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307 results for “nuclear DNA”
Figure 3 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 3. Posterior probability distributions for mean rates of evolution estimated from the combined data under a partitioned analysis for the mitochondrial (A) and nuclear genes (B). The middle line of each box plot represents mean rates and the top and bottom lines indicate the 95% credibility intervals. CMOS; MXRA-5.
Figure 2 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 2. Age posterior probability distributions for each of the Eulaemus crown groups. Vertical black line represents the Miocene-Pliocene boundary (5.33 Mya).
Figure 1 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 1. Fifty per cent majority rule phylogram from the partitioned BEAST analyses of the combined data set (cytochrome b, 12S, CMOS, and MXRA5). Numbers above and below the nodes represent posterior probability values and mean estimates of divergence dates (in millions of years), respectively.
FIGURE 1 in Reinstatement of Alysicarpus pokleanus (Leguminosae, Papilionoideae: Desmodieae) based on ITS sequences of nuclear ribosomal DNA
FIGURE 1. Best ML tree obtained after analyzing 41 accessions from previous study (Gholami et al. 2017) including 3 outgroups using RaXML (Stamatakis 2014) on CIPRES Science gateway (Miller et al. 2010).
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
<span>Background</span> <p><em><span>Abies koreana</span></em><span> E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history.</span></p> <span>Results</span> <p><span>Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from <em>A. koreana</em>. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of <em>A. koreana</em>. The short inverted repeats (1,186 bp) of the <em>A. koreana</em> plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using <em>A. koreana</em> as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (<em>Balsamea</em>, <em>Momi</em>, and <em>Pseudopicea</em>) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization.</span></p> <span>Conclusions</span> <p><span>These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within <em>Abies</em> and new insights into the phylogenomic complexity of this genus.</span></p>
FIGURE 2 in Phylogenetics of two rhizomatous epiphytic species of Cymbidium (Orchidaceae; Cymbidieae): evidence from analyses of nuclear and plastid DNA
FIGURE 2. Maximum likelihood tree for Cymbidium based on combined nuclear and plastid DNA regions. The previously recognised sections from Liu et al. (2006) are highlighted by the colour of branches. Numbers near the nodes are bootstrap percentages and Bayesian posterior probabilities (BS ML, BS MP, PP). A dash (–) indicates that the node is inconsistent between the topology of the MP/ML trees and the Bayesian tree. "*" indicates that the node has 100 bootstrap percentage or 1.00 posterior probability.
FIGURE 1 in Phylogenetics of two rhizomatous epiphytic species of Cymbidium (Orchidaceae; Cymbidieae): evidence from analyses of nuclear and plastid DNA
FIGURE 1. Phylogenetic comparison between the ML/MP/BI trees of Cymbidium based on nuclear ribosomal ITS (left) and plastid DNA (right). Numbers near the nodes are bootstrap percentages and Bayesian posterior probabilities (BS, BS, PP). A dash (–) indicates that ML MP the node is inconsistent between the topology of the MP/ML trees and the Bayesian tree. "*" indicates that the node has 100 bootstrap percentage or 1.00 posterior probability.
Mitochondrial DNA and Nuclear SNPs to Predict Severity of COVID-19 Infection
ClinicalTrials.gov study NCT04750330. IPD Sharing: Not stated. Countries: 3. Publications: 41.
Oxidative Stress and Circulating Nuclear DNA (cfDNA) in Acute Kidney Injury and Continuous Renal Replacement Therapies.
ClinicalTrials.gov study NCT06646328. IPD Sharing: NO. Countries: 1. Publications: 55.
Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
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DNA matrix combined (nuclear and indels coded) datasets for Hyptidinae (Lamiaceae)
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Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
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Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers
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Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection
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Data from: Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell
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Data from: Nuclear DNA based species delineations of Coccus scale insects in symbiosis with plants and ants, and the role of plant epicuticular wax in structuring associations
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Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio
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Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
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Data from: Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.
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Data from: New DNA data from a Transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).
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International Brain Laboratory public data
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OpenNeuro
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