Nightjars are a group of nocturnal and aerial insectivorous birds that have experienced long-term decline likely driven primarily by habitat loss and declines in prey populations. Eastern Whip-poor-will (Antrostomus vociferus) and Chuck-will’s-widow (Antrostomus carolinensis), two nightjar species native to Illinois, declined 69% and 58% since 1966, respectively. Although previous survey efforts have documented presence of Chuck-will’s-widow and Whip-poor-will, their current distribution in the state is not well known. Using Autonomous Recording Units (ARUs) deployed in a uniform, systematic grid, I surveyed 142 locations from May – July 2022 on public and private lands across the southern eleven counties of Illinois to assess Whip-poor-will and Chuck-will’s-widow distribution and estimate species occupancy. I estimated species relationships with proportion of landcover types, forest patch configuration, and proximity to other landcover types. Additionally, I quantified disturbances from the past 15 years to estimate species relationships to the severity and duration of disturbances. I deployed ARUs for 710 survey days collecting 170,400 minutes or 3,000 hours of recordings. Acoustic bird call identification software, BirdNet, was highly accurate at detecting focal species and greatly reduced the time spent manually reviewing acoustic data. BirdNet identified 43,922 calls of Whip-poor-will and 31,447 calls of Chuck-will’s-widow. I detected Whip-poor-will on 78 surveys with 100% accuracy and Chuck-will’s-widow on 75 surveys with 76% accuracy. Whip-poor-will were positively associated with forest patches with large core areas that neighbored pastures. Additionally, Whip-poor-will were likely to occupy landscapes that had experienced low to moderate disturbance within the previous 15 years. Covariates used to model Chuck-will’s-widow occupancy explained little variation in detection or occupancy and there were no significant relationships with any covariate. However, examining non-significant trends suggest similar relationships as Whip-poor-will in the area. Results highlight the efficiency of passive acoustic monitoring for these birds and the need for further investigation into Chuck-will’s-widow species-environmental relationships. In southern Illinois, Chuck-will’s-widow populations appears to be consistent with previous estimates from the 1990s while Whip-poor-will follow the broader trend of decline.

This research investigated several aspects of passive acoustic monitoring (PAM) which were previously unexplored or understudied. A comparison of autonomous recording units (ARUs) for use with BirdNET for the purpose of bird monitoring was conducted. Four ARUs were compared, including AudioMoth, SM4, SMMicro, and SwiftOne. We found that, of the performance metrics for which ARU choice made a statistically significant difference (P>0.01), which included sensitivity, specificity, F1 harmonic mean, and Matthews Correlation Coefficient, (but not precision: P = 0.94), AudioMoth had the best performance for all statistically significant performance metrics except for specificity, for which SMMicro had the highest. The same audio was then processed using 18 combinations of Overlap and Sensitivity, including default settings. We found that Overlap and Sensitivity values were highly significant (P>0.001) for all performance metrics: precision, sensitivity, specificity, F1 harmonic mean, and Matthews Correlation Coefficient. No individual Overlap-Sensitivity setting combination performed outperformed others in most of the performance metrics; however, in general, as Overlap or Sensitivity increased, the number of true and false positive species reports increased while the number of false negatives decreased. Four confidence-based threshold types were then used to filter BirdNET output to compare threshold performances, comparing two arbitrary thresholds and two species-specific thresholds which were calculated using manual validation data. Of the thresholds tested, one of the arbitrary threshold types and one of the species-specific threshold types achieved a precision ≥ 0.95. We hope this research will help guide PAM decisions regarding ARU choice, BirdNET settings, and threshold type choice.

Coral reefs around the world are threatened by a variety of sources, from localized impacts, including overfishing and coastal development, to global temperature increases and ocean acidification. Conserving these marine biodiversity havens requires both global and local action informed by scientific research. In this thesis, I use data collected from the coral reefs around Kiritimati atoll (Republic of Kiribati) in the central equatorial Pacific, first to assess the applicability of two common metrics used in passive underwater acoustic research, and second to examine the effects of a marine heatwave and local human disturbance on an assemblage of corallivorous fish. Using acoustic data recorded in 2017 and 2018 on reefs around Kiritimati, I assess how sound pressure level (SPL) and the acoustic complexity index (ACI) respond to changes in fish sounds in a low frequency band (160 Hz – 1 kHz) and snapping shrimp snaps in a high frequency band (1 kHz – 22 kHz). I found that while SPL was positively correlated with increases in fish sounds and snap density, changes in ACI were dependent upon the settings chosen for its calculation, with the density of snaps negatively correlated with ACI across all settings. These findings provide evidence that despite its quick and prolific adoption, acoustic metrics like ACI should be thoroughly field-tested and standardized before they are applied to new ecosystems like coral reefs. Next, using underwater visual censuses (UVCs) of reef fish assemblages, I quantified how two functional groups of corallivores, obligate and facultative, responded to a mass coral mortality event created by the 2015-2016 El Niño. Declines in abundance of both groups were largely driven by the response of coral-associated damselfishes, Plectroglyphidodon johnstonianus in the obligate group and Plectroglyphidodon dickii in the facultative group, to heat stress and subsequent coral mortality. I also observed a significant decline in the species richness of obligate corallivores, and a continued decline in the abundance of obligate corallivores three years after the mass coral mortality event. Additionally, facultative corallivore abundance increased with disturbance, although the effect was modulated by year, likely due to their more adaptable diets. Corallivore assemblage structure was also influenced by the heat stress event, recovery, and local human disturbance. These results detail how an entire corallivorous assemblage is impacted by a coral mortality event and incidentally provide a timeline for corallivore decline. Together, these results provide information about new ways of monitoring coral reefs, and the ways in which two components of the reef fish community, obligate and facultative corallivores, respond to a mass coral mortality event. / Graduate / 2022-01-15