Academic literature on the topic 'Mitogenomics'
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Journal articles on the topic "Mitogenomics"
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Osca, David, José Templado, and Rafael Zardoya. "Caenogastropod mitogenomics." Molecular Phylogenetics and Evolution 93 (December 2015): 118–28. http://dx.doi.org/10.1016/j.ympev.2015.07.011.
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Ho, Simon Y. W., and M. Thomas P. Gilbert. "Ancient mitogenomics." Mitochondrion 10, no. 1 (2010): 1–11. http://dx.doi.org/10.1016/j.mito.2009.09.005.
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Halasan, Lorenzo C., and Hsiu-Chin Lin. "Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes." Organisms Diversity & Evolution 24, no. 3 (2024): 417–34. https://doi.org/10.1007/s13127-024-00648-9.
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Halasan, Lorenzo C., Lin, Hsiu-Chin (2024): Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes. Organisms Diversity & Evolution 24 (3): 417-434, DOI: 10.1007/s13127-024-00648-9, URL: https://doi.org/10.1007/s13127-024-00648-9
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Horreo, Jose L. "Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances." PeerJ 5 (September 18, 2017): e3828. http://dx.doi.org/10.7717/peerj.3828.
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The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.
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Bellini, Bruno Cavalcante, Feng Zhang, Paolla Gabryelle Cavalcante de Souza, Renata Clicia dos Santos-Costa, Gleyce da Silva Medeiros, and Nerivânia Nunes Godeiro. "The Evolution of Collembola Higher Taxa (Arthropoda, Hexapoda) Based on Mitogenome Data." Diversity 15, no. 1 (2022): 7. http://dx.doi.org/10.3390/d15010007.
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Mitogenomes represent useful tools for investigating the phylogeny of many metazoan clades. Regarding Collembola, the use of mitogenomics has already shown promising results, but few published works include sufficient taxon sampling to study its evolution and systematics on a broader scale. Here, we present a phylogenetic study based on the mitogenomes of 124 species from 24 subfamilies, 16 families, and four orders—one of the most comprehensive datasets used in a molecular study of Collembola evolution to date—and compare our results with the trees from recently published papers and traditional systematic hypotheses. Our main analysis supported the validity of the four orders and the clustering of Poduromorpha with Entomobryomorpha (the traditional Arthropleona). Our data also supported the split of Symphypleona s. str. into the Appendiciphora and Sminthuridida suborders, and the division of the Neelipleona into two subfamilies: Neelinae and Neelidinae subfam. nov. On the other hand, the traditional Symphypleona s. lat., Isotomoidea, and all the Isotomidae subfamilies were refuted by our analyses, indicating a need for a systematic revision of the latter family. Though our results are endorsed by many traditional and recent systematic findings, we highlight a need for additional mitogenomic data for some key taxa and the inclusion of nuclear markers to resolve some residual problematic relationships.
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Botero-Castro, Fidel, Marie-ka Tilak, Fabienne Justy, François Catzeflis, Frédéric Delsuc, and Emmanuel J.P. Douzery. "Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)." Molecular Phylogenetics and Evolution 69, no. 3 (2013): 728–39. https://doi.org/10.5281/zenodo.13421392.
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(Uploaded by Plazi for the Bat Literature Project) Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
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Botero-Castro, Fidel, Marie-ka Tilak, Fabienne Justy, François Catzeflis, Frédéric Delsuc, and Emmanuel J.P. Douzery. "Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)." Molecular Phylogenetics and Evolution 69, no. 3 (2013): 728–39. https://doi.org/10.5281/zenodo.13421392.
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(Uploaded by Plazi for the Bat Literature Project) Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
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Schierwater, Bernd, Peter Stadler, Robert DeSalle, and Lars Podsiadlowski. "Mitogenomics and metazoan evolution." Molecular Phylogenetics and Evolution 69, no. 2 (2013): 311–12. http://dx.doi.org/10.1016/j.ympev.2013.08.009.
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Vieira, Gabriel A., and Francisco Prosdocimi. "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data." PeerJ 7 (January 24, 2019): e6271. http://dx.doi.org/10.7717/peerj.6271.
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The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.
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Xu, Shiwen, Yunfei Wu, Yingqi Liu, et al. "Comparative Mitogenomics and Phylogenetic Analyses of Pentatomoidea (Hemiptera: Heteroptera)." Genes 12, no. 9 (2021): 1306. http://dx.doi.org/10.3390/genes12091306.
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Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.
Dissertations / Theses on the topic "Mitogenomics"
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Briscoe, Andrew G. "Advancing mitogenomics : a case study in the Araneae." Thesis, Bangor University, 2013. https://research.bangor.ac.uk/portal/en/theses/advancing-mitogenomics--a-case-study-in-the-araneae(f642bbb7-75fa-49ea-a59d-23274019e8fa).html.
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Wasef, Sally A. "Ancient Egyptian Sacred Ibis Mummies: Evolutionary Mitogenomics Resolves the History of Ancient Farming." Thesis, Griffith University, 2016. http://hdl.handle.net/10072/367796.
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Animal mummies were extremely important to the people of ancient Egypt. The extraordinary number of different animal species that were mummified is evidence of this importance. The vast majority of these mummies served as ritual offerings by pilgrims to please the gods. These are known as “votive offerings”, and are thought to have flourished from the Twenty-Sixth Dynasty (664-525 BC) to the Graeco-Roman Period (30 BC–300 AD). Of these, none are found in quantities as great as the Sacred Ibis (Threskiornis aethiopicus) that were offered to the God of Wisdom and Writing, Thoth. It is estimated that 4 million Sacred Ibis mummies were deposited in dedicated catacombs throughout Egypt, with approximately 10,000 mummies interred each year. Such massive numbers suggest that ancient Egyptians perhaps kept and reared Ibis on an industrial-scale. However, there is limited evidence in ancient writings that support this suggestion. Sacred Ibis were once prevalent in Egypt but were driven to extinction as early as the mid 1800's.
Mummified Sacred Ibis specimens were collected from the main Sacred Ibis catacombs at Saqqara, Tuna el Gebel, Abydos and Thebes, as well as other mummified samples collected from worldwide museums. The aim of this research was to determine if there was evidence that Sacred Ibises were farmed for mummification purposes. If so, is there evidence for the existence of large central farm(s) from which mummies were distributed to the different catacombs by pilgrims? Alternatively, Sacred Ibises may have been reared in smaller enclosures adjacent to each of the main Thoth worshipping temples. Another possibility is that locals and / or priests may have caught wild Sacred Ibises each year from migrating populations? Alternatively, did the mummification industry source Sacred Ibis from a mix of both farmed and wild Sacred Ibises in order to meet the extraordinary demand?<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>Griffith School of Environment<br>Science, Environment, Engineering and Technology<br>Full Text
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McCullagh, Bonnie. "Sequence evolution among divergent mitochondrial haplotypes within species of Junonia butterflies." Journal of Asia-Pacific Entomology, 2015. http://hdl.handle.net/1993/31105.
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The New World Junonia butterflies include well-studied model organisms yet their phylogeny remains unresolved by traditional cox1 DNA barcodes. Sixteen Junonia mitochondrial genomes were sequenced using next generation MiSeq technology. Junonia lemonias, an Old World species, has mitochondrial genome features typical of Ditrysian Lepidoptera, and synteny is maintained throughout Junonia. Analysis of Junonia mitogenomes produced a robust phylogeny that was used with biogeographic information to infer that Junonia crossed the Pacific Ocean to invade the New World on 3 separate occasions. Junonia vestina, a high elevation species from the Andes Mountains, shows high altitude adaptation in the mitochondrial protein coding loci atp6, atp8, cox1, cob, nad1, and nad2, with the strongest effects seen in cox1 and nad1. There is some overlap between these genes with human loci that have disease associations with the same amino acid positions which could help elucidate the function of high elevation mutations in J. vestina.<br>February 2016
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Finnegan, Kimberly A. "A Mitogenomics View of the Population Structure and Evolutionary History of the Basking Shark Cetorhinus maximum." NSUWorks, 2014. http://nsuworks.nova.edu/occ_stuetd/13.
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The basking shark, Cetorhinus maximus, has historically been a target of international fisheries, leading to well-documented declines in parts of its global distribution. Currently, the basking shark is listed as globally ‘Vulnerable’ and regionally ‘Endangered’ (North Pacific and Northeast Atlantic) on the IUCN Red List of Threatened Species, rendering the species an international conservation priority. Here, we assessed the global matrilineal genetic population structure and evolutionary history of the basking shark by completing the first whole mitochondrial genome sequence level survey of animals sampled from three globally widespread geographic regions: the western North Atlantic (n = 11), the eastern North Atlantic (n = 11), and within New Zealand territorial waters (n = 12). Despite the relatively large amount of sequence data assessed (~16,669 bp per individual), whole mitogenome analyses showed no evidence of population differentiation (ΦST = -0.047, P > 0.05) and very low nucleotide diversity (π = 0.0014 ± 0.000) across a global seascape. The absence of population structure across large distances and even between ocean basins is indicative of long-dispersal by this species, including an ability to cross known biogeographic barriers known to differentiate populations of other highly vagile pelagic fishes. Notably, evolutionary analyses of the mitogenome sequences revealed two globally sympatric but evolutionary divergent lineages, with a Bayesian framework estimated coalescence time of ~2.46 million years ago. Coalescent-based Bayesian skyline analysis uncovered subtle evidence of Pleistocene demographic flux for this species, including a potential decline in female effective population size. Thus, historical population changes may be responsible for the occurrence of the two highly divergent, yet sympatric lineages, as population declines may have resulted in the loss of intermediate haplotypes and resulted in an overall loss of genetic diversity. This work supports the recognition of basking sharks as a single matrilineal global population, and as such requires the application of a cooperative multiagency and international approach to fisheries management to conserve this highly vulnerable and ecologically unique species.
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Tabata, Ryouichi. "The origin, history and mitogenome evolution of fishes in Lake Biwa." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215345.
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Botero-Castro, Fidel. "Systématique, phylogénie et évolution moléculaires des Phyllostomidae (Mammalia, Chiroptera) : une approche mitogénomique comparative." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20053/document.
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L'acquisition des données moléculaires a été bouleversée par le développement des techniques de séquençage haut-débit. Celles-ci ont augmenté la quantité des données et ont fait diminuer le coût de manière considérable. Ces nouvelles approches ont également redonné accès à des sources de matériel biologique qui étaient auparavant inutilisables en raison de la faible quantité et la forte dégradation de l'ADN qu'elles fournissent, notamment des tissus anciens, des échantillons de musée voire du matériel fossile. Un avantage supplémentaire c'est la possibilité de multiplexer les échantillons, c'est-à-dire, les mélanger et les séquencer simultanément grâce à l'utilisation de « tags » ou étiquettes permettant de les séparer après avec des outils bioinformatiques. Un marqueur qui a grandement bénéficié de ces technologies est le génome mitochondrial. En effet, nous montrons que grâce au ratio élevé entre l'ADN mitochondrial et l'ADN nucléaire par cellule, il est possible l'obtention de mitogénomes entiers, avec de couvertures adéquates, sans qu'un enrichissement préalable de l'échantillon soit nécessaire. Ceci permet d'envisager la réalisation de projets de mitogénomique comparative pour de groupes riches en espèces, requérant un échantillonnage taxonomique exhaustif et dont les divergences génétiques rendrait difficile l'usage du séquençage classique. C'est dans ce contexte que cette thèse aborde la systématique, la phylogénie et l'évolution moléculaires d'une famille de chauves-souris néotropicales : les Phyllostomidae. Cette famille est riche en espèces, avec plus de 160 taxons mais aussi en traits d'histoire de vie contrastés notamment le régime alimentaire. Cette diversité résulte en des morphologies convergentes dont les caractères sont en conséquence peu appropriés pour reconstruire l'histoire évolutive de ce groupe. La mitogénomique a prouvé être un outil efficace dans ce dessein, mais à présent aucune étude de ce type a été conduite pour cette famille. Nous avons d'abord réussi à séquencer les mitogénomes de représentants de toutes les lignées majeures couvrant également la diversité de traits d'histoire de vie. Nous montrons ensuite que l'utilisation de ces mitogénomes permet de résoudre les relations de parenté au niveau intrafamilial avec une résolution similaire à celle d'une concaténation de marqueurs mitochondriaux et nucléaires avec un soutien statistique robuste pour la plupart des nœuds de la phylogénie. Ceci nous a permis de clarifier plusieurs relations qui restaient controversées dans des études précédentes et confirmer plusieurs des clades proposés par celles-ci. Ensuite, nous abordons l'évolution du mitogénome en relation avec les traits d'histoire de vie en utilisant comme exemple le clade des vampires, les seules Mammifères hématophages, dont le génome mitochondrial semble avoir été touché par une accélération du taux d'évolution comme conséquence de l'action combinée de forces neutres et sélectives pour répondre aux contraintes imposées par ce régime alimentaire. Finalement, le cadre phylogénétique robuste proportionné par les 100 mitogénomes que nous avons séquencés pourra être utilisé comme référence pour étudier la diversification des Phyllostomidae<br>New sequencing technologies have revolutionized the acquisition of molecular data by increasing the amount of sequences at a considerably lower cost. These new technologies have also given access to samples previously neglected because they resulted in low-quantity and degraded DNA yields, as for example, old tissues, museum specimens and even fossil rests. An additional advantage comes from the possibility of multiplexing; this is, mixing several taxa in a single sample thanks to the use of tags or labels allowing late separating the sequences using bioinformatic tools. A molecular marker that has greatly benefited from these technologies is the mitochondrial genome. Indeed, we show that, thanks to the high per-cell ratio of mitochondrial to nuclear DNA, it's possible to obtain whole well-covered mitochondrial genomes without previous sample enrichment. This allows the accomplishment of projects of comparative mitogenomics for species-rich groups needing exhaustive taxon sampling and for which strong genetic divergences would difficult the use of classical sequencing.It is in this context that this thesis tackles the molecular systematics, phylogenetics and evolution of a Neotropical family of bats: the Phyllostomidae. This species-rich family, accounting for more than 160 species, is also the family of Mammals with the highest diversity of life history traits, for example, feeding on almost every possible source of food. This diversity results in convergent morphologies that make this kind of characters inadequate for reconstructing the evolutionary history of this group. Mitogenomics has proven useful in similar cases but no study of this kind has been conducted for this family. We got to sequence whole mitogenomes for representatives of all major lineages and covering the diversity of life history traits. We then show that using these mitogenomes allows solving intrafamilial relationships with a resolution similar to that resulting from a concatenation of mitochondrial and nuclear markers and with solid statistical support for most of the nodes of the phylogeny. This allowed clarifying several controversial relationships and confirming several clades proposed in previous studies. Next, we illustrate the evolution of mitogenomes and the influence of life history traits using the clade of vampire bats, the only hematophagous Mammals, whose mitogenome seem to have undergone an acceleration of evolutionary rate as a consequence of the combined action of neutral and selective forces in order to counter the constraints imposed by this feeding habit. Finally, the robust phylogenetic frame provided by the 100 mitogenomes that we sequenced, will be used for future studies about, for exemple, the diversification process of Phyllostomids
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Shen, Hong. "Mitogenomic analysis of decapod phylogeny." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16505.
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Für eine umfassende Untersuchung der Phylogenie der Decapoda wurden von mir die mitochondrialen Genome von 13 Dekapoden sequenziert. Zusammen mit den in der GenBank verfügbaren Sequenzen von 31 Dekapoden und dem von der Universität Bonn zur Verfügung gestellten mitochondrialen Genom von Dromia personata deckt dieser Datensatz alle großen Teilgruppen der Decapoda ab. Maximum likelihood (ML)-Analysen und Bayesian inference (BI)-Analysen der Nucleotidsequenzen und Aminosäuresequenzen ergaben bezüglich der Verwandtschaft der hochrangigen Taxa ähnliche Topologien: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Gleichwohl wurde mit den Polychelida ein problematisches Taxon mit ungewissen Verwandtschaftsbeziehungen identifiziert. Auf der Eben der Unterordnungen sind die Thalassinida paraphyletisch, was mit einigen morphologischen und einigen jüngeren molekularen Studien konsistent ist, alle anderen gebräuchlichen Taxa sind monophyletisch. Es handelt sich um eine Inversion, die sich vom S-E-F tRNA cluster bis zum I-Q-M tRNA cluster erstreckt und in Procambarus fallax f. virginalis und Homarus gammarus auftritt. Im Vergleich mit dem Genarrangement des Limulus polyphemus zeigen beide Astaciden in dieser Region exakt dieselbe Inversion wie der Priapulide Priapulus caudatus, die daher innerhalb der Ecdysozoa als konvergent angenommen werden muss. Auch neben dieser Inversion innerhalb der Astacidea zeigen die Genarrangements aller verfügbaren Dekapoden mehrere interessante Eigenschaften. Um die beobachteten einzigartigen genomischen Eigenschaften zu erklären, schlage ich mit dem „inversion triggered duplication“ Model ein neues Modell für Gen-Rearrangements vor.<br>For a comprehensive study of decapod phylogeny at the mitochondrial genome level, I have sequenced the mitochondrial genome of 13 decapods. Together with available sequences of 31 decapods from GenBank, and the mitochondrial genome of Dromia personata provided by the Bonn University, the dataset now cover all major decapod taxa. Maximum likelihood (ML) and Bayesian inference (BI) of the nucleotide and amino acid datasets reveal similar topologies at the higher level relationships: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Nevertheless, one problematic taxon, Polychelida, with ambiguous affinities is recognized. At the lower level, most taxa are monophyletic, whereas the Thalassinida is paraphyletic, which is consistent with some morphological and molecular results. An inversion spanning from S-E-F tRNA cluster to the I-Q-M tRNA cluster occurred in Procambarus fallax f. virginalis, Homarus gammarus, and one priapulid Priapulus caudatus. Compared with the gene arrangement of the horseshoe crab Limulus polyphemus, both astacids and the priapulid exhibit the same inversion, which is therefore supposed to be a convergent event of the clade Astacidea and Priapulida among Ecdysozoa. Other than this notable feature observed in astacids, the gene arrangements in all available decapods show some interesting characters. To explain these unique genomic features observed here, a new gene rearrangement model is proposed, which is called the “inversion triggered duplication” model.
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Zadra, Nicola. "Genome-scaled molecular clock studies of invasive mosquitoes and other organisms of societal relevance." Doctoral thesis, Università degli studi di Trento, 2022. http://hdl.handle.net/11572/351463.
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Molecular dating (or molecular clock) is a powerful technique that uses the mutation rate of biomolecules to estimate divergence times among organisms. In the last two decades, the theory behind the molecular clock has been intensively developed, and it is now possible to employ sophisticated evolutionary models on genome-scaled datasets in a Bayesian framework. The molecular clock has been successfully applied to virtually all types of organisms and molecules to estimate timing of speciation, timing of gene duplications, and generation times: this knowledge allows contextualizing past and present events in the light of (paleo)ecological scenarios. Molecular clock studies are routinely used in evolutionary and ecological studies, but their use in applied fields such as agricultural and medical entomology is still scarce in particular because of a paucity of genome data. Genome-scaled clocks have been successfully applied, for example, to various model organisms such as Anopheles and Drosophila, as well as to invasive mosquitoes Aedes aegypti and Aedes albopictus. Many other invasive pests are emerging worldwide aided by global trade, increased connectivity among countries, lack of prevention, and flawed invasive species management. Among them, there is Aedes koreicus and Aedes japonicus, two invasive mosquito species which are monitored for public health concerns because of their harboured human pathogenic viruses. For these, as well as for other insects of societal relevance, such as the parasitoid Trissolcus japonicus, there is a paucity of gene markers and no genome data for large scale molecular clock studies. Invasive pests are typically studied using microevolutionary approaches that tackle events at an intraspecific level: these approaches provide important information for the pest management, for example, by revealing invasion routes and insecticide resistances. Approaches that tackle the deep-time evolution of the pest, such as the molecular clock, are instead less used in pest science. Many important traits associated with invasiveness have evolved by speciation over a long time frame: the molecular clock can reveal the paleo-ecological conditions that favoured these traits helping a better understanding of pest biology. Molecular clock, when coupled with phylogenomics, can further identify genes and patterns that characterize the pest: this knowledge can be used to enhance management practices. Although this is a data-driven thesis, its major aim is to provide new results to demonstrate the utility of the molecular clock in pest science. This has been done by systematically apply the molecular clock to various neglected organisms of medical and agricultural relevance. To this aim, I generated new genome data and/or assembled the largest genome-scaled data to date. I studied the molecular clock in mosquitoes, focusing on the Aedini radiation (Chapter 2) and identified a strong incongruence between the mitochondrial and nuclear phylogeny for what concerns their molecular clock. This result highlighted the importance of employing genome scaled data for these species to exclude stochastic effects due to poor/inaccurate sampling in clock studies. To tackle the absence of data, I further assembled the whole mitogenome of emerging invasive species Aedes koreicus and Aedes japonicus with the aim of producing useful data for molecular typing and of inferring divergence estimates using whole mitogenomes (Chapter 3). Dated phylogenies point toward more recent diversification of Aedini and Culicini compared to estimates from previous works, addressing the issue of taxon sampling sensitivity in dated phylogeny. Although it is possible to perform molecular clock studies on single/few gene markers, the current trend is to couple this methodology with genome-scaled datasets to reduce the stochastic effect of using few genes. For this reason, I sequenced the draft genome of A. koreicus and A. japonicus (Chapter 4). The assemblies were extremely fragmented, highlighting the problem of sequencing large genomes using short reads. The assemblies provided, however enough information for genome skimming allowing extraction of BUSCO genes for downstream analyses, whole mitogenome assemblies (used in Chapter 3), and characterisation of the associated metagenome. These data need to be integrated by long reads; it provides, however a first framework to investigate the genome evolution of these species. I further sequenced and assembled the genome of Trissolcus japonicus, the parasitoid wasp of the invasive pest Halyomorpha halys. To elucidate its divergence, estimate and define an intraspecific typing system to differentiate strains for biocontrol strategies, I reconstructed the mitochondrial genomes of two populations: the mitogenomes were surprisingly identical, suggesting that they belong to the same de facto population. I further provide a detailed clock investigation of Zika, a virus harboured and transmitted by some Aedes species (Chapter 5). Using the largest set of genomes to date, I could set the origin of ZIKV in the middle age and its first diversification in the mid-19th century. From a methodological point of view, the clocking of this virus highlighted the importance of checking for recombination and for cell-passages to obtain correct divergence estimates. I finally show my contributions to molecular clock studies of three other invasive species (Chapter 6): I helped disentangle the divergence times of Bactrocera, a genus of invasive fruit files pest of agriculture; I contributed in performing a phylogenomics study of opsin genes in Diptera; I used chloroplast and nuclear genome data to reconstruct the divergences of the invasive reed Arundo. In the various Chapters of my thesis, I highlighted the limits and the problems of current molecular clock methodologies and identified the best practices for different types of organisms in order to develop a cross-discipline understanding of the molecular clock techniques. The various results presented in this thesis further demonstrate the utility of the molecular clock approach in pest studies.
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BRANDINI, STEFANIA. "Employing mitogenomes to reconstruct migration and dispersal events." Doctoral thesis, Università degli studi di Pavia, 2017. http://hdl.handle.net/11571/1203286.
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The mitochondrial genome is organized as a small circular molecule of DNA, present in hundreds/thousands of copies per cell and characterized by a much greater evolutionary rate than the average nuclear gene. The mitochondrial DNA (mtDNA) is transmitted as a non-recombining unit only through the mother and its variability is originated only by the sequential accumulation of new mutations. During millennia, this process of molecular divergence has given rise to monophyletic units (haplogroups) that are generally restricted to specific geographic areas or population groups. The study of the geographical distribution, the internal variability and the coalescence age of each haplogroup allow us to make inferences about the demographic history of populations, such as dispersals, range expansions, or migrations.
During my PhD studies, I analysed the sequence variation of the mtDNA at the highest level of resolution, that of complete sequence (mitogenome), in order to reconstruct the migration events of both human and animal populations. In particular, I mainly focused my research activity on three projects.
The first project aimed to date the events that brought to the initial peopling in Sardinia and to clarify the genetic history of Europe. Sardinians are "outliers" in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about the genetic ancestry of Sardinians, we analyzed 3491 modern and 21 ancient mitogenomes from Sardinia and observed that the age estimates of three Sardinian-specific haplogroups are >7800 years, the archeologically-based upper boundary of the Neolithic in the island. This finding supports archeological evidence of a Mesolithic occupation of the island, but also reveals a dual ancestral origin of the first Sardinians. Indeed, one of the Sardinian-specific haplogroups harbors ancestral roots in Paleolithic Western Europe, but the other two are most likely of Late Paleolithic Near Eastern ancestry, and among those that are often assumed to have spread from Anatolia only with the Neolithic. Thus, their ages are compatible with the scenario of a Late Glacial recolonization of Mediterranean Europe from the Near East prior to the migration wave(s) associated with the onset of farming.
The second project aimed to further assess the mitogenome variation of Native Americans origin. Specifically, I focused on Ecuador and Peru, two geographical areas of particular interest because of their location along the Pacific coast, in order to shed light on the peopling of South America. Phylogenetic analyses encompassing both novel and previously reported mitogenomes, allowed the identification of 50 new sub-haplogroups and the finding of a number of sub-clades shared with Native Americans from North and Central America, thus increasing the number of founding mtDNA lineages that entered South America from the North. Our phylogeographic analyses confirmed that the North to South expansion was extremely rapid, and most likely occurred along both the Pacific and Atlantic coasts.
The third study was aimed to acquire information about the diffusion process of the Asian tiger mosquito Ae. albopictus by analysing the mitogenome variation of representatives from Asia, America and Europe. Phylogenetic analyses revealed five haplogroups in Asia, but population surveys showed that only three of these were involved in the recent worldwide spread. We also found out that a sub-haplogroup, which is now common in Italy, most likely arose in North America from an ancestral Japanese source.
During these three years I also contributed to two additional projects whose goals were to reconstruct the ancient migratory events involving the Arabian Peninsula and Eastern Africa by the study of a rare haplogroup named R0a and to acquire new insights on the initial events that brought to the diffusion of domestic cattle (Bos taurus) outside the Near East.
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Shen, Hong [Verfasser], Gerhard [Akademischer Betreuer] Scholtz, Thomas [Akademischer Betreuer] Stach, and Lars [Akademischer Betreuer] Podsiadlowski. "Mitogenomic analysis of decapod phylogeny : (Crustacea, Malacostraca) / Hong Shen. Gutachter: Gerhard Scholtz ; Thomas Stach ; Lars Podsiadlowski." Berlin : Humboldt Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://d-nb.info/1022837559/34.
Full textBooks on the topic "Mitogenomics"
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Kulik, Tomasz, Anne D. Van Diepeningen, and Georg Hausner, eds. The Significance of Mitogenomics in Mycology. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-479-5.
Full textBook chapters on the topic "Mitogenomics"
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Pisani, Davide, Robert Carton, Lahcen I. Campbell, Wasiu A. Akanni, Eoin Mulville, and Omar Rota-Stabelli. "An Overview of Arthropod Genomics, Mitogenomics, and the Evolutionary Origins of the Arthropod Proteome." In Arthropod Biology and Evolution. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-662-45798-6_3.
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Fortes, Gloria Gonzales, and Johanna L. A. Paijmans. "Analysis of Whole Mitogenomes from Ancient Samples." In Whole Genome Amplification. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2990-0_13.
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Cunha, Divino Bruno da, Luis Fernando da Silva Rodrigues‐Filho, and João Bráullio de Luna Sales. "A Review of the Mitogenomic Phylogeny of the Chondrichthyes." In Chondrichthyes - Multidisciplinary Approach. InTech, 2017. http://dx.doi.org/10.5772/intechopen.70028.
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Gáspárdy, András. "Reality of Mitogenome Investigation in Preservation of Native Domestic Sheep Breeds." In Landraces - Traditional Variety and Natural Breed. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.95768.
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This chapter deals with the study of extranuclear hereditary material and the possibilities of using it to maintain endangered animal breeds. The chapter characterizes mtDNA, presents its genes and their functions, while also emphasizing the hypervariable control region. It reports on the results of previous researches, referring to international publications. It sheds light on promising areas of mitogenomic research. It shows the maternal genetic background of local native varieties according to the results of the study of available country/geographical region. It deals with reasons for endangerment and the arguments for preservation of autochthonous breeds. In addition, it gives place to discuss some exciting professional concepts in rare breed preservation.
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"Cutthroat Trout: Evolutionary Biology and Taxonomy." In Cutthroat Trout: Evolutionary Biology and Taxonomy, edited by Michael K. Young, Kevin S. McKelvey, Tara Jennings, et al. American Fisheries Society, 2018. http://dx.doi.org/10.47886/9781934874509.ch11.
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<em>Abstract</em>.—Identifying units of conservation of aquatic species is fundamental to informed natural resources science and management. We used a combination of mitochondrial and nuclear molecular methods to identify potential units of conservation of Westslope Cutthroat Trout <em>Oncorhynchus clarkii lewisi</em>, a taxon native to montane river basins of the northwestern United States and southwestern Canada. Mitogenomic sequencing identified two major lineages composed of nine monophyletic clades, and a well-supported subclade within one of these, largely delineated by river basins. Analyses of microsatellites and single nucleotide polymorphisms corroborated most of these groupings, sometimes with less resolution but demonstrating more complex connections among clades. The mitochondrial and nuclear analyses revealed that Pleistocene glacial cycles profoundly influenced the distribution and divergence of Westslope Cutthroat Trout, that this taxon crossed the Continental Divide in two separate events, and that genetically pure but nonindigenous fish were widely distributed. Herein, we recognize nine geographically discrete, cytonuclear lineages largely circumscribed by major river basins as potential units of conservation: (1) John Day; (2) Coeur d’Alene; (3) St. Joe; (4) North Fork Clearwater; (5) Salmon; (6) Clearwater headwaters; (7) Clearwater–eastern Cascades; (8) neoboreal, consisting of most of the Columbia upstream from central Washington, the Fraser in British Columbia, and the South Saskatchewan in Alberta; and (9) Missouri.
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Ureña, Irene, Silvia Guimarães, Simon J. M. Davis, et al. "An Archaeogenetics Study of Cattle Bones from Seventeenth Century Carnide, Lisbon, Portugal." In Cattle and People. Lockwood Press, 2022. http://dx.doi.org/10.5913/archbio04.08.
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Inheritable traits of cattle were modified in various ways at different times by diverse cultures. A large collection of seventeenth century cattle remains excavated from 71 silos in the Largo do Coreto in Carnide, Lisbon, included 47 com- plete and 44 distal ends of metacarpals. These provide an opportunity to make a detailed osteometric and archaeogenetics study. While morphological changes such as size increase, as detected in bone measurements, indicate improvement for larger animals, ancient DNA is useful for studying evolutionary trajectories and modes of improvement of domestic animals. High-throughput sequencing can show evolutionary processes at unprecedented resolution. We generated whole-genome shotgun resequencing data for 6 Carnide specimens on the Illumina HiSeq X Ten platform. Mean en- dogenous DNA content for these samples varied between 1% (CAR008) and 4% (CAR014), and their mitogenomes were sequenced to between 3.56x and 33.44x mean depth of coverage, respectively. The Carnide cattle belong to the Europe- an-T3 (CAR002 and CAR021) and African-T1 haplogroups (CAR008, CAR009, CAR014, and CAR016). These haplogroups are also present in extant native breeds from the Iberian Peninsula, corroborating the hypothesis of a genetic continuity of maternal lineages over time. The admixture of African taurine cattle observed in these specimens from the Modern period supports the idea that current genetic diversity of Iberian cattle derives from the dispersal of a heterogeneous population since early times along the Mediterranean basin. In addition, the biological sex of the Carnide specimens was consistently determined by our genomic analysis and osteometric measurements. Further analyses of whole-genome nuclear data are needed to infer specific biological properties, for example, the coat color of these animals, as well as the variability of genes linked to body size, meat, and milk production traits.
Conference papers on the topic "Mitogenomics"
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Gillett, Conrad. "Weevil mitogenomics." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.94502.
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Straeuli, Rieze, and Barbara van Asch. "Mitogenomics and Phylogeny of Seven African Saturniidae (Lepidoptera)." In The 1st International Electronic Conference on Entomology. MDPI, 2021. http://dx.doi.org/10.3390/iece-10372.
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"Mitogenomics and phylogenetics of vulnerable and endangered birds of genera Aratinga and Psittacus." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-148.
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Yan, Liping. "A mitogenomic perspective on calyptrate phylogeny." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.109353.
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M., KUSLIY, GRAPHODATSKY A., and TISHKIN A. "GENETIC STUDIES OF ANCIENT AND MODERN HORSES OF ALTAI AND ADJACENT TERRITORIES." In MODERN SOLUTIONS TO CURRENT PROBLEMS OF EURASIAN ARCHEOLOGY. Altai State Univercity, 2023. http://dx.doi.org/10.14258/msapea.2023.3.15.
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Over 40 years of ancient DNA research, both fragments and complete sequences of mitogenomes and nuclear genomes of many ancient, medieval and modern horses of Altai and adjacent territories have been studied. The mentioned region attracts attention because already extinct species (Equus lenensis, Equus ovodovi) as well as wild and domestic horses lived there. Modern native breeds of this region are reservoirs of unique genetic diversity. The obtained results expanded the boundaries of distribution of horses of the Botai Eneolithic culture and confirmed the origin of ancient domestic horses of Asia from horses bred by the carriers of the Sintashta culture of the Southern Urals. A close genetic relationship was also revealed between the horses of the Khereksur and Deer Stone culture of Mongolia and the Aldy-Bel culture of Tuva, between the horses of the Pazyryk culture of Altai and the Xiongnu culture of Inner Asia.