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45 results for “mitogenome sequencing”
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
<p>Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each model a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate heterotachy, and a model partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could be biological after all.</p>
Fig. 1 in First complete mitogenome sequence of Korean Gloydius ussuriensis (Viperidae: Crotalinae)
Fig. 1. Maximum likelihood (ML) phylogenetic tree constructed with 37 viper mitogenomes, based on 13 concatenated protein-coding genes. Achalinus meiguensis (FJ424614) was used as an outgroup species and bootstrap values are shown at the nodes. The mitogenome of Gloydius ussuriensis (OR680782) was determined in this study.
Figure S1 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure S1. Map of the Gigantometra gigas mitogenome using Sanger method (GenBank accession number: MF177288). Genes in the outer circle indicate the direction of transcription of the majority strand (J-strand), and those in the inner circle indicate that of the minority strand (N-strand). The GC content, GC skew+, and GC skew- are separately shown in the circle.
Figure 6 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 6. Two examples of the heteroplasmic sites in Sanger sequencing which correspond to the differently sequenced sites. Panels A and B indicate the sites at which the second-peak is obviously higher than the third-peak and fourth-peak, and the base state of the second-peak can be obtained by at least one result of HTS. The different fluorescence densities of base situated at np 1923 in the cox1 are shown in the panel A, and the panel B shows the nucleotides with amino acids at np 1923 in the results of Sanger and HTS methods. The nucleotides are C in the results of HTS sequencing, while the corresponding nucleotides are T in the results of Sanger method in both positions, and the different nucleotides lead not to the amino acids changed. Panels C and D indicate the site at the unobvious second-peak, which is slightly higher than the third-peak and fourth-peak, and the base state of the second-peak can also be obtained by at least one result of HTS. Panel C shows the unobvious second-peak at np 7125, and the nucleotide and amino acid of the site in the results of Sanger and HTS methods are shown in panel D. The amino acids are listed using single-letter amino acid abbreviations.
Figure 4. Intraspecific pairwise K2P in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 4. Intraspecific pairwise K2P distance of G. gigas based on barcode fragment size of cox1 (Sanger). The red boxplot shows the genetic distances of individuals in all three collecting sites, and the boxplots (blue, green, and yellow) separately show the distances of individuals within each place (HNYG, HNDL, and VIET). The pink boxplot shows the distances of the corresponding cox1 sequences obtained by the two sequencing methods. Abbreviation: HNYG—Yinggeling Nature Reserve, Hainan; HNDL— Diaoluoshan Nature Reserve, Hainan; VIET—northern Vietnam.
Figure S5 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure S5. The coverage of short fragments at each position in the assembly results of HTS. The three results of HTS method were separately used as reference sequences to be mapped back onto the corresponding HTS scaffolds, and the mitochondrial genes were shown below the corresponding coverage. The scale bar had an indicator at the mean coverage level and the coverage for each nucleotide position was indicated by the height of the blue line.
Figure 3 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 3. The different nucleotides in the ITS-1 and ITS-2 regions are shown. The result shows the different nucleotides at nucleotide position np 1897 (G nucleotide and T nucleotide) and np 2790 (C nucleotide and T nucleotide) obtained by Sanger and HTS methods.
Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C. The narrow distribution of G. gigas.
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
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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>
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>
Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
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Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
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Alignments of reindeer/caribou mitogenome sequences
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Data from: Fin whale (Balaenoptera physalus) mitogenomics: a cautionary tale of defining sub-species from mitochondrial sequence monophyly
The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.
Supplementary material 1 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Inferred secondary structure of 22 tRNA genes in the mitochondrial DNA of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata). :
Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens
Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.
Supplementary material 5 from: Sullivan JP, Hopkins CD, Pirro S, Peterson R, Chakona A, Mutizwa TI, Mukweze Mulelenu C, Alqahtani FH, Vreven E, Dillman CB (2022) Mitogenome recovered from a 19 th Century holotype by shotgun sequencing supplies a generic name for an orphaned clade of African weakly electric fishes (Osteoglossomorpha, Mormyridae). ZooKeys 1129: 163-196. https://doi.org/10.3897/zookeys.1129.90287
Measurements and counts of Heteromormyrus specimens and relevant mormyrid types from existing literature and taken from photographs & radiographs of newly sequenced individuals
Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens
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