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452 results for “Mitogenomics”
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
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Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
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Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction
<p class="CxSpFirst">Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (<i>Enhydra lutris</i>) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (N=20) represent ten haplotypes, which cluster with haplotypes from Alaska, Washington, and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.</p>
Mitogenome alignment of 159 unique haplotypes representing 455 individual killer whales
<p><span>Genome sequences can reveal the extent of inbreeding in small populations. Here we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (F<sub>ROH</sub> </span><span></span><span> 0.65). Detected recombination events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with three modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among different social groups within this morphotype. Limitations to the insights gained in this study stem from the </span><span>non-independence of the three closely related modern genomes, the short coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for coupling of genetic barriers to gene flow with other killer whale populations, and the distinctive morphology. </span></p>
Alignments of reindeer/caribou mitogenome sequences
<p>Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about their colonisation routes and timings. At the end of the last ice age, reindeer/caribou (<em>Rangifer tarandus</em>) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical, and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land, and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat. </p>
Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
<p>Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer (<em>Rangifer tarandus platyrhynchus</em>), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17–20th centuries. Here we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.</p>
Figure 5 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 5. Predicted secondary structures of Pontia callidice and Pontia daplidice 22 tRNA genes.
Figure 10 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 10. Predicted secondary structure of Pontia callidice srRNA gene.
Figure 8 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 8. Predicted secondary structure of Talbotia naganum srRNA gene.
Figure 6 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 6. Predicted secondary structure of Baltia butleri srRNA gene.
Figure 4 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 4. Predicted secondary structures of Baltia butleri and Talbotia naganum 22 tRNA genes.
Figure 12 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 12. Predicted secondary structure of Pontia daplidice srRNA gene.
Transitioning from environmental genetics to genomics using mitogenome reference databases
<p><span>Species detection using eDNA is revolutionizing the global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon's resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial "barcode" regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon's fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the "PCR-free" environmental genomics methods of the future can best leverage this information.</span></p>
Data from: Independent evolution of highly variable, fragmented mitogenomes of parasitic lice
<p>The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.</p>
Mammal mitogenomics from invertebrate-derived DNA (iDNA)
<p>Mitogenomic capture of Non-human Primates from invertebrate derived DNA using hybridisation capture. </p> <p>Files are in fastq format and sequenced with illumina Mi-Seq using the Mi-Seq Reagent Kit v3 (2 x 250bp; illumina) .</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>
Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild
<p>Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the microendemic Tanzanian Kihansi spray toad (<em>Nectophrynoides asperginis</em>) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation, however a subsequent outbreak of chytridiomycosis caused by <em>Batrachochytrium dendrobatidis </em>(<em>Bd</em>) led to the spray toads extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of <em>Bd </em>from archived toad mortalities that the outbreak was caused by invasion of the <em>Bd</em>CAPE lineage and not the panzootic lineage <em>Bd</em>GPL. Molecular dating reveals an emergence of <em>Bd</em>CAPE across Southern Africa overlapping with the timing of the spray toads extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by <em>Bd</em>CAPE yet no signs of ill-health or decline suggests these other species can tolerate <em>Bd</em> when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams' construction, invasion by <em>Bd</em>CAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.</p>
Fig. 3 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 3. Relative synonymous codon usage of Protein-coding genes in Oxyurichthys ophthalmonema.
Fig. 2 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 2. Gene map of Oxyurichthys microlepis mitogenome.
Fig. 1 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 1. Gene map of Oxyurichthys ophthalmonema mitogenome.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.