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Understanding the diversity, evolutionary relationships, and geographic distribution of species is foundational knowledge in biology. However, this knowledge is lacking for many diverse lineages of the tree of life. This is the case for the desert stink beetles in the tribe Amphidorini LeConte, 1862 (Coleoptera: Tenebrionidae) – a lineage of arid-adapted flightless beetles found throughout western North America. Four interconnected studies that jointly increase our knowledge of this group are presented. First, the darkling beetle fauna of the Algodones sand dunes in southern California is examined as a case study to explore the scientific practice of checklist creation. An updated list of the species known from this region is presented, with a critical focus on material now made available through digitization and global aggregation. This part concludes with recommendations for future biodiversity checklist authors. Second, the psammophilic genus Trogloderus LeConte, 1879 is revised. Six new species are described, and the first, multi-gene phylogeny for the genus is inferred. In addition, historical biogeographic reconstructions along with novel hypotheses of speciation patterns within the Intermountain Region are given. In particular, the Kaibab Plateau and Kaiparowitz Formation are found to have promoted speciation on the Colorado Plateau. The Owens Valley and prehistoric Bouse Embayment are similarly hypothesized to drive species diversification in southern California. Third, a novel phylogenomic analysis for the tribe Amphidorini is presented, based on 29 de novo partial transcriptomes. Three putative ortholog sets were discovered and analyzed to infer the relationships between species groups and genera. The existing classification of the tribe is found to be highly inadequate, though the earliest-diverging relationships within the tribe are still in question. Finally, the new phylogenetic framework is used to provide a genus-level revision for the Amphidorini, which previously contained six valid genera and 253 valid species. This updated classification includes more than 100 taxonomic changes and results in the revised tribe consisting of 16 genera, with three being described as new to science.
ContributorsJohnston, Murray Andrew (Author) / Franz, Nico M (Thesis advisor) / Cartwright, Reed (Committee member) / Taylor, Jesse (Committee member) / Pigg, Kathleen (Committee member) / Arizona State University (Publisher)
Created2018
Description
This dissertation critically evaluated methodologies and devices for assessing and protecting the health of human populations, with particular emphasis on groundwater remediation and the use of wastewater-based epidemiology (WBE) to inform population health. A meta-analysis and assessment of laboratory-scale treatability studies for removing chlorinated solvents from groundwater found that sediment microcosms operated as continuous-flow columns are preferable to batch bottles when seeking to emulate with high fidelity the complex conditions prevailing in the subsurface in contaminated aquifers (Chapter 2). Compared to monitoring at the field-scale, use of column microcosms also showed (i) improved chemical speciation, and (ii) qualitative predictability of field parameters (Chapter 3). Monitoring of glucocorticoid hormones in wastewater of a university campus showed (i) elevated stress levels particularly at the start of the semester, (ii) on weekdays relative to weekend days (p = 0.05) (161 ± 42 μg d-1 per person, 122 ± 54 μg d-1 per person; p ≤ 0.05), and (iii) a positive association between levels of stress hormones and nicotine (rs: 0.49) and caffeine (0.63) consumption in this student population (Chapter 4). Also, (i) alcohol consumption determined by WBE was in line with literature estimates for this young sub-population (11.3 ± 7.5 g d-1 per person vs. 10.1 ± 0.8 g d-1 per person), whereas caffeine and nicotine uses were below (114 ± 49 g d-1 per person, 178 ± 19 g d-1 per person; 627 ± 219 g d-1 per person, 927 ± 243 g d-1 per person). The introduction of a novel continuous in situ sampler to WBE brought noted benefits relative to traditional time-integrated sampling, including (i) a higher sample coverage (93% vs. 3%), (ii) an ability to captured short-term analyte pulses (e.g., heroin, fentanyl, norbuprenorphine, and methadone), and (iii) an overall higher mass capture for drugs of abuse like morphine, fentanyl, methamphetamine, amphetamine, and the opioid antagonist metabolite norbuprenorphine (p ≤ 0.01). Methods and devices developed in this work are poised to find applications in the remediation sector and in human health assessments.
ContributorsDriver, Erin Michelle (Author) / Halden, Rolf (Thesis advisor) / Conroy-Ben, Otakuye (Committee member) / Kavazanjian, Edward (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2018
Description
The influence of climate variability and reclaimed wastewater on the water supply necessitates improved understanding of the treatability of trace and bulk organic matter. Dissolved organic matter (DOM) mobilized during extreme weather events and in treated wastewater includes natural organic matter (NOM), contaminants of emerging concern (CECs), and microbial extracellular polymeric substances (EPS). The goal of my dissertation was to quantify the impacts of extreme weather events on DOM in surface water and downstream treatment processes, and to improve membrane filtration efficiency and CECs oxidation efficiency during water reclamation with ozone. Surface water quality, air quality and hydrologic flow rate data were used to quantify changes in DOM and turbidity following dust storms, flooding, or runoff from wildfire burn areas in central Arizona. The subsequent impacts to treatment processes and public perception of water quality were also discussed. Findings showed a correlation between dust storm events and change in surface water turbidity (R2=0.6), attenuation of increased DOM through reservoir systems, a 30-40% increase in organic carbon and a 120-600% increase in turbidity following severe flooding, and differing impacts of upland and lowland wildfires. The use of ozone to reduce membrane fouling caused by vesicles (a subcomponent of EPS) and oxidize CECs through increased hydroxyl radical (HO●) production was investigated. An "ozone dose threshold" was observed above which addition of hydrogen peroxide increased HO● production; indicating the presence of ambient promoters in wastewater. Ozonation of CECs in secondary effluent over titanium dioxide or activated carbon did not increase radial production. Vesicles fouled ultrafiltration membranes faster (20 times greater flux decline) than polysaccharides, fatty acids, or NOM. Based upon the estimated carbon distribution of secondary effluent, vesicles could be responsible for 20-60% of fouling during ultrafiltration and may play a vital role in other environmental processes as well. Ozone reduced vesicle-caused membrane fouling that, in conjunction with the presence of ambient promoters, helps to explain why low ozone dosages improve membrane flux during full-scale water reclamation.
ContributorsBarry, Michelle (Author) / Barry, Michelle C (Thesis advisor) / Westerhoff, Paul (Committee member) / Fox, Peter (Committee member) / Halden, Rolf (Committee member) / Hristovski, Kiril (Committee member) / Arizona State University (Publisher)
Created2014
Description
Arsenic (As) and chromium (Cr) occur naturally in AZ surface and groundwaters, pose different health impacts, and exhibit different treatment efficacies. Hexavalent chromium (Cr(VI)) has newly recognized human health concerns, and State and Federal agencies are evaluating a low Cr(VI)-specific maximum contaminant level (MCL) for drinking water. Occurrence of Cr and As in municipal drinking waters and industrial cooling tower waters was quantified by grab samples and compared with sampling results obtained from a new passive sampler developed specifically for Cr(VI). Cr(VI) and As concentrations in groundwater used for cooling tower make-up water concentrations were ~3 ppb and ~4 ppb, respectively, and were concentrated significantly in blowdown water (~20 ppb and ~40 ppb). Based upon pending Cr(VI), As, and other metal regulations, these blowdown waters will need routine monitoring and treatment. Cr(VI) concentrations in a water treatment plant (WTP) raw and finished water samples varied from 0.5 and 2 ppb for grab samples collected every 4 hours for 7 consecutive days using an ISCO sampler. The development of an ion exchange (IX) based passive sampler was validated in the field at the WTP and yielded an average exposure within 1 standard deviation of ISCO sampler grab data. Sampling at both the WTP and cooling towers suggested sources of Cr(III) from treatment chemicals or wood preservatives may exist. Since both facilities use chlorine oxidants, I quantified the apparent (pH=5) second-order rate constant for aqueous chlorine (HOCl/OCl-) with Cr(III) to form Cr(VI) as 0.7 M-1s-1. Under typical conditions (2 ppb Cr(III) ; 2 mg/L Cl2) the half-life for the conversion of Cr(III) to the more toxic form Cr(VI) is 4.7 hours. The occurrence studies in AZ and CA show the Cr(VI) and As treatment of groundwaters will be required to meet stringent Cr(VI) regulations. IX technologies, both strong base anion (SBA) and weak base anion (WBA) resin types were screened (and compared) for Cr removal. The SBA IX process for As removal was optimized by utilizing a reactive iron coagulation and filtration (RCF) process to treat spent IX brine, which was then reused to for SBA resin regeneration.
ContributorsBowen, Alexandra (Author) / Paul, Westerhoff K. (Thesis advisor) / Hristovski, Kiril (Committee member) / Halden, Rolf (Committee member) / Arizona State University (Publisher)
Created2014
Description
Six high-production-volume neonicotinoids were traced through a municipal wastewater treatment plant (WWTP) and engineered wetland located downstream, in a study motivated by reports on these insecticides posing threats to non-target invertebrate species and potentially playing a role in the global honeybee colony collapse disorder. An array of automated samplers was deployed in a five-day monitoring campaign and resultant flow-weighted samples were analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) using the isotope dilution method. Concentrations in WWTP influent and effluent were 54.7 ± 2.9 and 48.6 ± 2.7 ng/L for imidacloprid, respectively, and 3.7 ± 0.3 and 1.8 ± 0.1 ng/L for acetamiprid, respectively. A mass balance over the WWTP showed no (p=0.09, CI = 95%) removal of imidacloprid, and 56 ± 6% aqueous removal of acetamiprid. In the constructed wetland downstream, a lack of removal was noted for both imidacloprid (from 54.4 ± 3.4 ng/L to 49.9 ± 14.6 ng/L) and acetamiprid (from 2.00 ± 0.03 ng/L to 2.30 ± 0.21 ng/L). Clothianidin was detected only inconsistently in the WWTP and wetland (>2 to 288 ng/L; 60% detection frequency), whereas thiamethoxam (<10 ng/L), thiacloprid (<2 ng/L), and dinotefuran (<180 ng/L) were not detected at all. Thus, imidacloprid and acetamiprid were identified as recalcitrant sewage constituents (estimated U.S. WWTP discharge of 1920- 4780 kg/y) that persist during conventional wastewater treatment to enter U.S. surface waters at potentially harmful concentrations.
ContributorsSadaria, Akash Mahendra (Author) / Halden, Rolf (Thesis advisor) / Fox, Peter (Committee member) / Popat, Sudeep (Committee member) / Arizona State University (Publisher)
Created2015
Environmental releases of neonicotinoid and fipronil insecticides via U.S. wastewater infrastructure
Description
This dissertation is focused on environmental releases from U.S. wastewater infrastructure of recently introduced, mass-produced insecticides, namely neonicotinoids as well as fipronil and its major degradates (sulfone, sulfide, amide, and desulfinyl derivatives), jointly known as fiproles. Both groups of compounds recently have caught the attention of regulatory agencies worldwide due to their toxic effects on pollinators and on aquatic invertebrates at very low, part-per-trillion levels (Chapter 1). Mass balance studies conducted for 13 U.S. wastewater treatment plants (WWTPs) showed ubiquitous occurrence (3-666 ng/L) and persistence of neonicotinoids (Chapter 2). For the years 2001 through 2016, a longitudinal nationwide study was conducted on the occurrence of fiproles, via analysis of sludge as well as raw and treated wastewater samples. Sludge analysis revealed ubiquitous fiprole occurrence since 2001 (0.2-385 µg/kg dry weight) and a significant increase (2.4±0.3-fold; p<0.005) to elevated levels found both in 2006/7 and 2015/6. This study established a marked persistence of fiproles during both wastewater and sludge treatment, while also identifying non-agricultural uses as a major source of fiprole loading to wastewater (Chapter 3). Eight WWTPs were monitored in Northern California to assess pesticide inputs into San Francisco Bay from wastewater discharge. Per-capita-contaminant-loading calculations identified flea and tick control agents for use on pets as a previously underappreciated source term dominating the mass loading of insecticides to WWTPs in sewage and to the Bay in treated wastewater (Chapter 4). A nationwide assessment of fipronil emissions revealed that pet products, while representing only 22±7% of total fipronil usage (2011-2015), accounted for 86±5% of the mass loading to U.S. surface waters (Chapter 5). In summary, the root cause for considerable annual discharges into U.S. surface waters of the neonicotinoid imidacloprid (3,700-5,500 kg/y) and of fipronil related compounds (1,600-2,400 kg/y) is domestic rather than agricultural insecticide use. Reclaimed effluent from U.S. WWTPs contained insecticide levels that exceed toxicity benchmarks for sensitive aquatic invertebrates in 83% of cases for imidacloprid and in 67% of cases for fipronil. Recommendations are provided on how to limit toxic inputs in the future.
ContributorsSadaria, Akash Mahendra (Author) / Halden, Rolf (Thesis advisor) / Fraser, Matthew (Committee member) / Perreault, Francois (Committee member) / Mascaro, Giuseppe (Committee member) / Arizona State University (Publisher)
Created2017
Description
Uncertainty is inherent in predictive decision-making, both with respect to forecasting plausible future conditions based on a historic record, and with respect to backcasting likely upstream states from downstream observations. In the first chapter, I evaluated the status of current water resources management policy in the United States (U.S.) with respect to its integration of projective uncertainty into state-level flooding, drought, supply and demand, and climate guidance. I found uncertainty largely absent and discussed only qualitatively rather than quantitatively. In the second chapter, I turned to uncertainty in the interpretation of downstream observations as indicators of upstream behaviors in the field of Wastewater-Based Epidemiology (WBE), which has made possible the near real-time, yet anonymous, monitoring of public health via measurements of biomarkers excreted to wastewater. I found globally, seasonality of air and soil temperature causes biomarker degradation to vary up to 13-fold over the course of a year, constituting part of the background processes WBE must address, or detrend, prior to decision-making. To determine whether the seasonal change in degradation rates was introducing previously unaccounted for uncertainty with respect to differences in observed summertime and winter-time populations, I evaluated demographic indicators recorded by the Census Bureau for correlation with their distance from all major wastewater treatment plants across the U.S. The analysis identified statistically significant correlation for household income, education attainment, unemployment, military service, and the absence of health insurance. Finally, the model was applied to a city-wide case study to test whether temperature could explain some of the trends observed in monthly observations of two opiate compounds. Modeling suggests some of the monthly changes were attributed to natural temperature fluctuation rather than to trends in the substances’ consumption, and that uncertainty regarding discharge location can dominate even relative observed differences in opiate detections. In summary, my work has found temperature an important modulator of WBE results, influencing both the type of populations observed and the likelihood of upstream behaviors disproportionally magnified or obscured, particularly for the more labile biomarkers. There exists significant potential for improving the understanding of empirical observations via numerical modeling and the application of spatial analysis tools.
ContributorsHart, Olga (Author) / Halden, Rolf (Thesis advisor) / Mascaro, Giuseppe (Committee member) / Renaut, Rosemary (Committee member) / Nelson, Keith (Committee member) / Arizona State University (Publisher)
Created2019
Description
Plastic pollution has become a global threat to ecosystems worldwide, with microplastics now representing contaminants reported to occur in ambient air, fresh water, seawater, soils, fauna and people. Over time, larger macro-plastics are subject to weathering and fragmentation, resulting in smaller particles, termed ‘microplastics’ (measuring < 5 mm in diameter), which have been found to pollute virtually every marine and terrestrial ecosystem on the planet. This thesis explored the transfer of plastic pollutants from consumer products into the built water environment and ultimately into global aquatic and terrestrial ecosystems.
A literature review demonstrated that municipal sewage sludge produced by wastewater treatment plants around the world contains detectable quantities of microplastics. Application of sewage sludge on land was shown to represent a mechanism for transfer of microplastics from wastewater into terrestrial environments, with some countries reporting as high as 113 ± 57 microplastic particles per gram of dry sludge.
To address the notable shortcoming of inconsistent reporting practices for microplastic pollution, this thesis introduced a novel, online calculator that converts the number of plastic particles into the unambiguous metric of mass, thereby making global studies on microplastic pollution directly comparable.
This thesis concludes with an investigation of a previously unexplored and more personal source of plastic pollution, namely the disposal of single-use contact lenses and an assessment of the magnitude of this emerging source of environmental pollution. Using an online survey aimed at quantifying trends with the disposal of lenses in the US, it was discovered that 20 ± 0.8% of contact lens wearers flushed their used lenses down the drain, amounting to 44,000 ± 1,700 kg y-1 of lens dry mass discharged into US wastewater.
From the results it is concluded that conventional and medical microplastics represent a significant global source of pollution and a long-term threat to ecosystems around the world. Recommendations are provided on how to limit the entry of medical microplastics into the built water environment to limit damage to ecosystems worldwide.
A literature review demonstrated that municipal sewage sludge produced by wastewater treatment plants around the world contains detectable quantities of microplastics. Application of sewage sludge on land was shown to represent a mechanism for transfer of microplastics from wastewater into terrestrial environments, with some countries reporting as high as 113 ± 57 microplastic particles per gram of dry sludge.
To address the notable shortcoming of inconsistent reporting practices for microplastic pollution, this thesis introduced a novel, online calculator that converts the number of plastic particles into the unambiguous metric of mass, thereby making global studies on microplastic pollution directly comparable.
This thesis concludes with an investigation of a previously unexplored and more personal source of plastic pollution, namely the disposal of single-use contact lenses and an assessment of the magnitude of this emerging source of environmental pollution. Using an online survey aimed at quantifying trends with the disposal of lenses in the US, it was discovered that 20 ± 0.8% of contact lens wearers flushed their used lenses down the drain, amounting to 44,000 ± 1,700 kg y-1 of lens dry mass discharged into US wastewater.
From the results it is concluded that conventional and medical microplastics represent a significant global source of pollution and a long-term threat to ecosystems around the world. Recommendations are provided on how to limit the entry of medical microplastics into the built water environment to limit damage to ecosystems worldwide.
ContributorsRolsky, Charles (Author) / Halden, Rolf (Thesis advisor) / Green, Matthew (Committee member) / Neuer, Susanne (Committee member) / Polidoro, Beth (Committee member) / Smith, Andrew (Committee member) / Arizona State University (Publisher)
Created2020
Description
Next-generation sequencing is a powerful tool for detecting genetic variation. How-ever, it is also error-prone, with error rates that are much larger than mutation rates.
This can make mutation detection difficult; and while increasing sequencing depth
can often help, sequence-specific errors and other non-random biases cannot be de-
tected by increased depth. The problem of accurate genotyping is exacerbated when
there is not a reference genome or other auxiliary information available.
I explore several methods for sensitively detecting mutations in non-model or-
ganisms using an example Eucalyptus melliodora individual. I use the structure of
the tree to find bounds on its somatic mutation rate and evaluate several algorithms
for variant calling. I find that conventional methods are suitable if the genome of a
close relative can be adapted to the study organism. However, with structured data,
a likelihood framework that is aware of this structure is more accurate. I use the
techniques developed here to evaluate a reference-free variant calling algorithm.
I also use this data to evaluate a k-mer based base quality score recalibrator
(KBBQ), a tool I developed to recalibrate base quality scores attached to sequencing
data. Base quality scores can help detect errors in sequencing reads, but are often
inaccurate. The most popular method for correcting this issue requires a known
set of variant sites, which is unavailable in most cases. I simulate data and show
that errors in this set of variant sites can cause calibration errors. I then show that
KBBQ accurately recalibrates base quality scores while requiring no reference or other
information and performs as well as other methods.
Finally, I use the Eucalyptus data to investigate the impact of quality score calibra-
tion on the quality of output variant calls and show that improved base quality score
calibration increases the sensitivity and reduces the false positive rate of a variant
calling algorithm.
This can make mutation detection difficult; and while increasing sequencing depth
can often help, sequence-specific errors and other non-random biases cannot be de-
tected by increased depth. The problem of accurate genotyping is exacerbated when
there is not a reference genome or other auxiliary information available.
I explore several methods for sensitively detecting mutations in non-model or-
ganisms using an example Eucalyptus melliodora individual. I use the structure of
the tree to find bounds on its somatic mutation rate and evaluate several algorithms
for variant calling. I find that conventional methods are suitable if the genome of a
close relative can be adapted to the study organism. However, with structured data,
a likelihood framework that is aware of this structure is more accurate. I use the
techniques developed here to evaluate a reference-free variant calling algorithm.
I also use this data to evaluate a k-mer based base quality score recalibrator
(KBBQ), a tool I developed to recalibrate base quality scores attached to sequencing
data. Base quality scores can help detect errors in sequencing reads, but are often
inaccurate. The most popular method for correcting this issue requires a known
set of variant sites, which is unavailable in most cases. I simulate data and show
that errors in this set of variant sites can cause calibration errors. I then show that
KBBQ accurately recalibrates base quality scores while requiring no reference or other
information and performs as well as other methods.
Finally, I use the Eucalyptus data to investigate the impact of quality score calibra-
tion on the quality of output variant calls and show that improved base quality score
calibration increases the sensitivity and reduces the false positive rate of a variant
calling algorithm.
ContributorsOrr, Adam James (Author) / Cartwright, Reed (Thesis advisor) / Wilson, Melissa (Committee member) / Kusumi, Kenro (Committee member) / Taylor, Jesse (Committee member) / Pfeifer, Susanne (Committee member) / Arizona State University (Publisher)
Created2020
Pathways of Distinction Analysis of Liver Cancer Data: Genetic Differences Between Males and Females
Description
The Pathways of Distinction Analysis (PoDA) program calculates relationships between a given group of genes contained within a pathway, and a disease state. It was used here to investigate liver cancer, and to explore how genetic variability may contribute to the different rates of development of the disease in males and females. The goal of the study was to identify germline variation that differs by sex in hepatocellular carcinoma. Using the program, multiple pathways and genes were identified to have significant differences in their relationship to liver cancer in males and females. In animal studies, the genes which were identified using the PoDA analysis have been shown to impact liver cancer, often with different results for males and females. While these genes are often the focus in animal models, they are absent from current Genome Wide Association Studies (GWAS) catalogs for humans. By working to bridge the results of animal studies and human studies, the results help to identify the causes of liver cancer, and more specifically, the reason the disease affects males at much higher rates. The differences in pathways identified to be significant for the two sexes indicate the germline variance may play sex-specific roles in the development of hepatocellular carcinoma. Additionally, these results reinforce the capacity of the PoDA analysis to identify genes that may be missed by more traditional GWAS methods. This study lays the groundwork for further investigations into the identified genes and pathways, and how they behave differently within males and females.
ContributorsOlson, Erik Jon (Author) / Buetow, Kenneth (Thesis advisor) / Wilson, Melissa (Committee member) / Cartwright, Reed (Committee member) / Arizona State University (Publisher)
Created2021