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Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.

Environmental managers need a rapid and cost‐effective monitoring tool for tracking the spread of invasive species, particularly at the onset of introduction. The macroalgae Caulerpa prolifera is considered an invasive species outside its native range, colonizing large patches of seafloor, reducing native species, and altering ecosystem functioning. Here, we developed a droplet digital PCR assay for detection of C. prolifera from environmental DNA seawater samples using the internal transcribed spacer (ITS) region. While the assay itself was confirmed to be highly efficient, we discovered concentrations of C. prolifera eDNA were present below detectable levels in the water column surrounding an outbreak. To understand why, we conducted tank‐based experiments for two California invasive algae species, Caulerpa prolifera and Sargassum horneri. The steady‐state eDNA concentration (eDNA copies/ gram of biomass detected) of C. prolifera was found to be two orders of magnitude lower than S. horneri. A meta‐analysis of steady‐state concentrations reported in the literature showed a remarkable range from ~104–1011 (copies/g), revealing C. prolifera to have the lowest recorded steady‐state concentrations of eDNA of any known species. We attribute C. prolifera's low steady‐state eDNA concentration to its unique biology as a unicellular macroscopic algae which reduces the possible modes of eDNA release compared to similarly sized multicellular organisms. Critically our results demonstrate the potential limits of eDNA approaches, the influence of shedding rates in the reliability of species detections, and the vital importance of benchmarking and validating eDNA assays in both field and laboratory settings. The invasive Caulerpa prolifera's presence was unable to be detected in field surveys using a custom droplet digital PCR environmental DNA assay. Lab‐based experiments show that this is due to its low steady‐state eDNA concentration, attributable to its unique biology as a unicellular macroscopic algae.

Higher education institutions have long played a key role in solving society's most pressing problems. However, as the scale and complexity of socio‐environmental problems has grown, there has been a renewed debate about the role that academic institutions should play in developing solutions and how institutional structures should be redesigned to encourage greater interdisciplinarity. In the following pages, we present a graduate student perspective on this debate. Specifically, we identify challenges facing interdisciplinary graduate student researchers and present a series of recommendations for how institutions can better prepare them to become the next generation of leaders in interdisciplinary, action‐oriented research focused on solving socio‐environmental problems. Higher education institutions have long played a key role in solving society's most pressing problems. However, as the scale and complexity of socio‐environmental problems has grown, there has been a renewed debate about the role that academic institutions should play in developing solutions and how institutional structures should be redesigned to encourage greater interdisciplinarity. In the following pages, we present a series of recommendations for how institutions can better prepare them to become the next generation of leaders in interdisciplinary, action‐oriented research focused on solving socio‐environmental problems.

Environmental DNA metabarcoding (eDNA) is an evolving methodology of biodiversity monitoring. By leveraging shed and excreted DNA from organisms in a marine environment, researchers can perform DNA amplification and sequencing to identify what species were present at a site without the need for visual identification. This thesis uses eDNA to evaluate conservation efforts in Southern California as well as further establish and refine eDNA as a survey tool. In Chapter 1, I evaluate seagrass beds in three distinct geographic settings in Southern California. We demonstrate that nearly half of community composition is associated with whether seagrass was found off the mainland, off an island, or in an embayment. In addition, when compared to traditional monitoring, eDNA was able to identify roughly ~50% to 400% greater number of fish species at each site. In Chapter 2, I create a novel eDNA droplet digital PCR assay for the detection of the invasive species Caulerpa prolifera that was found in Newport Bay in 2021 and found it to have the lowest eDNA steady state of any previously tested species. We demonstrate the critical importance of benchmarking eDNA assays before their use by managers and highlight some limitations for using eDNA in species detection. In Chapter 3, we perform two years of monthly sampling of MPAs using community scientists and UCLA researchers. We find that MPAs are distinct from nonMPAs in multivariate space for both fish and metazoan communities and that metazoan communities in MPAs are more diverse and stable compared to nonMPAs. We also show the scalability that eDNA has in biodiversity monitoring through the incorporation of volunteers into field sampling. Together, these chapters better our understanding of marine conservation in Southern California and further demonstrate the utility and limitations of eDNA metabarcoding for monitoring marine biodiversity.

Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.

The macroalgae Caulerpa prolifera is considered an invasive species in many environments and can colonize large patches of seafloor, reduce native species, and alter ecosystem functioning. Environmental managers need a rapid and cost-effective monitoring tool for tracking the spread of this invasive species. We developed a digital PCR assay for detection of C. prolifera from environmental DNA seawater samples. We demonstrate, in both field and laboratory experiments, that the invasive algae C. prolifera is undetectable in practical applications of eDNA due to its minimal shedding. To test why, we conducted tank-based shedding experiments for two California invasive algae species, C. prolifera and Sargassum horneri. Copy numbers of C. prolifera eDNA detected in the experimental tanks were found to be two orders of magnitude lower than S. horneri. A meta-analysis of steady state eDNA produced by aquatic organisms reported in the literature show C. prolifera to have the lowest recorded steady state concentrations of eDNA in the water column. We attribute C. prolifera low eDNA shedding to its unique biology as a unicellular, multinucleate, macroscopic siphonous algae which reduces the possible modes of eDNA release compared to multicellular organisms. Our results highlight the value of benchmarking and validating eDNA surveys in both field and laboratory settings and potential limits of eDNA approaches for some applications. These results also emphasize the importance of organismal physiology in eDNA shedding rates, variations in mechanisms of eDNA shedding between organisms, and characterizing shedding rates for accurate interpretation of eDNA results.

Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these changes are affecting biodiversity over time. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.

Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning–derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.

Patient-reported outcomes (PROs) in randomized controlled trials pertaining to inflammatory bowel disease are important in identifying patients’ perspective of treatment. Incompletely reported PROs within trials could misrepresent information for clinicians and may contribute to treatment which lacks accommodation of patient input. Our study evaluates completeness of reporting of PROs and risk of bias (RoB) to identify how well trialists are adhering to known resources for trials. We used MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials to identify eligible trials from 2006 to 2020 with at least 1 PRO measure related to inflammatory bowel disease. The trials were screened in duplicate using Rayyan. We then compared trial completion of reporting to the Consolidated Standards of Reporting Trials (CONSORT)-PRO adaptation, and assessed RoB using the Cochrane Collaboration RoB 2.0 tool. To measure trial and reporting characteristics, we performed bivariate regression analyses. Among a sample of 29 trials, the mean completion percentage for CONSORT-PRO was 46.77%. We found PROs as a secondary outcome had significantly lower CONSORT-PRO reporting (p<0.05). In addition, per cent completeness of reporting was significantly higher with both a ‘therapy’ intervention, and trials published following the development of CONSORT-PRO (p<0.05). Incomplete PRO reporting is common in trials focused on inflammatory bowel disease. This suboptimal reporting indicates the need for adherence to reporting guidelines. Trialists should use the CONSORT-PRO checklist, as endorsed by Patient-Reported Outcomes Tools: Engaging Users and Stakeholders, to assess their studies in order to enhance reporting adherence.