Browsing by Subject "Biology, Botany"
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Item Open Access A Molecular Phylogenetic Study of Historical Biogeography and the Evolution of Self-Incompatibility RNases in Indian Ocean Coffea (Rubiaceae)(2010) Nowak, Michael DennisA fundamental goal in the diverse field of evolutionary biology is reconstructing the historical processes that facilitated lineage diversification and the current geographic distribution of species diversity. Oceanic islands provide a view of evolutionary processes that may otherwise be obscured by the complex biogeographic histories of continental systems, and have thus provided evolutionary biology with some of its most lasting and significant theories. The Indian Ocean island of Madagascar is home to an extraordinarily diverse and endemic biota, and reconstructing the historical processes responsible for this diversity has consumed countless academic careers. While the flowering plant genus Coffea is but one lineage contributing to Madagascar's staggering floral diversity, it is representative of the common evolutionary theme of adaptive radiation and local endemism on the island. In this dissertation, I employ the genus Coffea as a model for understanding historical biogeographic processes in the Indian Ocean using methods of molecular phylogenetics and population genetics. In the molecular phylogenetic study of Coffea presented in chapter 2, I show that Madagascan Coffea diversity is likely the product of at least two independent colonization events from Africa, a result that contradicts current hypotheses for the single origin of this group.
Species of Coffea are known to exhibit self-incompatibly, which can have a dramatic affect on the geographic distribution of plant genetic diversity. In chapter 3, I identify the genetic mechanism of self-incompatibility in Coffea as homologous to the canonical eudicot S-RNase system. Baker's Rule suggests that self-incompatible lineages are very unlikely to colonize oceanic islands, and in chapter 4, I test this hypothesis by characterizing the strength of self-incompatibility and comparing S-RNase polymorphism in Coffea populations endemic to isolated Indian Ocean islands (Grande Comore and Mauritius) with that of Madagascan/African species. My findings suggest that while island populations show little evidence for genetic bottleneck in S-RNase allelic diversity, Mauritian endemic Coffea may have evolved a type of "leaky" self-incompatibility allowing self-fertilization at some unknown rate. Through the application of traditional phylogenetic methods and novel data from the self-incompatibly locus, my dissertation contributes a wealth of new information regarding the evolutionary and biogeographic history of Coffea in the Indian Ocean.
Item Open Access Host Constraints on the Post-glacial Migration History of the Parasitic Plant, Epifagus Virginiana(2009) Tsai, Yi-Hsin EricaBecause 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 (Epifagus virginiana, beechdrop) that has an obligate and host specific relationship with a common eastern North American hardwood tree (Fagus grandifolia, 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.
Item Open Access Seed Dispersal, Gene Flow, and Hybridization in Red Oak(2010) Moran, Emily VictoriaUnderstanding the ecological and evolutionary responses of plant species to shifts in climate (and other rapid environmental perturbations) will require an improved knowledge of interactions between ecological and evolutionary processes as mediated by reproduction and gene flow. This dissertation research examines the processes of seed dispersal, intra- and inter-specific gene flow, and reproductive success in two red oak populations in North Carolina; the variation in these processes from site to site; and their influence on genetic structure, population dynamics, and migration potential.
Using genetic and ecological data collected from two large long-term study sites, I develop a hierarchical Bayesian model to identify the parents of sampled seedlings and characterize the scale of effective seed and pollen dispersal. I examine differences in scale of dispersal between the Appalachian and Piedmont sites in light of the spatial genetic structure and ecological differences of the two sites. I then use the pedigree and dispersal estimates derived from these analyses to examine variation in reproductive success and to test hypotheses about the causes and consequences of such variation. Using parentage estimates and measures of genetic differentiation between species, I study the likely extent of hybridization in these mixed-species secondary forests. Finally, using the SLIP stand simulator, I explore the implications of new genetic dispersal estimates for migration potential in oaks.
I find that effective seed dispersal distances are longer than estimated using seed trap data. While at the Piedmont site the large number of seedling found >100 m from their mother trees suggests that animal dispersers play a vital role, at the Appalachian site seedling distributions conform more closely to the original gravity-created pattern of seed density. Individual trees vary widely in their reproductive success. Seedling production was found to be positively associated with annual seed production, but exhibited hump-shaped or reversing relationships with age (suggesting the effect of senescence) and growth rate (suggesting tradeoffs in allocation). Germination fraction was negatively associated with fecundity, suggesting that density-dependent mortality may be acting on the high concentrations of seeds near highly fecund adults. Due to overlapping generations and variation in individual reproductive success, effective population size is estimated to be less than half the size that numbers of "adult" individuals would suggest, with consequences for the relative strength of drift and selection. Hybridization may boost effective population size somewhat; my analyses suggest that inter-specific gene flow is common at both study sites. Finally, simulations show that dispersal has a relatively stronger effect on migration rate and population growth than fecundity or size at maturity, and that genetic estimates of seed dispersal can yield significantly higher rates of migration and/or population persistence than seed-trap based estimates under both competitive and non-competitive conditions.
Item Open Access Systematics of the Lichen Family Verrucariaceae and Evolution of the Rock-inhabiting Habit within a Group of Ecologically Diverse Fungi (Chaetothyriomycetidae, Ascomycota)(2007-12-04) Gueidan, CecileVerrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats.Item Open Access The Effects of Dispersal on Macroecological Patterns(2008-10-17) Dexter, Kyle GrahamEcologists have long sought to uncover the mechanisms behind large-scale, macroecological patterns in the distribution and abundance of species. Macroecological patterns are often attributed to the dynamics of dispersal (e.g. dispersal limitation or widespread dispersal). However, few studies actually measure dispersal to determine if dispersal rates are commensurate with the observed macroecological patterns. In this dissertation, I use population genetic analyses across many species to obtain community-level estimates of dispersal rates for two different ecological systems: birds on islands and trees in tropical rainforests. These independent estimates of dispersal then allow me to determine if macroecological patterns in these two systems can be attributed to dispersal dynamics.
In chapter two, I explore the contrasting macroecological patterns of two groups of Lesser Antillean birds. The groups' differing macroecological patterns could be due to differences in dispersal, but other authors have advocated different mechanisms. Population genetic analyses show that the two groups do differ significantly in rates of inter-island dispersal, indicating that dispersal dynamics can explain their contrasting macroecological patterns. In chapter three, I turn my attention to tropical tree communities. In contrast to studies of birds on islands, studies of trees in tropical rainforests may suffer from misidentification of individuals in the field. Using a phylogenetic approach, I determine errors rates in identification, and then assess the effect of these errors on macroecological patterns and other ecological analyses of tropical tree communities. I find that error rates are substantial, but that they have little effect on macroecological patterns. In contrast, species-level ecological analyses can be dramatically affected by these errors.
In chapter four, I return to the influence of dispersal on macroecological patterns, this time in tropical tree communities. One notable macroecological pattern in Amazonian tree communities is a high correlation in the relative abundances of species shared across communities, which could indicate high rates of dispersal between communities. However, population genetic analyses show that dispersal is severely limited between communities. Thus, some factor besides dispersal, such as differences in competitive ability or susceptibility to disease, must be driving species to achieve similar relative abundances in geographically separated communities. In contrast, I show that dispersal limitation is the likely cause of another macroecological pattern frequently observed in tropical tree communities: the decline in the compositional similarity of communities with distance. However, this is not steady-state dispersal limitation in an equilibrium framework as is conventionally thought. Instead, the dispersal limitation appears to be historical in nature, which implies a heretofore unnoticed role for historical contingency in the assembly of Amazonian tree communities.