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274 results for “nuclear sequence”
Fig. 2 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 2. — The single most parsimonious tree resulting from the combined analysis of ITS + trnL-trnF + 5S spacer sequences, based on the identical 24-taxon sampling as used in Fig. 1; tree length = 349 steps; consistency index = 0.663; retention index = 0.770. Values along nodes are bootstrap percentages; nodes with dashed branches have bootstraps below 70%. Identical or near identical clades (labeled A-E) from Fig. 1 are also labeled, as is the placement of Polyscias sambucifolia and P. microbotrys (asterisks), as discussed in text. Outgroups indicated by "OG."
Fig. 4 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 4. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 40 trnL-trnF sequences; tree length = 122 steps; consistency index = 0.938; retention index = 0.972. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).
Fig. 5 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 5. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 26 5S spacer sequences; tree length = 147 steps; consistency index = 0.744; retention index = 0.849. Values along branches are bootstrap percentages.
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 3 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 3. The single most-parsimonious tree (L = 951; CI = 0.568; RI = 0.793) obtained from the maximum parsimony analysis of combined (16S + ITS1) sequence dataset. Maximum likelihood analysis produced a largely congruent topology (HKY model; Ln likelihood = - 7034.61154) with the only difference being Pisidium dubium sister to Sphaerium/Musculium clade. Taxonomic names are arranged according to suggested sphaeriinid taxonomy in the present study and five major monophyletic lineages are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups. MP bootstrap values are shown to the left of the slash and decay index values to the right above the branches. Numbers below the branches indicate ML bootstrap values.
Figure 1 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 1. Strict consensus of the four equally most parsimonious trees (L = 526; CI = 0.447; RI = 0.743) obtained from the phylogenetic analysis of sphaeriid mitochondrial 16S rDNA sequences. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Dataset for NMR quadrature echo and T1 saturation recovery pulse sequences underlying the publication 'On the quantification of solid phases in hydrated cement paste by 1H nuclear magnetic resonance relaxometry'
<p>This record comprises the datasets of combined 1H NMR quadrature echo and T1 saturation recovery pulse sequences underlying the publication “On the quantification of solid phases in hydrated cement paste by 1H nuclear magnetic resonance relaxometry” by Robert Schulte Holthausen & Peter J. McDonald, Cement and Concrete Research, https://doi.org/10.1016/j.cemconres.2020.106095.</p> <p><br> In this work different solid phases, important to cement paste hydration, are investigated with low-field bench top 1H nuclear magnetic resonance with a view to developing an alternate characterisation methodology that requires minimal invasive or destructive sample preparation.</p> <p><br> A combination of the well-established quadrature echo pulse sequence with variable pulse gap together with a T1 saturation recovery quadrature echo pulse sequence is used.</p>
Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi
<p><span>No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal 'subfossil' remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur <i>Megaladapis edwardsi </i>(~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, <i>Eulemur rufifrons</i> and <i>Lepilemur mustelinus</i>, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur vertebrates. Our phylogenetic results confirm that <i>Megaladapis</i> is most closely related to the extant Lemuridae (typified in our analysis by <i>E. rufifrons</i>) to the exclusion of <i>L. mustelinus</i>, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between <i>M. edwardsi</i> and extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore <i>Lepilemur</i>.</span></p>
The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China
<p>Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.</p>
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
Data from: Phylogenomics of superrosids and core rosids based on nuclear sequences and synteny
<p class="MsoListParagraph">Superrosids form one of the largest clades of angiosperms, including 18 orders (Vitales, Saxifragales and core rosids) which exhibits remarkable morphological and ecological diversity. However, phylogenetic relationships within superrosids remain unclear.</p> <p class="MsoListParagraph">To resolve the phylogeny of superrosids, we screened 122 single copy nuclear genes from 37 species, representing all 18 orders.</p> <p class="MsoListParagraph">Vitales was revealed as sister to all other superrosids. Within core rosids, the fabids should be restricted only to the nitrogen-fixing clade, while Picramniales, the CM clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales composed an "expanded" malvids. The COM clade (sensu APG IV) did not form a monophyletic group. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either malvids or fabids. The difficult phylogeny of superrosids is likely due to the combined effects of ancient reticulation and incomplete lineage sorting.</p> <p class="MsoListParagraph">To provide broader genomic representation of Saxifragales, we constructed a high-quality chromosome-level genome assembly for <em>Tiarella polyphylla</em> (Saxifragaceae). Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, which also indicated that Saxifragales has a closer relationship with core rosids.</p> <p class="MsoListParagraph">Our findings contribute to a better understanding of the phylogeny and evolution of angiosperms.</p>
Microsatellite data, chloroplast and nuclear rRNA sequences of Avicennia marina from Vietnam, Malaysia, and The Philippines
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Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi
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Concatenated data matrix of DNA sequences from two nuclear and four chloroplast gene regions
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Data from: Phylogenomics of superrosids and core rosids based on nuclear sequences and synteny
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Sequences of the nuclear gene ADH for thirteen species of willows and two poplars: Investigating patterns of habitat specialization in fifteen co-occurring willow and poplar species.
Thirteen willow (Salix) species occur in southeastern Minnesota and often co-occur within the same wetlands. This high local diversity is challenging to explain since closely related species are often functionally similar and density-dependent interactions such as competition and susceptibility to pests and pathogens should limit their co-occurrence. However, if willow species are partitioning resources, or if they are phylogenetically structured so that closely related species rarely co-occur, then the impact of these density-dependent processes could be reduced. In this study, I examined the role of niche partitioning in maintaining local willow diversity by documenting species distributions in plots across a water availability gradient and comparing species physiology in the field and greenhouse. By taking a phylogenetic approach, I also investigated whether willow communities exhibit phylogenetic community structure and whether there is evidence for environmental filtering.
Datasets from: Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode
<p>Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (<i>metaMATE</i>) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. <i>metaMATE</i> requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mtDNA haplotypes) or non-authentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. <i>metaMATE</i> (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of non-authentic ASVs and the collateral effects on the removal of authentic ASVs. The output from <i>metaMATE</i> facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the <i>metaMATE</i> software, available at https://github.com/tjcreedy/metamate).</p>
Data from: Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi)
The Gonorynchiformes are the sister lineage of the species-rich Otophysi and provide important insights into the diversification of ostariophysan fishes. Phylogenies of gonorynchiforms inferred using morphological characters and mtDNA gene sequences provide differing resolutions with regard to the sister lineage of all other gonorynchiforms (Chanos vs. Gonorynchus) and support for monophyly of the two miniaturized lineages Cromeria and Grasseichthys. In this study the phylogeny and divergence times of gonorynchiforms are investigated with DNA sequences sampled from nine nuclear genes and a published morphological character matrix. Bayesian phylogenetic analyses reveal substantial congruence among individual gene trees with inferences from eight genes placing Gonorynchus as the sister lineage to all other gonorynchiforms. Seven gene trees resolve Cromeria and Grasseichthys as a clade, supporting previous inferences using morphological characters. Phylogenies resulting from either concatenating the nuclear genes, performing a multispecies coalescent species tree analysis, or combining the morphological and nuclear gene DNA sequences resolve Gonorynchus as the living sister lineage of all other gonorynchiforms, strongly support the monophyly of Cromeria and Grasseichthys, and resolve a clade containing Parakneria, Cromeria, and Grasseichthys. The morphological dataset, which includes 13 gonorynchiform fossil taxa that range in age from Early Cretaceous to Eocene, was analyzed in combination with DNA sequences from the nine nuclear genes and a relaxed molecular clock to estimate times of evolutionary divergence. This "tip dating" strategy accommodates uncertainty in the phylogenetic resolution of fossil taxa that provide calibration information in the relaxed molecular clock analysis. The estimated age of the most recent common ancestor (MRCA) of living gonorynchiforms is slightly older than estimates from previous node dating efforts, but the molecular tip dating estimated ages of Kneriinae (Kneria, Parakneria, Cromeria, and Grasseichthys) and the two paedomorphic lineages, Cromeria and Grasseichthys, are considerably younger.
Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the remaining Spiranthinae) and the Eurystyles, Pelexia, Spiranthes and Stenorrhynchos clades. Eighteen of the 27 genera of Spiranthinae for which more than one species was included in our analyses are monophyletic. Paraphyly of large genera, such as Cyclopogon and Sarcoglottis, resulted from segregation of particular species or groups of species exhibiting minor modifications of structures directly involved in pollination (e.g. nectary, rostellum and viscidium). Conversely, polyphyly has resulted from convergent evolution of floral attributes in distantly related species (e.g. Mesadenus). Some of the morphological characters used traditionally for generic delimitation and in non-molecular cladistic analyses of Spiranthinae are discussed against the evolutionary framework set by our molecular trees, emphasizing putative synapomorphies and problems derived from inappropriate character coding or incorrect homology assessments. Our ancestral area analysis indicates that Spiranthinae originated in eastern South America, with subsequent migrations and secondary radiations in Mesoamerica and North America, plus a derived migration from the latter region to the Old World (Spiranthes).
Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
Premise of the study: Untapped information about allelic diversity within populations and individuals (i.e. heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allelic data across unlinked loci and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target enriched Illumina sequencing libraries. Methods: We perform supermatrix phylogeny reconstruction and species tree estimation of Artocarpus based on three methods of accounting for heterozygous sequences: a consensus method based on de novo sequence assembly, the use of ambiguity characters, and a novel method for phasing alleles. We characterize the extent to which highly heterozygous sequences impeded phylogeny reconstruction and determine whether the use of allele sequences improves resolution or decreases topological uncertainty. Key Results: We show that it is possible to infer phased alleles from target enriched Illumina libraries. We find that highly heterozygous sequences do not contribute disproportionately to poor phylogenetic resolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency. Conclusions: We provide a framework for inferring phased alleles from target enrichment data and for assessing the contribution of allelic diversity to phylogenetic reconstruction. In our dataset, the impact of allele phasing on phylogeny is minimal compared to the impact of using phylogenetic reconstruction methods that account for gene tree incongruence.
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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.