BIOTAS: BIOTelemetry Analysis Software, for the semi-automated removal of false positives from radio telemetry data

Introduction Radio telemetry, one of the most widely used techniques for tracking wildlife and fisheries populations, has a false-positive problem. Bias from false-positive detections can affect many important derived metrics, such as home range estimation, site occupation, survival, and migration timing. False-positive removal processes have relied upon simple filters and personal opinion. To overcome these shortcomings, we have developed BIOTAS (BIOTelemetry Analysis Software) to assist with false-positive identification, removal, and data management for large-scale radio telemetry projects. Methods BIOTAS uses a naïve Bayes classifier to identify and remove false-positive detections from radio telemetry data. The semi-supervised classifier uses spurious detections from unknown tags and study tags as training data. We tested BIOTAS on four scenarios: wide-band receiver with a single Yagi antenna, wide-band receiver that switched between two Yagi antennas, wide-band receiver with a single dipole antenna, and single-band receiver that switched between five frequencies. BIOTAS has a built in a k-fold cross-validation and assesses model quality with sensitivity, specificity, positive and negative predictive value, false-positive rate, and precision-recall area under the curve. BIOTAS also assesses concordance with a traditional consecutive detection filter using Cohen’s $$\kappa$$ κ . Results Overall BIOTAS performed equally well in all scenarios and was able to discriminate between known false-positive detections and valid study tag detections with low false-positive rates (< 0.001) as determined through cross-validation, even as receivers switched between antennas and frequencies. BIOTAS classified between 94 and 99% of study tag detections as valid. Conclusion As part of a robust data management plan, BIOTAS is able to discriminate between detections from study tags and known false positives. BIOTAS works with multiple manufacturers and accounts for receivers that switch between antennas and frequencies. BIOTAS provides the framework for transparent, objective, and repeatable telemetry projects for wildlife conservation surveys, and increases the efficiency of data processing.

Seizures Caused by Exposure to Hyperbaric Oxygen in Rats Can Be Predicted by Early Changes in Electrodermal Activity

Hyperbaric oxygen (HBO2) is breathed during undersea operations and in hyperbaric medicine. However, breathing HBO2 by divers and patients increases the risk of central nervous system oxygen toxicity (CNS-OT), which ultimately manifests as sympathetic stimulation producing tachycardia and hypertension, hyperventilation, and ultimately generalized seizures and cardiogenic pulmonary edema. In this study, we have tested the hypothesis that changes in electrodermal activity (EDA), a measure of sympathetic nervous system activation, precedes seizures in rats breathing 5 atmospheres absolute (ATA) HBO2. Radio telemetry and a rodent tether apparatus were adapted for use inside a sealed hyperbaric chamber. The tethered rat was free to move inside a ventilated animal chamber that was flushed with air or 100% O2. The animal chamber and hyperbaric chamber (air) were pressurized in parallel at ~1 atmosphere/min. EDA activity was recorded simultaneously with cortical electroencephalogram (EEG) activity, core body temperature, and ambient pressure. We have captured the dynamics of EDA using time-varying spectral analysis of raw EDA (TVSymp), previously developed as a tool for sympathetic tone assessment in humans, adjusted to detect the dynamic changes of EDA in rats that occur prior to onset of CNS-OT seizures. The results show that a significant increase in the amplitude of TVSymp values derived from EDA recordings occurs on average (±SD) 1.9 ± 1.6 min before HBO2-induced seizures. These results, if corroborated in humans, support the use of changes in TVSymp activity as an early “physio-marker” of impending and potentially fatal seizures in divers and patients.

Reduced diurnal activity and increased stopover duration by molting Swainson’s Thrushes

Migration consists of a sequence of small- to large-scale flights often separated by stopovers for refueling. Tradeoffs between minimizing migration time (more flights, shorter stopovers) and maximizing energy gain (fewer flights, longer stopovers) will affect overall migration timing. For example, some individuals make long-term stopovers in high-quality habitat that maximize energy gain (e.g., molt-migration), but movement to those habitats likely costs time. We used radio telemetry and blood plasma metabolite levels to examine physiological and behavioral tradeoffs between molt-migrant (birds molting at the molt stopover; n = 59) and post-molt (birds that presumably completed their molt elsewhere; n = 19) migrant Swainson’s Thrushes (Catharus ustulatus) near Montreal, Canada. Molt-migration was a large time investment as the average stopover duration for molt-migrants was of 47 ± 9 days (~13% of the entire annual cycle), almost twice as long as previously assumed from banding records, and far longer than stopovers of post-molting individuals (7 ± 2 days). Daily mortality rate during the molt stopover was similar to the average annual daily mortality rate. Molt-migrants’ circadian rhythms closely matched light levels, whereas post-molting birds had irregular rhythms and averaged 1 hr greater activity per day than molt-migrants. Despite being less active, molt-migrants had similar refueling rates based on metabolite profiles. As compared with migrants that completed molt earlier, molt-migrants at this stopover site had slower subsequent migration rates. Thus, birds using long-term stopovers appeared to tradeoff energy (efficient refueling) for time (slower subsequent migration).

Winter Roosting by Eastern Red Bats in Ozark Mountain Forests of Missouri

The eastern red bat (Lasiurus borealis Müller, 1776) is a widespread species that roosts in evergreen or dead foliage suspended in trees during winter but retreats to leaf litter during colder periods. Roosting in leaf litter by eastern red bats makes them vulnerable to prescribed fires in winter. Using radio telemetry, we tracked 33 male eastern red bats to 101 winter (November–February) roosts and quantified roost locations, habitat surrounding roosts, and landscape attributes of roost locations. When roosting in trees, bats preferred oaks but generally avoided other tree species; they used pines in proportion to their availability. During colder periods, bats retreated to roosts in leaf litter where 21% suffered mortality either from predation/scavenging or unknown causes while roosting on the ground. Models of roost selection indicated that southerly aspect was the most important factor determining roost selection, and both tree- and leaf-litter roosts were predominately (≥94%) on upper south-facing slopes. Prescribed burning in late morning/early afternoon on clear days when temperatures under leaf litter are warmest in winter could reduce potential mortality by allowing faster arousal time for hibernating bats.

The Spatial Ecology of the Timber Rattlesnake (Crotalus horridus) in southeastern Louisiana

The Timber Rattlesnake (Crotalus horridus) has a large distribution spanning much of the eastern United States. Because temperature, habitat type, prey composition and abundance, and a variety of other factors may dictate reptile behavior, populations of conspecific species may exhibit behavioral differences across latitudinal and elevational gradients. Using radio telemetry, we tracked 10 adult Timber Rattlesnakes (7 males, 3 females) from May 2016 to June 2017 in southeastern Louisiana to examine the spatial ecology of male and non-gravid female snakes. Mean annual and seasonal home ranges of non-gravid female Timber Rattlesnakes were not statistically different from that of males. Mean seasonal home range sizes and average distances travelled of both sexes was smallest in winter, and had a general increasing trend beginning in spring with a peak in fall. These increases seemed to coincide with the breeding season, taking place from early July until the end of November. Comparison of this study with other studies throughout its distribution could have implications towards future management of conservation for other southern populations of Timber Rattlesnakes.

Verification of the Detection Performance of Drone Radio Telemetry for Tracking the Movement of Frogs

Elucidating the various behavioral and ecological uses of animal habitats is the basis for the conservation and management of animal species. Therefore, tracking the movement of animals is necessary. Biotelemetry is used for tracking the movement of animals. By mounting a radio telemetry receiver and antenna on a drone, the time and labor required for surveying animals can be reduced. In addition, it is easy to track difficult-to-reach areas such as rice paddies and forests, and the environment is not invaded by the survey. We think that this drone radio telemetry will be the best method for tracking the movement of small amphibians, such as frogs. However, in order to put the method to practical use, the accuracy of the system needs to be verified. Approximately 26 ha of area in Sogabe, Kameoka City, Kyoto Prefecture, Japan was investigated in this study. We selected and validated the location where frogs are likely to enter farmlands. The location where the detection of movement is expected to be stable are 5 cm deep areas in the soil, gaps in masonry, and under plastic bags, whereas areas in which the detection is likely to be unstable are areas deeper than 5 cm in the soil, covered concrete channels, and grass. By calculating the geographic center, the location of the nanotag could be estimated with an accuracy of less than 16 m. We successfully showed that the drone radio telemetry system used in this study is capable of detecting and tracking the movement of animals with high spatial and temporal resolutions. However, we suggest that the detection of movement may be interrupted depending on the location of the target animal and more than three detections are needed to guarantee the accuracy of the estimation.

Kereru in Urbanised Landscapes

<p>Urban areas are quickly supplanting other land covers on a global scale as a direct result of a rapid human population growth and associated anthropogenic disturbances. Although the concept of a city as an ecosystem is now widely accepted, relatively little is still known about how wildlife responds to urbanised landscapes. In addition, the factors affecting habitat selection of highly mobile avian species within urbanised landscapes have seldom been quantified at multiple spatial scales. Understanding the human social aspects of urban ecology is also vital to wildlife conservation because as the majority of the world’s population continues to shift into cities, they are becoming increasingly “disconnected” from nature. However, people can contribute both directly through involvement in wildlife research, and indirectly through knowledge acquisition and environmental awareness. The kereru (New Zealand pigeon, Hemiphaga novaseelandiae) is a large, highly mobile, fruit-eating pigeon endemic to New Zealand. Although once in nationwide decline, kereru appear to have slowly increased in numbers across New Zealand, most notably in urbanised landscapes. Kereru recovery may be due to the control of mammalian predators and competitors, as well as a reflection of the kereru’s ability to adapt to and exploit novel suburban habitat. However, little is known about how kereru select amongst urbanised habitat, the impacts of injuries sustained within this habitat on post-rehabilitation success or how researchers can integrate urban residents into the conservation of kereru. This thesis aims to (1) advance current knowledge of kereru ecology within urbanised landscapes and to explore the concept of kereru as an “urban adapted” species, and (2) to examine the role of people in urban avian ecology, from the perspectives of both the researcher and the public. I applied a multi-scale approach to examine habitat selection by kereru at regional (first-order), winter range (second-order), and site (third-order) levels, using a citizen-generated dataset and by monitoring a marked and radio-tagged population in Wellington City. At the first-order of selection, citizens’ sightings of kereru revealed that birds selected areas with intermediate levels of building and road coverage when possum (Trichosurus vulpecula) control measures were undertaken. Radio-telemetry of kereru revealed that habitat selection within Wellington’s residential ecosystems occurred at the third- but not second-order of selection. Sites within winter ranges were selected based upon the presence of a native food source, conspecifics and possum control. My results suggest that possum control may be creating a buffered “safe zone” for kereru within suburban areas whereby predation risk is lowered, or more likely, competition for native food sources is reduced. While it is encouraging to see increasing numbers of kereru in urbanised areas, this environment is often the cause of injuries not normally sustained in the wildlands. I monitored kereru during the early post-release period following rehabilitation in two variably urbanised landscapes. Results of my modelling suggested that the sex of the bird, release site, severity of the injury sustained, and the time of year a bird was released were important determinants of early rehabilitation success. This thesis ends with a study that integrated local school children into my field research as part of a conservation education program. Using kereru as a focal species, I tested whether incorporating biological researchers into the classroom and hands-on experiences with radio-telemetry of wild birds in local green space increased wildlife knowledge, environmental awareness and intentions to act amongst children. No significant increases in wildlife knowledge were found in either treatment group, however those children who participated in exercises with researchers in local green space demonstrated, and retained, higher levels of nature awareness than groups who participated in the schoolyard. In summary, applying multiple methods and considering both the biological and social aspects of urban avian ecology have allowed me to gain a more holistic picture of the kereru's ability to adapt to urbanised landscapes and how people living in cities can contribute towards the conservation of kereru.</p>

Kereru in Urbanised Landscapes

<p>Urban areas are quickly supplanting other land covers on a global scale as a direct result of a rapid human population growth and associated anthropogenic disturbances. Although the concept of a city as an ecosystem is now widely accepted, relatively little is still known about how wildlife responds to urbanised landscapes. In addition, the factors affecting habitat selection of highly mobile avian species within urbanised landscapes have seldom been quantified at multiple spatial scales. Understanding the human social aspects of urban ecology is also vital to wildlife conservation because as the majority of the world’s population continues to shift into cities, they are becoming increasingly “disconnected” from nature. However, people can contribute both directly through involvement in wildlife research, and indirectly through knowledge acquisition and environmental awareness. The kereru (New Zealand pigeon, Hemiphaga novaseelandiae) is a large, highly mobile, fruit-eating pigeon endemic to New Zealand. Although once in nationwide decline, kereru appear to have slowly increased in numbers across New Zealand, most notably in urbanised landscapes. Kereru recovery may be due to the control of mammalian predators and competitors, as well as a reflection of the kereru’s ability to adapt to and exploit novel suburban habitat. However, little is known about how kereru select amongst urbanised habitat, the impacts of injuries sustained within this habitat on post-rehabilitation success or how researchers can integrate urban residents into the conservation of kereru. This thesis aims to (1) advance current knowledge of kereru ecology within urbanised landscapes and to explore the concept of kereru as an “urban adapted” species, and (2) to examine the role of people in urban avian ecology, from the perspectives of both the researcher and the public. I applied a multi-scale approach to examine habitat selection by kereru at regional (first-order), winter range (second-order), and site (third-order) levels, using a citizen-generated dataset and by monitoring a marked and radio-tagged population in Wellington City. At the first-order of selection, citizens’ sightings of kereru revealed that birds selected areas with intermediate levels of building and road coverage when possum (Trichosurus vulpecula) control measures were undertaken. Radio-telemetry of kereru revealed that habitat selection within Wellington’s residential ecosystems occurred at the third- but not second-order of selection. Sites within winter ranges were selected based upon the presence of a native food source, conspecifics and possum control. My results suggest that possum control may be creating a buffered “safe zone” for kereru within suburban areas whereby predation risk is lowered, or more likely, competition for native food sources is reduced. While it is encouraging to see increasing numbers of kereru in urbanised areas, this environment is often the cause of injuries not normally sustained in the wildlands. I monitored kereru during the early post-release period following rehabilitation in two variably urbanised landscapes. Results of my modelling suggested that the sex of the bird, release site, severity of the injury sustained, and the time of year a bird was released were important determinants of early rehabilitation success. This thesis ends with a study that integrated local school children into my field research as part of a conservation education program. Using kereru as a focal species, I tested whether incorporating biological researchers into the classroom and hands-on experiences with radio-telemetry of wild birds in local green space increased wildlife knowledge, environmental awareness and intentions to act amongst children. No significant increases in wildlife knowledge were found in either treatment group, however those children who participated in exercises with researchers in local green space demonstrated, and retained, higher levels of nature awareness than groups who participated in the schoolyard. In summary, applying multiple methods and considering both the biological and social aspects of urban avian ecology have allowed me to gain a more holistic picture of the kereru's ability to adapt to urbanised landscapes and how people living in cities can contribute towards the conservation of kereru.</p>

Female Scarcity and Natal Dispersal Differences Between Sexes Among Bellbirds (Anthornis melanura)

<p>Sex ratio imbalances in wild bird populations have been a challenge for wildlife managers for decades. Differences between sexes during natal dispersal has long been thought to promote sex ratio imbalances. Natal dispersal distances may differ between sexes because of competition for food and space, or intrasexual competition and aggression. I investigated natal dispersal and intrasexual competition as mechanisms for a sex ratio imbalance in a small, translocated population of a New Zealand honeyeater, the bellbird (Anthornis melanura) in the Karori Wildlife Sanctuary- Zealandia, Wellington, New Zealand. I analysed long term records of population size and structure to document annual variation in sex ratios since the reintroduction of bellbirds to Zealandia. Radio telemetry was used to track the 2008/2009 cohort of bellbirds for five months after fledging to observe movements and distances travelled from their hatching location. Observations at a supplemental food source that was used by both adults and fledglings, were used to study intrasexual competition and aggression. Dispersal distances did not differ between the sexes for any of the measurement types used. Males did however significantly dominate the use of a supplemental food source and were significantly more aggressive around this food source, which is most likely responsible for the lower feeding rate among females. Therefore, I conclude that the sex ratio imbalance in the bellbird population in Zealandia may not result from a difference in natal dispersal, but from males dominating a supplemental food source, raising their population and fitness over that of females.</p>