The biomass size spectrum - the power-law scaling relationship between average individual size and total biomass - has often been studied in lake and marine ecosystems, but rarely in lotic systems. The objective of this study was to test for characteristic biomass spectra in small temperate streams. Seasonal fish and macroinvertebrate data, including population abundance and biomass estimates, were collected in three wadeable, southern West Virginia streams from October 2013 to May 2015. Fish abundances were estimated with 3-pass electrofishing (depletion) surveys and individuals were weighed in the field. Macroinvertebrates were collected with a Hess sampler and returned to the lab for identification to the lowest practical level (usually genus). Published length-mass regressions were then used to estimate individual mass. All size spectra relationships (linear regression of log-log data) were highly significant (p<0.001). Size spectra intercepts were variable and may reflect seasonal differences in fish and invertebrate densities. Size spectra slopes were more consistent, with a mean slope of approximately -0.73, suggesting a common scaling relationship between stream consumers at differing trophic levels.

Bayou St. John (BSJ) and City Park Lakes and Lagoons (CPLL) are urban waterways in New Orleans, Louisiana. I studied habitat selection of red drum in BSJ, and fish assemblage change in BSJ and CPLL over 40 years. Temperature was found to be the best predictor of red drum habitat selection in Bayou St. John, while salinity and change in depth also were found to be good predictors for certain sites. Potential prey item abundance did not appear to influence habitat selection. Using data from 1971 – 2010, nearshore habitats in CPLL were affected by Hurricane Katrina, but have sense recovered and nearshore habitats in BSJ were found to have decreased diversity. Pelagic habitats in both areas were found stable across 40 years. Since 2006, nearshore assemblages were similar for CPLL and BSJ with a decrease in fishes from Order: Cyprinodontiformes and an increase in other fishes seen across years.

Phylogeography aims to understand the processes that underlie the distribution of genetic variation within and among closely related species. Although the means by which this goal might be achieved differ considerably from those that spawned the field some thirty years ago, the foundation and conceptual breakthroughs made by Avise are nonetheless the same and are as relevant today as they were two decades ago. Namely, patterns of neutral genetic variation among individuals carry the signature of a species’ demographic past, and the spatial and temporal environmental heterogeneity across a species’ geographic range can influence patterns of evolutionary change. Aquatic systems throughout Mexico provide unique opportunities to study phenotypic plasticity and evolution in relation to climatic and environmental selective forces. There are several unique, often isolated aquatic environments throughout Mexico that have a history of geographic isolation and reconnection. The first study presented herein shows significant mitochondrial sequence divergence was also discovered between L. megalotis populations on either side of the Sierra de San Marcos that bisects the valley of Cuatro Ciénegas and that the populations in the valley are genetically distinct from those found outside of the valley. The second study recovered signals of two divergence events in Cuatro Ciénegas for six codistributed taxa, and reveals that both events occured in the Pleistocene during periods of increased aridity suggesting that climatic effects might have played a role in these species’ divergence. The final study presents an Illumina-based high-resolution species phylogeny for Astyanax mexicanus providing added support that there are multiple origins to cave populations and further clarifying the uniqueness of the Sabinos and Rio Subterráneo caves.

In Lake Pontchartrain Basin, commercial fishing in estuarine habitats impacts many non-target species collected as bycatch. I investigated the bycatch assemblages collected by commercial vessels and compared these to assemblages collected by typical fishery-independent methods. I compared assemblages using analysis of similarity (ANOSIM) and determined important species by weight and abundance using similarity percentages analyses (SIMPER). I also examined differences in size-class distributions by gear type using density kernel plots and Mann-Whitney U tests. The two gear types collected significantly different assemblages (ANOSIM R = 0.522, p = 0.001) and gear type explained more composition differences than other factors such as month, daytime, or location. Fishery-independent gear underestimated the importance of many species. Although fishery-independent data are invaluable for monitoring assemblage dynamics, fishery-independent gear collects different assemblages than commercial gear. Larger fishes of important species were caught less often in bycatch, but completely absent from fishery-independent gear.

Few studies have rigorously assessed the adaptive value of diel rhythms in animals. We laid the groundwork for assessing the adaptive rhythm hypothesis by assaying diel rhythms of foraging and antipredator behavior in the orb-weaving spider Cyclosa turbinata. When confronted with a predator stimulus in experimental arenas, C. turbinata exhibited thanatosis behavior more frequently and for longer durations during the day. However, assays of antipredator response within webs revealed more complex diel patterns of avoidance behaviors and no pattern of avoidance behavior duration. Assays of prey capture behavior found that the likelihood of exhibiting prey capture behavior varied significantly across times of day and test subjects, but only test subject predicted attack latencies. Although C. turbinata foraging aggression changed over the diel cycle, we found no evidence of a trade-off between foraging behavior and predator vigilance. However, overall patterns of vigilance may be masked by diel changes in antipredator strategies.

Performance is key to survival. From day-to-day foraging events, to reproductive activities, to life-or-death crises, how well an organism performs these tasks can determine success or failure. Selection, therefore, both natural and sexual, act upon performance, and performance demands on individuals shape a population’s morphological and physiological trait distributions. While studies of morphological adaptations to ecological pressures implicitly center on the idea that responses to selection improve performance via changes in morphology, the relationships between morphology, performance, and fitness are not always well understood. In this dissertation, I investigate these relationships explicitly, as well as determine the effects that different ecological and genetic contexts have on selection and how populations respond to performance pressures. Using a model of lizard locomotor performance, I address three issues that may impact selection on performance that are often overlooked in performance studies. First, performance is not a static trait. Rather, individuals possess a range of performance abilities or intensities that can be expressed as needed. Using a novel, individual-based, quantitative genetic simulation model, I demonstrate the effects of variable performance expression and genetic constraints on how a population experiences and responds to selection on sprint and endurance performance. Second, sex differences in performance are expected in sexually dimorphic species, but empirical evidence for this is lacking. To this end, I measured and analyzed multivariate morphology and performance in Anolis carolinensis to identify sex-specific patterns in functional morphology and functional trade-offs within a broad suite of performance traits. Third, intralocus sexual conflict should constrain the evolution of the multivariate performance phenotype in both sexes. By extending the simulation model to include correlated trait inheritance between sexes and sex-specific selection on certain performance traits, I demonstrate the extent to which this sexual conflict constrains performance evolution. In combining studies of natural populations with simulation studies of selection, this dissertation embraces the complexity of performance to address the multiple contributing factors and constraints on performance evolution, and demonstrates the importance of accounting for such complexity when studying animal performance.

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency of nucleotide polymorphisms. Domain II was observed to be the most conserved, and Domain I was the most variable domain of the control region, in agreement with studies of other vertebrate control regions. The second goal of this study was to ascertain the phylogeny of R. osculus in Southern California in relation to other speckled dace in California. Seventy-four specimens of R. osculus were collected from five different watersheds located in three geographic regions of California: Southern California, the Central California Coast, and the Eastern Desert of the Owens River valley. Phylogenetic analysis of sequence data revealed that the Santa Ana Speckled Dace is a genetically distinct population from R. osculus inhabiting the Central Coast or Eastern Desert regions, which both differ from the Santa Ana Speckled Dace by a genetic distance of more than 7 percent. The Santa Ana Speckled Dace inhabiting the watersheds of Southern California form a reciprocally monophyletic clade with respect to the Central Coast dace and the Eastern Desert dace, which are sister clades to one another. The third goal of this study was to describe the population genetics of R. osculus in Southern California. Population genetic analysis demonstrated that a high degree of geographic population structure exists for the Speckled Dace in California, with 96% of molecular variance attributable to regional differences through isolation by distance. A high degree of population structure also exists among populations within the Southern California region as well. It was found that 45% of molecular variance in the Santa Ana Speckled Dace is attributable to differences among tributaries. This study finds that the distribution of speckled dace in Southern California best fits a model of population structure by individual tributary, with episodes of localized population bottlenecks followed by sudden population expansion, most likely linked to climatic variation. It is proposed the Santa Ana Speckled Dace constitutes an Evolutionarily Significant Unit (ESU) that qualifies it as a separate subspecies on the basis that it is geographically separated from other populations, genetically distinct from other dace populations due to restricted gene flow, and possesses unique phenotypic characteristics. This information suggests conservation and management strategies for the speckled dace populations which remain in existence in Southern California.

Atribacteria (OP9), candidate phylum with no representatives in pure culture, is found in various anaerobic environments worldwide. “Caldatribacterium”, a lineage within Atribacteria that is predicted to be a strictly anaerobic sugar fermenter based on cultivation-independent genomic analyses, is currently being maintained in lab enrichment cultures with fucose as its sole growth substrate. Metagenomics and 16S rRNA gene tag sequencing indicated that the fucose culture was a co-culture of “Caldatribacterium” and an uncultivated member of the genus Thermodesulfobacterium. Due to failed attempts to isolate “Caldatribacterium” by dilution-to-extinction and plating, it was hypothesized that “Caldatribacterium” is dependent in some way on the Thermodesulfobacterium. To better understand the possible interaction, multiple isolates of the sulfate reducer were obtained under sulfate-reducing conditions with H2 as an electron donor, and one of the isolates was characterized. Whole genome and 16S rRNA gene sequence comparisons of the isolate and other related members of the genus Thermodesulfobacterium suggested the isolate represents a distinct species in this genus, for which the name T. auxiliatoris is proposed. T. auxiliatoris was capable of using H2, formate, and lactate as sole electron donors, but not fucose or other sugars, suggesting that its growth in the co-culture might be dependent on one or more fermentation substrates produced by “Caldatribacterium”. Addition of T. auxiliatoris to highly diluted samples of the co-culture that likely contained only “Caldatribacterium”, which did not exhibit growth on their own, demonstrated that T. auxiliatoris was sufficient to support growth of “Caldatribacterium” on fucose. When this dilution experiment was repeated with various other organisms and substrates, it was found that several other thermophilic sulfate reducers (T. commune, T. hveragerdense, or Thermodesulfovibrio yellowstonii) could also support growth, as well as supernatant from the T. auxiliatoris pure culture or yeast extract. This last finding allowed for isolation of “Caldatribacterium”, which could form colonies on solid media when yeast extract and casamino acids were present. Fluorescent in situ hybridization and nanometer-scale secondary ion mass spectrometry demonstrated that “Caldatribacterium” took up a variety of sugars and amino acids in mixed culture, and that addition of acetate or bicarbonate, substrates of T. auxiliatoris, stimulated sugar uptake in “Caldatribacterium”. These results support a model where T. auxiliatoris and “Caldateribacterium” are dependent on each other in co-culture on fucose, where “Caldatribacterium” provides growth substrates for T. auxiliatoris, which in turn provides “Caldatribacterium” with some sort of soluble, essential compound(s) that can be produced by other sulfate reducers and are present in yeast extract. Further characterization of the “Caldatribacterium” isolate, the first representative of the phylum Atribacteria, will allow for detailed study of its metabolic capabilities that can be extended to other members of this phylum. Further analysis of responses of T. auxiliatoris and “Caldatribacteirum” when grow in co-culture and the specific metabolite(s) that are exchanged between the two organisms could allow for testing whether these interactions occur in more complex, natural systems.

A novel lepidopteran sex pheromone lure which was thought to be species-specific to the citrus pest Marmara gulosa (Lepidoptera: Gracillariidae) Guillén (McElfresh et al. 2009) has attracted male moths exhibiting two distinct morphologies. The morphological features examined were the sclerotized parts that make up the male genitalia; which include the valvular lobes, costal lobes, cucullar lobes, and the aedeagus. The sclerotized parts were methodically dissected and mounted on microscope slides. Digital images captured of the slide-mounted specimens proved to be inconsistent with the illustrations provided in the original Marmara gulosa species description (Guillén et al. 2001). The morphologies of all specimens from both the San Joaquin and Coachella valley show remarkable consistency; regardless of host plant origin, collection method, and collection date. Two specimen groups (one from an orchard in Northern Mexico and the other from backyard citrus in Riverside, California) exhibited entirely different morphological features in which the three lobes mentioned above are fused together. This difference in morphology can only be noticed when examining the sclerotized parts of the male genitalia under a microscope; it is otherwise indistinguishable from M. gulosa via macroscopic features such as antennae shape and wing pattern. These two specimen groups with fused lobes are considered a new species belonging to the genus Marmara and currently remain undescribed. A genetic study conducted at UC Riverside, which concentrated on the CO1 region of mitochondrial DNA, reported significant differences in genetics based on the geographic origins of specimens (Vickerman and Stouthammer 2006). Geographically, the genetic distribution described in the 2006 study does not coincide with the distribution of morphologies described in this paper. The species description of Marmara gulosa is in need of revision. In addition, further collection and research is required in order to describe and name the newly discovered Marmara species.

Rain-on-snow (ROS) occurs when warm, wet air moves into latitudes and/or elevations having vulnerable snowpacks, where it can alter water inputs to infiltration, runoff and erosion. The Pacific Northwest is particularly susceptible: winter storms off the Pacific cause locally heavy rain plus snowmelt almost annually, and disastrous flooding and landsliding intermittently. In maritime mountainous terrain, the effects seem more likely and hydrologically important where warm rains and seasonal snowpacks are liable to coincide, in middle elevations. Several questions arise: (1) In the PNW, does ROS affect the long-term frequency and magnitude of water delivery to the ground, versus total precipitation (liquid and solid), during big storms? Where and how much? (2) If so, can we determine which elevations experience maximum hydrologic effects, the peak ROS zone? Probabilistic characteristics of ROS are difficult to establish because of geographic variability and sporadic occurrence: scattered stations and short observational records make quantitative frequency analysis difficult. These problems dictate a modeling approach, combining semi-random selection of storm properties with physical rules governing snow and water behavior during events. I created a simple computer program to perform Monte Carlo simulation of large storms over 1000 "years", generating realizations of snowpack and storm-weather conditions; in each event precipitation falls, snow accumulates and/or melts, and water moves to the ground. Frequency distributions are based on data from the Washington Cascades, and the model can be applied to specific sites or generalized elevations. Many of the data sets were based on observations at Stampede Pass, where high-quality measurements of weather and snow at the Cascade crest have been made since the 1940s. These data were used to inform the model, and to test its reliability with respect to the governing data distributions. In addition, data from ROS events at Stampede, and at research sites in southwest Oregon, were used to confirm that the model's deterministic calculations of snow accumulation, snowmelt, and percolation (yielding water available for runoff) adequately simulate conditions observed in the field. The Monte Carlo model was run for elevations ranging from 200 to 1500 m, each over a hypothetical millennium. Results indicate that the presence of snow in some storms reduces the amount of water reaching the ground. This occurred more often in highlands but also at middle and lower elevations, affecting the long-term frequency-magnitude relations across the landscape. In these conditions, the rain-gauges overestimate the amount of liquid water actually reaching the ground. For many storms, however, ROS enhances water reaching the ground, most significantly at elevations between ~500-1100 m. At lower and higher elevations, the water available for runoff exceeds precipitation in ~2% of events, but this proportion rises to ~20-30% at ~800 m. Other metrics (e.g., series statistics, exponential regression coefficients, frequency-magnitude factors) also indicate that this middle-elevation band (around ~800 m) experiences ROS most often and with greatest water available for runoff. Of the west-central Washington Cascades study region, about one-third to one-half the landscape is susceptible to significant ROS influence. These results indicate areas where ROS currently has the greatest hydrologic consequence on ecosystems and human works, and possibly the greatest sensitivity to changes in land-use and climate.