The problem of species diversity and co-existence in hyper-diverse communities remains. Traditionally ecologists have approached this problem from examining patterns of co-occurrence, interaction matrices and abundance distributions. This work, while productive, generally has rarely explored the role of shared ancestry and species-specific quantitative function in promoting species diversity and co-existence. This has been a critical oversight as simply analyzing the list of Latin binomials in an assemblage ignores the relatedness between taxa as well as the diversity in organismal form and function--the very information relevant to evolutionary, ecological, and historical hypotheses about the distribution of diversity and community assembly. The following research is designed to investigate the role of phylogenetic and functional similarity on species diversity and co-existence through space and time in diverse tropical tree communities. Specifically, I investigate: (i) the role of phylogenetic relatedness in determining community structure from very local to large regional spatial scales; (ii) the role of phylogeny in determining the structure of tree communities at different strategraphic levels in the canopy; (iii) the power of recently developed phylogenetic analyses to detect non-random patterns of co-existence in communities when the phylogenetic tree used is not completely resolved; (iv) the role of functional similarity in promoting co-existence in a Neotropical dry forest through space and across body sizes; (v) whether decadal long trends in forest composition can be explained on the basis of species-specific function; and (vi) variability in a key functional trait across New World forest communities and along the Angiosperm phylogeny.

Mutation, recombination, selection, and demographic processes (such as gene flow and genetic drift) have shaped genetic variation, but the relative impact of these evolutionary forces remains poorly understood. This problem motivates this study which examines three regions of the genome -beta-globin, the Y-chromosome, and mtDNA- in a two part approach to assess the relative impact of evolutionary forces on human genetic variation in Africa. The first approach characterizes levels of nucleotide variability and linkage disequilibrium across thebeta-globin gene and recombinational hotspot in a sample of malarial-resistance alleles (HbC and HbS). Results suggest that the age of the HbC allele is <5,000 years and selection coefficients are 0.04-0.09 and, recombination is observed within 1-kb of the selected site on >1/3 of the chromosomes sampled. A long-standing question regarding the HbS allele is whether it originated multiple times via recurrent mutation or whether it arose once and was transferred to different haplotypic backgrounds through recombination. These results indicate that recombination played a critical role in generating haplotypic diversity at beta-globin and can explain the origins of the Bantu and Senegalese HbS haplotypes. The second approach examines Y-chromosome and mtDNA variation to disentangle the relative effects of demographic forces. A detailed characterization of the Y-chromosome and mtDNA in >1000 individuals from ~40 populations reveals that patterns of variation from these paternally- and maternally-inherited loci are remarkably different, suggesting that sex-specific demographic processes have influenced African genetic variation, particularly among agriculturalists. Hunter-gatherer populations carry a suite of Y-chromosomes that differ from those of agricultural populations. The examination of Y-SNP and Y-STR variation in eight hunter-gatherer populations reveals the presence of a very old, >50-kya, derived lineage (B2b) shared among these populations, which is absent in agricultural populations, suggesting that hunter-gatherer populations share an ancient common ancestry. Finally, the Y-chromosome results are placed into a broader evolutionary context in a phylogeographic summary as it relates to archeological and linguistic variation in Africa. Together these results underscore the vastly different effects that various evolutionary forces have had on shaping human genetic variation in Africa.

A study was undertaken on a strip mine in Campbell County, Tennessee to determine what site characteristics permit vegetation establishment and growth on some spoils while preventing it on adjacent ones. Fifty plots were established and spoil samples, 300 each on vegetated and nonvegetated spoils, were taken at depths of 0-5 cm, 10-15 cm, and 25-30 cm to be analyzed for pH, Ca, Mg, K, P, Fe, Al, Mn, Zn, compaction, moisture content, surface temperature, and color. It was found that K, P, Mn, and Zn were in the deficiency range of most plants. The solubility of aluminum and iron increases with low pH, thus increasing the probability of their interactions with and decreased availability of other plant nutrients. Applications of dolomitic limestone to some plots increased pH and may have decreased the availability of some nutrients such as iron.

The growth, nutrient absorption, and internal moisture status of selected woody species in coal mine spoil in response to an induced infection by the ectomycorrhizal fungus Pisolithus tinctorius was studied. Nursery grown loblolly and Virginia pine seedlings infected with Pisolithus and control seedlings were outplanted on a coal mine spoil in Tennessee which had been previously hydroseeded with a mixture of herbaceous ground cover species. Granular fertilizer was applied by broadcasting to one-half of the seedlings of each ectomycorrhizal treatment at the rate of 112 kg/ha NPK. After three years, the survival and growth of loblolly pine infected with Pisolithus was superior to that of the control seedlings, and chemical analyses of foliar samples revealed that the seedlings with Pisolithus ectomycorrhizae had a higher foliar concentration of NO3 and a lower concentration of Zn than the control seedlings. The survival, growth, and nutrient absorption of Virginia pine was not significantly affected by the infection with Pisolithus after two years, but both loblolly and Virginia pine seedlings with Pisolithus ectomycorrhizae exhibited an enhanced ability to absorb water during periods of high moisture stress, as determined by the pressure chamber technique. Fertilization substantially reduced the survival of the seedlings of both species. Sweet birch and European alder were grown under high, intermediate, and low fertility regimes in sand culture containing a mycelial inoculum of Pisolithus tinctorius for five months and then transplanted to coal mine spoil containing an identical Pisolithus inoclum. Control seedlings of each species were similarly grown except that no inoculum was incorporated into the potting media. The nutrient treatments initiated in the sand culture were continued throughout the study. Examinations of the roots of the sweet birch seedlings revealed that high fertility significantly reduced the development of Pisolithus ectomycorrhizae, but Pisolithus formed abundant ectomycorrhizae on the roots of sweet birch grown under the intermediate and low fertility regimes and these seedlings were significantly larger than comparable control seedlings. Chemical analyses of foliar samples revealed that sweet birch seedlings with Pisolithus ectomycorrhizae had a significantly higher foliar concentration of total N and a lower concentration of Mg and Al than the control seedlings. No ectomycorrhizal fungi were found to have infected the roots of the European alder seedlings of any of the ectomycorrhizal-nutrient treatment combinations.

Assessing how environmental change affects plants is increasingly important as terrestrial ecologists attempt to predict future patterns from current processes. However, this challenge is complicated because plant communities can respond to environmental variation at different, but overlapping scales. Additionally, both patterns and the processes that drive them are sensitive to the methods that scientists use to study them. Consequently, a variety of experimental and theoretical approaches are necessary to improve our understanding of how organisms, communities, and ecosystems will respond to future change. Collectively, the studies in this thesis employ a diverse array of approaches to test important ecological theories, including long-term observational studies, manipulative experiments, and analyses that leverage both local and global datasets. The Enquist lab has been measuring subalpine meadow carbon fluxes and climate variables at the Rocky Mountain Biological Laboratory (RMBL), for over 13 years at the time of this writing. Examining correlations between climate and carbon flux over this time has led to the identification of interesting patterns between snowmelt, precipitation events, and rates of carbon exchange. Despite the longer growing season, early snowmelt dates ultimately result in lower productivity in these systems. Pairing this study with the results of a soil moisture manipulation experiment aided in the discovery that the strength and duration of the foresummer drought was directly related to rates of carbon exchange and biomass accumulation in these systems. Thus, integrating long-term observational work with an experimental manipulation served to link pattern and process in a way that was not possible with either study alone. The studies in this thesis range in scale from sub-organismal (chapter 3), to community ecosystem (chapters 1 and 2), to continental (chapter 4). Across all scales afunctional trait ecology approach contributes a holistic view of how these changes may impact organismal, ecosystem, and evolutionary responses to environmental variation. Plants are frequently faced with fundamental performance tradeoffs, which arise due to physical, chemical, genetic/evolutionary, and/or ecological constraints. As a result, functional trait measurements can reflect ecological strategies or resource acquisition strategies. Functional ecology offers a promising approach to linking the attributes of individuals to and communities to ecosystem processes. Understanding how individuals, communities, and ecosystems will respond to environmental change is a fundamental question in ecology. I address this topic using a variety of novel experimental methods and statistical techniques. I use a functional ecology approach by considering not only the species in a community, but also the distribution of functional traits that those species represent. It is in this way that I test ecological hypotheses regarding plant responses to environmental change over physiological, ecological, and evolutionary time scales.

Spumaretrovirus, among retrovirus clades, has an extensive accumulation of evidence for an ancient origin. Recent discoveries indicate that the Spumaretrovirus ancestor could have been the first retrovirus to appear during the evolution of vertebrates. If they indeed appeared in ancient marine environments hundreds of millions of years ago, we should expect significant undiscovered diversity of foamy-like endogenous retroviruses in fish genomes. I report the discovery of these elements in 23 novel teleost hosts. These viruses have very large genomes compared to all other retroviruses, possess an unprecedented array of accessory genes, and form a robust reciprocally monophyletic sister clade with sarcopterygian host foamy viruses, with class III mammal endogenous retroviruses being the immediate sister group to both clades. I estimated that some of these viruses integrated recently into host genomes, and exogenous descendants of these viruses may be extant.

Evidence suggests that human-driven changes to the earth are having clear and profound effects on many species, as well as the species with which they associate. Disruptions in the interactions between species can change the community structure, in turn changing the dynamics of entire ecosystems. The following dissertation examines how the impacts of climate change related events and invasive species may influence biotic interactions and impact orchid populations and range distributions. Here I quantify how orchid pollinators and mycorrhiza vary between species with different life histories, and between and within habitats. The results showed that orchids with wide range distributions (i.e. geographic or elevational) were more generalized in their mycorrhizal fungi requirements than co-occurring rare and/or narrow ranging species; the rarer species were also more likely to be affected by antagonistic fungal interactions. This dissertation makes a critical contribution to understanding plant and orchid ecology, to assisting ongoing orchid recovery efforts worldwide, and ultimately to developing more comprehensive management plans to mitigate future biodiversity losses.

Research designed to elucidate artificial reef efficacy in attraction and production is lacking. Delineation of the rock reef habitat, coupled with faunal patterns of substrate use within artificial and natural reef regions, will allow elucidation of the potential of artificial reefs to attract sport fishes, and function as surrogate natural habitat for the conservation of endemic fish species. We compared faunal assemblages and habitat complexity between artificial and natural reefs to access the efficacy of artificial reefs in conservation of the native community, and attraction of sport fishes. We used hydroacoustics to map artificial and natural rock reefs within Bear Lake. We compared the accuracy of Visual Bottom Typer (VBT, BioSonics, Seattle, WA) software to observed substrate in three regions of varying slope and rock complexity within Bear Lake. VBT demonstrated an ability to distinguish substrates regardless of rock complexity and slope, although inaccuracies were present. VBT biased classification towards predominant substrate in the survey regions. We compared benthic invertebrate and fish catch in natural and artificial reef regions to assess the utility of artificial reefs in fisheries management. We assessed the potential of artificial reefs to function as foraging habitat for endemic fishes within Bear Lake. We compared benthic invertebrate taxa abundances and diversity between one region of artificial reefs, and two natural reefs in spring and summer. The artificial reefs hosted prey consumed by endemic Bonneville whitefish and Bear Lake sculpin. We assessed the potential of artificial reefs to function in attraction of sport fishes, and conservation of endemic fishes. We compared differences in fish catch per unit effort (CPUE) and diversity on rock and soft substrate between one artificial and two natural reef regions. Sport fishes attraction to the artificial reefs was minimal. Winter cisco and whitefish used the artificial reefs similarly to natural reefs. Fall lake trout, crayfish, and yellow perch used artificial and natural reefs dissimilarly.

No description available.

Ecologists have long known that complex habitats often provide prey with refugia from predation in a wide variety of habitat types and for a wide variety of prey species. Despite the recognized importance of structural habitat complexity, ecologists have measured complexity in many different ways. I propose four new indices of structural habitat complexity that are dimensionless, that can be applied across various habitat types and scales, and that directly measure how structural complexity interferes with a predator's foraging ability. These indices are: (1) Ct/At, the total area of cover within a habitat (Ct) divided by the area of the habitat (At), (2) Cw/Pw, the average width of the individual structures within a habitat (Cw) divided by the appropriate width of the prey organism (Pw), (3) Sp/Pr, the average inter-structural space size within a habitat (Sp) divided by the width of the predator (Pr), and Sp/Py, the average inter-structural space size within a habitat (Sp) divided by the width of the prey (Py). I predicted that prey survivorship should (1) increase hyperbolically with increasing Ct/At, (2) increase hyperbolically with increasing Cw/Pw, and (3) decrease sigmoidally with increasing Sp/Pr. I also predicted that different sized fauna should respond differently to artificial seagrass plots deployed in a seagrass bed, based upon the size of the inter-structural spaces relative to their body sizes (Sp/Py). I found that prey survivorship increased hyperbolically with increasing Ct/At, and decreased sigmoidally with increasing Sp/Pr. I found no effect of Cw/Pw on prey survivorship. I found that small fauna responded positively to increased structure in artificial seagrass plots deployed in a seagrass bed, but after controlling for structural surface area within each plot there was no difference between treatments, indicating no effect of Sp/Py on small fauna. Larger fauna responded slightly differently than the small fauna, but the pattern of their response did not support the hypothesis that Sp/Py was important. The smaller fauna also appeared to respond positively to increased water flow speeds within the seagrass bed. Overall, these indices may be useful to both ecologists and managers interested in predator-prey-habitat issues.