Telomeres are important protein-DNA structures at the ends of linear eukaryotic chromosomes that are necessary to prevent chromosome fusions and exonuclease attack. We found that telomere tracts in Arabidopsis are fairly uniformly distributed throughout a size range of 2-9kb. Unexpectedly, telomeres in WS plants displayed a bimodal size distribution with some individuals exhibiting 4-8 kb telomeres and others 2-5 kb telomeres. We also examined the dynamics of telomere tracts on individual chromosome ends. Following the fate of telomeres in plants through successive generations, we found that the shortest telomeres were typically elongated in the subsequent generation, while the longest telomeres were usually shortened. Thus, telomere length homoeostasis is achieved through intermittent telomerase action on shorter telomeres to attain an optimal size.Single-strand telomere binding proteins were also analyzed. Four major telomere binding protein complexes from cauliflower were identified and their DNA-binding properties characterized. The DNA-binding component of one of the complexes was purified and analyzed by mass-spectrometry. Peptide mass data was used to search for putative protein candidates from the Arabidopsis thaliana database. Additionally, two Arabidopsis genes, AtPot1 and AtPot2, were identified and characterized. The genes encode two single-strand telomeric DNA binding proteins. AtPot1 and AtPot2 proteins can homo- and heterodimerize in vitro. Pot1 protein predominantly localizes to the nucleolus, whereas Pot2 is exclusively nuclear. Plants over-expressing full-length Pot1 and Pot2 proteins had no obvious phenotype, while over-expression of P2DBD and P1∆DBD caused moderate telomere shortening. Plants over-expressing P2DBD had severe morphological and reproductive defects, multiple chromosome abnormalities and aneuploidy. Over-expression of a chimeric protein DBD-P1∆DBD led to rapid telomere shortening, confirming the involvement of Arabidopsis Pot proteins in telomere length maintenance. Intriguingly, telomerase in DBD-P1∆DBD-EYFP plants is inactivated, suggesting that Pot proteins are also involved in regulation of telomerase activity. The analysis of Arabidopsis telomeres and telomere binding proteins will provide additional information towards understanding the role of the telomeric nucleoprotein complex in eukaryotic chromosome biology.

Telomeres are important protein-DNA structures at the ends of linear eukaryotic chromosomes that are necessary to prevent chromosome fusions and exonuclease attack. We found that telomere tracts in Arabidopsis are fairly uniformly distributed throughout a size range of 2-9kb. Unexpectedly, telomeres in WS plants displayed a bimodal size distribution with some individuals exhibiting 4-8 kb telomeres and others 2-5 kb telomeres. We also examined the dynamics of telomere tracts on individual chromosome ends. Following the fate of telomeres in plants through successive generations, we found that the shortest telomeres were typically elongated in the subsequent generation, while the longest telomeres were usually shortened. Thus, telomere length homoeostasis is achieved through intermittent telomerase action on shorter telomeres to attain an optimal size.Single-strand telomere binding proteins were also analyzed. Four major telomere binding protein complexes from cauliflower were identified and their DNA-binding properties characterized. The DNA-binding component of one of the complexes was purified and analyzed by mass-spectrometry. Peptide mass data was used to search for putative protein candidates from the Arabidopsis thaliana database. Additionally, two Arabidopsis genes, AtPot1 and AtPot2, were identified and characterized. The genes encode two single-strand telomeric DNA binding proteins. AtPot1 and AtPot2 proteins can homo- and heterodimerize in vitro. Pot1 protein predominantly localizes to the nucleolus, whereas Pot2 is exclusively nuclear. Plants over-expressing full-length Pot1 and Pot2 proteins had no obvious phenotype, while over-expression of P2DBD and P1∆DBD caused moderate telomere shortening. Plants over-expressing P2DBD had severe morphological and reproductive defects, multiple chromosome abnormalities and aneuploidy. Over-expression of a chimeric protein DBD-P1∆DBD led to rapid telomere shortening, confirming the involvement of Arabidopsis Pot proteins in telomere length maintenance. Intriguingly, telomerase in DBD-P1∆DBD-EYFP plants is inactivated, suggesting that Pot proteins are also involved in regulation of telomerase activity. The analysis of Arabidopsis telomeres and telomere binding proteins will provide additional information towards understanding the role of the telomeric nucleoprotein complex in eukaryotic chromosome biology.

Glyphosate-resistant (GR) giant ragweed (Ambrosia trifida L.) has been confirmed in several states across the mid-western and mid-southern U.S. Greenhouse and lab studies were conducted to investigate possible mechanism of glyphosate resistance in a suspect population from Monroe County, Mississippi. Translocation of 14C-glyphosate in the susceptible biotype was 77%, compared to 12% in the resistant biotype at 120 hours after treatment, suggesting that the glyphosate resistance mechanism for this giant ragweed biotype is reduced translocation. Dose response studies were conducted to confirm and characterize glyphosate resistance in suspect biotypes from Mississippi (MS-R) and Tennessee (TN-R). The ED50 for MS-R and TN-R were 3.9- and 6.3-fold higher than a susceptible biotype. Results from a fallow field study conducted in 2016 in Monroe County revealed PRE and POST treatments containing dicamba and mesotrione alone and in various combinations provided effective control of GR giant ragweed. Studies were conducted to measure fitness, phenotypic, and genetic variation among GR biotypes from MS-R, TN-R, and Ohio (OH-R). Non-destructive measurements of plants over an eight-week period revealed rapid early growth of two GR accessions from MS in the absence of glyphosate. However, no differences in vegetative biomass were recorded after eight weeks with the exception of OH-R biotype which exhibited lower biomass due to photoperiod sensitivity. Vegetative biomass and fecundity were similar. Multivariate and PCA analysis of traits grouped biotypes based on state of origin. Groupings by state of origin can be significant as managers could design similar methods of control to address giant ragweed in these areas. Simple sequence repeat (SSR) markers were used to record genetic diversity among and within biotypes. Genetic diversity values were high at 0.514, 0.502, and 0.525 within biotypes from MS, TN, and OH, respectively. However, genetic diversity did not differ due to glyphosate response or level of glyphosate resistance. High levels of genetic variation can be an indicator of the ability of giant ragweed biotypes to adapt to changing environments and conditions.

Trophic ecology is a key component in describing patterns of variation between and within populations, particularly in Arctic marine systems wherein climate change is impacting food webs. This thesis investigates the trophic ecology of Arctic char (Salvelinus alpinus) in the Cumberland Sound region using a multi-indicator approach. My data show trophic niche differences between resident and anadromous ecotypes and evidence for estuarine feeding by residents. I document a shift in the marine diet of Arctic char from zooplankton to capelin (Mallotus villosus) – a novel prey species in this region – that has occurred in less than a decade. Changes in Arctic char growth imply population-level effects of this shift; however, more research is required. Finally, I find lipid effects on δ13C and lipid-extraction effects on δ15N and δ34S for Arctic char muscle tissue. Lipid-correction models did not provide adequate δ13C estimates; thus, chemical extraction or ecotype-specific validation of models is recommended.

Trophic ecology is a key component in describing patterns of variation between and within populations, particularly in Arctic marine systems wherein climate change is impacting food webs. This thesis investigates the trophic ecology of Arctic char (Salvelinus alpinus) in the Cumberland Sound region using a multi-indicator approach. My data show trophic niche differences between resident and anadromous ecotypes and evidence for estuarine feeding by residents. I document a shift in the marine diet of Arctic char from zooplankton to capelin (Mallotus villosus) – a novel prey species in this region – that has occurred in less than a decade. Changes in Arctic char growth imply population-level effects of this shift; however, more research is required. Finally, I find lipid effects on δ13C and lipid-extraction effects on δ15N and δ34S for Arctic char muscle tissue. Lipid-correction models did not provide adequate δ13C estimates; thus, chemical extraction or ecotype-specific validation of models is recommended.

Restoration of resilient plant communities in response to environmental degradation is a critical task, and a changing climate necessitates the introduction of plant communities adapted to anticipated future conditions. Ecotypes of dominant species can affect associated organisms as well as ecosystem function. The extent of ecotypic variation in dominant tallgrass prairie species and the consequences of this variation for ecosystem functioning were studied by manipulating two potential drivers of plant community dynamics: climate and the soil microbial community. Climate was manipulated indirectly through the use of reciprocal restorations across a rainfall gradient where regional sources of dominant grasses Andropogon gerardii and Sorghastrum nutans were seeded with 8 other native species that occur in tallgrass prairie. Four dominant grass sources (originating from central Kansas [CKS], eastern Kansas [EKS], southern Illinois [SIL], or a mixture of these) were reciprocally planted within four sites that occurred across a precipitation gradient in western KS (Colby, KS), CKS (Hays, KS), EKS (Manhattan, KS) and SIL (Carbondale, IL). The three grass sources and mixture of sources were sown into plots according to a randomized complete block design at each sites (n=16, 4 plots / block at each site). Aboveground net primary productivity (ANPP) was measured at the end of the 2010 and 2011 growing season at each site. In 2010, total ANPP declined from western to eastern Kansas, but increased across the geographic gradient in 2011. The dominant grasses did not comprise the majority of community ANPP in WKS, CKS or SIL in either year but did contribute most to total ANPP at the EKS site in 2011. In 2010, volunteer forbs comprised the largest proportion of ANPP in WKS, whereas and in both years planted forbs comprised the largest proportion of ANPP in SIL. Ecotypic variation in ANPP of A. gerardii was not evident, but Sorghastrum nutans ANPP exhibited a site by source effect in 2010 that did not suggest a home site advantage. Variation in the competitive environment at each site may have masked ecotypic variation during community assembly. Further, ANPP responses suggest that grasslands in early stages of establishment may respond more stochastically to climatic variation than established grasslands. Longer term studies will clarify whether ecotypes of dominant prairie grasses affect ecosystem function or community trajectories differently during restoration. Ecotypes of dominant species may support different soil microflora, potentially resulting in plant-soil feedback. A second experiment tested for local adaptation of prairie plant assemblages to their soil microbial community. Native plant assemblages from Kansas and Illinois were tested for local adaptation to their `home' soil by reciprocally crossing soil and plant source in a greenhouse experiment. Seeds and soil were obtained from two remnant prairies, one in eastern Kansas and one in central Illinois, with similar species composition but differing climate. Seeds of four species (Andropogon gerardii, Elymus canadensis, Lespedeza capitata, Oligoneuron rigidum) common to both locations were collected, germinated, and transferred to pots to create 4-species assemblages from each region. Non-prairie (NP) soil from the edge of an Illinois agricultural field was also included as an inoculum treatment to increase relevance to restoration. Kansas and Illinois plant assemblages were subjected to a fully factorial combination of soil inocula [with associated microbial communities] (3 sources: KS, IL, NP) and soil sterilization treatment (sterilized or live). Plants were harvested after 20 weeks and soil was analyzed for microbial composition using phospholipid fatty acid (PLFA) markers. Soil sources had different nutrient concentrations and sterilization resulted in a flush of NH4+, which complicated detection of soil microbial effects. However, plant sources did exhibit variation in productivity responses to soil sources, with Kansas plants more responsive to live soil sources than Illinois plants. Despite confounding variation in soil fertility, soil inoculation was successful at manipulating soil microbial communities, and plant sources responded differently to soil sources. Consideration of feedback between soil and plants may be a missing link in steering restoration trajectories.

The thesis reports distribution and important aspects of biology (host spectrum, effect of the species on plant community and basic ecophysioogical characteristics) of the endangered early ecotype of hemiparasitic plant Melampyrum nemorosum (Orobanchaceae) in the Czech Republic. Comparisons to the frequently occurring late ecotype are also emphasised where relevant.

Biological invasions have been observed throughout the world for centuries, often with major consequences to biodiversity and food security. Tying invasion to species identity and associated traits has led to numerous hypotheses on why, and where, some species are invasive. In recent decades, attention to intraspecific variation among invaders has produced questions about their adaptation to climate, land use, and environmental change. I examined the intraspecific variation of invasive Johnsongrass's (Sorghum halepense (L.) Pers.) seedling stress response, propagule cold tolerance, and large-scale niche dynamics for correlation with populations' climatic and ecotypic (i.e., agricultural vs. non-agricultural) origin. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated more and faster, while non-agricultural seedlings showed uniform chlorophyll production regardless of home soil carbon origin, unlike their agricultural counterparts. Neither seedling stress response nor propagule cold tolerance interacted with ecotype identity; however, drought stress varied with population origins' aridity and soil fertility, and seed from warm/humid and cold/dry climates was most germinable. Comparison of seed and rhizome cold tolerance also suggested that the latter is a conserved trait that may be limiting S. halepense poleward range expansion. This physiological limit, an unchanged cold temperature niche boundary between continents and ecotypes, and a narrowed niche following transition to non-agricultural lands all imply low likelihood of spread based on climatic niche shift. Instead, evidence points to range expansion driven primarily by climate change and highlights agriculture's role in facilitating invasibility. This tandem approach to climate and land use as drivers of intraspecific variation is transferable to other taxa and can help refine our conception of and response to invasion in the Anthropocene. / Doctor of Philosophy / Exotic invasive species are a global problem, threatening biodiversity and biosecurity now and in the future. In the last several decades, ecologists have studied many individual invaders and their traits to understand what drives their spread. More recently, abundant differences in traits between populations within an invasive species have raised questions about humans' role in facilitating invasion through climate change, land use, and other disturbances. I studied the invasive Johnsongrass's (Sorghum halepense (L.) Pers.) response to drought, nutrient limitation, and freezing to detect differences between populations based on their climate and ecotype (agricultural vs. non-agricultural) origin. I also tracked differences in the climates the species occupied across the globe and North America and projected its future distribution under climate change. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated the most, while non-agricultural seedlings performed consistently regardless of soil carbon origin, unlike their agricultural counterparts. In addition, drought stress varied with population origins' rainfall and soil fertility, and seed germination favored warm/humid and cold/dry origin. Rhizome (underground stem) cold tolerance appears to be a trait that limits S. halepense poleward range expansion. Along with no change in the coldest climates occupied worldwide and no spread to new climates with transition to non-agricultural lands, this implies that Johnsongrass is unlikely to expand its range without external forces. Instead future range expansion will likely be driven by climate change. This coupled approach to climate and land use affecting invasion is transferable to other species and can help refine both our concepts and response strategies.

Les processus de diversification adaptative, qui sont au cœur de la diversité du monde vivant, ont été étudiés grâce à une stratégie d'évolution expérimentale, initiée par le Pr Richard Lenski en 1988. Douze populations, fondées à partir d'un ancêtre commun d'Escherichia coli, sont propagées indépendamment depuis plus de 55 000 générations par transferts journaliers dans un milieu minimum limité en glucose. Un événement de diversification a émergé après 6500 générations d'évolution dans une seule des douze populations, appelée Ara-2, conduisant à deux lignées cellulaires différenciées, appelées S et L, qui continuent de co-exister depuis notamment grâce à des interactions négatives dépendant de leur fréquence. Deux propriétés confèrent à ce polymorphisme une grande originalité et donc un intérêt d'étude important : sa durée car il s'agit du plus long polymorphisme jamais identifié lors d'expériences d'évolution en laboratoire, et son unicité puisqu'il ne s'est produit qu'une seule fois au sein des douze populations initiées à partir d'un ancêtre commun. L'objectif de ce travail a été d'identifier les mécanismes du maintien au long terme des lignées S et L, ainsi que les bases génétiques de leur émergence. Le maintien du polymorphisme est lié à une forte dynamique des relations écologiques entre S et L, l'une des lignées envahissant systématiquement les niches écologiques de l'autre, qui réagit en conséquence pour éviter l'extinction. L'émergence de la lignée S est due à une succession précise de trois mutations, nécessaires et suffisantes pour établir les phénotypes de la lignée S. Les trois mutations affectent toutes des gènes codant des régulateurs globaux de la transcription, dont deux sont impliqués dans la régulation du métabolisme central. Pour l'un d'entre eux, l'allèle évolué altère les propriétés de liaison à l'ADN de la protéine évoluée. Bien que ce polymorphisme soit unique, ces trois gènes sont pourtant les cibles de la sélection naturelle dans la majorité des autres populations de l'expérience d'évolution. Pour deux d'entre eux, seul l'allèle substitué dans la population Ara-2 confère en fait les phénotypes de la lignée S. Ainsi, l'unicité de cet événement de diversification est liée à une succession d'événements mutationnels très précis, qui affectent par ailleurs les réseaux globaux de l'expression des gènes. Ces modifications graduelles ont ainsi conduit à l'émergence du plus long polymorphisme mis en évidence à ce jour dans des expériences d'évolution en laboratoire. / Adaptive diversification events that underly the diversity of the living world have been studied by an experimental evolution strategy initiated by Richard Lenski in 1988. Twelve populations founded from a common ancestor of Escherichia coli are propagated independently since more than 55,000 generations by daily transfer in a glucose-limited minimal medium. A diversification event emerged after 6500 generations of evolution in only one of the twelve populations, called Ara-2, resulting in two lineages of differentiated cells, called S and L, that coexist ever since owing to negative frequency-dependent interactions. Two properties make this polymorphism original and important: its length as the longest one ever observed in evolution experiments, and its uniqueness as it occurred only once in the twelve populations founded from the same ancestor. The aim of this work was to identify the mechanisms of the long-term coexistence of the S and L lineages, together with the genetic bases of their emergence. The maintenance of the polymorphism is characterized by a strong dynamic of the ecological relationships between S and L, with with L seeming to encroach over time on the niche of S, which reacts to avoid extinction. The emergence of the S lineage is due to the succession of three mutations, necessary and sufficient to establish its phenotypes. All three mutations affect genes encoding global transcriptional regulators, with two of them being involved in the regulation of central metabolism. For one of them, the evolved allele alters the DNA binding ability of the evolved protein. Although this polymorphism is unique, the same three genes are targets of natural selection in most other populations of the evolution experiment. For two of them, only the substituted allele of the Ara-2 population results in the phenotypes of the S lineage. Thus, the uniqueness of this diversification event is linked to a succession of precise mutational events that affect the global regulatory network in the cell. Those gradual modifications lead thus to the emergence of the longest polymorphism ever identified during evolution experiments in the laboratory.

The smallest free living eukaryote known as Ostreococcus tauri became along with some related species great experimental models for iron uptake research in marine picoplankton. The ecological context of such topic is very interesting considering the nature of adaptation to iron limitation and its connection to the copper metabolism. Our experiments has simulated iron and copper limiting conditions of the ocean, as a control we used iron and copper repleted cultivation media. The maximum cell counts were two- to threefold higher in iron-repleted medium compared to iron- depleted one. There was the only exception showing no difference in growth - O. lucimarinus coming from open ocean with high irradiance levels and very low iron concentrations, which all together made it the best adapted species. The reinoculation of cell cultures after a week cultivation into to the same iron/copper containing media led to unmasking the copper effect on growth, which was much weaker than encountered with iron (again except of O. lucimarinus). Iron sufficiency positively affects heme b and chlorophyll a and b content with no significant copper dependency. The circadian timing of heme b and chlorophyll a and b content shows the increasing trend during the day followed by decrease at night. This might be caused by...