Through genome wide association of nonvolatile metabolites and leaf ecophysiological traits, historic breeding practices were found to have led to germplasm divergence within the cultivated sunflower Helianthus annuus. In genome-wide analyses of single nucleotide polymorphisms (SNPs) in relation to flower petal carotenoid content across the cultivated H. annuus germplasm, alternative methods of analysis proposed differing genetic architectures, which suggests that these methods can be used as complementary approach in prioritizing SNPs for function analysis. Leaf hyperspectral reflectance was leveraged in a machine learning framework to predict herbivore- and volatile induction across the genus with 95% accuracy, while characterizing changes in volatile metabolites. The body of work in this dissertation represents the first characterization of the standing genetic variation for nonvolatile specialized metabolite diversity in cultivated sunflower in the context of modern breeding practices, and the first assessment of hyperspectral reflectance and volatile metabolite diversity across the genus Helianthus.

Intraspecific phenotype diversity allows for local adaption and the ability for species to respond to changing environmental conditions, enhancing survivability. Phenotypic variation could be stochastic, genetically based, and/or the result of different environmental conditions. Mojave Rattlesnakes, Crotalus scutulatus, are known to have high intraspecific venom variation, but the geographic extent of the variation and factors influencing venom evolution are poorly understood. Three primary venom types have been described in this species based on the presence (Type A) or absence (Type B) of a neurotoxic phospholipase A2 called Mojave toxin and an inverse relationship with the presence of snake venom metalloproteinases (SVMPs). Individuals that contain both Mojave toxin and SVMPs, although rare, are the third, and designated Type A + B. I sought to describe the proteomic and transcriptomic venom diversity of C. scutulatus across its range and test whether diversity was correlated with genetic or environmental differences. This study includes the highest geographic sampling of Mojave Rattlesnakes and includes the most venom-gland transcriptomes known for one species. Of the four mitochondrial lineages known, only one was monophyletic for venom type. Environmental variables poorly correlated with the phenotypes. Variability in toxin and toxin family composition of venom transcriptomes was largely due to differences in transcript expression. Four of 19 toxin families identified in C. scutulatus account for the majority of differences in toxin number and expression variation. I was able to determine that the toxins primarily responsible for venom types are inherited in a Mendelian fashion and that toxin expression is additive when comparing heterozygotes and homozygotes. Using the genetics to define venom type is more informative and the Type A + B phenotype is not unique, but rather heterozygous for the PLA2 and/or SVMP alleles. Intraspecific venom variation in C. scutulatus highlights the need for fine scale ecological and natural history information to understand how phenotypic diversity is generated and maintained geographically through time.

Circadian rhythms are ubiquitous among organisms, influencing a wide array of physiological processes and behaviors including aggression. While many neurophysiological mechanisms are involved in the regulation of aggressive behaviors, relatively few studies have investigated the underlying components involved in the interplay between circadian rhythms and aggression. Spiders are an ideal model system for studying circadian regulation of aggression as they are ecologically both predators and prey. Recent studies have revealed a nocturnal orb- weaving spider Larinioides cornutus exhibits a diel and circadian rhythm in anti-predator behavior (i.e. boldness) that can be manipulated by administration of octopamine (OA) and serotonin (5- HT). Dosing of OA increases boldness of an individual while 5-HT decreases boldness levels. Thus, it appears the serotonergic and octopaminergic system are playing a key role in the daily fluctuations of boldness. This study took a holistic approach to investigate OA and 5-HT levels of head tissue and hemolymph (i.e. blood) as well as the genes involved in synthesis, signaling, and degradation of these monoamines throughout the day (0100, 0700, 1300, and 1900 hours) using HPLC-ED and RNA-sequencing. Although endogenous and circulating levels of OA did not significantly fluctuate, putative transcripts involved in synthesis and signaling did increase in relative expression levels at dusk when L. cornutus begins to actively forage for prey. Endogenous and circulating levels of 5-HT also did not significantly change at the four different time points, but clear patterns of upregulation of 5-HT synthesis enzymes as well as some receptor transcripts were upregulated during the day when L. cornutus would be mostly inactive in its retreat. Lastly, monoamine oxidase, a major catabolic enzyme of monoamines in vertebrates and some invertebrates, was identified in L. cornutus and exhibited substrate specificity for OA compared to 5-HT. Together with the higher enzymatic activity at mid-day compared to dusk, MAO appears to be playing a significant role in regulating the OA and 5-HT signaling in L. cornutus. In conclusion, these results allow a unique preliminary perspective on how OA and 5-HT are influencing the diel shifts in aggression-related behaviors in an ecologically dynamic arthropod.

Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated (FST= 0.000644) and there is weak isolation-by-distance structure, but ongoing gene flow is unlikely. Within populations, stand density and competitor effects contribute to inbreeding. I also show that previously measured traits are predominantly determined by genetics. Analyzing by sliding window in the genome, I show that connectivity patterns vary widely throughout the genome and identify several areas that are important to the genetic architecture of the phenotypic traits and plasticity (GxE). Overall, there is high connectivity, genetic similarity, and genetically based trait variation among and within populations of the northern subspecies of foxtail pine due to historical processes, despite biotic interactions driving inbreeding. Persistent genetic isolation, however, may make adaptation to future climate a challenge for the subspecies.

The translocation of organisms is becoming a frequently used tool in conservation biology. There are, however, a disproportionate number of unsuccessful attempts translocating populations of herpetofauna. Logistical and temporal limits of monitoring, combined with ambiguous metrics concerning "success," have led to few advances regarding reptile translocations. Successfully established and persistent populations are those in which both the founding population and subsequent generations show consistent or positive levels of survival and reproduction. A small population of the threatened Florida Sand Skink (Plestiodon reynoldsi) was translocated in 2007. Data collected from 2007 to 2009 confirmed survival and reproduction among the founding individuals, but the sampling did not include a long enough period to allow for the evaluation of the survival and reproduction of individuals born on the site. In this study, individuals were collected during two separate sampling events, one during the third spring and one during the sixth spring after the translocation occurred. Survival estimates, reproduction, population size and generation structure were calculated by combining and analyzing data from all years post-translocation. The numbers of both total and new individuals captured in the sixth year exceeded captures from every prior sampling event since monitoring began in 2008. Founding individuals represented only 14% of the total individuals captured, while the number of individuals born on site continued to increase. The proportion of recruits and increased number of hatchlings despite the loss of founders shows that the filial generations are producing offspring. The methods utilized in assessing this translocation effort will further the understanding of the population dynamics of the Florida Sand Skink and allow for more informed decisions in future management studies of this threatened species.

Soils are critical to ecosystem function as they provide essential nutrients for primary producers, habitat and organic energy for decomposers, and storage of organic matter. Irrigation with reclaimed water is an increasingly popular water conservation strategy; yet its high salinity and nutrient content potentially affect soil properties. In this study, set in a residential neighborhood of Tampa (U.S.). I tested whether there are distinct lawn system management strategies characterized by systematic differences in reclaimed water usage and irrigation and fertilization practices. I then investigated whether soil biogeochemistry responds to lawn system management strategy. My results indicated that amendment strategy, which includes water source type, frequency of fertilization, and frequency of irrigation varies among residents of comparable neighborhoods. In this case, these three categories of management behaviors tend to co-occur. Analysis of irrigation water samples collected in this study showed significant differences between potable and reclaimed water. Mainly, reclaimed water had higher conductivity and phosphate content than potable water. When looking at the soil biogeochemical characteristics of the study area I found that there were significant differences in soil nutrients and microbial biomass across amendment strategy. Soils with a high amendment strategy (frequently irrigation with nutrient-rich reclaimed water, plus frequent fertilizer addition) showed higher conductivity and a higher microbial biomass than soils on lawns with a low amendment strategy (infrequent irrigation with dilute potable water, plus infrequent fertilizer addition). A positive correlation between soil conductivity and microbial biomass was observed. These findings suggest that high amendment strategy increases the input flux of some nutrients to the soils and acts as a nutrient resource for soil microorganisms. The differences between soil and microbial biomass amendment strategy support the idea that decisions made by individuals about which management intensity strategy to use do affect the spatial variability of the ecosystem. These results contribute to the hypothesis of urban ecological urbanization by looking at the vertical social interactions between municipalities and individual homeowners. These interactions might explain the observed spatial variability of ecological characteristics. The results of this research affect the way information about the advantages of using reclaim water is advertised, in particular to homeowners.

Thesis (Ph. D.)--Rutgers University, 2009. / "Graduate Program in Physiology and Integrative Biology." Includes bibliographical references (p. 95-114).

Investigations were made examining the relationships between gastropod species richness and abundance across 20 phosphate and 20 natural lakes in Central Florida. In additional to lake category, age of phosphate lakes was used to determine if phosphate lakes ever approximate natural lakes. Additional physical, chemical, and biological parameters, including chlorophyll a, Ca, secchi, phosphorous, conductance, fish predation, and recreational lake use were investigated in order to determine if they affected gastropods with lake age. Comparisons were also made between gastropod species richness and average abundance and two groups of dominant vegetation categories: Panicum, a structurally complex macrophyte, and Typha, a less structurally complex macrophyte. After phosphate mining operations are completed, Florida state regulations require the establishment of ecologically viable habitat (created lakes) which reflects the properties of regional natural lakes including vegetation structure, littoral zone, bank slope, and lake depth. The littoral zone is part of the mandated structure of the lake, and is of considerable importance to the uptake, storage, transformation and release of nutrients. Within the littoral zone, gastropods are a critical link in the food web with implications for the long term structure and function of a lake. They are known for their close associations with macrophytes and are common environmental indicators since they have limited mobility, high diversity, are well studied, are representative of their habitat type and have a widespread geographic range. They are also an important food sources for many predators in aquatic environments, include migratory waterfowl and game fish. Gastropod species richness and abundance data were collected via standard net sweep methodology. Abundance was presented in catch per unit effort, therefore all abundance data were averages. Initial comparisons between gastropod species richness and average abundance yielded no significant differences between natural and phosphate lakes. However, when age was applied as a covariate, there was a significant difference between lake age as a continuous variable in species richness comparisons. Additionally, categorical comparisons between lakes older or younger than 30 years indicated significantly higher species richness and average abundance of gastropods in lakes phosphate lakes older than 30 years. Physical and chemical properties of the lakes did not appear to influence gastropod populations between lakes of different ages. Fish predation interactions did not indicate any significant influence either. However, the presence of boat ramps did indicate a positive relationship between average gastropod abundance and species richness and recreational lake use. Littoral zone macrophyte comparisons between dominant vegetation Typha and Panicum indicated a significantly positive relationship between gastropod species richness and average abundance in older phosphate lakes dominated by the more structurally complex Panicum macrophytes. Confidence in the Typha and Panicum results was confounded by lack of access to younger, Typha dominated, phosphate lakes. An increase in sample size for younger Typha lakes, with additional site access, may further support these findings.

The Wrinkle-lipped free-tailed bat (T. plicata) in Thailand and the Brazilian free-tailed bat (T. brasiliensis) in south-central Texas are integral in the control of agricultural pests. The effect on the production of rice and cotton is determined by the bats consumption of a particular pest species in that region. In Thailand, it is the White-Backed Planthopper (Sogatella furcifera), while in south-central Texas, it is the cotton bollworm (Helicoverpa zea). The ecological service these bat species provide is measured in millions of dollars saved by farmers each year. Finally, a conclusion was made about which species had a greater effect on the economy when compared to each other.

Bees are necessary pollinators for a vast array of different plants, including many which we rely on for food. In order to grow sufficient crops to feed the world’s growing population, we need to make sure our crops are visited by the most effective possible pollinators. However, this is complicated by the fact that there are over 4,000 bee species in North America, many of which vary in their pollination effectiveness and are difficult to identify. My dissertation’s first two data chapters focus on classifying the species of the xeric solitary bee group Anthophora subgenus Micranthophora, including seven newly described species, while also providing identification resources for telling them apart. With this group’s classification fixed, my third chapter then uses differences in the DNA of these species to reconstruct evolutionary trees of their relationships; those with more similar DNA sequences are grouped more closely together. I then use powerful modern methods to and determine how quickly new species have arisen throughout the entirety of the group’s evolutionary history, in order to determine how desertification has influenced the evolution of these xeric bees. My results suggest that the Neogene Uplift, a mountain-building event, initially increases their diversification rates, but climatic cooling and niche competition later greatly decrease these rates. Finally, my last chapter looks at bee evolution from a contemporary perspective, viewed through the lens of a new species of bee that actually excavates its nests in sandstone, Anthophora pueblo, despite the obvious time and energy costs of this behavior. In addition to describing this fascinating new species, I also use interdisciplinary methods from biology and geology to demonstrate that, although they prefer to use weaker sandstone, intermediate levels of sandstone hardness are likely beneficial to them, enabling future generations of their relatives to reuse nest tunnels for many years without excavating. Preliminary evidence also suggests that these bees benefit from protections afforded to them against parasites and pathogens that can destroy their nests and kill their offspring. Overall, this species will provide a terrific system for future studies of bee evolution and life history trade-offs. By performing these studies, my dissertation will enable a wealth of additional studies on these poorly known solitary bees.