; g9, gonapophyses 9; gc8, gonocoxites 8; gc9, gonocoxites 9; go, gonangulum; g, groove; im8, intergonocoxal membrane of eighth segment; im9, intergonocoxal membrane of ninth segment; la8, laterotergites 8; la9, laterotergites 9; paf, posterior annular flange; pc, pars comunis; pi, pars intermedialis; R1, first rami; R2, second rami; T9, tergite of ninth segment; T10, tergite of tenth segment; tvi, thickenings of vaginal intima; X, tenth segment.
Figs 25–34. 25 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Figs 25–34. 25. Parastrachia japonensis (Parastrachiidae), male. Sternite VIII visible, not covered by segment VII. 26. Tessaratoma papillosa (Tessaratomidae), female. Tergite IX visible dorsally. 27. Pallantia macula (Pentatomidae), female. Tergite IX not visible dorsally, covered by apically positioned tergite VIII. 28. Urochela distincta (Urostylididae), female. Gonocoxites 9 in an ''M'' sclerite. 29. Phloea subquadrata (Phloeidae), female. Gonocoxites 9 completely fused. 30. Tectocoris diophtalmus (Scutelleridae), female. Gonocoxites 9 fused, with a distinct median fusion line. 31. Similiforstona bella (Pentatomidae), female. Laterotergites 9 contiguous covering segment X. 32. Pantochlora vivida (Pentatomidae), female. Laterotergites 9 separate with segment Xbetween them. 33. Lestonia haustorifera (Lestoniidae), female. Laterotergites 9 totally fused with segment X concealed. 34. Prionogaster serratus (Tessaratomidae), female. Laterotergites 9 larger than gonocoxites 8. g9, gonapophyses 9; gc8, gonocoxites 8; gc9, gonocoxites 9; go, gonangulum; la8, laterotergites 8; la9, laterotergites 9; M, ''M'' sclerite; R2, second rami; VII, seventh segment; X, tenth segment.
Fig. 15 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Fig. 15. Pretarsus: (15a) Lincus sp. (Pentatomidae); (15b) Arvelius sp. (Pentatomidae); (15c) Urostylis striicornis (Urostylididae); (15d) Sinopla sp. (Acanthosomatidae); (15e) Xyonysius californicus (Lygaeidae: Orsillinae), showing cylindrical claws (from Bonatto, 1988). Bp, basipulvillus; CGD, dorsal guard setae; CGL, lateral guard setae; Dp, distipulvillus; Dt, distitarsus; Em, empodium; Ga, claw; Pa, parempodia; Paa, accessory parempodia; PrGa, sharp projection of claw; PlU, unguitractor plate; Sp, parempodia support.
Fig. 14 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Fig. 14. Foretibial apparatus: 14a. Garsauria usambarica (Cydnidae); (14b) Serbana borneensis (Phloeidae); (14c) Aphylum syntheticum (Pentatomidae); (14d) Sciocoris longifrons (Pentatomidae); (14e) Bebaeus punctipes (Acanthosomatidae); (14f) Gynenica affinis (Pentatomidae); (14g) Eumenotes obscura (Dinidoridae); (14h) Platytatus ambiguus (Tessaratomidae); (14i) Amnestus sp. (Cydnidae).
Fig. 1 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Fig. 1. Diagrams showing hypotheses of Pentatomoidea classifications (Bonatto, 1988): (a) Singh-Pruthi, 1925; diagram and discussion; (b) Leston, 1958; Fig. 5; (c) China and Miller, 1959; Fig. 1; (d) Cobben, 1968; figs 269–270; (e) Cobben, 1978; several figures and text; (f) proposed phylogeny of Pentatomoidea (Gapud, 1991). [Captions removed; all taxon names rendered in current spellings; part (f) not from Bonatto (1988).]
Figs 7–13. 7a in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Figs 7–13. 7a. Antennal segments of Megymenum sp.; 7b. antennal segments of Eumenotes obscura; 7c. flattened 2nd antennal segment of E. obscura in cross-section; 7d. antennal segments of Natalicola pallidens; 7e. flattened 2nd antennal segment of N. pallidens in cross-section; 7f. antennal segments of Phloea corticata. 8. Thaumastella namaquensis (Thaumastellidae): lygaeid type of head (Štys, 1964a); humeral angles not developed. 9. Lestonia haustorifera (Lestoniidae). Scutellum long almost attaining apex of abdomen but not covering conexivum and corium of hemelytra; base of corium expanded. 10. Canopus caesus (Canopidae), dorsal view. Well-developed scutellum, completely covering abdominal dorsum and hemelytra; spheroid form. 11. Body foliations: 11a. Phloea corticata (Phloeidae), female; 11b. Serbana borneensis (Phloeidae), male. 12. Garsauriella haglundi (Cydnidae). Corium subdivided by a medial longitudinal fracture (mlf = median longitudinal fracture). 13. Tessaratoma papillosa (Tessaratomidae). Hindwing stridulitrum. (S = stridulitrum)
Figs 2–6. 2a in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)
Figs 2–6. 2a. Poecilometis sp. (Pentatomidae): post-ocular tubercles and ''neck'' absent; first antennal segment long; pronotum with humeral and posterior angles developed; claval comissure absent; 2b. Trisecus pictus (Idiostolidae): post-ocular tubercles absent; antenniferous tubercles lateral on head partially obscured by mandibular plates; 2c. Trisecus pictus (Idiostolidae): claval comissure well developed. 3. Urolabida sp. (Urostylididae). Base of head forming a ''neck''; first antennal segment long. 4a. Saileriola sandakanensis (Saileriolidae): antenniferous tubercles lateral on head, visible in dorsal view; head conical; ocelli closer; 4b. S. sandakanensis: claval comissure obsolete; 4c. Amnestus sp. (Cydnidae): claval comissure reduced. 5. Ceratocoris sp. (Plataspididae). Antenniferous tubercles ventral on head, completely covered by the development of mandibular plates. 6. Canopus caesus (Canopidae), ventral view. Prosternum deeply sulcate and strongly carinate; trichobothria longitudinal.
An amplicon sequencing protocol for attacker identification from DNA traces left on artificial prey
<ol> <li>Clay model studies are a popular tool to identify predator-prey interactions that are challenging to observe directly in the field. But despite its wide use, the method's applicability is limited by its low taxonomic resolution. Attack marks on clay models are usually identified visually, which only allows classification into higher taxonomic levels of predators. Thus, the method is often biased, lacks proof and, above all, standardization.</li> <li>Here, we tested whether precise identification of attackers can be provided by amplification and sequencing of mitochondrial DNA left in bite marks on clay models. We validated our approach in a controlled laboratory study as well as in a field experiment using clay models of a common European amphibian, the European fire salamander (<i>Salamandra salamandra</i>). DNA based taxonomic assignments were additionally compared to visual assessments of bite marks.</li> <li>We show that trace DNA of attackers can be routinely isolated and sequenced from bite marks, providing accurate species level classification. In contrast, visual identification alone yielded a high number of unassigned predator taxa. We also highlight the sensitivity of the method and show likely sources of contamination as well as probable cases of secondary and indirect predation.</li> <li>Our standardized approach for species level attacker identification opens up new possibilities far beyond the standard use of clay models to date, including food web studies at unprecedented detail, invasive species monitoring as well as biodiversity inventories.</li> </ol>
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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.