Small broomrape, a holoparasitic weed, is a relatively new weed introduction in the Pacific Northwest that has contaminated a limited number of red clover fields in Oregon. Greenhouse and field studies were conducted to evaluate small broomrape response to common crop and weed species in the Pacific Northwest. Host species in the greenhouse or field study included alfalfa, arrowleaf clover, carrot, celery, common vetch, crimson clover, lettuce, prickly lettuce, red clover, spotted catsear, subterranean clover, white clover, and wild carrot. False-host species included barley, birdsfoot trefoil, creeping bentgrass, cucumber, field corn, fine fescue, flax, Italian ryegrass, nasturtium, oat, orchardgrass, perennial ryegrass, snap bean, sugar pea, sunflower, sweet corn, tall fescue, tomato, and wheat. Non-host species included sugar beet and curly dock. The greenhouse polyethylene bag system provided a rapid and inexpensive screening for plant species host status to small broomrape. Germination and attachment to host roots are initiated by chemical exudates, that may change concentration in response to nutrient availability and microorganisms. Red clover was grown in varying concentrations of ammonium sulfate fertilizer with and without Rhizobium inoculation, and with small broomrape seeds. Neither Rhizobium inoculation nor ammonium concentration influenced the number of small broomrape attachments to red clover roots. A survey was conducted of red clover seed growers with small broomrape-contaminated fields in the Pacific Northwest. Red clover seed from six respondents were cleaned at the same cleaning facility, and the same respondents purchased their seed stock from this cleaning facility. Small broomrape was not identified in red clover fields prior to or during the first clover seed harvest of fall planted red clover in small broomrape-contaminated sites. / Graduation date: 2003

<p>Because species respond individually to climate change, understanding community assembly requires examination of multiple species from a diversity of forest niches. I present the post-glacial phylogeographic history of an understory, parasitic herb (<italic>Epifagus virginiana</italic>, beechdrop) that has an obligate and host specific relationship with a common eastern North American hardwood tree (<italic>Fagus grandifolia</italic>, American beech). The migration histories of the host and parasite are compared to elucidate potential limits on the parasite's range and to understand their responses to shared climate change. Two chloroplast DNA regions were sequenced and 9 microsatellite loci genotyped from parasite specimens collected throughout the host's range. These data were compared with available cpDNA sequences from the host (McLachlan et al. 2005) and host fossil pollen records from the last 21,000 years (Williams et al. 2004). Analyses of genetic diversity reveal high population differentiation in the parasite's southern range, a possible result of long term isolation within multiple southern glacial refuges. Estimates of migration rates and divergence times using Bayesian coalescent methods show the parasite initiating its post-glacial range expansion by migrating northward into the northeast from southern areas, then westward into the midwest, a pattern consistent with the development of high density beech forests. This result is strongly confirmed through spatial linear regression models, which show host density plays a significant role in structuring parasite populations, while the initial migration routes of the host are irrelevant to parasite colonization patterns. Host density is then used as a proxy for the parasite's habitat quality in an effort to identify the geographic locations of its migration corridors. Habitat cost models are parameterized through use of the parasite's genetic data, and landscape path analyses based on the habitat map show a major migration corridor south of the Great Lakes connecting the northeast and midwest. Host density was the major determinant controlling the parasite's range expansion, suggesting a lag time between host and parasite colonization of new territory. Parasites and other highly specialized species may generally migrate slower due to their complex landscape requirements, resulting in disassociation of forest assemblages during these times. From these results, the low migration capacities of highly specialized species may be insufficient to outrun extirpation from their current ranges.</p> / Dissertation

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs and a few non-bioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only ~1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole genome shotgun read depth is 1,400X coverage for the plastome, while the mitochondrial genome is covered at 40X and the nuclear genome at 2X. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally-active open reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in Hydnora visseri. A four stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs and a few non-bioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only ~1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole genome shotgun read depth is 1,400X coverage for the plastome, while the mitochondrial genome is covered at 40X and the nuclear genome at 2X. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally-active open reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in Hydnora visseri. A four stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

Une des contraintes biotiques majeures de la riziculture de bas-fond au nord du Togo est l’adventice parasite Rhamphicarpa fistulosa (Hochst.) Benth. Afin d’évaluer les options stratégiques pour contrôler efficacement R. fistulosa, notre étude a été conduite avec comme principaux objectifs : 1) l’identification de la répartition de R. fistulosa et l’étude des facteurs qui favorisent son infestation, 2) l’étude de l’impact des niveaux d’infestation sur la flore adventice du riz, et 3) la caractérisation des interactions hôte-parasite et de leurs impacts sur le développement de l’hôte et les performances reproductives du parasite. A l’issu des prospections de terrain, les plus fortes infestations ont été retrouvées sur des sols majoritairement à texture sableuse et très pauvres en matière organique. Une flore adventice très diversifiée a été retrouvée en présence de R. fistulosa, certaines adventices pouvant être parasitées et constituer éventuellement un réservoir pour accroître le stock semencier du parasite. En conditions contrôlées, R. fistulosa se développe et se reproduit aussi bien sur le riz que sur la tomate, alors que le soja retarde la reproduction du parasite. La germination des graines de R. fistulosa est maximale en présence de graines de plantes cultivées ou adventices. Les graines nouvellement récoltées ont une dormance de plus de six mois, mais leur germination a été stimulée par la présence de phytohormones. En conclusion, les meilleures stratégies de lutte doivent impliquer le contrôle par les semis tardifs, les rotations culturales avec les légumineuses comme le soja, l’arachide ou le niébé, et les cultures maraîchères. / Main biotic constraints to rain-fed lowland rice cultivation in northern Togo include the parasitic weed Rhamphicarpa fistulosa (Hochst.) Benth. In order to evaluate efficient strategies to control R. fistulosa, our study was performed taking into account the following main objectives: 1) Identification of the distribution of R. fistulosa and study of the factors favouring its infestation, 2) Study of the impacts of infestation levels on rice weed communities, and 3) Characterization of the host-parasite interactions and their impacts on the host development and the parasite reproduction. Following fields investigations, highest infestations were observed on sandy soils with low levels of organic matter.In addition, weed flora found in the presence of R. fistulosa was much diversified and some weeds were found to been parasitized and could possibly constitute reservoirs to increase the seed stock of the parasite. In controlled experiments, R. fistulosa grown and reproduced better on rice and tomato crops, than on soybean which delayed the reproduction of the parasite. Germination of R. fistulosa seeds was stimulated in presence of cultivated crops or weeds. New collected seeds shown six months dormancy but their germination was stimulated in presence of phytohormones. In conclusion, the best strategies to control R. fistulosa must include delayed sowing, crop rotation with leguminous species (i.e. soybean, peanut or cowpea) and vegetable cropsKeywords: Rhamphicarpa fistulosa, rice, lowland, parasitism, host-parasite interaction, weeds.