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763 results for “Mitochondrial DNA”
Figure 5 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 5. Phylogenetic informativeness of three mtDNA gene fragments (16S, 12S, and COI) in peppermint, cleaner, and semi-terrestrial shrimps. (A) Phylogenetic informativeness (PI) profiles of the three different mtDNA gene fragments studied through relative time in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. The sum of the instantaneous asymptotic informativeness of all sites in each gene is plotted. The arrows and numbers above or below them indicate the relative time (arrow) and magnitude (numbers) at which PI reaches its maximum value. (B) Tree topology resulting from the maximum-likelihood analysis of the sequences studied with a relative time-enforced branch length. This phylogeny was used to calculate the PI profiles in panel (A). Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3.
Figure 7. Neighbour-nets generated using SplitsTree4 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 7. Neighbour-nets generated using SplitsTree4 from the three mtDNA gene fragments studied (16S, 12S, and COI) in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3. Abbreviations: LA, Lysmata ankeri; LABP, Lysmata cf. vittata; LAM, Lysmata amboinensis; LARG, Lysmata argentopuctata; LBA, Lysmata bahia; LBO, Lysmata boggessi; LCA, Lysmata californica; LD, Lysmata debelius; LGA, Lysmata galapagensis; LGB, Lysmata grabhami; LGR, Lysmata gracilirostris; LH, Lysmata hochi; LHO, Lysmata holthuisi; LI, Lysmata intermedia; LIM2, Lysmata cf. intermedia; LK, Lysmata kuekenthali; LM, Lysmata moorei; LN, Lysmata nayaritensis; LNI, Lysmata nilita; LO, Lysmata olavoi; LP, Lysmata pederseni; LRA, Lysmata rafa; LSET, Lysmata seticaudata; LT, Lysmata cf. ternatensis; LV, Lysmata vittata; LU, Lysmata udoi; LWEF, Lysmata wurdemanni EFL; LWG, Lysmata wurdemanni TX; LWWF, Lysmata wurdemanni WFL; EXO, Exhippolysmata oplophoroides; EXE, Exhippolysmata ensirostris; MO, Merguia oligodon; MR, Merguia rhizophorae; and NSP, Nikoides sp.
Figure 3 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 3. Tree topology resulting from the combined analysis of the three mtDNA gene fragments studied (16S, 12S, and COI) for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML). Numbers above or below the branches represent the bootstrap values obtained from the maximum likelihood (ML) analysis in TREEFINDER and posterior probabilities from the Bayesian inference (BI) analysis in MrBayes (ML/BI). The general topology of the trees obtained from ML and BI analyses was the same.
Figure 1 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 1. Amino acid usage analysis (mean amino acid count per sequence) for COI reference sequences (from selected species of crustaceans: Macrobrachium rosenbergii, Exopalaemon caricaudinata, Halocaridina rubra, and Cherax destructor), for COI orthologous sequences obtained from shrimps from the genus Lysmata, and for COI-like cloned sequences from Lysmata seticaudata. The error bars in each graph represent the highest and lowest amino acid counts per sequence in the three data sets. Amino acid determination and naming follows the invertebrate mitochondrial translation code, and was performed in MEGA 5.
Figure 2 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 2. Tree topologies resulting from the analysis of COI-like cloned sequences from Lysmata seticaudata and mtDNA COI gene fragments for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML) and Bayesian inference (BI). Numbers above or below the branches represent the bootstrap values obtained from the ML analysis in TREEFINDER, and posterior probabilities from the BI analysis in MrBayes.
FIGURES 11–15 in Recovery of mitochondrial DNA for systematic studies of Pentatomoidea (Hemiptera: Heteroptera): successful PCR on early 20 century dry museum specimens
FIGURES 11–15. Trace files (electropherograms) showing the fragment (between 230/240bp and 340/350bp) of the subunit 16S. 11, Parastrachiidae: Dismegistus binotatus; 12–13, Thyreocoridae: Strombosoma impictum (12), Galgupha difficilis (13); 14–15. Dinidoridae: Coridius nepalensis (14), Megymenum brevicorne (15).
FIGURES 16–17 in Recovery of mitochondrial DNA for systematic studies of Pentatomoidea (Hemiptera: Heteroptera): successful PCR on early 20 century dry museum specimens
FIGURES 16–17. Trace files (electropherograms) showing the fragment (between 240bp and 350bp) of the subunit 16S. 16, Dinidoridae: Megymenum parallelum; 17, Tessaratomidae: Tessaratoma quadrata.
FIGURES 1–5 in Recovery of mitochondrial DNA for systematic studies of Pentatomoidea (Hemiptera: Heteroptera): successful PCR on early 20 century dry museum specimens
FIGURES 1–5. Trace files (electropherograms) showing the same fragment (between 120bp and 230bp) of the subunit 12S. 1– 2, Cydnidae: Chilocoris assmuthi (1), Linospa orbicularis (2); 3, Parastrachiidae: Dismegistus binotatus; 4–5, Thyreocoridae: Strombosoma impictum (4), Galgupha difficilis (5).
FIGURE 2 in Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA
FIGURE 2. Molecular phylogeny of the spoonbills based on maximum likelihood analysis of mitochondrial sequence data (cytochrome-b, ND2). Bootstrap support based on 1000 replicates (ML at top, MP in middle) and Bayesian posterior probability (at bottom) are indicated for each node.
FIGURE 1 in Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA
FIGURE 1. Distributions of Platalea species (following Hancock et al. 1992). The heavy gray line across Africa represents the southern edge of the winter range of migratory P. leucorodia.
Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)
<p>After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, <i>Etmopterus pusillus</i> in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has a 12 times coverage and a length of 16,741 basepairs. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple <i>E. pusillus</i> samples from various distant localities as well as sequences from a morphological similar species, the Shortfin Smooth Lantern Shark <i>Etmopterus joungi</i>. Results confirm the almost global distribution of <i>E. pusillus</i> and suggest <i>E. joungi </i>to be a junior synonym of <i>E. pusillus</i>. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet-collection type specimen for taxonomy.</p>
FIGURE 2 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 2. Scatter plot for the number of transitions (s) and transversions (v) versus TN distance of ITS1 and ITS2 in pairwise comparisons between spider mites.
FIGURE 1 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 1. Scatter plot for the number of transitions (s) and transversions (v) versus TN distance of COI gene in pairwise comparisons between spider mites, (a) all codon positions; (b) third codon position.
FIGURE 5 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 5. ML tree based on ITS2 sequences. Sequence data for the ITS2 was aligned from a total of 23 individuals from nine species. Demodex folliculorum and D. canis (GenBank nos. AM904564 and GU299785, respectively) were selected as the outgroups of ITS2 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).
FIGURE 3 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 3. Phylogeography of Gongylomorphus skinks in Mauritius based on 1102bp of combined mtDNA sequence data. Lower-case letters refer to collection localities in Fig. 1 and Table 1. Haplotype networks are drawn with the areas of circles proportional to number of individuals observed; dots represent unobserved haplotypes, and lines between them each represent a single nucleotide substitution. Filled circles represent samples collected from extant populations, and open circles samples from extinct ones.
FIGURE 2 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 2. Bayesian maximum likelihood tree for extinct and extant Gongylomorphus skinks and a range of outgroup taxa, based on 1473 bp of combined mitochondrial (12S rRNA, cytochrome b) and nuclear (c-mos) DNA sequence. Numbers adjacent to nodes indicate: Bayesian posterior probability/MP bootstrap support values for analyses conducted using all samples (top line, if present), and only a subset of samples with full-length sequence for all three genes (bottom or only line). Letters a-s indicate the sampling locality in Mauritius for each specimen (Fig. 1, Table 1). Letters in bold are specimens which were sequenced for all three genes. Letters suffixed by an * are specimens that represent extinct populations.
FIGURE 1 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 1. (A) Map of the west Indian Ocean showing the location of the Mascarene islands. (B) Mauritius showing collection localities for Gongylomorphus bojerii skinks used in the present study. (C) Mauritius showing collection localities for Gongylomorphus 'orange-tail' and G. fontenayi skinks used in the present study. * indicates extinct populations.
Figure 6 in Integrative insect taxonomy based on morphology, mitochondrial DNA, and hyperspectral reflectance profiling
Figure 6. Neighbour-joining (NJ) tree (Kimura two-parameter, K2P) for 37 sequences of combined cytochrome c oxidase subunit I (COI) and 16S. The node support: bootstrap NJ (K2P)/NJ (Tamura three-parameter, T3P)/minimum evolution (ME) (K2P). Bootstrap values of less than 50 are not displayed.
Figure 5 in Integrative insect taxonomy based on morphology, mitochondrial DNA, and hyperspectral reflectance profiling
Figure 5. Neighbour-joining tree (Kimura two-parameter, K2P) for 39 barcode cytochrome c oxidase subunit I (COI) sequences. The node support: bootstrap neighbour-joining (NJ) (K2P)/NJ (Tamura three-parameter, T3P)/minimum evolution (ME) (K2P). Bootstrap values of less than 50 are not displayed.
Figure 4 in Integrative insect taxonomy based on morphology, mitochondrial DNA, and hyperspectral reflectance profiling
Figure 4. Male: A–H, Bundera heichiana Li & Wang, 1991; I–P, Bundera emeiana Li & Wang, 1994. A, I, habitus, dorsal view; B, J, habitus, lateral view; C, K, head, dorsal view; D, L, face; E, M, pygofer, lateral view; F, N, aedeagal, lateral view; G, O, aedeagal, ventral view; H, P, connective and style, ventral view.
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Allen Brain Atlas
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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.