Mummichog (Fundulus heteroclitus) responses to chronic whole-ecosystem nutrient enrichment were examined near Plum Island Sound, Massachusetts. Dissolved fertilizer was released into replicate salt marsh creeks over 6 growing seasons to simulate agricultural run-off (bottom-up effects). Density, biomass, secondary production, growth rate, and condition factor were estimated in fertilized and reference creeks. Mummichog densities were also used to determine if mummichog growth or health varied with density. Over 7,600 mummichogs were marked and released into the treatment and control areas to measure responses. Over 900 mummichogs were recovered. Mummichog abundance was higher (p = 0.055) in nutrient-enriched creeks than reference creeks (0.81 ± 0.04 fish m-2 and 0.59 ± 0.07 fish m-2 respectively). Nutrient enriched-creek biomass of 522.9 ± 36.1 mg dw m-2 was significantly higher (p=0.028) than control-creek biomass of 338.5 ± 26.7 mg dw m-2. However, reference-creek growth rates of 0.105 ± 0.091 were significantly higher (p=0.04) than the nutrient enriched-creek growth rates of 0.073 ± 0.065 mm d-1. Secondary production and condition factor of mummichogs did not differ with nutrient enrichment. Nutrient enrichment likely stimulated primary production causing bottom-up effects in the food web, which increased mummichog abundance and biomass. However, as abundance increased, mummichog growth rates decreased, suggesting a density-dependent response, likely caused by either intraspecific competition or behavioral changes causing dietary shifts.

Most biogeographic studies on the Mexican biota have assumed that the dramatic climate cycles of the Pleistocene epoch and the prominence of the Trans-Mexico Volcanic Belt have played major roles in the origin and diversification of species. Here the pylogenetics and biogeography of four codistributed rodent species were studied. In each case, a phylogenetic hypothesis for the taxon and allied species using two mitochondrial (Cytochrome-b and 12S), and two nuclear genes (GHR and IRBP) was generated, appropriate taxonomic changes were recommended, and a temporal framework was generated to identify events that may have produced the phylogenetic pattern. Nelsons woodrat Neotoma nelsoni and the Perote ground squirrel Xerospermophilus perotensis, were confirmed as having their closest relatives in the Mexican Plateau. The findings also confirmed that N. nelsoni and X. perotensis are genetically well-differentiated from their sister taxa. Genetic distances in combination with low levels of morphological differentiation suggest that they should be recognized only at the subspecific level as N. leucodon nelsoni and X. spilosoma perotensis. Molecular estimates of divergence times suggested that N. l. nelsoni and X. s. perotensis diverged from their sister taxa to the north during early Pleistocene times. The rock mouse Peromyscus difficilis was divided into two well-supported clades, a northern clade including the subspecies P. d. difficilis and P. d. petricola, and a southern clade containing the subspecies amplus, felipensis, and saxicola. Molecular-based estimates of divergence times suggested that separation of these clades occurred in the Pleistocene. The study of the Phillips kangaroo rat, Dipodomys phillipsii, revealed a biogeographic pattern different from that seen for other taxa. D. phillipsii was divided into two well-supported clades: one distributed on the Mexican Plateau, and a southern clade in the TMVB. Several lines of evidence supported the decision to return the Mexican Plateau clade of D. phillipsii to full species status as D. ornatus. The study showed that D. phillipsii, D. ornatus, D. elator, and D. merriami form a well-supported clade of kangaroo rats, however, the dataset was unable to resolve relationships among these four species. Molecular-based analyses of divergence times suggests that D. phillipsii, D. ornatus, D. elator, and D. merriami diverged in mid-Pliocene times, probably in or near the Mexican Plateau. Unlike the Pleistocene divergence dates reported in previous chapters this Pliocence divergence suggests that the morphotectonic processes that gave rise to the Trans-Mexico Volcanic Belt may have influenced early diversification in Mexican species of Dipodomys.

Research in invasion ecology has focused on developing ecological theory that can predict how invasive species interact with invaded communities. However, empirical support for theoretical predictions has been inconsistent. Inconsistencies may be attributed to the lack of data in three core areas; (1) field data with enough resolution to determine population dynamics of invasive species in relation to native species, (2) manipulative field experiments that encapsulate natural variation found among micro-habitats, and (3) field data that incorporate effects of invasive species within and among spatial scales. This dissertation has addressed these concerns by examining the mechanisms responsible for the successful invasion and ecological impacts of the invasive grass smooth brome (Bromus inermis) within the prairies of North Dakota and Minnesota. GIS analyses revealed that native Spartina pectinata patch growth was two times greater in non-invaded areas versus areas heavily invaded with brome. The probability of extinction of native Spartina pectinata averaged 8 times more likely in areas of high versus low brome coverage. Field experiments determined differences in germination between invasive smooth brome and native prairie cordgrass were not driven by habitat differences or soil conditions. Following initial germination, invasive smooth brome had a negative impact on cordgrass establishment, which was primarily due to a 78% and 47% reduction in native cordgrass plant height and stems density, respectively. Throughout the field experiment invasive smooth brome was a dominant competitor under all habitats and soil conditions except in areas where soil salinity levels were highest. Results from the herbivore study indicated that smooth brome has the potential to have negative effects on local herbivore assemblages. Despite the large differences in herbivore species richness, diversity and evenness at our larger spatial scales, my results indicated no statistically significant effects of invasive smooth brome. Results indicated that plant species richness had a larger effect than invasive smooth brome on herbivore assemblages (i.e. plant species richness, predator abundances, landscape surroundings). Future directions for research concerning the impact of smooth brome on native herbivore assemblages should include incorporating herbivore community composition, predator abundances and landscape features (i.e. surrounding matrix, prairie isolation and management history).

Recurrent disturbances play an important role in maintaining longleaf pine savannas. Windstorms and fires contribute to the heterogeneity of pine savanna understory through generation of canopy gaps and fuel accumulation, distribution and consumption. The combination of windstorms and fires promotes native herbaceous species, but also promotes invasion of Japanese climbing fern (Lygodium japonicum). Lygodium japonicum is an invasive fern with subterranean rhizomes and copious spore production invading pine savannas along the southeastern Gulf Coast Region. This dissertation examines how fire, previous windstorm disturbances, and animal disruptions influence L. japonicum and native species abundance in a restored longleaf pine savanna. Studies were conducted at Girl Scout Camp Whispering Pines, an upland mesic site containing longleaf pine in Tangipahoa Parish, Louisiana. I experimentally examined L. japonicum response to various fire severities during prescribed fire by manipulating fine fuels in the understory. Three fine-fuel treatments (increased, reduction, unaltered) were applied to plots containing fern genets. The effect of fire severity through duration of heating was transient on frond emergence, suggesting that established fern genets survive subsequent fires. Native groundcover species abundance and composition was also transiently influenced by fire severity, as examined in a post hoc fuel manipulation study. Abundance and composition of native species within localized areas differed based on heterogeneity of fire severity, indicating sensitivity to prolonged heating. Heat released, a product of fuel accumulation, may stunt recovery of native groundcover in localized areas and contribute to understory patches susceptible to invasion by non-native species. Animal biopedturbations were strongly associated with stump locations, which provided refuge and foraging opportunities in the understory. Biopedturbations did not, however, promote or suppress L. japonicum frequency or density. Windstorms and fire disturbances contributed to heterogeneity of groundcover and, thus influenced L. japonicum spread. Particular growth characteristics of L. japonicum enabled persistence in certain locations. Areas with open canopy, where fire severity was low, were at higher risk of invasion than areas under pine trees. Fire is essential for restoration, yet promotes invasion by L. japonicum. Careful consideration of disturbance regime and characteristics of invasive species are required for successful maintenance of longleaf pine savannas.

This dissertation explores the effects of stress and disturbance on fungal endophyte diversity and composition in obligate wetland plants in southeast Louisiana. I explored two types of endophytes: root and foliar. Each of these groups is known to live within apparently healthy host plants without causing symptoms of disease; therefore, plants are thought to benefit from this association. Few studies, however, have shown that plants in wetlands associate with fungi. In this dissertation, I show that both root and foliar endophytes not only exist in wetland plants living in flooded and saline environments, but also are abundant within these plants. In the chapter two I explore the distribution of arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) in the roots of 18 plant species. Monocots were mostly colonized by DSE, and dicots, including woody species were mostly colonized by AMF. In the third chapter, I used a mesocosm approach, to explore the effects of soil conditions on foliar endophyte diversity and composition in two wetland plant species Sagittaria lancifolia and Taxodium distichum. Endophytes were abundant in both hosts, but S. lancifolia contained higher diversity. In addition, endophyte composition was shaped by different factors in each host: water quality shaped communities in T. distichum, and hydrology in S. lancifolia. In the fourth chapter I expand on the third chapter by including four more plant species that range from highly salt tolerant to intolerant and simulated a category 3 hurricane to explore its effects on endophytes within each plant species. I found that endophytes of grasses, irrespective of salt tolerance, did not change in diversity or composition following the simulated hurricane. Endophyte diversity T. distichum did not change, but composition was dependent on habitat type. Sagittaria lancifolias endophyte diversity decreased with hurricane conditions, but overall composition did not change. The results of these studies not only demonstrate that endophytes are present in wetland plants, but that they are abundant and common. Further, I show that host identity interacts with environmental conditions to influence diversity and composition and that habitat type is important in determining the outcome of endophyte composition after hurricanes.

Ecological speciation is a process involving adaptation to different environments leading to reproductive isolation between populations. Hybridization between Clapper and King rails (Rallus longirostris and R. elegans) is frequent but restricted to narrow bands of brackish marsh along the Gulf of Mexico and Atlantic coastlines of North America. In the second chapter I used mitochondrial and nuclear sequences to infer phylogenetic relationships in this species complex. The complex falls out into three distinct groups: South America; western North America; and eastern North America and the Caribbean. My results indicate that R. elegans as currently recognized is paraphyletic, with birds of highland Mexico sister to R. longirostris of California whereas R. elegans of eastern North America and Cuba forms a clade with eastern North American and Caribbean R. longirostris. My results support splitting the complex into four distinct species. In the third chapter I used morphological data, ecological data, and DNA sequences generated via next-generation methods to investigate the hybrid zone situated along a salinity gradient. Maximum-likelihood clines fitted to the five loci, body weight, salt gland weight, and water salinity revealed that the hybrid zone is narrow (mean genetic cline width = ~8.3 km), and that all clines are coincident and concordant with the water salinity cline. In the fourth chapter, I measured morphological characters on males collected across the hybrid zone to determine differences on opposite ends of the zone and to examine if these differences covaried and were correlated with genotypes from four nuclear markers; I also estimated dispersal distances using these characters. For four hybrid sites I found six of twelve correlations were significant, and ten of twelve estimates of covariance were greater than the expected covariance, suggesting selection against recombinants for the quantitative characters salt gland weight, bill length, and overall size. The estimates of dispersal distances for genetic and morphological characters were more than an order of magnitude lower than the only published estimate from a banding study. These results suggest that while rails are capable of dispersing across the zone, the hybrid zone constrains dispersal within it.

High in the Andes, a unique peatland habitat exists precariously above the frostline and below snowline. These bofedales, as they are called in Peru, support an extraordinary avifauna consisting of both boreal and austral migratory species and residents. This ecosystem is predicted to be significantly reduced as a result of global climate change. We endeavored to understand the habitat associations and seasonality of the avian assemblage occurring in these permanent wetlands. Numerous detections of species outside of their documented geographic range provided an opportunity to assess geographic ranges using niche modeling. This novel approach provided insights and inferences for assessing geographic ranges. Peatland study sites were visited in both the wet and dry season and habitat and seasonality associations were determined for the majority of species occurring therein. Peatlands are an important habitat for many migratory and resident bird species and seasonality is strong for many species. With the threat of climate change predicted for the Andes, we modeled the presence of peatland habitat for a large area of southern Peru using ground-truthed study sites and assessed the effects of the temperature change for these peatlands. Our model showed peatlands represent approximately 5% of the Puna. Peatland occurrence is correlated with several environmental variables including flow accumulation and presence of glaciers in the watershed. Using the model of peatland occurrence, we predicted what percentage of peatland habitat would no longer occur within the required climatic envelope. Within our study area, more than 75% of the peatlands would no longer occur above the frost line using temperature predictions for the next 80 years. In effect, habitat for already rare and isolated bird species will be dramatically reduced by weather alone. The additional pressures of pastoralism, peat harvesting, agriculture, and water diversion projects suggest these peatlands should be prioritized for conservation assessment and action. Finally, we identified several areas within our study area that are most likely to persist through the precipitation and temperature changes through the end of the century.

Alligators appear to swallow prey items that are large relative to their head size. Therefore, the intermandibulo-cervical envelope (i.e., the skin, Fascia superficialis, and constrictor musculature) was expected to be expandable. The three main layers of the intermandibulo-cervical envelope expand and recoil in tandem, but through different mechanisms. In the skin, which consists of hard-cornified scales and soft-cornified interscale skin segments, only the latter are expandable. Therefore, the width and orientation of the interscale skin segments determine the extent and direction of expansion of the skin. Whereas the intermandibular skin region is very expandable and enables the manipulation and crushing of large prey items in the mouth cavity, the gular and cervical skin regions can expand longitudinally, but have very limited circumferential expansibility. Elastic fibers in the dermis and Fascia superficialis provide the resilience needed to return the skin to its resting condition. The trilaminate Fascia superficialis expands by changing the orientation of its helically arranged collagen fibers. The three main skin regions, which are also characterized by particular scale and interscale skin patterns, are in congruence with the three parts of the underlying constrictor musculature. The expansibility of the constrictor muscles is determined by their proportion of muscle length to tendon length, because muscle fibers can lengthen passively, whereas collagenous tendon fibers resist lengthening. The expansibility of the constrictor muscles diminishes from rostral to caudal. Whereas the longitudinal expansibility of the intermandibulo-cervical envelope allows lateral and dorso-ventral movements of the head and neck, the limited circumferential expansibility of the gular and cervical regions constrains the size of prey items that can pass through the throat and matches the narrow isthmus of the thoracic inlet. Hence, the functional-morphological data of the intermandibulo-cervical envelope require a reinterpretation of feeding mechanics and prey choice of alligators.

Unionoids (freshwater mussels) are important in aquatic ecosystems, yet despite their continued decline in diversity, little is known about their distribution and ecology. To study Louisiana mussel species richness, abundance, and distribution I sampled 65 sites within six major watersheds in the Pine Hill region, Louisiana. Second through sixth order streams were surveyed for local instream variables, land use, hydrology, and co-occurring fish assemblage. To evaluate mussel species richness and abundance a structural equation model was created that suggested two major variables were important: 1) habitat stability, influenced by benthic shear stress, percent of silt substrate, and stream order and 2) anthropogenic disturbance influenced by agricultural land use in riparian corridors and water quality. Mussel species distribution in various stream sizes has been associated with hydrologic disturbance and their obligatory host fishes distribution. Few studies have looked at life history variation between mussel species to help explain their distributions. I contrasted the life history strategies, behavioral adaptations, and shell functional morphological of nine mussel species from the Amite River, Louisiana. The set of life history traits demonstrated two distinct groups of mussels: cosmopolitan species found through range of stream sizes and a set of large river specialist. The traits associated with cosmopolitan species includes: fast growth rates, early maturity, use of visual displays for host fish attraction, thin shells, and higher mobility. The traits of the large river species were: long lived, late to maturity, relatively sessile, none displaying methods of host attraction, and with thick sculptured shells. The sampled assemblages of mussels and fishes from the Pine Hill region were used to develop a Tiered Aquatic Life Unit (TALU) framework. The TALU is an efficient bioassessment tool, with conservation goals that are based on practical, systematic sampling of stream attributes. The developed TALU was created from metrics that are sensitive to anthropogenic disturbance. The model demonstrated to be quite conservative, resulting in only a 4% error rate in site allocation. Our framework is broadly applicable and easily modified to fit other eco-regions, and should prove useful for resource managers to monitor the health of rivers.

Cancer is characterized by unregulated growth. SV40 large tumor (T) antigen interacts with cellular proteins to cause transformation and tumors in rodents. Interaction with the retinoblastoma (Rb) family of tumor suppressors allows T antigen to inhibit growth arrest, while T antigen interaction with the p53 tumor suppressor blocks apoptosis. Transgenic mice that express T antigen (TAgwt) in intestinal enterocytes develop hyperplasia that progresses to dysplasia. Expression of a mutant of T antigen (TAg3213) that is unable to interact with Rb family members in enterocytes does not result in an intestinal phenotype. Thus, T antigen interaction with Rb family members (pRb, p130 and p107) is required for T antigen-induced intestinal neoplasia. pRb performs the majority of its tumor suppressive properties through repression of E2Fs, a family of transcription factors that regulate the expression of many genes required for S phase. T antigen binds Rb family members, disrupts p130/E2F complexes and induces E2F2 and E2F3a in villi. These E2Fs are bound to the promoters of up-regulated E2F-responsive genes, supporting a role for them in T antigen-induced hyperplasia. Expression of an amino-terminal truncation mutant of T antigen (TAgdl1137) in villi enterocytes is sufficient to induce hyperplasia, but not progression to dysplasia. We hypothesized the T antigen interaction with p53 is required for the progression to dysplasia. However, T antigen does not bind and stabilize p53 in villi enterocytes. Furthermore, TAgdl1137/p53-/- mice do not progress to dysplasia. Therefore, we propose that the p53 is not active in intestinal enterocytes and its inactivation is not required for T antigen-induced progression to dysplasia. These results suggest that distinct tumor suppressor proteins and pathways function in specific cell types to regulate normal or abnormal mechanisms of proliferation.