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763 results for “Mitochondrial DNA”
Mitochondrial DNA from Borsuka Cave
<p>Six infant human teeth and 112 animal tooth pendants previously found at Borsuka Cave in Poland were thought to be from a burial. Uncertainties around the dating of the assemblage and the association between the teeth and pendants have precluded their association to a specific archaeological industry. In this study, we combined dating and genetic analyses of a selection of the human teeth and herbivore tooth pendants to address these questions. We confirmed the Palaeolithic origin of the human remains and herbivore tooth pendants and identified the infant as female. </p>
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
<p>Cold-water corals build up reef structures or coral gardens and play an important role for many organisms in the deep sea. Climate change, deep-sea mining, and bottom trawling are severely compromising these ecosystems, making it all the more important to document the diversity, distribution, and impacts on corals. This goes hand in hand with species identification, which is morphologically and genetically challenging for Hexa- and Octocorallia. Morphological variation and slowly evolving molecular markers both contribute to the difficulty of species identification. In this study, a fast and cheap species delimitation tool for Octocorallia and Scleractinia of the Northeast Atlantic was tested based on 49 specimens. Two nuclear markers (ITS2 and 28S rDNA) and two mitochondrial markers (COI and mtMutS) were sequenced. The sequences formed the basis of a reference library for comparison to the results of species delimitation based on proteomic analysis using the MALDI-TOF MS method. The genetic methods were able to distinguish 17 of 18 presumed species. The MALDI-TOF MS method was able to distinguish 7 species. Species that could not be distinguished from one another still achieved good signals but were not represented by enough specimens for comparison. Therefore, it is predicted that with an extensive reference library of proteome spectra for Scleractinia and Octocorallia, MALDI-TOF MS may provide a rapid and cost-effective alternative for species discrimination in corals.</p>
Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses
<p>The present-day population structure of a species reflects the combination of oceanographic currents, life-history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star-shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species' response to future climate change.</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: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
<p>Biomonitoring surveys from environmental DNA make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species-level resolution. Here we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different long-fragment sequencing approaches using Oxford Nanopore sequencing coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ('mitoenrichment'). A second enrichment approach takes advantage of the CRISPR-Cas9 targeted scission on previously dephosphorylated DNA ('targeted mitosequencing'). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17-12.33 % of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83-55 % of sequences on target and a 38 to 2123-fold mean coverage. This produced complete the mitogenome of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA is possible and can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide.</p>
Fig. 5 in Variation In Cone And Seed Morphology Traits Among The Mitochondrial Dna Haplotypes Of Scots Pine (Pinus Sylvestris L.)
Fig. 5. Distribution of the seed wing shape (%, units) between and within Scots pine mitotypes.
Fig. 4 in Phylogeography of Hypostomus strigaticeps (Siluriformes: Loricariidae) inferred by mitochondrial DNA reveals its distribution in the upper Paraná River basin
Fig. 4. Network of haplotypes generated by the TCS program.
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.
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - HiSeq - M1-M4 - BAM
<p>Illumina HiSeq data of mixtures M1 (50%), M2 (10%), M3 (2%) and M4 (1%) of haplotypes H1c6 and U5a2e (decreasing).</p> <p>See <a href="https://doi.org/10.1371/journal.pone.0135643">https://doi.org/10.1371/journal.pone.0135643</a> for technical/lab-related informations</p>
Table 1 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species
<p><b>Table 1</b> Average values of detected genetic p-distances (±SD) in percentage per lineage of <i>H. savii</i> s.l. according to used marker set</p><table><tbody><tr><th></th><th></th><th>A</th><th>B</th><th>C</th><th>D</th><th>E</th></tr></tbody><tbody><tr><th>A</th><td>ND1:</td><td>0.46± 0.12</td><td></td><td></td><td></td><td></td></tr><tr><td>CytB:</td><td>0.32± 0.21</td><td></td><td></td><td></td><td></td></tr><tr><td>COI:</td><td>0.28± 0.24</td><td></td><td></td><td></td><td></td></tr><tr><td>16 S:</td><td>0.13± 0.11</td><td></td><td></td><td></td><td></td></tr><tr><th>B</th><td>ND1:</td><td>9.14± 0.28</td><td>0.47± 0.57</td><td></td><td></td><td></td></tr><tr><td>CytB:</td><td>8.03± 1.31</td><td>1.68± 0.96</td><td></td><td></td><td></td></tr><tr><td>COI:</td><td>7.90± 0.24</td><td>0.18± 0.19</td><td></td><td></td><td></td></tr><tr><td>16 S:</td><td>3.90± 0.27</td><td>0.34± 0.41</td><td></td><td></td><td></td></tr><tr><th>C</th><td>ND1:</td><td>6.79± 0.51</td><td>8.46± 0.35</td><td>0.62 ±0.68</td><td></td><td></td></tr><tr><td>CytB:</td><td>8.27± 0.68</td><td>9.01± 1.06</td><td>1.44 ±0.71</td><td></td><td></td></tr><tr><td>COI:</td><td>7.36± 0.25</td><td>8.92± 0.24</td><td>0.83 ±0.61</td><td></td><td></td></tr><tr><td>16 S:</td><td>/</td><td>/</td><td>/</td><td></td><td></td></tr><tr><th>D</th><td>ND1:</td><td>9.19± 0.30</td><td>9.12± 0.24</td><td>8.55 ±0.64</td><td>0.42±0.54</td><td></td></tr><tr><td>CytB:</td><td>/</td><td>/</td><td>/</td><td>/</td><td></td></tr><tr><td>COI:</td><td>8.91± 0.18</td><td>7.36± 0.28</td><td>10.15 ±0.38</td><td>0</td><td></td></tr><tr><td>16 S:</td><td>/</td><td>/</td><td>/</td><td>/</td><td></td></tr><tr><th>E</th><td>ND1:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>CytB:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>COI:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>16 S:</td><td>12.8± 0.65</td><td>11.81 ±0.89</td><td>/</td><td>/</td><td>0.59± 0.30</td></tr><tr><th>X</th><td>ND1:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>CytB:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>COI:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>16 S:</td><td>4.62± 0.23</td><td>5.12± 0.29</td><td>/</td><td>/</td><td>9.97± 0.31</td></tr></tbody></table>
Table 2 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species
<p><b>Table 2</b> Estimated divergence times (in MYa) between mitochondrial lineages, obtained by BI analysis of the different marker datasets. Node heights (mean ages) are given, with 95% HPD intervals in square brackets. FIS indicates the first internal split within what we consider <i>H. savii</i> s.l. (including all four lineages – A, B, C and D), while SNN denotes the split from its nearest neighbour in the tree (most commonly <i>H. alaschanicus</i>). In the case of 16 S dataset, SNN does not include lineage E, as it is placed significantly more basal (see Fig. 2d). E is also excluded from <i>H. savii</i>, alongside X (Fig. 1c), in case of concatenated dataset. (C1, C2) refers to dating of the split within lineage C. Hstu – <i>H. stubbei</i>, Hara – <i>H. arabicus</i>, sc – sister clade</p><table><tbody><tr><th></th><th>ND1</th><th>CytB</th><th>COI</th><th>16 S</th><th>Conc.</th></tr></tbody><tbody><tr><th>(A, C)</th><td>2.17 [1.62–2.70]</td><td>2.16 [1.75–2.60]</td><td>2.58 [1.94–3.30]</td><td></td><td>3.21 [2.56–3.89]</td></tr><tr><th>(A, B)</th><td></td><td></td><td></td><td>3.31 [2.13–4.52]</td><td></td></tr><tr><th>(B, D/Hstu)</th><td>2.38 [1.89–2.92]</td><td></td><td>2.54 [1.87–3.24]</td><td></td><td>3.12 [2.46–3.82]</td></tr><tr><th>(B, (A, C))</th><td></td><td>2.50 [2.08–2.94]</td><td></td><td></td><td></td></tr><tr><th>(C1,C2)</th><td>0.51 [0.32–0.70]</td><td>0.54 [0.36–0.73]</td><td>0.44 [0.24–0.66]</td><td></td><td>0.64 [0.43–0.85]</td></tr><tr><th>(E, sc)</th><td></td><td></td><td></td><td>11.18 [8.15–14.39]</td><td>9.93 [7.79–12.19]</td></tr><tr><th>(X, (A, B))</th><td></td><td></td><td></td><td>4.31 [2.97–5.76]</td><td></td></tr><tr><th>(X, Hara)</th><td></td><td></td><td></td><td></td><td>2.47 [0.00-5.44]</td></tr><tr><th>FIS</th><td>2.79 [2.32–3.28]</td><td></td><td>3.29 [2.67–3.95]</td><td></td><td>3.89 [3.22–4.62]</td></tr><tr><th>SNN</th><td>3.12 [2.58–3.67]</td><td>3.36 [2.81–3.93]</td><td>3.61 [2.95–4.34]</td><td>5.96 [4.68–7.37]</td><td>4.51 [3.72–5.30]</td></tr></tbody></table>
Mitochondrial DNA and RNA interactomes
<p>Protocol for isolation of mitochondrial DNA and RNA interacting proteins and MS data results.</p>
Data from: Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation
Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snappers). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species (L. campechanus). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favor the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. While we find evidence of introgression in geographically neighboring populations in northern South America, the genetic differences strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.
Figure 5 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 5. Altitudinal distribution across habitat types of members of the genus Oreobates.
Seascape genetics of the Atlantic spotted dolphin (Stenella frontalis) based on mitochondrial DNA
<p>The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population-level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.</p>
Mitochondrial DNA assay of 63 Chinook-Coho salmon hybrids
<p>Mitochondrial DNA sequences can identify the maternal species involved in hybridization events and provide behavioural clues of the matings. In this study, Mitochondrial DNA indicated hybrids were the offspring of female Coho salmon spawning with Chinook salmon males (all but two individuals from a reciprocal cross). This finding suggested two possible scenarios: accidental fertilization in crowded spawning grounds or heterospecific choice of mate when conspecifics were not available (e.g. differential abundance).</p>
The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management
<p>There are only about 7,100 adolescent and adult cheetahs (<em>Acinonyx</em> <em>jubatus</em>) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the <em>A</em>. <em>j</em>. <em>soemmeringii</em> specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.</p>
Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling (datasets)
<p>Supplemental data files that include the results of complexome profiling experiments from the manuscript entitled "<strong>Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling" by Potter et al</strong>. </p> <p>Supplemental Data 1: comparison of mitochondrial complexomes obtained with either Blue Native (BNE) or high resolution Clear Native (hrCNE) gel electrophoresis. </p> <p>Supplemental Data 2: comparison of mitochondrial complexomes obtained with hrCNE from samples supplemented or not with DNase I. </p> <p>Supplemental Data 3: comparison of mitochondrial complexomes obtained with hrCNE from samples supplemented with only DNase I or a combination of DNase I and RNase A. </p> <p>Supplemental Data 4: comparison of mitochondrial complexomes obtained with hrCNE from control cells, cells treated with ethidium bromide and cells recovering after ethidium bromide treatment.</p> <p>Supplemental Data 5: results of LFQ-based analysis of profiles obtained from samples supplemented or not with DNase I.</p> <p>Supplemental Data 6: individual profiles (replicates), alignment and mass calibration results for the presented data.</p>
Diversity of mitochondrial DNA in three species of great whales before and after modern whaling
<p>The 20th-century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for three great whales in the South Atlantic, the blue, humpback and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th-century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all three species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere. </p>
Mitochondrial DNA from Borsuka Cave
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