The pecan weevil, Curculio caryae Horn, is an obligate nut feeder of all North American hickory (Carya) and a key pest of the pecan, C. illinoinensis Koch. This study investigated population structure of the pecan weevil. Gene flow and genetic variation was estimated for 90 pecan weevil specimens sampled from the entire Carya range. Cladistic and nested clade analyses, as well as an analysis of molecular variance (AMOVA) of mitochondrial DNA cytochrome oxidase I (mtDNA COI) were performed. The data indicate C. caryae diverged from its sister species, C. nasicus approximately 4.3 million years before present (mybp). Six-hundred and forty equally parsimonious trees of 31 haplotypes demonstrated high genetic diversity across all pecan weevil samples, and significant regional subdivision. Three clades recovered in the parsimony and nested clade analyses were strongly associated with western, eastern and central localities sampled within C. caryae's range. The current distribution of C. caryae and population structure were explained by past glaciation events. Lineage divergence between the western and eastern populations occurred during the Pleistocene (approx. 1.1 million years ago), and a more recent divergence occurred between C. caryae populations east and west of the Appalachian mountain range (870,000 yrs. ago). Haplotypes were segregated by region, but further sampling is necessary to test for gene flow among these regions.

Given the high salinity, prevailing annual high temperatures, and ultra-oligotrophic conditions in the Red Sea isolation and characterization of important microbial groups thriving in this environment is important in understanding the ecological significance and metabolic capabilities of these communities. By using a high-­throughput cultivation technique in natural seawater amended with minute amounts of nutrients, members of the rare biosphere (PS1), methylotrophic Betaproteobacteria (OM43), and the ubiquitous and abundant SAR11 group (Pelagibacterales), were isolated in pure culture. Phylogenetic analyses of Red Sea isolates along with comparative genomics with close representatives from disparate provinces revealed ecotypes and genomic differentiation among the groups. Firstly, the PS1 alphaproteobacterial clade was found to be present in very low abundance in several metagenomic datasets form divergent environments. While strain RS24 (Red Sea) harbored genomic islands involved in polymer degradation, IMCC14465 (East (Japan) Sea) contained unique genes for degradation of aromatic compounds. Secondly, methylotrophic OM43 bacteria from the Red Sea (F5, G12 and H7) showed higher similarities with KB13 isolate from Hawaii, forming a ‘H-­RS’ (Hawaii-­Red Sea) cluster separate from HTCC2181 (Oregon isolate). HTCC2181 members were shown to prevail in cold, productive coastal environments and had an nqrA-­F system for energy generation by sodium motive force. On the contrary, H-­RS cluster members may be better adapted to warm and oligotrophic environments, and seem to generate energy by using a proton-­translocating NADH:Quinone oxidoreductase (complex I; nuoA-­N subunits). Moreover, F5, G12, and H7 had unique proteins related to resistance to UV, temperature and salinity, in addition to a heavy metal ‘resistance island’ as adaptive traits to cope with the environmental conditions in the Red Sea. Finally, description of the Red Sea Pelagibacterales isolates from the Ia (RS39) and Ib (RS40) subgroups, principally revealed unique putative systems for iron uptake and myo-inositol utilization in RS39, and a potential phosphonates biosynthetic pathway present in RS40. The findings presented here reflect how environments influence the genomic repertoire of microbial communities and shows novel metabolisms and putative pathways as unique adaptive qualities in diverse microbes encompassing from rare to predominant bacterioplankton groups from the Red Sea.

The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.

The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.

Eriophorum crinigerum (Scirpeae, Cyperaceae) has been placed in either the genus Scirpus (club-rushes) or Eriophorum (cottograsses), but a unique combination of bristle and inflorescence features suggests that it could represent a new generic lineage. In addition, prior field studies and initial analyses suggested that E. crinigerum could consist of two species. Using molecular, morphological, anatomical, embryological and geographical data, I examine relationships within the hyperdiverse Cariceae + Dulichieae + Scirpeae clade (ca. 2055 species)to which E. crinigerum belongs and I explore whether this species could contain undocumented species diversity. Results demonstrate not only that E. crinigerum represents a new genus within Cyperaceae, here called Calliscirpus, but it can be divided into two allopatric species, C. criniger and C. brachythrix sp. nov. Calliscirpus brachythrix is confined to the Sierra Nevada Mountains and C. criniger is confined to the Klamath-Siskiyou and North Coastal Mountains; all three mountain ranges are found within the California Floristic Province (USA) which is well known for its high generic and species endemism. My results suggest that Calliscirpus is distantly related to Eriophorum, but that it could be most closely related to the Cariceae, a osmopolitan clade representing almost 40% of all Cyperaceae diversity.

Eriophorum crinigerum (Scirpeae, Cyperaceae) has been placed in either the genus Scirpus (club-rushes) or Eriophorum (cottograsses), but a unique combination of bristle and inflorescence features suggests that it could represent a new generic lineage. In addition, prior field studies and initial analyses suggested that E. crinigerum could consist of two species. Using molecular, morphological, anatomical, embryological and geographical data, I examine relationships within the hyperdiverse Cariceae + Dulichieae + Scirpeae clade (ca. 2055 species)to which E. crinigerum belongs and I explore whether this species could contain undocumented species diversity. Results demonstrate not only that E. crinigerum represents a new genus within Cyperaceae, here called Calliscirpus, but it can be divided into two allopatric species, C. criniger and C. brachythrix sp. nov. Calliscirpus brachythrix is confined to the Sierra Nevada Mountains and C. criniger is confined to the Klamath-Siskiyou and North Coastal Mountains; all three mountain ranges are found within the California Floristic Province (USA) which is well known for its high generic and species endemism. My results suggest that Calliscirpus is distantly related to Eriophorum, but that it could be most closely related to the Cariceae, a osmopolitan clade representing almost 40% of all Cyperaceae diversity.

Parmi les espèces de levures du clade CTG, certaines sont responsables de candidoses tandis que d’autres présentent des potentiels en biotechnologie. Depuis quelques années, nous assistons à une intensification des recherches sur ces levures. Cependant, leur code génétique particulier a ralenti la mise au point d’outils génétiques pour la plupart d’entre elles. Cette thèse vise à développer des outils moléculaires standardisés pour un grand nombre d’espèces de levures du clade CTG. Nous avons d’abord conçu des vecteurs d’expression adaptés à l’espèce M. guilliermondii. Par la suite, nous avons caractérisé le gène de résistance à l’acide mycophénolique IMH3.2 afin de l’utiliser comme marqueur de sélection lors de la transgénèse d’espèces du clade CTG. Enfin, nous avons mis au point une série de vecteurs permettant la manipulation génétique de ces espèces. Ce travail a conduit à la conception d’une large gamme d’outils utilisable dans un grand nombre de ces levures, pré-requis essentiel aux futurs recherches en mycologie médicale et au développement de stratégies de biologie synthétique. / The fungal CTG clade includes well-known yeasts of clinical importance and/or biotechnological potential. Thus, albeit being intensively studied over the last 30 years, their uncommon genetic code precludes the use of the widely available markers and reporter systems for genetic approaches in these microorganisms. We provide here a toolbox to genetically manipulate a wide range of CTG clade species. Firstly, we developed a new series of versatile controllable expression vectors for M. guilliermondii. After, we characterized MPA-resistant gene IMH3.2 et used it as a drug resistance marker in several yeast species. Finaly, we provide a molecular toolbox suitable to genetically manipulate a broad range of prominent species from the CTG clade. This versatile toolkit represents a new starting point for successful developments of research in medical mycology in the CTG clade but also will expedite synthetic biology strategies in these microorganisms for biotechnological applications.

No description available.

Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems since they burrow into pine cone tissues for egg deposition, causing the death of the seeds. Management of these beetles in natural and commercial stands of pines has been problematic due to lack of understanding about species limits and distribution. This study was conducted to investigate the phylogeography and phylogenetics of the genus. Several species represented by disjunct populations appear to be monophyletic including Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C. ponderosae is polyphyletic with many distinct clades isolated by geography. This study explored whether host use or geography has played a greater role in the diversification of this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis. In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a phylogeny of the genus, and the distribution and host use were compared to investigate whether these factors were significantly associated. The second study addressed population structure and possible historical influences on the C. edulis and C. ponderosae populations using a nested clade analysis of the mtDNA haplotypes. Despite potential limitations due to sampling, several conclusions could be drawn. Three separate haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was significantly associated with the phylogeny at greater distances (>900km), but host use was not significant. At the species level, association with geography is variable. Population structure for C. ponderosae at the species level is minimal, and suggests that there has not been much time for lineage sorting of the haplotypes based on the nested clade analysis as compared to C. edulis.

The phylogeny of Clematis, section Viorna, was characterized in this study using molecular data. Two nuclear introns were sequenced for a variety of taxa: actin and nitrate reductase. Actin intron sequence data yielded very little phylogenetic information. Some basal clades were resolved, but there were very few well supported relationships between species of the Viorna section in both the neighbor joining and maximum parsimony analyses. Nitrate reductase intron sequence data was slightly more variable. The number of well supported relationships in both the neighbor joining and maximum parsimony analyses for nitrate reductase was greater, but still not sufficient to yield an informative tree. Two possible explanations for the lack of variation are that these species have not evolved many differences in these intron sequences or that common alleles are flowing between the species. Hybrid analysis using the actin intron was inconclusive because the experimentally generated hybrid possessed an allele that neither parents tested had. More sampling from multiple individuals from both parent and multiple hybrid individuals is necessary to answer this question. The hybrid specimen tested was homozygous for the nitrate reductase intron marker, and both parents also possessed the allele. This did not directly support or refute the use of these markers for tracking the hybridization history within Clematis.