Dissertations / Theses on the topic 'Homoplasie'

Les relations phylogénétiques des Rhacophorinae sont très méconnues. J'ai étudié 1712 pb de trois gènes (12S, 16S et Rhodopsine), sur 83 Rhacophorinae et 35 autres Ranidae. Et j'ai également étudié 83 caractères de morphologie externe sur 40 Rhacophorinae et 28 autres Ranidae. L'homophylétisme des Rhacophorinae est soutenu. Buergeria se positionne basalement en leur sein. L'étroite relation entre Theloderma et Nyctixalus a été mise en évidence. Les espèces de Philautus se regroupent par ensembles géographiques. Toutes les espèces caractérisées par un développement direct de leurs larves formeraient un groupe particulier. Kurixalus pourrait être le groupe-frère de toutes ces espèces de Philautus. La capacité à fabriquer des nids d'écume soutient en une branche les genres Rhacophorus, Polypedates, Chirixalus et Chiromantis. L'espèce-type de Chirixalus ressort comme l'espèce-sœur du genre africain Chiromantis. Les résultats morphologiques sont soutenus par des données moléculaires. L'homoplasie n'est pas répartie de façon homogène sur le corps des Anoures ; les membres, surtout, gardent des traits de caractères témoins d'un lien de parenté
The phylogenetic relations among Rhacophorinae are undefined. I studied 1712 pb of three genes (12S, 16S and Rhodopsin), on 83 Rhacophorinae and 35 other Ranidae. And I also studied 83 external morphological characters on 40 Rhacophorinae and 28 other Ranidae. The homophyletism of Rhacophorinae is constant. Buergeria appears to be the sister-group of all remaining Rhacophorinae. The close relation between Theloderma and Nyctixalus is strongly supported. The species of Philautus groups by geographical sets. All these species characterized by larvae with direct development form a particular group. Kurixalus could be the sister-group of all these species of Philautus. The ability to make foam nests supports a particular branch the genus Rhacophorus, Polypedates, Chirixalus and Chiromantis. The type-species of Chirixalus arises like the sister-group of the African genus Chiromantis. The morphological results are supported by the molecular data. The homoplasy is not distributed in a homogeneous way on the body of the Anura; the members, especially, keeps more easily characters of the past

La symétrie bilatérale (ou zygomorphie) est un caractère floral apparu de manière récurrente et indépendante au cours de l’évolution des angiospermes, à partir de formes ancestrales de fleurs à symétrie radiale. La zygomorphie est considérée comme une innovation clé des plantes à fleur et est souvent associée à des phénomènes de radiations adaptatives. Certains facteurs génétiques impliqués dans la mise en place de la zygomorphie sont désormais connus chez quelques espèces modèles d’eudicots dérivées et le gène CYCLOIDEA, identifié chez Antirrhinum majus (Plantaginaceae), joue un rôle clé dans le déterminisme de ce caractère. Cependant, les causes moléculaires de la zygomorphie restent encore mal connues chez les eudicots basales et les monocots et il demeure de ce fait impossible de déterminer dans quels groupes taxonomiques l’évolution répétée de la zygomorphie résulte d’une évolution parallèle ou convergente. L’apparition répétée de ce caractère homoplasique résulte aussi probablement de l’action de contraintes de développement, le canalisant au cours de l’évolution dans certaines directions privilégiées. Ce travail de thèse a tout d’abord consisté à identifier de potentielles contraintes de développement dans le groupe des Asteridae (core eudicots), grâce à des méthodes phylogénétiques comparatives. Dans ce groupe, une mérosité variable du périanthe et des étamines nombreuses se sont avérés être des facteurs limitant les transitions vers la zygomorphie. Une comparaison avec un travail similaire effectué sur les Ranunculales a montré que le développement des Asteridae était plus canalisé et moins apte à former des combinaisons variées de caractères. Ces résultats laissent supposer l’existence d’un contrôle génétique de la zygomorphie différent entre les eudicots dérivées et basales. Afin de tester cette hypothèse, les bases moléculaires de la zygomorphie ont été étudiées chez les Ranunculaceae (Ranunculales) par une approche évo-dévo de type gène candidat. La diversité ainsi que les profils d’expression des gènes homologues de CYCLOIDEA (RANACYL) ont été examinés dans différentes espèces et pour différents organes et stades de développement. Le développement des espèces étudiées a auparavant été décrit, en insistant particulièrement sur la mise en place de la zygomorphie. L’approche évo-dévo a montré que les gènes RANACYL ont subi une première duplication avant la divergence des Ranunculaceae et une seconde, cette fois-ci avant la divergence du seul clade à fleurs zygomorphes de la famille. La duplication spécifique aux Delphinieae est un argument en faveur d’un rôle des gènes RANACYL dans la zygomorphie, mais les profils d’expression, à ce stade de l’étude, n’apportent pas de véritable confirmation. La poursuite de ce travail nécessitera l’utilisation de techniques de génétique inverse (VIGS) et de biologie moléculaire (études fonctionnelles par hybridations in situ) pour déterminer si l’évolution de la zygomorphie chez les Ranunculaceae résulte du même type de mécanismes moléculaires que ceux identifiés chez les eudicots dérivées
Floral bilateral symmetry (zygomorphy) evolved several times independently in angiosperms, from radially symmetrical ancestors. The evolution of this floral trait is generally associated with adaptive radiation and high speciation rates. The genetic control of zygomorphy is well described in some core eudicot species and it was shown that the CYCLOIDEA gene, characterized in Antirrhinum majus (Plantaginaceae), is a major determinant of this character. However, molecular investigations of bilateral symmetry control are still patchy in basal eudicots and monocots and determining in which taxonomic group the repeated evolution of this homoplasious character is the result of convergent or parallel evolution is still a challenging question. Moreover, flower symmetry is an integrated phenotype, whose establishment during development can be controlled by historical associations among morphological traits, revealing either physical constraints or common genetic bases. The objectives of this study were to compare the morphological and phylogenetic contexts in which zygomorphy evolved in core and basal eudicots, and then to conduct an evo-devo approach combining a developmental study with the investigation of a candidate gene diversity and expression in Ranunculaceae. This work aimed first at identifying potential developmental constraints in Asteridae (core eudicots), using Phylogenetic Comparative Methods. The impact of perianth merism and stamen number on floral symmetry evolution was evidenced. A comparison with Ranunculales (basal eudicots) showed that in core eudicots there were fewer evolutionary trends associated with transitions toward zygomorphy and that development was more canalized. These results could indicate a different molecular control of zygomorphy between core eudicots and Ranunculales. The second step was to investigate the role of CYCLOIDEA homologs in shaping floral symmetry in Ranunculaceae (Ranunculales). The evo-devo approach showed that the lineage of CYCLOIDEA homologs of Ranunculaceae (RANACYL genes) was duplicated first before the divergence of Ranunculaceae and a second time likely in the lineage leading to the single zygomorphic clade of the family. The expression patterns of the members of the RANACYL multigenic family were uncovered in different species, organs and developmental stages. These were chosen after having described the development of our study species, giving a timing of the major landmarks and focusing on the establishment of zygomorphy. Even if a gene duplication specific to Delphinieae is an argument in favor of the involvement of RANACYL genes in controlling symmetry, the way these genes are expressed during development does not show clear evidence for this for the moment. This evo-devo study must be continued to assess whether the molecular pathways responsible for zygomorphy in Antirrhineae and Ranunculaceae are similar or not

Parmi les paramètres influençant l'inférence d'arbres phylogénétiques, nous nous sommes penchés d'une part sur (i) l'utilisation et l'efficacité de différents marqueurs et (ii) l'influence de la radiation évolutive (la succession rapide d'événements de spéciation) dans la construction d'arbres phylogénétiques et, d'autre part, sur l'applicabilité du modèle de substitution nucléotidique GTR (General Time Reversible).

La première partie de ce travail étudie l'évolution des cétacés en se basant sur les séquences des génomes mitochondriaux, sur le motif d'insertion de rétroposons SINEs (short interspersed elements) nouvellement isolés et les loci nucléaires de ces derniers. Le choix des cétacés est motivé par la présence, durant leur évolution, de radiations évolutives, qui sont propices au tri différentiel de lignées généalogiques: si des séquences de gènes ou des allèles restent polymorphes entre des événements de spéciations, il est possible, et même probable, d'observer une incompatibilité entre les histoires évolutives de ces marqueurs, malgré que celles-ci soient bien correctes. Nous abordons l'étude du tri différentiel des lignées généalogiques par le biais des SINEs, dont l'insertion aléatoire et irréversible confère à ces marqueurs un risque de convergence particulièrement faible.

Notre approche multi-marqueur nous permet de reconstruire un arbre robuste à partir duquel nous analysons ces différents marqueurs à l'aide des rapports signal/bruit (la qualité du contenu informatif du marqueur) et effort/signal (les efforts à mettre en oeuvre pour obtenir du signal phylogénétique). Nous discutons également les relations conflictuelles/incorrectes obtenues à partir des différents marqueurs, notamment des motifs d'insertion de SINEs pour lesquels nous décrivons un test objectif nous permettant de différencier le tri différentiel de lignées généalogiques et la convergence.

Les modèles de substitutions nucléotidiques sont à la base de nombreuses méthodes d'inférence phylogénétiques. Parmi ces modèles, le modèle GTR est un des plus complets et des plus utilisés. Waddell and Steel [1997] ont décrit une procédure qui permet d'estimer les distances et les taux instantanés de substitution pour des séquences évoluant selon les hypothèses du modèle GTR. Il existe néanmoins des conditions qui rendent cette procédure, et donc l'utilisation du modèle GTR, inapplicables.

Nous avons simulé l'évolution de séquences d'ADN le long de 12 arbres caractérisés par un ensemble de conditions biologiquement plausibles (différentes longueurs de branches, des conditions de (non-)homogénéité de la matrice de taux instantanés de substitution et différentes longueurs de séquences). Pour chaque ensemble de conditions, nous avons évalué (i) l'applicabilité du modèle GTR et (ii) la qualité des alignements obtenus à partir des données simulées.

Nos résultats indiquent que l'inapplicabilité de la procédure de Waddell and Steel [1997] peut effectivement être considérée comme un problème pratique car elle apparaît avant les difficultés d'alignement (étape nécessaire et préalable à toute inférence phylogénétique). La probabilité de cette inapplicabilité dépend du taux de substitution et de la taille des données.

Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished

La structure, l'organisation et les variations de la famille de l'adn ribosomique 5s nucleaire (adnr 5s) chez deux arbres forestiers sympatriques (chenes pedoncule et sessile) et chez deux arbres forestiers allopatriques (melezes d'europe et du japon). Comme chez la plupart des plantes superieures, cette famille multigenique est organisee en longues series d'unites repetees en tandem qui sont chacune constituee d'un gene 5s tres conserve entre les especes (120 pb) et d'un espaceur intergenique de taille variable. Une seule classe d'unites ( 350 pb) representee par 1000-2000 copies par genome a ete detectee chez les chenes. En revanche, deux classes d'unites tres divergentes, les unes courtes ( 650 pb) et les autres longues ( 870 pb), comportant chacune 1500-3000 copies par genome, ont ete observees chez les melezes. Ces unites courtes et longues alternent majoritairement au sein de series composites dont l'etablissement est sans doute ancien car le meme type d'organisation a ete retrouve chez 4 autres especes de melezes. L'analyse d'un croisement de chenes pedoncules et d'un croisement de melezes d'europe et du japon a montre que les marqueurs fournis par l'adnr 5s presentent generalement un mode d'heredite mendelien gouverne par un unique locus. Dans le cas du chene pedoncule, le locus a pu etre cartographie sur le groupe de liaison g5 correspondant a la paire de chromosomes n o2. Les unites d'adnr 5s evoluent en longueur par duplication en tandem, insertions et deletions surtout localisees dans la zone centrale des espaceurs. Les estimations de diversite nucleotidique intraspecifique des genes 5s (0,005-0,066), des espaceurs de chenes pedoncule et sessile (0,047-0,057), des espaceurs courts (0,098-0,067) ou longs (0,015-0,037) des melezes d'europe et du japon sont comparables a celles obtenues pour les especes herbacees a cycle court. Chez ces dernieres, le niveau de divergence interspecifique des espaceurs est bien correle au polymorphisme intraspecifique.

Patterns in the distribution of homoplasy are investigated from theoretical and empirical perspectives. The history of the term "homoplasy" as used by morphologists, evolutionary systematists, cladists, and others is reviewed, especially in relation to its complement, "homology." Homoplasy is defined relative to homology, which is viewed as any similarity shared through an unbroken line of common ancestry. An investigation of levels of homoplasy based on a statistical analysis of 60 published phylogenies reveals a strong dependence of homoplasy on the number of taxa included. This relation is independent of number of characters, type of data, taxonomic rank, or organism, and suggests that large taxa should be the focus of empirical studies of homoplasy. Hence, a phylogenetic analysis of the large genus Astragalus was undertaken using 113 representative species (and varieties) found in North America. Fifty-seven binary and multistate characters were scored and the resulting matrix was subjected to numerical cladistic analysis. Two large sets of equally parsimonious trees were found at 595 and 596 steps. The sets were analyzed using consensus methods, robust clades were discussed in detail, and the phylogenies were compared to previous classifications. Character evolution of a large set of taxonomically important and morphologically varied traits was investigated. Statistical tests were developed to detect patterns of topological clustering of homoplastic character changes in cladograms. The tests use Monte-Carlo computer simulations of four null models of character evolution in an attempt to reject the hypothesis of random homoplastic distributions. For the Astragalus data set only two of 17 characters were significantly clustered, and this is close to random expectation. Another data set from the literature was also tested, and in it no characters were clustered at the 5 percent level. The explanation for these negative findings regarding homoplastic "tendencies" is explored with respect to "scope", "scale", and character "resolution," factors believed to play an important role in the analysis of character evolution.

A transformação plastidial oferece uma série de vantagens em relação à transformação nuclear, como: altos níveis de expressão de proteínas, capacidade de expressar múltiplos transgenes em operons e contenção gênica pela ausência de transmissão pelo pólen. Devido ao alto número de cópias do genoma plastidial por cloroplasto e ao alto número de cloroplastos por células vegetais, são necessários ciclos de regeneração sob condições seletivas para obter transformantes homoplásmicos. A análise de homoplasmia é realizada pela metodologia de Southern blot ou pelo teste de herança do transgene pela germinação de sementes em meio seletivo. O Southern blot é trabalhoso, demorado e para maior sensibilidade envolve o uso de radioisótopos, enquanto o teste de germinação é realizado somente após a produção de sementes necessitando de um ciclo de reprodução da planta. Assim, o objetivo deste trabalho foi desenvolver um método rápido, sensível e eficaz para determinar o grau de homoplasmia de plantas transplastômicas, baseado na técnica de PCR em tempo real. Folhas de fumo foram transformadas com vetores compostos pelos genes 9 dessaturase (pMR1), 15 dessaturase (pMR3), -3 elongase (pMR5) e 12/3 dessaturase (pMR10), todos contendo o gene de seleção aadA. No total, 44 plantas foram obtidas, sendo 21 plantas positivas para a inserção do transgene. O grau de homoplasmia foi determinado pela proporção entre o número de cópias do transgene e o número de cópias do gene endógeno. Inicialmente, misturas de DNA de plantas transplastômicas homoplásmicas (pMR1 e pMR3) com DNA de planta tipo selvagem foram preparadas para simular diferentes graus de homoplasmia. DNA da planta transplastômica ou do plasmídeo foi diluído em série para construção das curvaspadrão, com a quantidade dos genes sendo estimada por meio da plotagem nessas curvas. Os índices de homoplasmia detectados na PCR em tempo real foram compatíveis com os resultados do teste de germinação com valores abaixo de 1 para plantas heteroplásmicas, 1 para a planta homoplásmica e 0 para as plantas sem a inserção do transgene. Os resultados das análises de amostras coletadas após o primeiro ciclo de regeneração mostraram que 13 das 21 plantas já se apresentavam em estado homoplásmico não sendo necessários mais ciclos de regeneração. A PCR em tempo real mostrou ser um método eficiente para análise do grau de homoplasmia de plantas transplastômicas.
Plastid transformation offers several advantages in relation to nuclear transformation, such as high-level of protein expression, the feasibility of expressing multiple transgenes in operons and gene containment through the lack of pollen transmission. Due to the high copy number of plastidial genome in chloroplasts and the high number of chloroplasts per plant cells, regeneration cycles under selective conditions are necessary to obtain homoplasmic transformants. Homoplasmy analysis is performed by Southern blot methodology or transgene inheritance test through seed germination in selective medium. Southern blot is laborious, time consuming and for more sensitivity it would require the use of radioisotopes, while germination test can be performed only after seed production which require a plant reproduction cycle. The objective of this study was to develop a fast, sensitive and effective method to determine the homoplasmy degree of transplastomic plants, based on real-time PCR. Tobacco leaves were transformed with vectors containing the 9 desaturase (pMR1), 15 desaturase (pMR3), -3 elongase (pMR5) and 12/3 desaturase (pMR10) each one with the aadA selection gene. In total, 44 plants were obtained, of which 21 were positive for the insertion of the transgene. The homoplasmy degree was determined by the proportion between the number of transgene copies and the number of endogenous gene copies. Initially, mixtures of homoplastomic plants DNA (pMR1 and pMR3) with wild-type plant DNA were prepared to simulate different degrees of homoplasmy. Transplastomic plant DNA or plasmid DNA was diluted to construct the standard curves and the gene amount was detected by plotting in this curves. The homoplasmy rate detected in real-time PCR were consistent with the results of germination test with values below 1 for heteroplasmic plants, 1 for homoplasmic plants and 0 for plants without the transgene insertion. The results obtained from the samples collected after the first regeneration cycle showed that 13 of the 21 plants were already in a homoplasmic state and did not require more cycles of regeneration. The real-time PCR proved to be an effective method for analyzing the homoplasmy degree of transplastomic plants.

Der Bewegungsapparat der Sciuromorpha, einer monophyletische Gruppe von ca. 300 Arten, wurde verwendet um den Effekt der Lebensweise und der Körpermasse auf die Scapula- und Femurmorphologie zu untersuchen. Diese Nagetierklade weist eine breite Vielfalt an Lebensweisen (arboreal, fossoriell, aerial) als auch Körpermassen (drei Größenordnungen umfassend) auf. Die fossorielle Lebensweise hat sich höchstwahrscheinlich dreimal unabhängig von einem arborealen Vorfahren entwickelt. Mehr als die Hälfte der rezenten Arten wurden untersucht. Die Scapulae wurden fotografiert, während Computertomographie (CT) und Oberflächenlaserscans für die Femora verwendet wurden. Es wurden funktionsrelevante Merkmale analysiert, wie die effektive Länge der Skelettelemente, die Muskeleigenschaften soweit aus der Geometrie der Knochen ableitbar, sowie die Robustheit. Die CT-Scans wurden verwendet, um die Querschnitts- und Trabekeleigenschaften des Femurs zu analysieren. Die Gestalt wurde mittels geometrischer Morphometrie untersucht. Phylogenetic comparative methods wurden unter anderem verwendet, um den Einfluss der Phylogenie zu beurteilen als auch, ob sich die unabhängige Aneignung einer fossoriellen Lebensweise in der Evolution homoplastischer Morphologien widerspiegelt. Die Phylogenie spielte bei der Merkmalsevolution eine vernachlässigbare Rolle. Das Auftreten signifikanter Merkmalsunterschiede zwischen den Lebensweisen sowie allometrischer Anpassungen aufgrund Veränderungen in der Körpermasse hingen von dem jeweiligen Merkmal ab. Bei einigen Merkmalen unterschied sich der Einfluss der Körpermasse signifikant zwischen den einzelnen Lebensweisen, was aber nicht die Regel zu sein scheint. Die Evolution homoplastischer Morphologien war sehr unwahrscheinlich bei den fossoriellen Gruppen. Diese Ergebnisse deuten auf eine komplexe, aber adaptive Evolutionsgeschichte dieser Skelettelemente bei den Sciuromorpha hin.
The vertebrate locomotor apparatus of Sciuromorpha, a monophyletic group of ca. 300 species, was used to investigate the effect of lifestyle and body mass on the scapular and femoral morphology. This rodent clade displays a broad diversity of lifestyles (arboreal, fossorial, aerial) and body masses spanning three orders of magnitude. The fossorial lifestyle evolved most probably three times independently from an arboreal ancestor. More than half of the extant species were included. Scapulae were photographed and computed tomography (CT) and surface laser scans were acquired for the femora. Functionally relevant traits were analysed, e.g., the effective length of the skeletal element, the properties of attaching muscles as inferred from the geometry of the bones, and robustness properties. The CT scans were used to analyse the cross-sectional and trabecular properties of the femur. Bone shape was investigated using geometric morphometrics. Phylogenetic comparative methods were utilized, e.g., to assess phylogenetic inertia and whether the independent acquisition of a fossorial lifestyle is reflected in the evolution of homoplastic morphologies. Phylogenetic inertia played a neglectable role in the trait evolution. Significant differences among lifestyles as well as allometric scaling adjustments depended on the trait under consideration. For some traits, scaling differed significantly among lifestyles, although this did not appear to be the rule. Morphological homoplasy was unlikely among the fossorial groups. The results suggest a complex, but adaptive evolutionary history of these skeletal elements in Sciuromorpha.

A central concept in Evolutionary theory is the character trait. It provides a context in which to explore differences and similarities among taxa, both extant and extinct. It is expanded in scope in Evolutionary Developmental theory to functional units with a biological role, "evolutionarily stable configurations." The talo-crural joint is such a configuration, a highly canalized structural unit in primates forming the interface between organism, and foot and substrate. It is a microcosm in which to examine the relationship of shape with environment and function and the interplay of genetics, ontogeny, and use. Geometric Morphometric analysis of landmark data was employed in studying the articular surfaces of the talus in a diverse sample of adult specimens in nine catarrhine taxa. The influence of four factors on talar shape was examined: superfamily, a proxy for phylogeny; size and mass, a proxy for physical attributes; and substrate preference, a proxy for behavior. All significantly affected shape, and substrate preference was unrelated to the others. Appositional articular morphology, the shape of the subchondral bone surfaces of the talo-crural joints in an expanded sample of 12 taxa, showed a significant effect of the four proxies on the tibial and talar components, and substrate preference was weakly related to the other proxies in each. Singular Warp analysis of the cross-covariance matrices of the joints demonstrated sorting of taxa by substrate use and signals of convergent and divergent evolution among hominoids and cercopithecoids in joint shape. The ontogeny of the appositional articular shape was examined using adult and subadult specimens grouped by molar eruption. Singular Warp analysis demonstrated a genetic signal in the subadults, strongest in the slowly maturing African hominoids, and an epigenetic signal across taxa to substrate use in the adults. The talo-crural joint, a highly canalized, modular, and integrated "evolutionarily stable configuration," provides a model for the study of the evolution of shape. The epigenetic signal observed is consistent with plasticity or developmental plasticity in response to the interaction of the joint complex with the environment due to a behavioral effect, substrate use. This dissertation included previously unpublished, co-authored material.

Chapter One Raven's 1985 phylogenetic analysis of the Mygalomorphae placed a number of previously unrelated genera into the rastelloid family Cyrtaucheniidae. Although Goloboff's 1993 reanalysis of mygalomorph relationships retained the familial composition of the Rastelloidina it di not support cyrtaucheniid monophyly. This study resolves the issue of cyrtaucheniid monophyly within the context of the Rastelloidina. Using 71 morphological characters scored for 29 mygalomorph taxa we find that the Cyrtaucheniidae is polyphyletic and propose the following families in its place: Cyrtaucheniidae, Kiamidae (new family), Aporoptychidae (new rank), Ancylotrypidae (new family) and Euctenizidae (new rank). We also propose two new euctenizid genera, Apachella and Sinepedica, revise the taxonomy of the euctenizids of the Southwestern United States, and present a key for these six genera. In addition to the morphologically based phylogeny we test and refine the euctenizid intergeneric phylogeny using molecular data (mitochondrial 16S rRNA and COI genes and 28S rRNA nuclear genes). The results of the combined morphological and molecular analysis are used to construct a composite rastelloid phylogeny that is used to investigate biogeographical relationships, burrow entrance evolution, and homoplasy. Chapter Two This systematic study of the predominately Californian trapdoor spider genus Aptostichus Simon, 1890 describes 28 species, 25 of which are newly described: A. atomus, A. improbulus, A. insulanus, A. icenoglei, A. ebriosus, A. muiri, A. cahuillus, A. luiseni, A. serranos, A. calientus, A. chemehuevi, A. shoshonei, A. pauitei, A. tipai, A. cochesensis, A. indegina, A. gertschi, A. kristenae, A. fornax, A. spinaserratus, A. brevifolius, A. brevispinus, A. agracilapandus, A. tenuis, and A. gracilapandus. Aptostichus stanfordianus Smith, 1908 is considered to be a junior synonym of A. atomarius Simon 1890. Using 72 quantitative and qualitative morphological characters we propose a preliminary phylogeny for this group. Based on the results of this phylogenetic analysis, we recognize the Atomarius, Simus, Hesperus and Pandus species groups. Additionally, our phylogenetic analysis indicates that adaptations favoring the invasion of the very arid desert habitats of southern California have evolved multiple times in the Aptostichus clade. The existence of both desert and non - desert species in three of the four species groups makes this genus an ideal candidate for the study of the evolutionary ecology of desert arthropods. Chapter Three Aptostichus simus is a trapdoor spider that is endemic to the coastal dunes of southern California and is recognized as a single species on morphological grounds. Mitochondrial DNA 16S rRNA sequences demonstrate that populations from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6 - 12%). These results are comparable to, or higher than recent reports of species - level differences in other invertebrate taxa. A molecular clock hypothesis shows that these four populations have been separated for 2 - 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. The time - limited genealogical perspective that is employed separates A. simus into two genetically distinct species. This study suggests that a species concept based on morphological distinctiveness in spider groups with limited dispersal capabilities probably underestimate taxonomic diversity.
Ph. D.

These studies compare neurotransmitter localization and the behavioral functions of homologous neurons in nudibranch molluscs to determine the types of changes that might underlie the evolution of species-specific behaviors. Serotonin (5-HT) immunohistochemistry in eleven nudibranch species indicated that certain groups of 5 HT-immunoreactive neurons, such as the Cerebral Serotonergic Posterior (CeSP) cluster, are present in all species. However, the locations and numbers of many other 5 HT-immunoreactive neurons were variable. Thus, particular parts of the serotonergic system have changed during the evolution of nudibranchs. To test whether the functions of homologous neurons are phylogenetically variable, comparisons were made in species with divergent behaviors. In Tritonia diomedea, which crawls and also swims via dorsal-ventral body flexions, the CeSP cluster includes the Dorsal Swim Interneurons (DSIs). It was previously shown that the DSIs are members of the swim central pattern generator (CPG); they are rhythmically active during swimming and, along with their neurotransmitter 5-HT, are necessary and sufficient for swimming. It was also known that the DSIs excite efferent neurons used in crawling. DSI homologues, the CeSP-A neurons, were identified in six species that do not exhibit dorsal-ventral swimming. Many physiological characteristics, including excitation of putative crawling neurons were conserved, but the CeSP A neurons were not rhythmically active in any of the six species. In the lateral flexion swimmer, Melibe leonina, the CeSP-A neurons and 5-HT, were sufficient, but not necessary, for swimming. Thus, homologous neurons, and their neurotransmitter, have functionally diverged in species with different behaviors. Homologous neurons in species with similar behaviors also exhibited functional divergence. Like Melibe, Dendronotus iris is a lateral flexion swimmer. Swim interneuron 1 (Si1) is in the Melibe swim CPG. However, its putative homologue in Dendronotus, the Cerebral Posterior ipsilateral Pedal (CPiP) neuron, was not rhythmically active during swim-like motor patterns, but could initiate such a motor pattern. Together, these studies suggest that neurons have changed their functional relationships to neural circuits during the evolution of species-specific behaviors and have functionally diverged even in species that exhibit similar behaviors.

Microsatellites are repetitive DNA characterized by tandem repeats of short motifs (2 – 5 bp). High mutation rates make them ideal for population level studies. Microsatellite allele genesis is generally attributed to strand slippage, and it is assumed that alleles are caused only by changes in repeat number. Most analyses are limited to alleles (electromorphs) scored by mobility only, and models of evolution rarely account for homoplasy in allele length. Additionally, insertion/deletion events (indels) in the flanking region or interruptions in the repeat can obfuscate the accuracy of genotyping. Many investigators use microsatellites, designed for a focal species, to screen for genetic variation in non-focal species. Comparative studies have shown different mutation rates of microsatellites in different species, and even individuals. Recent studies have used reciprocal comparisons to assess the level of polymorphism of microsatellites between pairs of taxa. In this study, I investigated the evolution of microsatellites within a phylogenetic context, using comparisons within the rodent family Bathyergidae. Bathyergidae represents a monophyletic group endemic to sub-Saharan Africa and relationships are well supported by morphological and molecular data. Using mitochondrial and nuclear DNA, a robust phylogeny was generated for the Bathyergidae. From my results, I proposed the new genus, Coetomys. I designed species-specific genotyping and microsatellite flanking sequence (MFS) primers for each genus. Sequencing of the MFS provided direct evidence of the evolutionary dynamics of the repeat motifs and their flanking sequence, including rampant electromorphic homoplasy, null alleles, and indels. This adds to the growing body of evidence regarding problems with genotype scores from fragment analysis. A number of the loci isolated were linked with repetitive elements (LTRs and SINEs), characterized as robust phylogenetic characters. Results suggest that cryptic variation in microsatellite loci are not trivial and should be assessed in all studies. The phylogenetic utility of the nucleotide variation of the MFS was compared to the well-resolved relationships of this family based on the 12S/TTR phylogeny. Variation observed in MFS generated robust phylogenies, congruent with results from 12S/TTR. Finally, a number of the indels within the MFS provided a suite of suitable phylogenetic characters.

碩士
國立中正大學
資訊工程所
98
Independent evolution of similar phenotypes or genotypes (called homoplasy) occurs repeatedly among different species exposed to identical ecological conditions. Homoplasy has been known to be manifested by natural selection. A few evidences of homoplasies have been found in primate and human evolution. However, little is known about the extent of homoplasy between human and chimpanzee. In this thesis, we develop a Hidden Markov Model for identifying homoplasies between chimpanzee and human populations and assess the statistical significance of each homoplasies. Our results indicate that homoplasies are widespread in the human genome. Using phylogenetic analysis, the underlying mechanisms of these homoplasies are further classified into parallel evolution, convergent evolution, and reversal. We found that the overwhelming majority of homoplasies were generated via reversal. The identified homoplasies are shown to be significant enriched in genes related to neuron and nervous system development. In addition to evidences from computer-assisted stereology, our results also support that homoplasies are indeed common in the evolution of nervous systems among primates.

The goal of my thesis is to understand the genetics of a complex behavioral trait, vocal learning, which serves as a critical substrate for human spoken language. With the available genomes of 23 mammals, I developed a novel approach based on molecular homoplasy to reveal Single Non-random Amino Acids Patterns (SNAAPs) that are associated with convergent traits, a task that proved intractable for standard approaches, e.g. dN/dS analyses. Of 73 genes I identified in mammalian vocal learners, ~25% function in neural connectivity, auditory or speech processing. Remarkably, these include a group of 6 genes from the ROBO1 axon guidance pathway. In birds, I found ROBO1 and its ligand SLIT1 show convergent differential expression in the motor output song nucleus of the three independent lineages of vocal learners but not in analogous brain areas of vocal non-learners, and ROBO1 is developmentally regulated during song learning critical periods in songbirds. In a different set of genes, I came across an unexpected discovery of the excess sharing of homoplastic substitutions in humans and domesticated species. I revealed biased nucleotide transitions (mostly favoring A/G mutation) for above amino acid substitutions and found that this rule was significantly relaxed during domestication for artificial selection. Overall, my thesis has resulted in a novel approach for studying convergent complex traits and provided critical insights into the evolution of vocal learning specifically, and complex traits generally.

Dissertation

This dissertation explores philosophical problems in biology, particularly those relating to macroevolutionary theory. It is comprised of a series of three papers drawn from work that is currently at the publication, re-submission, and review stage of the journal refereeing process, respectively. The first two chapters concern the overarching contours of complex life, while the third zeroes in on the short and long-term prospects of human evolution.

The rhetorical journey begins with a thought experiment proposed by the late paleontologist Stephen Jay Gould. Gould hypothesized that replaying the "tape of life" would result in radically different evolutionary outcomes, both with respect to animal life in general and the human species in particular. Increasingly, however, biologists and philosophers are pointing to convergent evolution as evidence for replicability and predictability in macroevolution. Chapters 1 and 2 are dedicated to fleshing out the Gouldian view of life and its antithesis, clarifying core concepts of the debate (including contingency, convergence, constraint and causation), and interpreting the empirical data in light of these conceptual clarifications. Chapter 3 examines the evolutionary biological future of the human species, and the ways in which powerful new biotechnologies can shape it, for better and for worse. More detailed chapter summaries are provided below.

In Chapter 1, I critique a book-length excoriation of Gould's contingency theory written by the paleobiologist Simon Conway Morris, in which he amasses and marshals a good bulk of the homoplasy literature in the service of promoting a more robust, counter-factually stable account of macroevolution. I show that there are serious conceptual and empirical difficulties that arise in broadly appealing to the frequency of homoplasy as evidence for robustness in the history of life. Most important is Conway Morris's failure to distinguish between convergent (`externally' constrained) and parallel (`internally' constrained) evolution, and to consider the respective implications of these significantly different sources of homoplasy for a strong adaptationist view of life.

In so doing, I propose a new definition of parallel evolution, one intended to rebut the common charge that parallelism differs from convergence merely in degree and not in kind. I argue that although organisms sharing a homoplastic trait will also share varying degrees of homology (given common decent), it is the underlying developmental homology with respect to the generators directly causally responsible for the homoplastic event that defines parallel evolution and non-arbitrarily distinguishes it from convergence. I make use of the philosophical concept of `screening-off' in order to distinguish the proximate generators of a homoplastic trait from its more distal genetic causes (such as conserved master control genes).

In Chapter 2, I critically examine a recent assessment of the contingency debate by the philosopher John Beatty, in which he offers an interpretation of Gould's thesis and argues that it is undermined by iterative ecomorphological evolution. I develop and defend alternative concepts of contingency and convergence, and show how much of the evidence generally held to negate the contingency thesis not only fails to do so, but in fact militates in favor of the Gouldian view of life. My argument once again rests heavily on the distinction between parallelism and convergence, which I elaborate on and defend against a recent assault by developmental biologists, in part by recourse to philosophical work on the ontological prioritization of biological causes.

In Chapter 3, I explore the probable (and improbable) evolutionary biological consequences of intentional germ-line modification, particularly in relation to human beings. A common worry about genetic engineering is that it will reduce the pool of genetic diversity, creating a biological monoculture that could not only increase our susceptibility to disease, but even hasten the extinction of our species. Thus far, however, the evolutionary implications of human genetic modification have remained largely unexplored. In this Chapter, I consider whether the widespread use of genetic engineering technology is likely to narrow the present range of genetic variation, and if so, whether this would in fact lead to the evolutionary harms that some authors envision. By examining the nature of biological variation and its relation to population immunity and evolvability, I show that not only will genetic engineering have a negligible impact on human genetic diversity, but that it will be more likely to ensure rather than undermine the health and longevity of the human species. To this end, I analyze the relationship between genotypic and phenotypic variation, consider process asymmetries between micro and macroevolution, and investigate the relevance of evolvability to clade-level persistence and extinction.

Dissertation

The Canary Island pine, Pinus canariensis, is an endemic tree that forms one of the main forest ecosystems within the archipelago, and whose distribution has been reduced in the last five centuries by clear cutting for the extraction of timber and tar. It was in the XXth century that exploitation declined and reforestation programs were brought forward for the restoration of an ecosystem that harbours a number of endangered endemic species of plants and animals. In addition to reforestation efforts, an understanding of population genetic processes is also necessary for the successful conservation management of the Canarian pine forest, particularly in light of gathering evidence for local adaptation.

In this thesis historical and contemporary gene flow within P. canariensis was studied with nuclear and chloroplast microsatellite markers. High immigration rates (0.68–0.75) were estimated as expected for an outcrossing windpollinated tree. Nevertheless, significant population differentiation (theta = 0.019, RST = 0.044) was detectable for sites separated by only a few kilometres. Within the context of reforestation programs the high levels of gene flow detected would appear to have a positive effect on reforested stands by facilitating the immigration of local alleles from natural stands into potentially genetically depauperate first generation gene pools of reforested stands.

Historical population growth was revealed with chloroplast microsatellites for most populations of P. canariensis. Population expansions for the pine parasite weevil Brachyderes rugatus were also detected, broadly coinciding with the population expansions within the Canary Island pine forests. Given the estimated times of expansion, these population demographic increases would seem likely related to the process of colonisation of newly emerged islands or local patches after volcanic disturbance. Detection and dating of these expansions from chloroplast microsatellites was, to some degree, negatively affected by homoplasy (i.e. parallel and back mutations).

Coalescent simulations of the evolution of chloroplast microsatellites were applied to study the effects of homoplasy in the statistical analysis of population structuring. Measures of genetic diversity based on number of haplotypes and genetic distances were differently affected. Genetic distances were underestimated but were proportional to the actual value. These effects help to explain the lower performance of statistical analyses for the detection and dating of population expansions. Further research on the effects of homoplasy in the analysis of population differentiation using chloroplast microsatellites is essential.

Les champignons mycorhiziens à arbuscules (CMA) sont des organismes microscopiques du sol qui jouent un rôle crucial dans les écosystèmes naturels et que l’on retrouve dans tous les habitats de la planète. Ils vivent en relation symbiotique avec la vaste majorité des plantes terrestres. Ils sont des biotrophes obligatoires, c'est-à-dire qu'ils ne peuvent croître qu'en présence d'une plante hôte. Cette symbiose permet entre autres à la plante d'acquérir des nutriments supplémentaires, en particulier du phosphore et du nitrate. Malgré le fait que cette symbiose apporte des services importants aux écosystèmes, la richesse des espèces, la structure des communautés, ainsi que la diversité fonctionnelle des CMA sont mal connues et l'approfondissement des connaissances dans ces domaines dépend d’outils de diagnostic moléculaire. Cependant, la présence de polymorphisme nucléaire intra-isolat combiné à un manque de données génomiques dans différents groupes phylogénétique de ces champignons complique le développement de marqueurs moléculaires et la détermination de l'affiliation évolutive à hauts niveaux de résolution (c.a.d. entre espèces génétiquement similaires et/ou isolats de la même espèce). . Pour ces raisons, il semble une bonne alternative d’utiliser un système génétique différent en ciblant le génome mitochondrial, qui a été démontré homogène au sein d'un même isolat de CMA. Cependant, étant donné le mode de vie particulier de ces organismes, une meilleure compréhension des processus évolutifs mitochondriaux est nécessaire afin de valoriser l'utilisation de tels marqueurs dans des études de diversité et en génétique des populations. En ce sens, mon projet de doctorat consistait à investiguerétudier: i) les vecteurs de divergences inter-isolats et -espèces génétiquement rapprochéesphylogénétiquement apparentées, ii) la plasticité des génomes mitochondriaux, iii) l'héritabilité mitochondriale et les mécanismes potentiels de ségrégation, ainsi que iv) la diversité mitochondriale intra-isolat in situ. À l'aide de la génomique mitochondriale comparative, en utilisant le séquençage nouvelle génération, on a démontré la présence de variation génétique substantielle inter-isolats et -espèces, engendrées par l'invasion d'éléments mobiles dans les génomes mitochondriaux des CMA, donnant lieu à une évolution moléculaire rapide des régions intergéniques. Cette variation permettait de développer des marqueurs spécifiques à des isolats de la même espèce. Ensuite, à l'aide d'une approche analytique par réseaux de gènes sur des éléments mobiles, on a été en mesure de démontrer des évènements de recombinaisons homologues entre des haplotypes mitochondriaux distincts, menant à des réarrangements génomiques. Cela a permis d'ouvrir les perspectives sur la dynamique mitochondriale et l'hétéroplasmie dans un même isolatsuggère une coexistence de différents haplotypes mitochondriaux dans les populations naturelles et que les cultures monosporales pourraient induirent une sous-estimation de la diversité allélique mitochondriale. Cette apparente contradiction avec l'homogénéité mitochondriale intra-isolat généralement observée, a amené à investiguer étudier les échanges génétiques à l'aide de croisements d'isolats génétiquement distincts. Malgré l'observation de quelques spores filles hétéroplasmiques, l'homoplasmie était le statut par défaut dans toutes les cultures monosporales, avec un biais en faveur de l'un des haplotypes parentaux. Ces résultats suggèrent que la ségrégation opère durant la formation de la spore et/ou le développement de la coloniedu mycélium. De plus, ils supportent la présence d'une machinerie protéique de ségrégation mitochondriale chez les CMAAMF, où l'ensemble des gènes impliqués dans ce mécanisme ont été retrouvé et sont orthologues aux autres champignons. Finalement, on est revenue aux sources avecon a étudié le polymorphisme mitochondrial intra-isolat à l'aide d'une approche conventionnelle de PCR en utilisant une Taq polymérase de haute fidélité, suivie de clonage et de séquençage Sanger, sur deux isolats de R. irregularis. Cela a permis l'observation d'hétéroplasmie in situ, ainsi que la co-expression de variantes de variantes de protéines'ARNm dans une souche in vitro. Les résultats suggèrent que d'autres études basées sur le séquençage nouvelle génération aurait potentiellement ignorée cette variation, offrant ainsi plusieurs nouveaux arguments permettant de considérer les CMA comme des organismes possédant une population de génomes mitochondriaux et nucléaires distincts.
The association between arbuscular mycorrhizal fungi (AMF) and plant roots is one of the most widespread symbioses involving plants, and thus has an important role in terrestrial ecosystems. In exchange for carbohydrates, AMF improve plant fitness by enhancing mineral nutrient uptake, especially in particular phosphate and nitrate. Although this symbiosisDespite the fact that these symbioses contribute provides to important services toin ecosystems, the species richness, community structure and functional diversity of AMF is not well understood due to a lack of reliable molecular tools. The intra-isolate genetic polymorphism of nuclear DNA observed in AMF, combined with a lack of genomic data in a broad range of phylogenetic groups, has made it difficult to develop molecular markers and to determine evolutionary relatedness at high levels of resolution (i.e. between genetically-similar species and/or isolates). For these reasons, it seems a good alternative to use a different genetic system by targeting the mitochondrial genome, which have been shown to be homogeneous within AMF isolates. However, given the peculiar lifestyle of these organisms, a better understanding of the mitochondrial evolutionary processes and dynamics were is necessary in order to validate the usefulness of such markers in diversity and population genetics studies. In that regard, the objectives of my PhD project were to investigate: i) the divergence between closely related species and isolates, ii) mitochondrial genomes plasticity, iii) mitochondrial heritability and potential segregation mechanisms and iv) in situ mitochondrial intra-isolate allelic diversity. With Using comparative mitochondrial genomics using and next generation sequencing (NGS) sequencing, we found substantial sequence variation in intergenic regions caused by the invasion of mobile genetic elements. This variation gives risecontributes to rapid mitochondrial genome evolution among closely related isolates and species, which makes it possible to design reliable intra- and inter-specific markers. Also, an extensive gene similarity network-based approach allowed us to provide strong evidence of inter-haplotype recombination in AMF, leading to a reshuffled mitochondrial genome. These findings suggest the coexistence of distinct mtDNA haplotypes in natural populations and raise questions as to whether AMF single spore cultivations artificially underestimates mitochondrial genetic diversity in natural population.. This apparent contradiction with the intra-isolate mtDNA homogeneity usually observed in these fungi, led to the investigation of mitochondrial heritability in the spore progeny resulting from crossed-cultures. Although an heteroplasmic state was observed in some daughter spores, we found that homoplasmy was the dominant state in all monosporal cultures, with an apparent bias towards one of the parental haplotypes. These results strongly support the presence of a putative mitochondrial segregation proteic machinery in AMF, whose complete set of genes were orthologous with those found in other fungi. Our findings suggest that segregation takes place either during spore formation or colony mycelium development. Finally, we performed a conventional PCR based approach with a high fidelity Taq polymerase, followed by downstream cloning and Sanger sequencing using the model organism Rhizophagus irregularis. We found in situ heteroplasmy along with substantial intra-isolate allelic variation within the mtDNA that persists in the transcriptome. Our study also suggest that genetic variation in Glomeromycota is higher than meets the eye and might be critically underestimated in most NGS based-AMF studies both in nuclei and mitochondria.

Les champignons mycorhiziens arbusculaires (CMA) sont très répandus dans le sol où ils forment des associations symbiotiques avec la majorité des plantes appelées mycorhizes arbusculaires. Le développement des CMA dépend fortement de la plante hôte, de telle sorte qu'ils ne peuvent vivre à l'état saprotrophique, par conséquent ils sont considérés comme des biotrophes obligatoires. Les CMA forment une lignée évolutive basale des champignons et ils appartiennent au phylum Glomeromycota. Leurs mycélia sont formés d’un réseau d’hyphes cénocytiques dans lesquelles les noyaux et les organites cellulaires peuvent se déplacer librement d’un compartiment à l’autre. Les CMA permettent à la plante hôte de bénéficier d'une meilleure nutrition minérale, grâce au réseau d'hyphes extraradiculaires, qui s'étend au-delà de la zone du sol explorée par les racines. Ces hyphes possèdent une grande capacité d'absorption d’éléments nutritifs qui vont être transportés par ceux-ci jusqu’aux racines. De ce fait, les CMA améliorent la croissance des plantes tout en les protégeant des stresses biotiques et abiotiques. Malgré l’importance des CMA, leurs génétique et évolution demeurent peu connues. Leurs études sont ardues à cause de leur mode de vie qui empêche leur culture en absence des plantes hôtes. En plus leur diversité génétique intra-isolat des génomes nucléaires, complique d’avantage ces études, en particulier le développement des marqueurs moléculaires pour des études biologiques, écologiques ainsi que les fonctions des CMA. C’est pour ces raisons que les génomes mitochondriaux offrent des opportunités et alternatives intéressantes pour étudier les CMA. En effet, les génomes mitochondriaux (mt) publiés à date, ne montrent pas de polymorphismes génétique intra-isolats. Cependant, des exceptions peuvent exister. Pour aller de l’avant avec la génomique mitochondriale, nous avons besoin de générer beaucoup de données de séquençages de l’ADN mitochondrial (ADNmt) afin d’étudier les méchanismes évolutifs, la génétique des population, l’écologie des communautés et la fonction des CMA. Dans ce contexte, l’objectif de mon projet de doctorat consiste à: 1) étudier l’évolution des génomes mt en utilisant l’approche de la génomique comparative au niveau des espèces proches, des isolats ainsi que des espèces phylogénétiquement éloignées chez les CMA; 2) étudier l’hérédité génétique des génomes mt au sein des isolats de l’espèce modèle Rhizophagus irregularis par le biais des anastomoses ; 3) étudier l’organisation des ADNmt et les gènes mt pour le développement des marqueurs moléculaires pour des études phylogénétiques. Nous avons utilisé l’approche dite ‘whole genome shotgun’ en pyroséquençage 454 et Illumina HiSeq pour séquencer plusieurs taxons de CMA sélectionnés selon leur importance et leur disponibilité. Les assemblages de novo, le séquençage conventionnel Sanger, l’annotation et la génomique comparative ont été réalisés pour caractériser des ADNmt complets. Nous avons découvert plusieurs mécanismes évolutifs intéressant chez l’espèce Gigaspora rosea dans laquelle le génome mt est complètement remanié en comparaison avec Rhizophagus irregularis isolat DAOM 197198. En plus nous avons mis en évidence que deux gènes cox1 et rns sont fragmentés en deux morceaux. Nous avons démontré que les ARN transcrits les deux fragments de cox1 se relient entre eux par épissage en trans ‘Trans-splicing’ à l’aide de l’ARN du gene nad5 I3 qui met ensemble les deux ARN cox1.1 et cox1.2 en formant un ARN complet et fonctionnel. Nous avons aussi trouvé une organisation de l’ADNmt très particulière chez l’espèce Rhizophagus sp. Isolat DAOM 213198 dont le génome mt est constitué par deux chromosomes circulaires. En plus nous avons trouvé une quantité considérable des séquences apparentées aux plasmides ‘plasmid-related sequences’ chez les Glomeraceae par rapport aux Gigasporaceae, contribuant ainsi à une évolution rapide des ADNmt chez les Glomeromycota. Nous avons aussi séquencé plusieurs isolats de l’espèces R. irregularis et Rhizophagus sp. pour décortiquer leur position phylogénéque et inférer des relations évolutives entre celles-ci. La comparaison génomique mt nous montré l’existence de plusieurs éléments mobiles comme : des cadres de lecture ‘open reading frames (mORFs)’, des séquences courtes inversées ‘short inverted repeats (SIRs)’, et des séquences apparentées aux plasimdes ‘plasmid-related sequences (dpo)’ qui impactent l’ordre des gènes mt et permettent le remaniement chromosomiques des ADNmt. Tous ces divers mécanismes évolutifs observés au niveau des isolats, nous permettent de développer des marqueurs moléculaires spécifiques à chaque isolat ou espèce de CMA. Les données générées dans mon projet de doctorat ont permis d’avancer les connaissances fondamentales des génomes mitochondriaux non seulement chez les Glomeromycètes, mais aussi de chez le règne des Fungi et les eucaryotes en général. Les trousses moléculaires développées dans ce projet peuvent servir à des études de la génétique des populations, des échanges génétiques et l’écologie des CMA ce qui va contribuer à la compréhension du rôle primorial des CMA en agriculture et environnement.
Arbuscular mycorrhizal fungi (AMF) are the most widespread eukaryotic symbionts, forming mutualistic associations known as Arbuscular Mycorrhizae with the majority of plantroots. AMF are obligate biotrophs belonging to an ancient fungal lineage of phylum Glomeromycota. Their mycelia are formed by a complex network made up of coenocytic hyphae, where nuclei and cell organelles can freely move from one compartment to another. AMF are commonly acknowledged to improve plant growth by enhancing mineral nutrient uptake, in particular phosphate and nitrate, and they confer tolerance to abiotic and biotic stressors for plants. Despite their significant roles in ecosystems, their genetics and evolution are not well understood. Studying AMF is challenging due to their obligate biotrophy, their slow growth, and their limited morphological criteria. In addition, intra-isolate genetic polymorphism of nuclear DNA brings another level of complexity to the investigation of the biology, ecology and function of AMF. Genetic polymorphism of nuclear DNA within a single isolate limits the development of efficient molecular markers mainly at lower taxonomic levels (i.e. the inter-isolate level). Instead, mitochondrial (mt) genomics have been used as an attractive alternative to study AMF. In AMF, mt genomes have been shown to be homogeneous, or at least much less polymorphic than nuclear DNA. However, by generating large mt sequence datasets we can investigate the efficiency and usefulness of developing molecular marker toolkits in order to study the dynamic and evolutionary mechanisms of AMF. This approach also elucidates the population genetics, community ecology and functions of Glomeromycota. Therefore, the objectives of my Ph.D. project were: 1) To investigate mitochondrial genome evolution using comparative mitogenomic analyses of closely related species and isolates as well as phylogenetically distant taxa of AMF; 2) To explore mt genome inheritance among compatible isolates of the model AMF Rhizophagus irregularis through anastomosis formation; and 3) To assess mtDNA and mt genes for marker development and phylogenetic analyses. We used whole genome shotgun, 454 pyrosequencing and HiSeq Illimina to sequence AMF taxa selected according to their importance and availability in our lab collections. De novo assemblies, Sanger sequencing, annotation and comparative genomics were then performed to characterize complete mtDNAs. We discovered interesting evolutionary mechanisms in Gigaspora rosea: 1) we found a fully reshuffled mt genome synteny compared to Rhizaphagus irregularis DAOM 197198; and 2) we discovered the presence of fragmented cox1 and rns genes. We demonstrated that two cox1 transcripts are joined by trans-splicing. We also reported an unusual mtDNA organization in Rhizophagus sp. DAOM 213198, whose mt genome consisted of two circular mtDNAs. In addition, we observed a considerably higher number of mt plasmidrelated sequences in Glomeraceae compared with Gigasporaceae, contributing a mechanism for faster evolution of mtDNA in Glomeromycota. We also sequenced other isolates of R. irregularis and Rhizophagus sp. in order to unravel their evolutionary relationships and to develop molecular toolkits for their discrimination. Comparative mitogenomic analyses of these mtDNAs revealed the occurrence of many mobile elements such as mobile open reading frames (mORFs), short inverted repeats (SIRs), and plasmid-related sequences (dpo) that impact mt genome synteny and mtDNA alteration. All together, these evolutionary mechanisms among closely related AMF isolates give us clues for designing reliable and efficient intra- and inter-specific markers to discriminate closely related AMF taxa and isolates. Data generated in my Ph.D. project advances our knowledge of mitochondrial genomes evolution not only in Glomeromycota, but also in the larger framework of the Fungal kingdom and Eukaryotes in general. Molecular toolkits developed in this project will offer new opportunities to study population genetics, genetic exchanges and ecology of AMF. In turn, this work will contribute to understanding the role of these fungi in nature, with potential applications in both agriculture and environmental protection.