Mitochondria are eukaryotic cellular organelles responsible for power-generation, believed to have come into existence by an endo-symbiontic event where a bacterial cell was incorporated by an un-specified "proto-eukaryote". Phylogenetic analysis have shown that the mitochondrial ancestor was most related to present-day alpha-proteobacteria, although the exact nature of the mitochondrial progenitor remains disputed. In this work, I have used phylogenetic and other methods to investigate the identity of the organism giving rise to mitochondria, by analysing the evolutionary history of select proteins, the events where they have been transfered to the eukaryotic nucleus, and the time-point of mitochondrial establishment. In addition, a search for mitochondrially related organisms in the ocean metagenome was performed, in the hope that something more related to the mitochondrial progenitor than anything previously identified could be found. Previous analysis have shown that a large fraction of mitochondrial proteins does indeed trace their descent to the alpha-proteobacteria, but I found that the amino-acyl tRNA-synthetases display more general bacterial descent, making it likely that these proteins are of a different origin from the mitochondria themselves. While the synthetases are encoded on the nuclear genome, most mitochondria still posses most of the tRNA on their own genomes. In the cases where the tRNA has been lost from the mitochondrial genome, I found that the probability of loss correspond to the evolutionary history of their synthetase. The ocean metagenome represents an order of magnitude more data than previously available, making it suitable for improving the analyses dealing with mitochondrial placement. This large of amount of data was utilised to improve the phylogenetic analyses, showing that previous works might have suffered from artefacts inflating the support for placement of mitochondria with a specific alpha-proteobacterial group. Eukaryotic/mitochondrial radiation was shown to be as old, or older, than radiation of extant alpha-proteobacteria, casting doubt on previous analysis identifying a specific alpha-proteobacterial group as the mitochondrial ancestor.

The contribution of yeast strain background, specifically auxotrophic markers, to stability and fidelity of mtDNA replication was investigated. In summary, the ade2, his3delta200, and hap1 mutations have complex effects on mitochondrial functions, the severity of which appears to depend on other components in the genetic background of the strain. These results are important as many commonly used laboratory strains are related to the respiratory hampered S288c strain and are used for studies of orthologous human mutations associated with various mitochondrial diseases. These observations have added to our understanding of fungal mtDNA replication and have informed the mitochondrial community of problematic strains that need to be considered when using this model organism. The function of the yeast mitochondrial DNA polymerase (Mip1p) carboxyl-terminal extension (CTE) was investigated both in vivo and in vitro by genetically engineering various truncations of the CTE. The respiratory competence of mip1delta175 and mip1delta205 cells, in which Mip1p lacks the C-terminal 175 and 205 residues respectively, are indistinguishable from that of wild-type. In contrast, strains harbouring Mip1pdelta351, Mip1pdelta279, Mip1pdelta241, and Mip1pdelta222 rapidly lose mtDNA. At a low frequency, mip1delta216 cells grow poorly on glycerol. Fluorescence microscopy and Southern blot analysis revealed lower levels of mtDNA in these cells, and rapid loss of mtDNA during fermentative growth. Therefore, only the polymerase-proximal segment of the Mip1p CTE is necessary for mitochondrial function. To determine more precisely the defects associated with polymerase truncation variants, these proteins were overexpressed in yeast and used in a novel non-radioactive mtDNA polymerase assay. The threonine-661 and alanine-661 variants, shown by others to be responsible for the increased mtDNA mutability of various laboratory yeast strains at increased temperature, were examined in combination with CTE-truncations. These experiments suggest that exonuclease function is not effected in the alanine-661 variant at 37 degrees Celsius whereas polymerase activity is, and this higher relative level of exonuclease activity could be a contributing factor to mtDNA instability in S288c-related strains. Lastly, isogenic CTE truncation variants all have less DNA polymerase activity than their parental wild-type. Based on these results, several possible roles for the function of the CTE in mtDNA replication are suggested. / October 2008

Les mitochondries, organites essentiels à la production d'énergie, possèdent leur propre matériel génétique : l'ADN mitochondrial (ADNmt). Chaque produit des gènes de I'ADNmt interagit avec des protéines codées par l'ADN nucléaire pour assurer la respiration mitochondriale. Dans le règne animal, I'ADNmt est transmis exclusivement de façon maternelle. La transmission maternelle permettrait d'éviter les conflits intergénomiques. Il existe un seul système mitochondrial qui transgresse singulièrement les lois de la transmission et de la génétique de I'ADNmt, il s'agit de la double transmission uniparentale [doubly uniparental inheritance (DUI)]. L'existence de la DUI a été démontrée chez sept familles de mollusques bivalves, dont les moules marines : Mytilidae; les palourdes marines : Veneridae, Solenidae et Donacidae et les moules d'eau douce : Unionidae, Margaritiferidae et Hyriidae. Les espèces possédant ce système atypique sont caractérisées par la présence de deux ADNmt distincts qui sont hérités de façon maternelle (ADNmt F) et paternelle (ADNmt M). Typiquement, les femelles sont homoplasmiques et contiennent uniquement I'ADNmt F tandis que les mâles sont hétéroplasmiques. Chez ces derniers, I'ADNmt F domine dans les tissus somatiques alors que la gonade contient presque exclusivement I'ADNmt M. Les divergences observées entre les ADNmt F et M chez les moules peuvent atteindre ~50% en acides aminés. Ce haut niveau de divergence observée entre les génomes M et F, coexistant à l'intérieur d'un même individu soulève de nombreuses questions d'ordre évolutives. La double transmission uniparentale représente, certes, un système atypique, mais les descriptions, les comparaisons et les analyses qu'elle permet contribuent à développer une image plus exacte de l'évolution non seulement au niveau de l'évolution de la DUI, mais aussi au niveau de l'évolution du génome mitochondrial dans son ensemble. L'objectif de la présente thèse est d'utiliser une approche comparative de données moléculaires pour mettre en évidence l'évolution des génomes mitochondriaux mâle et femelle du système de la double transmission uniparentale chez les moules unionoïdes. Chez ce groupe, la double transmission uniparentale semble évolutivement plus stable (aucun évènement de recombinaison ou de masculinisation n'a été recensé) et la divergence entre les ADNmt M et F est significativement plus élevée que chez les taxons marins. Le chapitre II est une revue de littérature sur le système de la double transmission uniparentale. Les observations qui ont menées à la découverte de la DUI y sont présentées de même que le modèle et les mécanismes de la DUI. Cette revue propose la DUI comme un système modèle qui pourrait permettre d'acquérir de nouvelles connaissances sur les interactions et la coadaptation des génomes nucléaires et mitochondriaux. L'objectif du chapitre III était de séquencer, d'annoter et de publier pour la toute première fois des génomes mâles complets d'Unionoïdés. Six nouveaux génomes mitochondriaux complets d'espèces d'Unionoïdés, soit le génome F et M de Venustaconcha ellipsiformis (Unionoida: Unionidae: Ambleminae: Lampsilini), Pyganodon grandis (Unionoida: Unionidae: Unioninae: Anodontini) et Quadrula quadrula (Unionoida: Unionidae: Ambleminae: Quadrulini) ont été séquencés avec succès et les caractéristiques génomiques propres à chaque lignée mâle ont été présentées et ont fourni un contexte pour les comparaisons des génomes mitochondriaux chez les lignées de bivalves possédant et ne possédant pas la DUI. La position basale des Unionoïdés à l'intérieur des autolamellibranches ainsi que la probable origine unique de la DUI suggère que la DUI serait apparue chez un ancêtre des autolamellibranches et aurait été subséquemment perdue chez plusieurs descendants. Les caractéristiques de la DUI observées chez les Unionoïdés s'approcheraient donc davantage de l'état ancestral de la DUI. Le chapitre IV est une étude phylogéographique du genre Pyganodon (Unionidae, Bivalvia) dans le nord-est de l'Amérique du Nord. Le genre Pyganodon a été choisi entre autres en raison de sa richesse taxonomique et de sa vaste répartition géographique dans le nord-est de l'Amérique du Nord. Cette analyse phylogéographique est basée sur l'étude du polymorphisme de gènes des ADNmt M et F ce qui a permis de comparer et confronter les signaux phylogénétiques rendus par les génomes M et F à l'intérieur de ce groupe. L'exploration de la distribution de la variation génétique entre et à l'intérieur des populations et des espèces de Pyganodon a permis de mettre en évidence la complexité du système, mais aussi de distinguer les processus démographiques des processus sélectifs. Ce chapitre renforce l'hypothèse de l'action de la sélection adaptative sur le génome mitochondrial mâle. Très tôt après la découverte du système du la DUI, un possible rôle de la sélection positive comme pression sélective majeure a été soupçonnée. Malgré l'accumulation de certains indices, un tel processus n'avait jamais été démontré. Dans le chapitre V de la présente thèse, en utilisant les données recueillies et cumulées dans le chapitre III soit l'ensemble des gènes mitochondriaux codants (sauf I'ATP8) de 29 espèces de mollusque bivalves de différentes familles, un test de sélection positive en maximum de vraisemblance a été effectué. Les résultats de ce test suggèrent que de nombreux sites d'acides aminés sont positivement sélectionnés sur le génome mâle des Unionoïdés. Quelques sites seraient également positivement sélectionnés dans I'ADNmt F des Unionoïdés et témoignent probablement de la coévolution cytonucléaire. Le test n'a pas mis en évidence de sélection positive dans les ADNmt M ni F de Mytilidés et confirment que les forces évolutives n'agissent pas de manière identique dans les différents groupes de bivalves possédant la DUI. Les résultats du test révèlent que des sites d'acides aminés seraient également positivement sélectionnés dans le troisième groupe de bivalves testé soit les Vénéridés. Toutefois, la concentration de ces sites sur certains gènes spécifiques de I'ADNmt F pourrait témoigner de l'action de la sélection positive suite à une réorganisation structurale du génome. Compte tenu du profond impact que peut avoir l'ensemble des résultats de ce chapitre sur notre compréhension actuelle des forces sélectives agissant sur le génome mitochondrial, la prudence est toutefois de mise dans leurs interprétations. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : ADN mitochondrial, génomique comparative, phylogéographie, sélection positive, double transmission uniparentale, bivalves

<p>TThe proposed research will provide a set of 16 near complete mtDNA gene orders. The observed gene rearrangements will be used to investigate the phylogeny of the Sub-Class Hydroidolina and the Family Hydractiniidae. All the medusozoan classes contain a linear mitochondrial genome (mtDNA genome), whereas the Class Anthozoa contains a circular mtDNA genome (Bridge et al., 1992). The linear structure of the medusozoan mtDNA genomes is the most likely reason why these genomes are underrepresented, because the most rapid methods of mtDNA genome sequencing take advantage of the circular nature of most animal mtDNA. In a circular genome where mtDNA gene order is unknown prior to isolation, the forward and reverse primer(s) are designed based on the sequences of one or two highly conserved regions. Linear mtDNA requires a more involved approach, making it more difficult to sequence in its entirety than circular mtDNAs. In chapter 1, a novel assay to determine linear mtDNA gene orders is presented. In chapter 2, the near-complete mtDNA genome sequences are presented, as well as 7 near-complete mtDNA gene orders determined by the mtDNA gene order assay. These data are used to investigate relationships in the Family Hydractiniidae. Finally, in chapter 3, an additional 9 near complete mtDNA gene orders are used to explore relationships in the sub-class Hydroidolina. This study significantly increases the number of known near-complete mtDNA genomes, as well as their mtDNA.</p> / Dissertation

As one of the major preys of many important economic fish species such as swordfish and dolphinfish in waters off estern Taiwan, flyingfish belongs to low-end consumers in the food chain with the function of maintaining the stability of the Kuroshio marine ecosystem. Hirundichthys oxycephalus is the primary component of flyingfish-egg fishery captures in the northeastern waters of Taiwan, and is also one of the dominant species of flyingfish in eastern waters of Taiwan. However, the significant drop of the flyingfish and flyingfish-egg catch from 2006 to 2007 and the effects on ecosystem and fishery caused major concern from the fishery sector and academic field. In order to manage this marine resource effectively, the phylogenetic relationships and population structure needed to be characterized first. In this study, the phylogenetic relationships of Hirundichthys oxycephalus of Northwestern Pacific was characterized based on the mitochondrial COI fragment. Totally 55 samples were collected between July, 2008 and November, 2010 in waters of Keelung, Ilan, Hualian, and Green Island. In addition, 12 more samples were obtained in Sebtember, 2009 from Tanegashima Island, and Yakushima Island of Japan. The DNA sequencing results of samples from Taiwan showed a total number of 29 haplotypes. The length of partial COI sequence was found to be 657 bp while the mean genetic distance was found to be 0.6%. In phylogenetic analyses, two major groups were identified in the phylogenetic trees by neighbor-joining and maximum-likelihood methods. The majority of "Keelung inshore group" came from Keelung and Ilan waters. The main population of "Kuroshio group" came from Green Island. The variation between two groups was found to be 61.75% by amova. The DNA sequencing results of samples from Japan showed a total number of 8 haplotypes. The length of partial COI sequences was found to be 657 bp with a mean genetic distance of 0.53%. In the phylogenetic tree, the samples from Japan were found to belong to "Kuroshio group". The variation between the two major groups was found to be 60% by amova. It was inferred that the differentiation of flyingfish into the two major groups in Taiwan was due to the flow pattern difference of Kuroshio in northeast waters of Taiwan. It was also inferred that phylogenetic similarity of the samples from Japan and the Kuroshio group was due to the distribution of both groups locating on the same path of the main current of Kuroshio. However, applying different distribution assumption may result in different conclusion such as one single stock hypothesis. Further studies will be needed to confirm the stock structure of the species.

The genus Capricornis Ogilby, 1837, is divided into three species and widely distributed in sourthern China, Tibet, Myanmar, IndoChinese peninsula, Malaysia peninsula, Sumatra, Japanese archipelagos and Taiwan. Using complete cytochrome b sequences (1140 bp) analyzes the genetic variation and phylogeny of genus Capricornis from Taiwan, Japan and Mainland China. Constructed by both distance and maximum parsimony methods, the phyloenetic tree distinguish the Capricornis to three clades: Formosan serow, Japanese serow, and Sumatran serow from mainland China. Formosan serow is more familiar with Sumatran serow than Japanese serow. Local populations of Formosan serow of Taiwan island and Japanese serow of the Japanese archipelagos are already differentiated. Serow and goral are apparently distinguishable. The results of Principal Component Analysis and Discriminant Analysis show that serows from Taiwan, Japan and mainland China and goral are apparently distinguishable at morphological characters. The variation of morphological analysis may be a good tool to identify serow and goral. From the paleogeology and fossil records of serow of Quaternary, we could infer that ancestors of serow from southwestern mountain of mainland China migrated to Taiwan island and Japanese archipelagos through the land bridge of east Asian islands to mainland China in the early Pleistocene caused by the glaciation of Quaternary, then separated from mainland of east Asia and speciation of serow occured in Taiwan island and Japanese archipelagos after the end of the glaciation of Quaternary.

Genetic analyses of two endangered species of mammals in the Lower Keys of Florida (Lower Keys marsh rabbit, LKMR, Sylvilagus palustris hefneri; silver rice rat, SRR, Oryzomys palustris natator) were performed to evaluate the genetic structure of their populations. Mitochondrial sequence data (control region; 763 base pairs (bp), LKMR; 788 bp, SRR) were used to explore patterns of genetic variation within and among island populations in both species. Analysis of the SRR also included 8 polymorphic nuclear microsatellite loci (9 to 16 alleles). Phylogenetic analyses of mitochondrial sequence data for both species revealed two main lineages corresponding to eastern and western localities, with high levels of genetic structuring (LKMR FST = 0.982, SRR ΦST = 0.916). The two species differed in the level of sequence divergence between eastern and western populations (LKMR, 19 bp; SRR 4 bp). In addition to an overall similar pattern of genetic subdivision, populations of both species possessed low levels of mtDNA variation (haplotypic diversity in the LKMR = 66.1%, SRR = 58.6%). Microsatellite analyses of the SRR revealed subdivision between eastern and western regions. Although less pronounced than the structure observed in mtDNA, the overall pattern was still apparent. Additional examination of divergence between mainland and Lower Keys rice rats revealed a genetic division that indicated a lack of recent gene exchange between the regions (i.e. no shared haplotypes, the presence of private alleles, and distinctive separation in numerous analyses). Although this degree of division does not warrant species designation, the levels and patterns of divergence, both morphological and genetic, do suggest genetic isolation of mainland and island forms. This fact, along with restricted gene flow between the Lower Keys and the Everglades, suggests that the SRR is on an evolutionary trajectory separate from its mainland counterparts and validates its identification as a separate subspecies, Oryzomys palustris natator. Finally, the genetic division between eastern and western populations of the SRR and LKMR suggests that populations of both species in these two regions of the Lower Keys should be treated as separate management units, especially when considering the enhancement of populations via translocations.

Thèse de doctorat : Parasitologie : Paris 12 : 2007. / Titre provenant de l'écran-titre. Pagination : 335 p. Bibliogr. p. 301-331.

Thèse de doctorat : Génétique évolutive : Paris 12 : 2005. / Version électronique uniquement consultable au sein de l'Université Paris 12 (Intranet). Titre provenant de l'écran-titre. Bibliogr. : 213 réf.

Thesis (Ph.D.)--East Carolina University, 2009. / Presented to the faculty of the Department of Exercise and Sports Science. Advisor: Joseph A. Houmard. Title from PDF t.p. (viewed Apr. 30, 2010). Includes bibliographical references.