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1,696 results for “DNA sequence”
FIGURE 1 in Species delimitation of Stemona (Stemonaceae) based on sequences of five plastid DNA regions
FIGURE 1. Sampling sites of the 23 Stemona populations from China and two populations from Indonesia.
FIGURE 2 in Species delimitation of Stemona (Stemonaceae) based on sequences of five plastid DNA regions
FIGURE 2. Bayesian tree produced by analysis of five non-coding plastid DNA regions. Clade support is for maximum parsimony bootstrap percentages, maximum likelihood bootstrap percentages and Bayesian posterior probabilities in this order. Different topologies between the BI, MP, and ML trees are marked by asterisks.
FIGURE 3 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 3. Bayesian maximum clade reliability trees based on combined nuclear At103 and chloroplast rps16, trnL-F datasets for Dracaena, Sansevieria, and selected outgroups. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP. Long branches were shortened by half their length (indicated by \\).
FIGURE 2 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 2. Bayesian maximum clade credibility trees based on nuclear At103 (A) and chloroplast rps16, trnL-F (B) datasets for Dracaena and Sansevieria. Outgroups were trimmed from the Figure. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP.
FIGURE 1 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 1. Representative morphological diversity in the dracaenoid genera, Dracaena and Sansevieria. A, Dracaena draco subsp. draco, Spain, Canary Islands, Tenerife, Icod de los Vinos; B, D. konaensis, origin: USA, Hawai'i, Big Island, Kona coast, in cultivation at Kew (Acc. No. 2008-239); C, D. arborea, Gabon, Woleu-Ntem Rd, Mitzic to Njole; D, D. laxissima, São Tomé and Príncipe, São Nicolau; E, D. goldieana, origin: Gabon, in cultivation at Kew (Acc. No. 1990-2300); F, D. aubryana, Gabon, Woleu-Ntem Rd Mitzic to Njole; G, Sansevieria frequens, Kenya, Laikipia District, Ngare Ndare Farm (type locality); H, S. aethiopica, Namibia, 74 km from Windhoek, on road to Walvis Bay; I, S. fischeri, Kenya, Munda, 18.9 km NE of Mwatate on Taveta road; J, S. pinguicula, Kenya, by Kowi airstrip, north bank of Tiva Lugga; K, S. ascendens, Kenya, Coast Province, Kwale District, around base of Taru Hill (type locality); L, S. kirkii var. pulchra, in cultivation (private collection, Miami, FL). Photographs by A, L. Mucina; B, I. Willey; C, E–F, T.H.J. Damen; D, J.J.F.E. de Wilde; G-K, L. E. Newton; L, S. Zona.
FIGURE 13 in Reinstatement of Phrix (Delesseriaceae, Rhodophyta) based on DNA sequence analyses and morpho-anatomical evidence
FIGURE 13. ML phylogeny of the Delesseriaceae inferred from partial LSU ribosomal DNA sequences. Bootstrap values for ML (>50%; left) and posterior probabilities for BI (>0.5; right) are given on each branch. The scale is in units of nucleotide substitutions per site.
FIGURE 14 in Reinstatement of Phrix (Delesseriaceae, Rhodophyta) based on DNA sequence analyses and morpho-anatomical evidence
FIGURE 14. ML phylogeny of the Delesseriaceae inferred from partial COI gene sequences. Bootstrap values for ML (>50%; left) and posterior probabilities for BI (>0.5; right) are given on each branch. The scale is in units of nucleotide substitutions per site.
FIGURES 7–11 in Reinstatement of Phrix (Delesseriaceae, Rhodophyta) based on DNA sequence analyses and morpho-anatomical evidence
FIGURES 7–11. Phrix spatulata (E.Y. Dawson) comb. nov. 7. Apex of blade with numerous fusiform spermatangial sori in series between lateral veins of the wings. Scale bar = 200 μm. 8. Permanent mount slide showing folded blade margin and sori (one indicated by arrow) with branching of spermatangial mother cells and spermatangia (one indicated by small arrow). Scale bar = 50 μm. 9. Excised mature blade 18 mm long with 6 secondary blades. Scale bar = 2 mm. 10–11. Permanent mount slide showing apical (10) and middle (11) parts of blade. Note undivided pericentral cells (arrows show one in each Fig) as well as incipient spermatangial sori (one indicated by asterisk in Fig. 11). Scale bars = 50 μm.
FIGURE 12 in Reinstatement of Phrix (Delesseriaceae, Rhodophyta) based on DNA sequence analyses and morpho-anatomical evidence
FIGURE 12. ML phylogeny of the Delesseriaceae inferred from partial rbcL gene sequences. Bootstrap values for ML (>50%; left) and posterior probabilities for BI (>0.5; right) are given on each branch. The scale is in units of nucleotide substitutions per site.
FIGURES 1–6 in Reinstatement of Phrix (Delesseriaceae, Rhodophyta) based on DNA sequence analyses and morpho-anatomical evidence
FIGURES 1–6. Phrix spatulata (E.Y. Dawson) comb. nov. 1. Living branches ramifying through dead blade. Scale bar = 50 μm. 2. Live filament extends through axial filament of dead blade and into culture medium. Scale bar = 150 μm. 3. This filamentous basal system attached to glass was derived from a single excised filament. The levorotary growth pattern expands outward. At the center of the basal disc numerous coalescent parallel filaments occur at the bases of developing blades. Scale bar = 1 mm. 4. Formation, coalescence and elongation of horizontal filaments. Shoot on right with central axial filament enclosed by parallel adherent branches bearing oblique uniseriate laterals projecting toward middle shoot also enclosed by parallel filaments. Middle shoot has 3 uniseriate laterals growing toward and attaching to uniseriate shoot on left. Scale bar = 100 μm. 5. Basal system of radiating filaments developing into thick structure of adherent parallel filaments projecting up and around lower blade. Scale bar = 70 μm. 6. Two young blades arising from thickened bases like that in Fig. 5 entangled with live filaments. Scale bar = 200 μm.
Sequence-specific, mechanophore-free mechanochemistry of DNA
<p>Original Data underpinning Figures, Schemes, and Tables of the Manuscript and Supplementary Information.</p>
Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
Data from: Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping
Skin swabbing, a minimally invasive DNA sampling method recently developed on adult amphibians, was tested on larvae of fire salamanders (Salamandra salamandra). The quality and quantity of the sampled DNA was evaluated by (i) measuring DNA concentration in DNA extracts, (ii) sequencing part of the mtDNA cytochrome b gene (692 bp) and (iii) genotyping eight polymorphic nuclear microsatellite loci. The multiple-tubes approach was used for calculating allelic dropout (ADO) and false allele (FA) rates to evaluate the reliability of the genotypes. DNA extracts from tissue samples of road-killed individuals were included in the study as positive controls. Our results showed that skin swabs of fire salamander larvae can provide DNA in sufficient quantity and quality, as sequencing was successful and no allelic dropouts or false alleles were detected. This method, tested for the first time on amphibian larvae, has proven to be an efficient and reliable alternative to the controversial tail fin clipping procedure.
Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
Figure 6 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 6. Maximum likelihood (ML) tree inferred using IQ-TREE, version 1.6. Bootstrap support values indicated on branches; scale bar represents the number of nucleotide substitutions per site.
Figure 5 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 5. Coccophagus yunnana sp.nov. female. (a) antenna; (b) fore wing; (c) F3 and clubs; (d) stigma vein of fore wing.
Figure 4 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 4. Coccophagus yunnana sp. nov. female. (a) head and mesosoma; (b) head in face view; (c) mesosoma; (d) ovipositor.
Figure 1 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 1. Coccophagus anchoroides (Huang), female. (a) antenna; (b) fore wing; (c) mesosoma and metasoma; (d) ovipositor, mid-tibia and tarsus. Scale bars = μm (from Huang 1994).
Figure 2 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 2. Coccophagus fumadus Hayat, female. (a) meso- and metasoma (gaster); (b) antenna; (c) fore wing; (d) dorsal mesosoma; (e) head.
Figure 3 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 3. Coccophagus yunnana sp. nov. female. (a) coccid scale host with C. yunnana pupa and meconia visible; (b) pupa in dorsal view; (c) pupa in ventral view; (d) body in dorsal view; (e) body in ventral 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
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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.