abstract: Although many studies have identified environmental factors as primary drivers of bird richness and abundance, there is still uncertainty about the extent to which climate, topography and vegetation influence richness and abundance patterns seen in local extents of the northern Sonoran Desert. I investigated how bird richness and abundance differed between years and seasons and which environmental variables most influenced the patterns of richness and abundance in the Greater Phoenix Metropolitan Area. I compiled a geodatabase of climate, bioclimatic (interactions between precipitation and temperature), vegetation, soil, and topographical variables that are known to influence both richness and abundance and used 15 years of bird point count survey data from urban and non-urban sites established by Central Arizona–Phoenix Long-Term Ecological Research project to test that relationship. I built generalized linear models (GLM) to elucidate the influence of each environmental variable on richness and abundance values taken from 47 sites. I used principal component analysis (PCA) to reduce 43 environmental variables to 9 synthetic factors influenced by measures of vegetation, climate, topography, and energy. I also used the PCA to identify uncorrelated raw variables and modeled bird richness and abundance with these uncorrelated environmental variables (EV) with GLM. I found that bird richness and abundance were significantly different between seasons, but that richness and winter abundance were not significantly different across years. Bird richness was most influenced by soil characteristics and vegetation while abundance was most influenced by vegetation and climate. Models using EV as independent variables consistently outperformed those models using synthetically produced components from PCA. The results suggest that richness and abundance are both driven by climate and aspects of vegetation that may also be influenced by climate such as total annual precipitation and average temperature of the warmest quarter. Annual oscillations of bird richness and abundance throughout the urban Phoenix area seem to be strongly associated with climate and vegetation. / Dissertation/Thesis / Masters Thesis Applied Biological Sciences 2019

The presence and spread of invasive tree species have caused great ecological and economic damages. Previous studies usually ignored the role of socioeconomic factors and seldom treated presence and abundance as different phenomena. Using Classification and Regression Trees (CART) analysis, important driving factors affecting the presence and abundance of invasive tree species in Mississippi were identified. Then these selected important factors were spatially analyzed using a spatial lag model at the plot and county levels. The empirical results from the spatial lag model showed that: 1) presence was associated with elevation, ownership, population density and per capita annual income; 2) abundance was related to stand age, elevation, growing stock and per capita annual income. These findings suggested that socioeconomic factors besides ecological factors played a significant role and factors affecting the presence and abundance were different. Thus, management prescriptions to monitor and control invasions should depend on difference factors.

Many insights into ecological and evolutionary processes have come from studies of island systems. Diversity, abundance, and movement of species are restricted on smaller islands, but these dynamics can become increasingly complex as island size increases. In recent decades urbanization and the human population on the Galápagos islands has increased rapidly, affecting wildlife in unknown ways. During 2005 and 2006, we sampled birds along a 4-km transect extending northeast of the city of Puerto Ayora, Santa Cruz Island. This allowed us to collect data on the potential impacts of rapidly growing urban center on passerine bird diversity and abundance. We also documented movement patterns of the medium ground finch (Geospiza fortis), the most abundant species on the transect, with a mark/recapture protocol. Although Darwin's finches have been an influencial model for the last 150 years, little is known about their movements on larger islands. Avian species diversity did not vary significantly along a transect from a periurban area into more remote habitat. Avian abundance, however, was inversely correlated with distance from the urban center. This latter finding is consistent with a well-documented trend in urban ecology, in which periurban areas show higher abundance as compared to adjacent, less developed regions. We also found recapture/re-sight rates for G. fortis within years were 7% and 11% in 2005 and 2006, respectively. The mean distance traveled by individual birds between recaptures or re-sightings was 430.4 m. The majority of movements were less than 500 m from the location of previous sighting. There was no relationship between the distance moved and the time between captures or re-sightings; birds were equally likely to move large distances over short intervals (days) as over longer intervals (years). There was no significant difference in movement distances between males and females. These data document the movement of G. fortis on a larger island. Further studies of gene flow among populations may provide further insight into the genetic and evolutionary consequences of movement patterns documented here.

Human population growth and development reduce the area and quality of natural communities and lead to a reduction of populations of the species associated with them. Certain species can be useful indicators or "focal species" for determining the quality of ecosystem remnants and the required management practices. Tree squirrels are good models for studies on the effects of fragmentation because they depend on mature forests. The Big Cypress fox squirrel, (Sciurus niger avicennia), a state-listed Threatened subspecies endemic to south Florida, appears sensitive to habitat fragmentation and fire regime. This research aims to assess the conservation status of the Big Cypress fox squirrel. I documented the current distribution of the fox squirrel by obtaining and mapping occurrence records and through interviews with biologists and other field personnel of public land-managing agencies, and private landowners including golf course managers. Transect sampling was used to survey and sample natural areas and private lands to evaluate the distribution, abundance, and habitat use of fox squirrels. Natural areas and suburban areas appear to support Big Cypress fox squirrels, but individuals are widely distributed and only found in low numbers throughout southwest Florida. The distribution of fox squirrel populations depends on land use and understory height, but not the size of trees. Fire suppression has resulted in a dense understory in large portions of parks and preserve lands, which is unsuitable for fox squirrels.

Production of hot peppers, Capsicum spp., in Jamaica is constrained by the aphid-transmitted potyviruses, tobacco etch virus (TEV) and potato virus Y (PVY). The virus epidemiology was not understood and no effective virus management system existed for these viruses. This study sought to identify possible management strategies for aphid-transmitted viruses of hot peppers in Jamaica, using TEV and Capsicum chinense, var. 'Scotch Bonnet' and 'West Indian Red', as models. Field spread of TEV to pepper was mainly by secondary spread from primary infections. Secondary infections were spatially correlated to primary infections for up to 25 meters. Natural infections of TEV were associated with aphid flight activity. Over 30 species of aphids were collected on pepper farms in St. Catherine parish. These aphids included five known vectors of TEV, Aphis gossypii Glover, A. craccivora Koch, A. spiraecola Patch, Lipaphis erysimi Hille Ris Lambers and M. persicae (Sulzer), and 12 new records for Jamaica, Aphis amaranthi Holman, Brachycaudus helichrysi (Kaltenbach),Capitophorus hippophaes (Walker), Geopemphigus floccosus (Moreira), Hysteroneura setariae (Thomas), Lipaphis erysimi Hille Ris Lambers, Rhopalosiphum padi (Linnaeus), Schizaphis graminum (Rondani), Schizaphis rotundiventris (Signoret), Trichosiphonaphis poligoni (van der Goot), Uroleucon ambrosiae complex (Thomas) and Uroleucon pseudoambrosiae (Olive). A. amaranthi and U. ambrosiae were associated with TEV spread. Weeds on and near farms influenced the abundance and species of aphids captured. West Indian Red pepper showed tolerance to TEV. Scotch Bonnet pepper yield reduction was greater if plants were infected with TEV during the vegetative stage through flower initiation rather than after the start of fruit set. Stylet oil and reflective mulch used together delayed the incidence of TEV in pepper plots for over two months. TEV management programs should aim to delay the virus from infecting peppers during the first two months after transplanting. A risk analysis is proposed for management of TEV and other aphid-borne viruses. / Ph. D.

Part I: Low complexity regions (LCRs) are common motifs in eukaryotic proteins, despite the fact that they are also mutationally unstable. For LCRs to be widely used and tolerated there must be regulatory mechanisms which compensate for their presence. I have endeavored to characterize the relationships and co-evolution of LCRs with the abundance of the proteins that host them as well as the transcripts which encode them. As the abundance of a gene product is ultimately responsible for its associated phenotype, any relationships have implications for the many neurodegenerative diseases associated with LCR expansion. I found that there are indeed relationships. LCRs are more associated with low abundance proteins, but the opposite is true at the RNA level: LCRs encoding transcripts have higher abundance. Investigating the co-evolution of LCRs and transcript abundance revealed that on short evolutionary timescales indels in LCRs influence the selective pressures on TAb. Viewing LCRs through the previously unexplored lens of abundance has generated new results. Results which, together with explorations of information flow and low-complexity in untranslated regions, expand our knowledge of the functional impacts of LCRs evolution. Part II: A commonly encountered problem in DNA sequencing is a situation where the DNA of interest makes up a small proportion of the DNA in a sample. This challenge can be compounded when the DNA of interest may come from many different organisms. Targeted metagenomics is a set of techniques which aim to bias sequencing results towards the DNA of interest. Many of these techniques rely on carefully designed probes which are specific to targets of interest. I have developed a bioinformatic tool, HUBDesign, to design oligonucleotide probes to capture identifying sequences from a given set of targets of interest. Using HUBDesign, and other methods, I have contributed to projects ranging in context from clinical to ancient DNA. / Thesis / Doctor of Science (PhD) / This thesis describes research in two fields: repetitive protein sequences and methods for sequencing the portions of a sample in which one is most interested. In the first part I describe the general properties of repetitive proteins, establish a connection between the presence of repeats in a protein and the amount of that protein which a cell maintains, and show that these two quantities evolve together. This informs our understanding of evolution and regulation with implications for repeat related diseases and further evolutionary research. In the second part I describe a method for selecting short nucleotide sequences which can be used to capture specifically the DNA of organisms of interest, as well as applications of this and other methods. These contributions are widely applicable as targeted sequencing is useful in fields as far apart as clinical sepsis diagnosis and determining the colour of ancient animals.

The Bog Turtle (Glyptemys muhlenbergii) is a federally threatened species that occupies isolated pockets of open-canopy fens. This long-lived species is susceptible to habitat loss and degradation; thus, the conservation of known populations and management of their habitat is critical to the species’ survival. Long-term (multi-decadal) assessment is important for determining population trends and responses to ongoing habitat management. I assessed population demographics (abundance, survival) and spatial distribution (home range) of two Bog Turtle populations in Massachusetts that have been managed since the late 1990s by treating invasive species, thinning woody vegetation, and mitigating flooding. The results of this study were compared to two previous studies conducted in 1994–1997 and 2005–2009 to evaluate the response to habitat management. Estimates of adult population abundance increased from the first study period (Site 1 X̅= 37.3 ± 10.4, Site 2 X̅= 36.2 ± 3.2) to the last study period (Site 1 X̅= 65.1 ± 17.9, Site 2 X̅= 42.5 ± 10.9) across both sites. Estimates of annual survival across all study periods remained above 90% at Site 1 and were 100% for two years at Site 2. I constructed 95% minimum convex polygon (MCP) and 95% kernel density estimation (KDE) home ranges for 71 turtles. At Site 1 there was no significant influence of the study period on home range estimates. The increase in abundance estimates, high survival, and stable home range sizes at Site 1 suggest that ongoing management has maintained quality habitat. At Site 2, the average home range size decreased by approximately half after the first study period in response to flooding but increased in the current study. Fluctuations in population abundance, and home range size at Site 2 throughout the study period reflect the cycles of habitat degradation and habitat management. My results indicate that habitat management efforts implemented since the late 1990s have provided quality habitat for the two Bog Turtle populations in Massachusetts while also mitigating long-term negative impacts on the populations. This further supports the need for long-term analysis of Bog Turtle populations, especially at sites where active habitat management is occurring.

No description available.

Little is known about how the leaf bacterial community is affected by the seed microbiota at different stages of plant development. The bacterial populations of spinach seed and leaves after germination were compared using DGGE, to assess bacterial community richness, and real-time PCR to compare the abundance of select phyla (total bacteria, <i>Actinobacteria, Bacteroidetes, Firmicutes, α-Proteobacteria and β- Proteobacteria</i>). To determine the effect of environment, the plants were grown in the field and growth chambers. Vertical transmission of bacterial community members was evident; the developmental stage of the plant affected the richness and abundance of select bacterial phyla. The bacterial richness of plants grown in the two environments was not affected. However, overall numbers of bacteria increased in field grown samples in comparison to those produced in growth chambers during development. A statistically significant interaction was seen between growth stage and environment with each of the selected phyla. Populations on cotyledons were smaller than mature leaves, but were not significantly different than the 3-4 leaf stage plants. The culturable populations of bacteria on seeds (~5 log CFU/g) were significantly smaller than determined using real time PCR (~7 log copies). Of these bacteria cultured from spinach seeds, isolates belonging to the genera <i>Pantoea</i> were found to inhibit growth of <i>E. coli</i> O157:H7 <i>in vitro</i>. This study highlights the importance of vertical transmission on the bacterial community of plants and suggests the importance of developing strategies to influence these communities on seed to control human and plant pathogens on the leaf surface. / Master of Science in Life Sciences / Master of Science

Understanding how species respond to anthropogenic changes and why species respond in the way that they do can help focus conservation planning. Hellbenders (Cryptobranchus alleganiensis) are a freshwater species of increasing conservation concern that are suspected to have declined due to loss of forest cover. However, quantitative evidence of land use effects on hellbenders is lacking. I used a multilevel approach to understanding whether hellbenders respond to land use by examining physiological indices, demographics and patterns of species occurrence as endpoints. My study area included two major river drainages in Virginia which mark a largely understudied portion of the species' range. In Chapter I, I described hellbender distribution and tested the hypothesis that hellbenders would be more likely to occur in heavily forested landscapes. Surprisingly, hellbenders occupied a relatively wide land use gradient (range = 50-90% forest in an upstream catchment) and current land use was an unreliable predictor of occurrence. In Chapter II I examined hellbender abundance and demographics at a subset of study sites stratified across a land use gradient. Abundance of sub-adult/adult hellbenders increased as forest cover increased in collective upstream riparian areas, primarily as the result of increased recruitment of new adults to local populations (rather than increased apparent survival of adults). Populations in lesser forested areas were declining and composed largely of relatively old adults, indicating that land use can lead to changes in hellbender distribution given sufficient time. In Chapter III, I examined three indices of physiological condition (body condition, hematocrit and leukocyte profiles) in hellbenders captured across a land use gradient. I found evidence suggesting low reproductive success may explain reduced recruitment in areas of low forest cover and evidence suggesting hellbender endocrinology during the breeding season may vary with land use. In Chapter IV I examine efficacy of artificial shelters as a monitoring tool and demonstrate their potential as tool to further our understanding of mechanisms underlying demographic responses of hellbenders to land use. I synthesize my findings in Chapter V and conclude that loss of forest cover in riparian areas poses a formidable threat to hellbender population viability in Virginia. / Ph. D.