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42 results for “mtDNA sequence”
Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period
<p><strong><span>Aim: </span></strong><span>Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations </span><span>is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. </span><span>This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene.</span></p> <p><span><strong>Location:</strong> </span><span>Europe</span></p> <p><strong><span>Taxon: </span></strong><span>Common vole (<em>Microtus arvalis</em>)</span></p> <p><strong><span>Methods: </span></strong><span>We generated a dataset comprised of a 4.2-kb-long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated.</span></p> <p><span><strong>Results:</strong> </span><span>We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than previous estimates. </span><span>We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition.</span><span> </span><span>In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM), even at high latitudes.</span></p> <p><strong><span>Main conclusions: </span></strong><span>The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas </span><span>climate </span><span>deterioration </span><span>during</span><span> the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.</span></p>
Fig. 3 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 3. Maximum likelihood trees and population structuring of Apatania (A) and Limnephilus (B) based on ddRAD SNP data.ML trees were inferred from RAxML analysis with 1,000 bootstrap replicates. The bootstrap values are indicated near the branches. Results of population STRUCTURE analyses with posterior probability plots of individual assignments to the inferred genetic clusters for K = 6 and 7 for Apatania and K = 4 for Limnephilus.
Fig. 2 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 2. Maximum likelihood trees based on mitochondrial COI sequences of Apatania (A) and Limnephilus (B). The bootstrap values are indicated near the branches (only shown for nodes supported with more than 50% of BS).
FIGURE 2. Phylogenetic relationships between T. cinnabarinus and T. urticae inferred from ITS2 in Genetic Relationship between the Carmine Spider Mite Tetranychus cinnabarinus (Boisduval) and the Two-spotted Mite T. urticae Koch in China Based on the mtDNA COI and rDNA ITS2 Sequences
FIGURE 2. Phylogenetic relationships between T. cinnabarinus and T. urticae inferred from ITS2 data of Neighbor- Joining methods. Phylogenetic tree was established by MEGA based on Kimura-2-parameter distance. Numbers on branches indicate the percentage of 100 bootstraps supporting the branching pattern shown. Two sequences of T. evansi and T. pacificus were used as outgroups.
FIGURE 1 in Genetic Relationship between the Carmine Spider Mite Tetranychus cinnabarinus (Boisduval) and the Two-spotted Mite T. urticae Koch in China Based on the mtDNA COI and rDNA ITS2 Sequences
FIGURE 1. Phylogenetic tree inferred from COI sequences of various samples of T. urticae and T. cinnabarinus. The Neighbor-Joining (NJ) method was used based on distances calculated using Kimura-2-parameter correction method. Numbers on branches indicate the percentage of 100 bootstraps supporting the branching pattern shown. The species Petrobia harti and Bryobia kissophila were used as outgroups. Mite colouration for each sample is indicated in brackets: (R) means red form of T. urticae; (G) means green form of T. urticae.
Fig. 4 in Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences
Fig. 4. The maximum-likelihood (ML) chronogram for the evolution of the Eremias persica complex of the Iranian plateau. The time scale was calibrated based on palaeogeographical evidence (see the text for details). The time bar represents the approximate time of past branching events in millions of years before the present. The numbers indicate the ML bootstrap values (200 replicates).
Fig. 2 in Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences
Fig. 2. Patterns of nucleotide substitution. Pairwise proportions of transitions (s) and transversion (v) versus JC69 distance, derived from the combined data set. The graph indicates there is low saturation in the data set.
Fig. 3 in Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences
Fig. 3. Bayesian inference phylogram (GTR + I + G model) based on 1533 base pairs of the cytochrome b and 12S sequence data set. The numbers next to the nodes are clade credibility values, from the Bayesian analysis, followed by maximum-parsimony bootstrap values (1000 replicates), and those next to the curved brackets indicate the localities in Figure 1.
Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period
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Figure 3. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species
Figure 3. D. hattamimizu detailed internal anatomy showing the disputed paired nephridial funnels ("n.m.") sketched for only three of the nephridia (after Hatai, 1930: fig. 4).
Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf
<p>Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf.</p> <p>Ludt, W.B., Jabado, R.W., Al Hameli, S.M., Freeman, L., Teruyama, G., Chakrabarty, P. & Al Dhaheri, S.S. (2020) Establishing a reference collection and DNA barcoding the coastal fishes of the United Arab Emirates. <em>Journal of the Ocean Science Foundation</em>, 35, 54–64.</p>
Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative analyses were also performed with a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case-studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA, and allowed an assessment of prey-DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
Figure 8 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 8. Relationship of diagnosability to Nei's net nucleotide divergence (dA, Nei and Kumar 2000). Colors indicate taxonomic level of comparison: species (blue), subspecies (green), and populations (red). Vertical lines indicate the binomial 95% CI around diagnosability. Note that x-axis for dA is log10-scaled.
Fig. 1 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 1. Geographical sampling maps for (A) Apatania and (B) Limnephilus.
Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
Open the record for dataset details and reuse information.
Next-Generation Sequencing of Human Mitochondrial DNA (mtDNA) from Postmortem Brain and Blood
GEO Series GSE118615. Homo sapiens. 93 samples. Type: Genome variation profiling by high throughput sequencing.
Multimodal sequencing (gene expression, chromatin accessibility, and mtDNA genotyping) of single cells of the RPE and choroid in human MELAS (m.3243A>G) and control samples
GEO Series GSE202886. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Next generation sequencing reveals no change in mtDNA deletions upon the loss of mitochondrial fusion in mouse hearts
GEO Series GSE124420. Mus musculus. 7 samples. Type: Other.
mtDNA sequencing of aged muscle stem cells (mouse)
GEO Series GSE180953. Mus musculus. 20 samples. Type: Genome variation profiling by high throughput sequencing.
Data from: Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.
Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Aves: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as successive sister groups to this clade. This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes.
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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.