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763 results for “Mitochondrial DNA”
Figure 4 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 4. Neighbour-joining (NJ) tree of the Iberus gualtieranus complex for the combined data set of the cytochrome oxidase subunit I (COI) and 16S rRNA genes. Bootstrap values under NJ (1000 replicates), MrBayes, and maximum parsimony are shown at each node (NJ/BA/MP)> 70%. G1, A2, C3, A4, A5, and A6 are the six major clades obtained. Subclades are indicated with lower case letters (a, b, c).
Figure 5 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 5. The molecular phylogeny of cytochrome oxidase subunit I (COI) (left) and 16S rRNA (right) by neighbourjoining (NJ) analyses. Bootstrap values under NJ (1000 replicates), MrBayes, and maximum parsimony are given at each node (NJ/BA/MP)> 70%. For abbreviations, see the legend to Figure 4.
Figure 2. Phylogenetic relationships among the 29 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 2. Phylogenetic relationships among the 29 specimens of Orthometopon species. Individuals from two other terrestrial isopod species were used as outgroup taxa: Ligidium sp. and Armadillidium vulgare. Phylogenetic analyses, maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), all produced trees with the same topology. Only the BI tree is presented here. Numbers above the branches indicate bootstrap values in the MP and ML analyses, respectively (MP/ML). Numbers below the branches indicate the posterior probabilities of the Bayesian analysis (BI).
Figure 4 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 4. Type localities of members of Oreobates: (1) O. quixensis, San José de Moti, Prov. Napo, Ecuador; (2) O. simmonsi, Río Piuntza, 1830 m a.s.l., Cordillera del Cóndor, Prov. Morona-Santiago, Ecuador; (3) O. saxatilis, Ponga de Shilcayo, 470 m a.s.l., Department San Martín, Peru; (4) O. lehri, Apurimac River Valley, 2445 m a.s.l., Department Cusco, Peru; (5) O. granulosus, Santo Domingo, Carabaya, Department Puno, Peru, 1800 m a.s.l.; (6) O. madidi, Arroyo Huacataya, Serranía Eslabón, 1500 m a.s.l., Department La Paz, Bolivia; (7) O. sanderi, Arroyo Bilunto, Chunirumi Valley, 1800 m a.s.l., near Santa Cruz de Valle Ameno, Department La Paz, Bolivia; (8) O. zongoensis, Valle de Zongo, 1250 m a.s.l., Department La Paz, Bolivia; (9) O. choristolemma, Serranía de Bellavista c. 1000 m a.s.l., Department La Paz, Bolivia; (10) O. cruralis, Department La Paz, Bolivia, 4000 m a.s.l. (in error); (11) O. heterodactylus, gruta Facendinha, State Mato-Grosso, Brazil; (12) O. ibischi, km 68.5 on Santa Cruz de la Sierra-Samaipata road c. 750 m a.s.l., Department Santa Cruz, Bolivia; (13) O. sanctaecrucis, El Chapé, Department Santa Cruz, Bolivia, 2060 m a.s.l.; (14) O. discoidalis, Tucumán, Prov. Tucumán, Argentina.
Figure 6 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 6. Type specimens of some members of Oreobates. A–B, holotype of O. cruralis (BM 1947.2.15.70); C–D, holotype of O. simmonsi (KU 147068); E–F, paralectotype of O. discoidalis (BM 1947.2.15.63); G–H, holotype of O. granulosus (BM 1947.2.15.72); I–J, lectotype of O. quixensis (MNCN 1708).
Figure 1 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 1. Majority rule consensus tree based on maximum parsimony (MP) and Bayesian phylogenetic analyses of combined data from the partial cytochrome b (c. 350 bp) and 16S (c. 590 bp) mitochondrial DNA. The numbers above branches indicate boostrap support (± 50%) for the MP topology, followed by Bayesian posterior probabilities for the Bayesian topology (± 95).
Figure 2 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 2. Majority rule consensus tree based on Bayesian phylogenetic analyses of partial 16S (c. 590 bp) mitochondrial DNA of some members of the genera Oreobates, Eleutherodactylus, and Craugastor. The numbers above branches are Bayesian posterior probabilities, followed by boostrap support for maximum parsimony topology. Values lower than 0.90 Bayesian posterior probability, or lower than 60 for boostrap, are not depicted.
Figure 1 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 1. Map showing the sampling localities of the 29 specimens used for the DNA analysis. The numbers correspond to those listed in Table 1.
Figure 6 in Mitochondrial DNA variation and the evolutionary history of the Mediterranean species of Cicada L. (Hemiptera, Cicadoidea)
Figure 6. Post-glacial colonization routes of Cicada orni (black arrow) and C. barbara (crosshatched arrow) in Europe (top map) and distribution of Cicada haplotypes in the Aegean area (map below). Pie charts represent the proportion of each haplotype in each locality. Hatched circle surrounds C. orni haplotypes, grey circle groups C. mordoganensis and crosshatched circle groups C. cretensis. Smaller black circles highlight populational substructure within C. orni.
Figure 5 in Mitochondrial DNA variation and the evolutionary history of the Mediterranean species of Cicada L. (Hemiptera, Cicadoidea)
Figure 5. Neighbour-joining (NJ) phylogenetic tree [the maximum likelihood (ML) consensus tree had the same topology and is not shown) obtained for Cicada in the Mediterranean area, based on 12S rRNA gene haplotypes. Two hundred bootstrap replicates for the ML tree and 1000 for the NJ tree were performed to assess the statistical significance of internal nodes (only bootstrap values> 50% are shown, ML bootstrap values followed by the NJ ones). For each clade, an oscillogram (time vs. amplitude) of the calling song of one male of C. orni, C. mordoganensis, C. cretensis, C. lodosi and C. barbara is shown. A locality code follows the haplotype: WE, Western Europe (including most Iberian Peninsula and France specimens but also Croatia, Macedonia and Slovenia); IP, Iberian Peninsula; Gc, Greece continental – in all other codes the last letter stands for country: P, Portugal; S, Spain; M, Morocco; F, France; G, Greece; C, Crete; T, Turkey; and the first letter(s) stands for locality: M, Monforte; SH, St. Hippolyte; P, Portel; C, Caparica; L, Lisbon; Le, Lesbos; Sk Skyros; Cr, Crato; Ki, Kithira; N, Naxos; S, Samos; R, Rhodes; K, Kos; H, Heraklion; G, Gordes; Mè, Mèknes; Se, Sevilla; F, Fès; Mo, Moura; T, Toledo; A, Alcalar; FC, Foz Côa.
Mitochondrial DNA Variation in Southern Tunisian Populations
<p>mtDNA (HVR-I and HVR-II) data of five southern Tunisian human populations:</p> <p>- Douz (abbreviation: Douz)</p> <p>- Matmata (abbreviation: MAT)</p> <p>- Nouvelle Zraoua (abbreviation: ZRA)</p> <p>- R'Baya (abbreviation: rba)</p> <p>- Tamezret (abbreviation: TAM)</p>
Figure 3 in Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA
Figure 3. Global Mantel's correlation test for genetic and geographic distance of the Aedes vexans populations analyzed.
Figures 4–5. Phylogenetic tree for Aedes vexans populations constructed from 395 in Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA
Figures 4–5. Phylogenetic tree for Aedes vexans populations constructed from 395 haplotypes from the COI gene by using Bayesian Inference, BI (4) and Maximum Likelihood, ML (5). The evolutionary history for both analyses was inferred by using the GTR + G model, as suggested by jModelTest version 2.1.10. The BI tree was obtained by using 2-million generations, while the ML used 1,000 replicas. For BI, the support of the branches is indicated by the subsequent probability values, while for ML the bootstrap values are shown. Numbers in blue represent sequences from the A. nipponii subspecies. In both figures the colors below denote the continents and their respective countries: (z) America (Canada and USA) + Europe (Turkey); (z) Asia (China, India, Japan, Singapore and South Korea); (z) Europe (Sweden and Belgium) + Asia (China); (z) Eurasia (Romania, Sweden, Belgium, Russia, Kosovo, the Netherlands, China, Spain, Germany, Iran, Austria and Hungary); (z) Africa (South Africa); (z) America (USA) + Africa (South Africa).
Figures 1–2 in Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA
Figures 1–2. Map (1) showing the origin of COI gene sequences for Aedes vexans, and haplotype network (2) based on COI sequences showing the genetic relationship between populations. On the map (1), the circles indicate the location of the sequences used and the arrows, the genetic relationships between the populations. In the haplotypes network (2), the size of the circles is proportional to the haplotype frequency and each circle in color belongs to a haplotype that is respectively numbered; black docks represent ancestral haplotypes. On the map (1) and in the haplotype network (2), the following colors, group the cluster observed on the network and in the ML and BI trees (see Figs 4, 5 for details): (z) America (Canada and USA) + Europe (Turkey); (z) Asia (China, India, Japan, Singapore and South Korea); (z) Europe (Sweden and Belgium) + Asia (China); (z) Eurasia (Romania, Sweden, Belgium, Russia, Kosovo, the Netherlands, China, Spain, Germany, Iran, Austria and Hungary); (z) Africa (South Africa); (z) America (USA) + Africa (South Africa).
Mitochondrial DNA (mtDNA) Data
<p>Dataset taken from https://sites.google.com/site/consensusmotifs/</p> <p>Stored on Zenodo as backup for Stumpy Consensus Motif Search</p>
Mitochondrial DNA (mtDNA) Data
<p>Dataset taken from https://sites.google.com/site/consensusmotifs/</p> <p>Stored on Zenodo as backup for Stumpy Consensus Motif Search</p>
Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
<p>Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (<i>Rhincodon typus</i>) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna<i> </i>(<i>Euthynnus affinis</i>), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from <i>E</i>. <i>affinis</i>. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and non-target sequences as well as presence of non-target species at the sampling site, is crucial to consider. Environmental DNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.</p>
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - MiSeq - U5-H1-M1-M2-M3-M4-M5 - BAM
<p>mtDNA mixture model of 2 mtDNA sequences belonging to haplogroups U5 and H1. Run on Illumina MiSeq with 3 different polymerases (Clontech, Herculase, NEB Taq), and different DNA extraction protocols - <strong>BAM FILES </strong></p> <p>M1 = Mixture 1:2 i.e. 50%</p> <p>M2 = Mixture 1:10 i.e. 10%</p> <p>M3 = Mixture 1:50 i.e. 2%</p> <p>M4 = Mixture 1:100 i.e. 1%</p> <p>M5 = Mixture 1:200 i.e. 0.5%</p>
Data from: Strong selective effects of mitochondrial DNA on the nuclear genome
<p>Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod <i>Tigriopus californicus</i> to disrupt putatively coevolved mitonuclear genotypes in reciprocal F<sub>2</sub> hybrids. We utilized inter-individual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and <i>in vitro </i>ATP synthesis rates of mitochondria isolated from high fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high or low fitness hybrids. Significant biases for maternal alleles were detected on five (of 12) chromosomes in high fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that inter-genomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.</p>
Data from: Hare pseudo-reference genome from: the genomic impact of historical hybridization with massive mitochondrial DNA introgression
<p><b>Background:</b> The extent to which selection determines interspecific patterns of genetic exchanges enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, <i>Lepus granatensis</i>, displays in its northern range extensive mitochondrial DNA introgression from <i>L. timidus</i>, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.</p> <p><b>Results:</b> Although the average nuclear and mtDNA introgression patterns are strongly contrasted, they fit a single neutral model of post-glacial invasive replacement of <i>timidus</i> by <i>granatensis</i>. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X-chromosome and in low recombining regions.</p> <p><b>Conclusion:</b> General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.</p>
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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.