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Iron is one of the most important micronutrients used by living organisms. Iron is frequently a limiting nutrient for plant growth, and plants are a major source of iron for human nutrition. The most prominent symptom of iron deficiency in plants is interveinal chlorosis, or yellowing between the veins, which appears first in the youngest leaves. Iron deficiency anemia (IDA) is the number one human nutritional deficiency worldwide. In order to solve the problem of iron deficiency, it is desirable to breed plants that have increased iron in those parts that are consumed by humans. To do this, we must first understand the molecular basis of Fe uptake, transport, and storage in plants. In soil, iron is quickly oxidized to Fe(III), and Fe(III) is relatively insoluble, thus difficult for plants to obtain. Our lab has been working on metal ion homeostasis mechanisms in plants and the ultimate goal of our research is to understand the mechanisms by which plants maintain the correct levels of iron, zinc and copper in each cell and tissue. The Yellow Stripe-like (YSL) family of proteins has been identified based on sequence similarity to maize Yellow stripe 1 (YS1). YS1 transports Fe(III) that is complexed by phytosiderophores (PS), strong Fe(III) chelators of the mugineic acid family of compounds. Non-grass species of plants neither make nor use PS, yet YSL family members are found in non-grass species including Arabidopsis thaliana. YSLs in non-grasses have been hypothesized to transport metals that are complexed by nicotianamine (NA), an iron chelator that is structurally similar to PS and which is found in all higher plants. In this dissertation, Arabidopsis YSL1 and YSL3 are demonstrated to be important in iron transport and also responsible for loading Fe, Cu, and Zn from leaves into seeds. Arabidopsis YSL4 and YSL6 are demonstrated to be involved in iron transport and metal mobilization into seeds. The transport function of Arabidopsis YSL1 and YSL2 are shown be partially overlapping to the function of Arabidopsis YSL3 in vegetative structures, but distinct in reproductive organs. Arabidopsis YSL3 and YSL6 are shown to have distinct functions in planta.

Suspended and epiphytic bacteria were studied in calcareous headstreams of the Yorkshire Wolds and in acid headstreams of the Galloway Hills. Mean concentrations of suspended bacteria were marginally greater in the calcareous streams, while heterotrophic activity was substantially greater. Mean cell volume was also greater. The concentration and activity of suspended bacteria in the calcareous streams usually showed linear downstream increase, while in the acid streams, the downstream increase was less, and was frequently not observed. In Mill Beck (a calcareous stream) it was found that the population of epiphytic bacteria near the source was easily sufficient to sustain the observed downstream increase in suspended bacteria. In Dungeon Burn (an acid stream) a substantial population of epiphytic bacteria was also found, but there was no downstream change in concentration of suspended bacteria; reasons are suggested for the apparent non-release of epiphytes in the Galloway stream. The mean volume of suspended bacteria in Mill Beck changed between the source and downstream limit of a vegetated section, to resemble that of epiphytic bacteria, suggesting that suspended bacteria were dislodged epiphytes. Estimates were made of the attachment rate of suspended bacteria to submerged vegetation in Mill Beck; daily attachment represented only a small proportion of the total standing crop of epiphytic bacteria. A further study in Mill Beck, over a Spring growing period, demonstrated a temporal change in the density of epiphytic bacteria, which was related to change in discharge and temperature. The results supported the suggestion that epiphytic bacteria might largely be the source of suspended bacteria in this headstream.

Hybridisation is a common evolutionary process that can arise in primary or secondary contact. Gene ow and/or reproductive isolation between hybridising taxa can be explored in hybrid zones. Therefore, a (homoploid) hybrid zone in north-west Spain between Hyacinthoides non-scripta and H. hispanica was studied. The centre occurs west to east across the Galicio-Duero Mountains with H. non-scripta distributed north, and H. hispanica south of the centre. The hybrids' genome sizes and phenotypes represented a range of intermediate states between their parents. Crossing and seed germination experiments revealed a low inter-speci c barrier, and the hybrids showed similarly good tness. Genome wide markers for large genome species were designed from transcriptomes. Diagnostic SNPs between H. non-scripta and H. hispanica were targeted and re-sequenced with multiplexing PCR. Coalescence analyses suggested a Pleistocene origin of parapatric speciation between H. non-scripta and H. hispanica. These results are supported by shared inter-speci c polymorphisms, the lack of recent hybrid generations and of parental individuals in sympatry. Di erential introgression patterns between the organellar and nuclear genomes revealed that formerly H. hispanica ranged further north but was swamped by H. non-scripta alleles. Asymmetric hybridisation was reasoned by absence of backcrosses between northern hybrids to H. non-scripta, but presence between southern hybrids and H. hispanica. Combining these results, a southwards movement of the hybrid zone centre caused by climate change (and adaptive introgression), or inter-speci c di erences in owering time was suggested. Cline patterns revealed cyto-nuclear incompatibilities, which could evolve through divergent adaptation of the organelle to climate and a delayed selection on nuclear inter-acting loci. Both species are in secondary contact in the UK due to recent introduction(s) of H. hispanica and garden variants, which is considered to cause genetic pollution of native H. non-scripta. Therefore, a conservation study is in progress, in which this diagnostic marker system for bluebells is applied.

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Plants often modify microsite conditions important for seedling establishment. Palms may reduce light levels and produce deep leaf litter; both may suppress seedlings, affecting the local abundance, distribution, and species composition of tree seedlings. The abundance and composition of palms were examined along a tropical forest chronosequence at the Barro Colorado Nature Monument, Panama. Palms were sampled along transects in secondary (20, 40, 70, and 100 y in fallow) and old-growth forests. Palm abundance and basal area significantly increased with forest age. Palm distribution was driven by the most abundant palm, Oenocarpus mapora, which accounted for 60% of the total stems. I examined the effects of O. mapora, on seedling distributions on Barro Colorado Island, Panama. I asked: a) what are the effects of O. mapora on light availability and leaf litter accumulations; b) how does O. mapora affect abundances of seedlings; c) does seed size of established seedlings differ between palm and non-palm sites? Seedling composition, light availability, leaf litter, and palm presence were measured in 1-m² contiguous plots along transects in one late second growth and two old growth forest stands. I conducted a seedling transplant experiment to determine the effect of O. mapora and its leaf litter on growth and mortality rates of Gustavia superba seedlings. Leaf litter depth was higher and light availability was lower in plots where palms were present. There was a lower probability of seedling presence where large palms were present. The probability of seedling presence increased with light availability. Seed size was greater for seedlings in palm plots relative to non-palm plots. Seedling survival was significantly lower for palm and litter treatments relative to controls. I conclude that O. mapora creates poor establishment conditions for seedlings which may affect the local abundance, distribution, and species composition of the seedling pool.

An increasingly urgent task in the field of conservation biology is to identify changes in abiotic and biotic interactions that result when large areas of forest are converted to small fragments surrounded by anthropogenic landscapes. My research, conducted in lowland dipterocarp rain forest at the 2,500-ha Pasoh Forest Reserve in Peninsular Malaysia, investigated a novel but strongly negative edge effect - namely, a tremendous increase in the density of wild pigs (Sus scrofa) and the resulting deleterious impacts on the understory plant community. The absence of feline predators due to the small size of the reserve and the presence of a year-round food supply in the agricultural areas surrounding the reserve are believed to be the main factors contributing to increased pig density. Line transects were conducted to determine pig density within Pasoh. Density in 1996 and 1998 was estimated to be 47 and 27 pigs/km², respectively, or 10 100 times historical levels. Fences were constructed to exclude pigs from control plots to quantify the impact of soil rooting and seed predation on plants in the understory. After two years, plots inside exclosures had three times more recruits, greater species richness, and 53% more height growth among plants 1 7 m tall than did adjacent plots to which pigs had access. Surveys were conducted in 1995, 1996, and 1998 to determine the number of reproductive nests constructed by pigs. Pigs constructed an estimated 6.0 nests/ha/year during this time, with an average nest composed of 145 snapped saplings and 117 uprooted saplings. Nest building accounted for 28.9% of all mortality for trees 1 2 cm diameter at breast height. Uprooted stems died, but snapped stems produced a leafless stump that could resprout. Observations of >1,800 stumps for 36 months revealed large differences in resprouting among species, families, and groups of plants with similar life history characteristics. Overall, the results of the different studies suggest that if elevated pig densities continue there could be a shift away from the currently dominant Dipterocarpaceae and Euphorbiaceae.

Chloroplasts generate important cellular signals and synthesize diverse products. The chloroplast-localized protein, Nitric Oxide Associated-1 (NOA1), is implicated in nitric oxide (NO) accumulation and linked to the methylerythritol phosphate (MEP) pathway, but its role is undefined. I report that NOA1 is not essential for NO accumulation because the noa1 mutant accumulates NO when provided sucrose-supplemented media. Therefore, chloroplast function and fixed carbon, but not NOA1 are likely critical for plant NO accumulation. noa1 is also resistant to fosmidomycin, an inhibitor of the MEP pathway. This phenotype led to uncovering a potential link between the MEP and tetrapyrrole pathways. I report that fosmidomycin toxicity is light dependent and reduced by phytol supplementation. Downregulation of the tetrapyrrole pathway enhances fosmidomycin resistance, suggesting that reduced tetrapyrrole biosynthesis alleviates fosmidomycin toxicity. These findings reveal new insight into how impairment of the MEP pathway affects plants and the importance of metabolic balance for chloroplast function.

Organisms on earth evolved a circadian clock that matches the planet's 24-hour rotation. The plant clock controls many behaviors and proper entrainment of the clock to the environment leads to a competitive overall growth advantage. Despite the finding that many wound-inducible genes are also circadian regulated, it was uncertain whether this regulation is important for plant defense against herbivorous insects. We found that plants entrained to light-dark cycles 12 hours out of phase with the predator, Trichoplusia ni (cabbage loopers), were more susceptible to T. ni herbivory than plants entrained in phase with T ni . In contrast, arrhythmic clock and jasmonate-deficient mutants were equally susceptible to T. ni herbivory whether entrained in the same or reciprocal 12-hour light-dark cycles. These results suggest that the circadian rhythms, acting through jasmonate signals and the clock, add selective advantage to plants through enhanced anticipation of and defense against herbivory.

Phylogenetic relationships and classification of Chrysothamnus, Ericameria, Xylothamia and related genera were investigated. The internal transcribed spacer and 3' external transcribed spacers (ITS and ETS) of the nuclear ribosomal (nr) DNA were analyzed separately and combined employing different optimality criteria. These analyses indicated that the previous classifications and hypotheses of relationships were not monophyletic. Chrysothamnus, Ericameria, Xylothamia, and related genera were placed in separate lineages irrespective of data set and optimality criteria. Chrysothamnus species, as traditionally delimited, were resolved in four, not necessarily closely related lineages affiliated with the Solidagininae. Previous sectional classification of Chrysothamnus based primarily on morphology was not supported by the present molecular data. Ericameria was placed in a clade separate from both Chrysothamnus and Xylothamia. Associated with, but basal to, the Ericameria lineage was a clade composed of Pentachaeta, Rigiopappus, and Tracyina. Prior infrageneric classification of Ericameria was in part consistent with the results of this investigation. Species were placed in three, rather than four, lineages within the genus. The three annual genera and Ericameria represent a lineage separate from the Solidagininae and Hinterhuberinae. Species of Xylothamia were not monophyletic but were placed in at least five separate lineages. Four species were aligned with Gundlachia, while the others were strongly supported in a separate clade. Within that clade, however, the other species were usually in distinct, but unresolved lineages. Xylothamia and its relatives were resolved in a clade distinct from other Solidagininae and merits recognition of their distinctiveness. Both Stenotus and Tonestus were polyphyletic. Type species of both genera were associated with other clades, and the relationship of most of the other species remains unclear. These results suggest a reclassification of these taxa into novel, distinct genera. In general, the results of this study were incongruent with relationships inferred from morphology.