Thesis (Ph.D.)--University of California, San Diego, 2005. / (UnM)AAI3208810. Advisers: Lisa A. Levin; A. Aristides Yayanos. Source: Dissertation Abstracts International, Volume: 67-03, Section: B, page: 1244.

Thesis (Ph.D.)--Aberdeen University, 2009. / Title from web page (viewed on Mar. 30, 2010). Includes bibliographical references.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-07, Section: A, page: 2700. Adviser: Bruce M. Hannon. Includes bibliographical references (leaves 167-184) Available on microfilm from Pro Quest Information and Learning.

Thesis (Ph. D.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 85-94). Also available on the World Wide Web.

The discovery of deep-sea chemosynthesis-based ecosystems including hydrothermal vents and cold seeps has greatly expanded our view of life on Earth. Nevertheless, for many benthic organisms in these ecosystems, little is known about where they come from, how scattered populations are connected by larval dispersal, and how they adapt to the local environments. Mussels of Bathymodiolus platifrons (Bivalvia: Mytilidae) are one of the dominant and foundation species in deep-sea chemosynthesis-based ecosystems. They are known to have a wide geographic distribution, and are also one of the few deep-sea species capable of living in both hydrothermal vents [in Okinawa Trough (OT)] and methane seeps [in the South China Sea (SCS) and Sagami Bay (SB)]. Previous population genetics studies of B. platifrons mostly relied on one to several genes, which suffered from the lack of sensitivity required to resolve their fine-scale genetic structure, and were unable to reveal their adaptation to the local environments. With the repaid development of molecular techniques, it is now possible to address their demographic mechanisms and local adaptation from a genome-wide perspective. Therefore, in the first part of my thesis, I aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for B. platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) approach, assess the potential use of SNPs in detecting fine-scale population genetic structure and signatures of diversifying selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781 720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified from 28 B. platifrons individuals collected from a methane seep in the SCS and a hydrothermal vent in the middle OT (M-OT), with nine outlier SNPs showed significant evidence of diversifying selection. The small FST value (0.0126) estimated based on the neutral SNPs indicated high genetic connectivity between the two populations. However, the permutation test detected significant differences (P < 0.00001), indicating the two populations having clearly detectable genetic differentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the neutral or outlier SNPs also showed that the two populations were genetically differentiated. This initial study successfully demonstrated the applicability of combining genome sequencing and 2b-RAD in population genomics studies of B. platifrons. Besides, using the survey genome of B. platifrons as a reference, a total of 10 199, 6429, and 3811 single nucleotide variants (SNVs) were detected from three bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides, and Idas sp. These results highlighted the potential of cross-species and cross-genus applications of the B. platifrons genome for SNV/SNP identification among different bathymodioline lineages, which can be further used in various evolutionary and genetic studies. To have a deeper understanding of how individuals of B. platifrons are connected among and adapt to their habitats, in the second part of my thesis, I used both mitochondrial genes and genome-wide SNPs to conduct a more comprehensive population genetics/genomics study of B. platifrons. Three mitochondrial genes (i.e. atp6, cox1, and nad4) and 6398 SNPs generated by 2b-RAD were obtained from 110 B. platifrons individuals from six representative locations along their known distribution range in the Northwestern Pacific. The small FST values based on both types of genetic markers all revealed high genetic connectivity of B. platifrons, which may have been driven by the strong ocean currents (i.e. Kuroshio Current, North Pacific Intermediate Water). However, when using SNP datasets rather than mitochondrial genes, individuals in the SCS were identified as a distinct genetic group, indicating the Luzon Strait may serve as a dispersal barrier that limits their larval exchange between the SCS and the open area in the Northwestern Pacific. Moreover, a genetic subdivision of B. platifrons in the southern OT (S-OT) from those in M-OT and SB was observed when using 125 outlier SNPs for data analyses. The outlier-associated proteins were found to be involved in various biological processes, such as DNA and protein metabolism, transcription and translation, and response to stimulus, indicating local adaptation of B. platifrons even they are confronted with extensive gene flow in the OT-SB region. Furthermore, by using SNP datasets, populations in S-OT were revealed to be the source of gene flow to those in the SCS, M-OT, and SB. Overall, these results offered novel perspectives on the potential forces that may have led to the genetic differentiation and local adaptation of B. platifrons, which can serve as an example for other deep-sea species with high dispersal potential, and contribute to the designation of marine protected areas and conservation of deep-sea chemosynthesis-based ecosystems. Molluscan shell formation is one of the most common and abundant biomineralization processes in metazoans. Although composed of less than 5 wt% of the molluscan shells, shell matrix proteins (SMPs) are known to play multiple key roles during shell formation, such as providing a gel-like micro-environment to favour mineral precipitation, promoting crystal nucleation, as well as guiding and inhibiting crystal growth. To date, all studies on SMPs have focused on molluscs in terrestrial and shallow-water ecosystems with no reports for those living in the deep ocean. Herein, the third part of my thesis was to study the shell proteomes of B. platifrons and its shallow-water relative Modiolus philippinarum with the aim to bridge such knowledge gaps in biomineralization studies. A total of 94 and 55 SMPs were identified from the shell matrices of B. platifrons and M. philippinarum, respectively, with 31 SMPs shared between two species. These SMPs can be assigned into six broad categories, comprising calcium binding, polysaccharide interaction, enzyme, extracellular matrix-related proteins, immunity-related proteins, and those with uncharacterized functions. Many of them, such as tyrosinases, carbonic anhydrases, collagens, chitin-related proteins, peroxidases, as well as proteinase and proteinase inhibitor domain-containing proteins, have been widely found in molluscan shell matrices and other metazoan calcified tissues (e.g. exoskeletons of corals, tubes of tubeworms), whereas some others, such as cystatins, were found for the first time in molluscan shell matrices, and ferric-chelate reductase-like proteins and heme-binding proteins were to be detected for the first time in metazoan calcified tissues. This is the first report of the shell proteome of deep-sea molluscs, which will support various follow-up studies to better understand the functions of these SMPs, especially in relation to environmental adaptation. Overall, my population genetics/genomics studies have improved our understanding of the population dynamics, genetic connectivity, fine-scale genetic structure, and local adaptation of B. platifrons in the Northwestern Pacific, and my proteomics study has shed light on the biomineralization processes of molluscs in the deep ocean.

Doctor of Philosophy / Department of Biology / Jack F. Cully, Jr. / Black-tailed prairie dogs (Cynomys ludovicianus) are epizootic hosts for plague (Yersinia pestis); however, alternate enzootic hosts are important for the maintenance of the pathogen. We determined small rodents and prairie dog associations and quantified rodent and flea relationships in the presence and absence of prairie dog colonies and plague. We identified potential alternate hosts and flea vectors for the maintenance and transmission of plague in the prairie ecosystem. This is the first multi-year study to investigate associations between prairie dogs, rodents and fleas across the range of the black-tailed prairie dog. Few rodent species associated with black-tailed prairie dogs and were found to be highly abundant on colonies. Rodent species implicated in plague were present at study areas with and without plague. Peromyscus maniculatus and Onychomus leucogaster, two widely occurring species, were more abundant in areas with a recent history of plague. Flea community characteristics varied within each study area in the presence and absence of prairie dogs. Based on flea diversity on rodents, and the role of rodents and fleas in plague, we identified P. maniculatus and O. leucogaster and their associated fleas, Aetheca wagneri, Malareus telchinus, Orchopeas leucopus, Peromyscopsylla hesperomys, and Pleochaetis exilis to be important for the dynamics of sylvatic plague in our study areas. Peromyscus maniculatus and O. leucogaster were consistently infected with Bartonella spp., another blood parasite. Presence of prairie dog fleas on other rodents at both off and on prairie dog colonies suggests the potential for intra and interspecific transmission of fleas between rodent hosts, and between other small rodents and prairie dogs.

Doctor of Philosophy / Department of Biology / David C. Hartnett / In perennial grasslands, the belowground population of meristems (the bud bank) plays a fundamental role in local plant population structure and dynamics. I tested the “meristem limitation hypothesis” prediction that bud banks increase along an increasing precipitation/productivity gradient in North American grasslands. I sampled bud populations quarterly at six sites across a 1,100 km gradient in central North America. Bud banks increased with average annual precipitation, which explained 80% of variability in bud banks among sites. Seasonal changes in grass bud banks were surprisingly similar across a 2.5-fold range in precipitation and a 4-fold range of aboveground net primary productivity (ANPP). Secondly, I tested the hypothesis that tallgrass prairie plants respond to increases in a limiting resource (nitrogen) through demographic effects on the bud bank. I parameterized matrix models for individual genets, considering each genet as a population of plant parts (buds and stems). Nitrogen addition significantly impacted bud bank demography of both Sporobolus heterolepis and Koeleria macrantha. In 2005, emergence from the bud bank and growth rates (λ) of the tiller population were significantly higher in S. heterolepis genets that received nitrogen. In contrast, nitrogen addition decreased λ in K. macrantha. Both prospective and retrospective analyses indicated that bud bank dynamics are the key demographic processes driving genet responses to nutrient availability. Lastly, I tested the hypothesis that the effects of fire and grazing on plant species composition and ANPP are mediated principally through demographic effects on bud banks. I found that plants respond to fire and grazing with altered rates of belowground bud natality, bud emergence, and both short-term (fire cycle) and long-term changes in bud density. The size of the bud bank is an excellent predictor of long-term ANPP, supporting my hypothesis that ANPP is strongly regulated by belowground demographic processes. Meristem limitation due to water or nutrient availability or management practices such as fire and grazing may constrain grassland responses to inter-annual changes in resource availability. An important consequence is that grasslands with a large bud bank may be the most responsive to future climatic change or other phenomena such as nutrient enrichment, and may be most resistant to exotic species invasions.

Master of Science / Department of Biology / Brett K. Sandercock / Translocations are a useful management tool for restoring wildlife species to their native ranges, but require post-release monitoring to determine project success. We report results of a 4-year effort to reestablish a breeding population of Evermann's Rock Ptarmigan (Lagopus mutus evermanni) on Agattu Island in the Aleutian Archipelago, Alaska. This endemic subspecies of ptarmigan was extirpated from most of the Near Islands by introductions of arctic fox by fur traders, and natural recolonizations did not occur after fox eradication. All females surviving the 2-week post-release period attempted to nest but initiated clutches later in the season and laid fewer eggs than resident females. Nest success was similar for resident and translocated females. Brood survival was greater for translocated than resident females and differed significantly; however, brood survival varied among years and was reduced by adverse weather conditions in 2006. Seasonal survival of radio-marked birds during the breeding season was 100% for translocated and resident ptarmigan. Over-winter mortality resulted in a low return rate in 2006. Returning birds in 2006 showed strong site fidelity and nest locations in two consecutive years were closely spaced. We examined nest site selection and determined brood movements and home range size of recently translocated and resident females. Nest sites of translocated females averaged 4.2 km from their respective release location and were not different from nest locations of resident females with regard to topographical features. Female nest site selection was influenced by percent composition of rock and forb coverage but was unaffected by slope, aspect, or general habitat. Broods of both resident and translocated females made movements to higher elevations after hatching. While size of brood home range was similar for resident and translocated females, distances traveled between the nest site and the arithmetic center of the brood home range were greater for translocated females. Overall, we conclude that translocations are an effective technique for reestablishing island populations of Rock Ptarmigan. Our study provides successful methods which may benefit future projects to reestablish endemic populations of ptarmigan and landbirds elsewhere in the Aleutian Islands.

Master of Science / Department of Biology / David C. Hartnett / Herbivory is one of the major biotic interactions shaping the structure and dynamics of grassland plant populations and community structure. The two major grass growth forms, rhizomatous and caespitose species, may show different grazing tolerance and short-term overcompensation may offset long-term reductions in plant performance and fitness. The objectives of this study were to assess 1) the effects of long-term ungulate grazing on plant architecture, population structure, and life history traits of the caespitose perennial grass, Schizachyrium scoparium (little bluestem), and the rhizomatous Bouteloua curtipendula (sideoats grama) in tallgrass prairie, and 2) the effects of grazing intensity (frequency of defoliation) on growth responses of little bluestem. Long-term bison grazing decreased the cover, frequency, tiller height, and proportion of tillers producing seed in little bluestem, but caused no changes in tiller density and total genet size. Grazed little bluestem plants maintained a significantly larger below ground bud bank. Bison grazing had no long-term effect on the abundance, bud bank densities, or rhizome growth of the rhizomatous side-oats grama grass. Biomass, tiller density, relative growth rates, and proportion of tillers flowering in little bluestem all decreased with increasing frequency of defoliation. However, even an intense grazing regime (9 defoliations over a 12 month period) caused no plant mortality and no changes in new tiller emergence rates, or bud bank densities. Increasing defoliation frequency did result in shifts in plant architecture, as an increasing proportion of extravaginal tillers led to a more lateral, decumbent growth form. These results show that the rhizomatous side-oats grama grass has a significantly higher grazing tolerance than does little bluestem, and/or that bison selectively graze little bluestem. Results from responses to the experimental defoliation regimes suggest that little bluestem shows lower tolerance to high frequency of defoliation, and its maintenance of a reserve below ground bud bank may be its primary tolerance mechanism, allowing tiller populations to recover following severe defoliation.

Doctor of Philosophy / Department of Biology / Anthony Joern / Aboveground and belowground food webs are linked by plants, but their reciprocal influences are seldom studied. Because phosphorus (P) is the primary nutrient associated with arbuscular mycorrhizal (AM) symbiosis, and evidence suggests it may be more limiting than nitrogen (N) for some insect herbivores, assessing carbon (C):N:P stoichiometry will enhance my ability to discern trophic interactions. The objective of this research was to investigate functional linkages between aboveground and belowground invertebrate populations and communities and to identify potential mechanisms regulating these interactions using a C:N:P stoichiometric framework. Specifically, I examine (1) long-term grasshopper community responses to three large-scale drivers of grassland ecosystem dynamics, (2) food selection by the mixed-feeding grasshopper Melanoplus bivittatus, (3) the mechanisms for nutrient regulation by M. bivittatus, (4) food selection by fungivorous Collembola, and (5) the effects of C:N:P on invertebrate community composition and aboveground-belowground food web linkages. In my analysis of grasshopper community responses to fire, bison grazing, and weather over 25 years, I found that all three drivers affected grasshopper community dynamics, most likely acting indirectly through effects on plant community structure, composition and nutritional quality. In a field study, the diet of M. bivittatus was dominated by forbs with grasses constituting only a minor fraction of their diet under ambient soil conditions, but grass consumption approximately doubled as a result of changes in grass C:N:P. M. bivittatus was found to rely primarily on selective consumption of foods with varying nutritional quality, rather than compensatory feeding or altering post-ingestive processes, to maintain C:N homeostasis in a laboratory experiment. In a soil-based mesocosm study, I show that Collembola feed on both saprophytic and AM fungi, in some cases exhibiting a slight preference for AM fungi. In the final study, although I did not find the expected indirect relationship between soil Collembola and aboveground herbivory as mediated through host plant quality, there were significant effects of root C:N and AM colonization on Collembola density and of plant C:N on aboveground herbivory. Overall, this research shows that host plant C:N:P stoichiometry can influence both above- and belowground invertebrate population, community, and food web dynamics.