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307 results for “nuclear DNA”
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.
FIGURE 3 in The taxonomic status of Lepus melainus (Lagomorpha: Leporidae) based on nuclear DNA and morphological analyses
FIGURE 3. Maximum likelihood (ML) tree of the nuclear TG gene. Numbers above nodes represent bootstrap values. The sequence names correspond to the sample codes listed in Table 1. The letters A and B in the terminal names represent the two alleles of heterozygotic individuals.
FIGURE 4 in The taxonomic status of Lepus melainus (Lagomorpha: Leporidae) based on nuclear DNA and morphological analyses
FIGURE 4. Maximum likelihood (ML) tree of the nuclear MGF gene. Numbers above nodes represent bootstrap values. The sequence names correspond to the sample codes listed in Table 1. The letters A and B in the terminal names represent the two alleles of heterozygotic individuals.
FIGURE 2 in The taxonomic status of Lepus melainus (Lagomorpha: Leporidae) based on nuclear DNA and morphological analyses
FIGURE 2. Plot of scores for principal components 1 and 2 of Lepus melainus, L. mandshuricus, and L. timidus. See able 3 for factor loadings, eigenvalues and percentage of variance of principal components.
FIGURE 1 in The taxonomic status of Lepus melainus (Lagomorpha: Leporidae) based on nuclear DNA and morphological analyses
FIGURE 1. Geographical distribution of the samples examined in this study and the species ranges of Lepus melainus and L. mandshuricus in China.
Figure 4 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 4. Comparison of three alternative hypotheses on the ancestral 2n number of chromosomes of Nabidae: fusions, proposed by Nokkala et al. (2007); autosomal polyploidy, suggested by Kuznetsova & Maryańska-Nadachowska (2000) and supported by nuclear DNA content data from the present study; and the hypothetical fission theory. Abbreviations: 2C, nuclear DNA content; F, autosomal fusions; Fis, fissions; P, polyploidy.
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C peaks represent diploid cells, and 4C peaks represent cells in the G2 phase of the cell cycle, with replicated DNA. Standard used: Solanum pseudocapsicum 2C = 2.61 pg. A, Himacerus apterus female with 2n = 36 + XX and 2C = 9.71 pg. B, Nabis maoricus female with 2n = 16 + XX and 2C = 4.21 pg.
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 1 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 1. Sampling localities of Mesocarabus specimens used in this study and identified by voucher number, as listed in Table 1. Colour code: brown, Carabus riffensis; red, Carabus macrocephalus; orange, Carabus macrocephalus barcelecoanus; purple, Carabus dufourii; yellow, Carabus lusitanicus; pink, Carabus lusitanicus baguenai; blue, Carabus problematicus; and green, Carabus problematicus, from Ochagavía.
Figure 5 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 5. Ultrametric time-calibrated tree for combined DNA markers (ALL-B data set) in Carabus. Numbers above nodes represent posterior probabilities. Grey bars on nodes represent the 95% confidence intervals for node ages (Myr), with mean ages indicated inside the bars. Labels A–D indicate the cladogenetic events for Mesocarabus and Iberian Oreocarabus referred to in the main text; labels G1 and G2 indicate nodes used as calibration priors. Specimen illustrated: Carabus (Mesocarabus) lusitanicus from Albacete, Spain.
Figure 4. Bayesian 50 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 4. Bayesian 50% majority rule consensus tree for the total evidence data set (ALL-B). Numbers besides nodes represent posterior probabilities and bootstrap values for maximum-likelihood and maximum-parsimony analyses, respectively. Labels A–D indicate the cladogenetic events for Mesocarabus and Iberian Oreocarabus referred to in the text. The species colour codes are as described in Figure 1. Voucher numbers are indicated in brackets. Vertical bars represent the main lineages, as proposed by Imura (1996) and Deuve (2004). Specimens illustrated: 1, Carabus (Mesocarabus) lusitanicus from Tarragona, Spain; 2, Carabus (Mesocarabus) macrocephalus from León, Spain; 3, Carabus (Mesocarabus) riffensis from El Biutz, Morocco; 4, Carabus (Oreocarabus) guadarramus from Madrid, Spain; 5, Carabus (Oreocarabus) amplipennis from León, Spain; 6, Carabus (Orinocarabus) concolor from Bex, Switzerland; 7, Carabus (Nesaeocarabus) abbreviatus from Tenerife, Spain; 8, Carabus (Eurycarabus) faminii from Rif Massif, Morocco.
Figure 2 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 2. Distribution map of some Carabus lineages within the Metacarabi in the western Palaearctic region.
Figure 3. Bayesian 50 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 3. Bayesian 50% majority rule consensus trees from (a) nuclear (NUC) and (b) mitochondrial (MIT) data sets. The numbers beside nodes represent posterior probabilities and bootstrap values for maximum-likelihood and maximumparsimony analyses, respectively. Labels A–D indicate cladogenetic events referred to in the text for Mesocarabus (in blue) and Iberian Oreocarabus (in red). Asterisks indicate incongruent nodes between MIT and NUC data sets. The species colour codes are as described in Figure 1. Voucher numbers are indicated in brackets. Specimens illustrated: 1, Carabus (Mesocarabus) lusitanicus from Salamanca, Spain; 2, Carabus (Oreocarabus) ghiliani from Segovia, Spain.
Figure 6 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 6. Ultrametric time-calibrated tree for combined DNA markers (ALL-B data set) in Carabus showing ancestral area inferences (A, Iberian Peninsula; B, Eurasia; C, North Africa and Canary Islands). Pie charts represent the probability for each area reconstruction. The grey bars on nodes represent the 95% confidence intervals for node ages (Myr), with mean ages indicated inside bars. The palaeogeographic reconstructions are taken from Andeweg (2002).
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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
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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.