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763 results for “Mitochondrial DNA”
SSCS and DCS fq data for NZB conplastic mice mitochondrial DNA profiling
<p>The SSCS and DCS fq files for NZB conplastic mice associated with https://doi.org/10.5281/zenodo.10127101 repo. </p>
SSCS and DCS fastq data for AKR conplastic mice mitochondrial DNA profiling
<p>The SSCS and DCS fq files for AKR conplastic mice associated with https://doi.org/10.5281/zenodo.10127101 repo. </p>
Processed data files for conplastic mice mitochondrial DNA profiling
<p>This dataset contains all tables used and generated in analyses for the conplastic mice mitochondrial DNA profiling project. Please refer to serrano2023_directory<em>_</em>of_files.pdf for a description of the files. The serrano2023_directory_of_files.pdf also contains field descriptions for: </p> <ul> <li>somatic_mutations.vcf</li> <li>haplotype_mutations.vcf</li> <li>supertable.txt</li> <li>cleaned_read_depth_per_pos.txt</li> <li>adjusted_mut_freq_for_haplotypes.csv</li> <li>mut_freq_per_type.csv</li> </ul> <p>All scripts that generate the files in this zenodo repo can be found at <a href="https://github.com/sudmantlab/conplastic_mt_profiling">https://github.com/sudmantlab/conplastic_mt_profiling </a></p> <p> </p> <p>Single stranded and duplex consensus fastq files can be found at the following zenodo repositories:</p> <p><a href="https://doi.org/10.5281/zenodo.10403218">(Wildtype) B6 fastq files</a></p> <p><a href="https://doi.org/10.5281/zenodo.10403087">B6-mtAKR fastq files</a></p> <p><a href="https://doi.org/10.5281/zenodo.10397996">B6-mtALR fastq files</a></p> <p><a href="https://doi.org/10.5281/zenodo.10294450">B6-mtFVB fastq files</a></p> <p><a href="https://doi.org/10.5281/zenodo.10211698">B6-mtNZB fastq files</a></p>
Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)
<p><em>Obovaria olivaria</em> is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. <em>Obovaria olivaria </em>uses the similarly imperiled <em>Acipenser fulvescens</em> (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of <em>O. olivaria</em> from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise <em>F</em><sub>ST</sub> ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of <em>O. olivaria</em> is consistent with the existing literature on <em>Acipenser fulvescens</em> and suggest that, although northern and southern <em>O. olivaria</em> populations are genetically distinct, genetic structure in <em>O. olivaria</em> is largely clinal rather than discrete across its range. Conservation and restoration efforts of <em>O. olivaria</em> should prioritize the maintenance and restoration of locations where <em>O. olivaria </em>remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of <em>Acipenser fulvescens</em> and movement of encysted glochidia.</p>
Figure 4 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 4: Maximum likelihood phylogenetic tree inferred from the alignment of ITS1 sequences. Support values are shown as in Figure 3. The ribotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Alaria esculenta was used as an outgroup to root the tree. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site).
Figure 3 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 3: Maximum likelihood phylogenetic tree inferred from the alignment of the combined cox3 and tatC–tLeu sequences. Bootstrap values and Bayesian posterior probabilities>50% are shown, and "-" indicates a value <50%. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site). Refer to Uwai et al. (2006a) for explanation of the haplotype names and classification of the clades I to IV. The haplotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Lessoniopsis littoralis was used as an outgroup to root the tree.
Figure 2 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 2: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of ITS1 sequences. The color areas in the pie charts are proportional to the ribotype frequency in the map. Small circles indicate undetected ribotypes. Each line connecting ribotypes represents one base mutation. The ribotypes detected in the Chinese samples in the present study are indicated in the ribotype network by the same colors as those in the map.
Figure 1 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 1: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of the combined cox3 and tatC–tLeu sequences. The color areas in the pie charts are proportional to the haplotype frequency in the map. Refer to Uwai et al. (2006a) and Table 3 for explanation of the haplotype names and classification of the clades I to IV, which are enclosed by boxes with lines of different patterns. Small circles indicate undetected haplotypes. Each line connecting haplotypes represents one base mutation. The haplotypes detected in the Chinese samples in the present study are indicated in the haplotype network with the same colors as those in the map.
Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA
<p>The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching, and fragmentation. Here we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186bp and cytochrome b 487bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared to the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126,cytochrome b 0.0528) and high FST statistics (D-loop 0.725,cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.</p>
Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages. in Suidae
Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages.
Supplementary material 1 from: Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K (2022) A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). Metabarcoding and Metagenomics 6: e78756. https://doi.org/10.3897/mbmg.6.78756
A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)
FIGURE 12 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 12. Ranges of the species based on existing information. A—H. spatzi, B—H. nitidulus, C—H. dintelmanni, D—H. sp. 1, E—H. tuberculatus, F—H. bangwae, G—H. parallelus, H—H. marmoratus, I—H. marginatus, J—H. noblei, K—H. goetzei, L—H. glandicolor, M—H. mariae, N—H. viridiflavus.
FIGURE 11 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 11. Illustrations of typical colour patterns in the Hyperolius viridiflavus complex: A—H. viridiflavus, from an illustration of 1845 by J. Vignaud; B—H. marmoratus, Storms River, South Africa, photo A. Channing; C—H. marginatus, North Luangwa National Park, Zambia, photo A. Channing; D—H. parallelus, PEM A12451, Cuanavale Source, Angola, photo W. Conradie; E—H. nitidulus, Lamto, Côte d'Ivoire, photo M.-O. Rödel; F—H. glandicolor, Kinangop, Kenya, photo A. Channing; G—H. tuberculatus, ZMB 91677, Dja Reserve, Cameroon, photo M.-O. Rödel; H—H. mariae, Kiloza, Tanzania, photo A. Channing; I—H. noblei, PEM A10608, Quinonga, Mozambique, photo W. Conradie; J—H. goetzei, Iringa, Tanzania, photo A. Channing; K—H. spatzi, Senegal, photo A. Hillers; L—H. dintelmanni, CAS 254137, Edib Hills, Cameroon, photo D. Portik.
FIGURE 10 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 10. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius noblei (A), H. goetzei (B), H. spatzi (C) and H. dintelmanni (D). Locality codes are explained in Table 3.
FIGURE 8 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 8. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius nitidulus (A), H. mariae (B) and H. sp 1 (C). Locality codes are explained in Table 3.
FIGURE 9 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 9. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius bangwae (A), H. tuberculatus (B), and H. glandicolor (C). Locality codes are explained in Table 3.
FIGURE 6 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 6. Localities of sequences (black circles), type locality (star) and location of junior synonyms of Hyperolius marginatus. Locality codes are explained in Table 3.
FIGURE 7 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 7. Localities of sequences (black circles), type locality (star) and location of junior synonyms of Hyperolius parallelus. Locality codes are explained in Table 3.
FIGURE 5 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 5. Localities of sequences (black circles), type locality (star) and location of junior synonyms of Hyperolius marmoratus. Locality codes are explained in Table 3.
FIGURE 1 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 1. Localities from where sequences were obtained (black circles), and from where available names were described (red triangles). The dashed lines indicate the range of the Hyperolius viridiflavus species complex.
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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.