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140 results for “mitochondrial diversity”
Figure S2 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure S2. ABGD results of COXI gene. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 21): Anatolia, China, Asian and European parts of Russia; Group 2 (n: 16): Serbia, Hungary.
Figure S1 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure S1. ABGD results of CYTB gene region. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 56): Anatolia, Georgia, Armenia, Iran, Siberia, China, Asian parts of Russia and one sample from Ukraine; Group 2 (n: 31): European parts of Russia, three samples from Ukraine, Western, Central and Eastern Europe.
Figure 7 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 7. Bayesian tree obtained from IRBP sequences based on HKY + G parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.
Figure 6 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 6. Median-joining network obtained from IRBP haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.
Figure 5 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 5. Bayesian tree obtained from COXI sequences based on HKY + I parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.
Figure 4 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 4. Median-joining network obtained from COXI haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.
Figure S3 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure S3. ABGD results of IRBP gene region. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 28): Anatolia, Serbia, Hungary, Iberian Peninsula; Group 2 (n: 1): one sample from Anatolia.
Figure 3 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 3. Bayesian tree obtained from CYTB sequences based on HKY+I+G parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.
Figure 1. Figure 1 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 1. Figure 1. Location map of AUMAC samples and GenBank Sequences (modified from Yiğit et al. 20161). Black line is the border of arvalis and obscurus forms; dotted lines show possible hybridization zone of the two forms. Western Europe (1: Orkney Island, 2: Spain, 3: France, 4: Belgium), Central Europe (5: Germany, 6: Switzerland, 7: Czech Republic), Eastern Europe (8: Austria, 9: Slovenia, 10: Bosnia, 11: Montenegro, 12: Serbia, 13: Hungary, 14: Poland, 15: Ukraine, 16: European Russia/Vladimir, 17: European Russia/ Arkhangelsk Oblast) groups are 'arvalis' form. Anatolia and its surroundings (18: Anatolia/Ardahan, Kars and Erzurum provinces, 19: Iran, 20: Armenia) and Asia (21: Russia/Orenburg Oblast, 22: Russia/ Chelyabinsk Oblast, 23: China/Xinjiang, 24: Siberia) belong to 'obscurus' form.
Datasets: Population genomics and mitochondrial DNA reveal cryptic diversity in North American Spring Cavefishes (Amblyopsidae, Forbesichthys)
<p>Forbesichthys_allsites.vcf: Dataset in VCF format used to perform Effective Population Size estimation.</p> <p>Forbesichthys_SNPs_NoLD.vcf: Dataset in VCF format used to perform PCA, fastStrucuture, and phylogenetic analyses.</p> <p>Files with extension .sfs contain site spectrum frequencies generated with the program easySFS.py.</p>
Linked collectors and determiners for: Uncovering a hidden diversity: a new species of freshwater shrimp Macrobrachium (Decapoda: Caridea: Palaemonidae) from Neotropical region (Brazil) revealed by morphological review and mitochondrial genes analyses.
Natural history specimen data linked to collectors and determiners held within, "Uncovering a hidden diversity: a new species of freshwater shrimp Macrobrachium (Decapoda: Caridea: Palaemonidae) from Neotropical region (Brazil) revealed by morphological review and mitochondrial genes analyses". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/de12a630-0709-4600-b356-971f170b10be">https://bionomia.net/dataset/de12a630-0709-4600-b356-971f170b10be</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/de12a630-0709-4600-b356-971f170b10be">https://gbif.org/dataset/de12a630-0709-4600-b356-971f170b10be</a>. Formatted as a Frictionless Data package.
Figure 1 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 1. Images of the three morphotypes of the Iberus gualtieranus complex. A, Iberus gualtieranus, with a keeled, flattened shell and closed umbilicus. B, Iberus alonensis, with a globose and non-umbilicated shell. C, Iberus campesinus, with a rounded, umbilicated shell and an expanded peristome. Scale bar: 2 cm.
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.
Setting files from: Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe
<p><strong>Simulated Data and Simulation Program</strong></p> <p>This dataset release permits to simulate the scenarios investigated in the article entitled "Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe" by Broccard et al, using the program SPLATCHE3, which is included.</p> <p>There is a zipped folder "Broccard_et_al_SimulationData.zip" that contains i) a "ReadMe.txt" file with the instructions to launch the simulations; ii) the executable called "SPLATCHE3-Linux-64b"; iii) the input settings file for the various scenarios.</p> <p>See Broccard, N, Silva, NM and & Currat M., American Journal of Biological Anthropology (2021), for background and http://www.splatche.com/splatche3 for more information about the simulation program.</p>
Global patterns of nuclear and mitochondrial genetic diversity in marine fishes
Open the record for dataset details and reuse information.
Data from: Diversity of land snail tribe Helicini (Gastropoda: Stylommatophora: Helicidae): where do we stand after 20 years of sequencing mitochondrial markers?
<p>Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy, and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of <i>Helix</i> is revised by placing <i>Helix godetiana</i> back in the genus and new synonymies are suggested within the genera <i>Codringtonia</i> and<i> Helix</i>. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.</p>
The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies
<p>Abstract: Motivation<br>Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies.</p> <p>Main types of variables contained<br>A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes.</p> <p>Spatial location and grain<br>The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude.</p> <p>Time period and grain<br>DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022.</p> <p>Major taxa and level of measurement<br>Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level.</p> <p>Software format<br>Data and functions to manage the dataset are provided in the iodatabase R package (<a href="https://github.com/leondap/iodatabase" rel="noopener noreferrer">https://github.com/leondap/iodatabase</a>) and in Dryad</p>
Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence
Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.
EGP Mitochondrial Genome Analysis on Human Genome Diversity Project Whole-Genome Sequencing Data
<p><strong>Summary: </strong>This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the HGDP. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno.</p> <p><strong>Author: </strong>Tychele N. Turner, Ph.D.</p> <p><strong>Short Writeup: EGP version 1.3 on Simons Genome Diversity Project</strong>: Short-read WGS CRAM files were downloaded from the EMBL-EBI Public Data Globus Endpoint from the <code>/1000g/ftp/data_collections</code> directory. Post-download, the data was run through EGP version 1.3. The results are shown below:</p> <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>2b388c1fa446ecec70e33ea0471e06f8</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>50b80ed32b1ae542c8967cc31986dd19</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Variant Tables</td> <td>995f30b74c4bb094a674b1a994853246</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Copy Number</td> <td>e79e61efab4c491fa2825b7d1853df58</td> </tr> </tbody> </table> </div> <div>Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open.</div>
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Allen Brain Atlas
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International Brain Laboratory public data
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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.