Long-term habitat changes in a protected area: Implications for herpetofauna habitat management and restoration

Point Pelee National Park, located at the southern-most tip of Canada's mainland, historically supported a large number of herpetofauna species; however, despite nearly a century of protection, six snake and five amphibian species have disappeared, and remaining species-At-risk populations are thought to be in decline. We hypothesized that long-Term changes in availability and distribution of critical habitat types may have contributed to the disappearance of herpetofauna. To track habitat changes we used aerial image data spanning 85 years (1931±2015) and manually digitized and classified image data using a standardized framework. Change-detection analyses were used to evaluate the relative importance of proportionate loss and fragmentation of 17 habitat types. Marsh habitat diversity and aquatic connectivity has declined since 1931. The marsh matrix transitioned from a graminoid and forb shallow marsh interspersed with water to a cattail dominated marsh, altering critical breeding, foraging, and overwintering habitat. Reduced diversity of marsh habitats appears to be linked to the expansion of invasive Phragmites australis, which invaded prior to 2000. Loss of open habitats such as savanna and meadow has reduced availability of high quality thermoregulation habitat for reptiles. Restoration of the northwestern region and tip of Point Pelee National Park to a mixed landscape of shallow wetlands (cattail, graminoid, forb, open water) and eradication of dense Phragmites stands should improve habitat diversity. Our results suggest that long-Term landscape changes resulting from habitat succession and invasive species can negatively affect habitat suitability for herpetofauna and protection of land alone does not necessarily equate to protection of sensitive herpetofauna

Thermal characteristics of overwintering habitats for the Blanding’s Turtle (Emydoidea blandingii) across three study areas in Ontario, Canada

Habitat restoration is a necessary strategy to protect populations of Blanding’s Turtles (Emydoidea blandingii) living in settled areas. Relatively little is known about thermal tolerances and requirements of this species in situ during the overwintering period, except that these turtles must find water bodies that do not freeze completely and that are sufficiently cool to allow them to stay dormant throughout the winter. We used water temperature data associated with Blanding’s Turtle populations in a northern, central, and southern study area within Ontario, Canada to determine thermal characteristics of occupied overwintering habitats. From fall through spring from 2012 to 2014, we measured water temperature of 20 potential overwintering habitats within the three study areas. We also radio tracked 48 adult turtles to determine which habitats they occupied during winter. Water temperatures of all occupied habitats ranged from 0.44° C to 3.68° C, with a mean of 1.77° C (± 0.03° C), and showed slow steady declines throughout the overwintering period. Regardless of location, average water temperatures at all confirmed overwintering habitats remained above the freezing point of turtle body fluids (-0.6° C). Average water temperature at five of the six confirmed overwintering habitats never dropped below 0° C, but dropped to -0.33° C for eight days at the sixth overwintering habitat. Determining thermal parameters of overwintering sites can provide knowledge useful for habitat restoration and creation to ensure habitats provide suitable overwintering conditions in the face of global climate change

Effects of European common reed on Blanding's turtle spatial ecology

European common reed (Phragmites australis; common reed) is an aggressive invader of North American wetlands that forms homogenous patches and replaces native flora. Dense patches of common reed generally provide poor habitat for many species, although specific effects on at-risk turtles are largely unknown. We created 3 predictive scenarios to relate the amount of common reed in the landscape to amount of effective habitat for Blanding's turtles (Emydoidea blandingii) and investigated the spatial ecology of 46 adult Blanding's turtles using Euclidean distance analysis within 2 wetland complexes in southern Ontario, Canada. At the home-range scale, we identified a positive association between turtle home ranges and common reed. At the individual scale, turtle radio-locations were significantly farther from common reed patches than from random points, consistent with the hypothesis that they avoided common reed patches locally. When we analyzed habitat selection by sex, results were similar to population-level results except for nesting females. During nesting migrations, females did not avoid common reed patches at the individual scale but instead interacted with common reed, potentially placing themselves at risk of being stranded within dense patches. Our results are consistent with our dynamic home range plus saturation hypothesis that invasion of common reed reduces the amount of effective habitat for at-risk turtles in wetlands because Blanding's turtles significantly avoided common reed patches at individual scales. Management of common reed is an important step to restore habitat for Blanding's turtles and future research is needed to determine best restoration practices. © 2018 The Wildlife Society

Mutual information rate and bounds for it

The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two data sets (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators

UNMANNED AERIAL VEHICLES PRODUCE HIGH-RESOLUTION, SEASONALLY-RELEVANT IMAGERY FOR CLASSIFYING WETLAND VEGETATION

With recent advances in technology, personal aerial imagery acquired with unmanned aerial vehicles (UAVs) has transformed the way ecologists can map seasonal changes in wetland habitat. Here, we use a multi-rotor (consumer quad-copter, the DJI Phantom 2 Vision+) UAV to acquire a high-resolution (< 8 cm) composite photo of a coastal wetland in summer 2014. Using validation data collected in the field, we determine if a UAV image and SWOOP (Southwestern Ontario Orthoimagery Project) image (collected in spring 2010) differ in their classification of type of dominant vegetation type and percent cover of three plant classes: submerged aquatic vegetation, floating aquatic vegetation, and emergent vegetation. The UAV imagery was more accurate than available SWOOP imagery for mapping percent cover of submergent and floating vegetation categories, but both were able to accurately determine the dominant vegetation type and percent cover of emergent vegetation. Our results underscore the value and potential for affordable UAVs (complete quad-copter system < $3,000 CAD) to revolutionize the way ecologists obtain imagery and conduct field research. In Canada, new UAV regulations make this an easy and affordable way to obtain multiple high-resolution images of small (< 1.0 km2) wetlands, or portions of larger wetlands throughout a year

Use of fixed-wing and multi-rotor unmanned aerial vehicles to map dynamic changes in a freshwater marsh1

We used a multi-rotor (Phantom 2 Vision+, DJI) and a fixed-wing (eBee, senseFly) unmanned aerial vehicle (UAV) to acquire high-spatial-resolution composite photos of an impounded freshwater marsh during late summer in 2014 and 2015. Dominant type and percent cover of three vegetation classes (submerged aquatic, floating or emergent vegetation) were identified and compared against field data collected in 176 (2 m × 2 m) quadrats during summer 2014. We also compared these data against the most recently available digital aerial true colour, high-resolution photographs provided by the government of Ontario (South-western Ontario Orthophotography Project (SWOOP), May 2010), which are free to researchers but taken every 5 years in leaf-off spring conditions. The eBee system produced the most effective data for determining percent cover of floating and emergent vegetation (58% and 64% overall accuracy, respectively). Both the eBee and the Phantom were comparable in their ability to determine dominant habitat types (moderate kappa agreement) and were superior to SWOOP in this respect (poor kappa agreement). UAVs can provide a time-sensitive, flexible, and affordable option to capture dynamic seasonal changes in wetlands, information that ecologists often require to study how species at risk use their habitat

Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study

BACKGROUND: Quantitative molecular methods (QMMs) such as quantitative real-time polymerase chain reaction (q-PCR), reverse-transcriptase PCR (qRT-PCR) and quantitative nucleic acid sequence-based amplification (QT-NASBA) are increasingly used to estimate pathogen density in a variety of clinical and epidemiological contexts. These methods are often classified as semi-quantitative, yet estimates of reliability or sensitivity are seldom reported. Here, a statistical framework is developed for assessing the reliability (uncertainty) of pathogen densities estimated using QMMs and the associated diagnostic sensitivity. The method is illustrated with quantification of Plasmodium falciparum gametocytaemia by QT-NASBA. RESULTS: The reliability of pathogen (e.g. gametocyte) densities, and the accompanying diagnostic sensitivity, estimated by two contrasting statistical calibration techniques, are compared; a traditional method and a mixed model Bayesian approach. The latter accounts for statistical dependence of QMM assays run under identical laboratory protocols and permits structural modelling of experimental measurements, allowing precision to vary with pathogen density. Traditional calibration cannot account for inter-assay variability arising from imperfect QMMs and generates estimates of pathogen density that have poor reliability, are variable among assays and inaccurately reflect diagnostic sensitivity. The Bayesian mixed model approach assimilates information from replica QMM assays, improving reliability and inter-assay homogeneity, providing an accurate appraisal of quantitative and diagnostic performance. CONCLUSIONS: Bayesian mixed model statistical calibration supersedes traditional techniques in the context of QMM-derived estimates of pathogen density, offering the potential to improve substantially the depth and quality of clinical and epidemiological inference for a wide variety of pathogens

Factors Affecting Coastal Wetland Occupancy for Eastern Musk Turtles (Sternotherus odoratus) in Georgian Bay, Lake Huron

In many jurisdictions, rare species and their habitats can receive protection if species are assessed as being at risk of declining. The assessment process requires data on habitat occupancy as well as identification of threats to a species critical habitat, both of which are difficult to obtain when the species occurs across large spatial scales. Such is the case for Eastern Musk Turtles (Sternotherus odoratus), which are obligate coastal wetland species in the Laurentian Great Lakes. We use data collected between 2003 and 2015 to map occupancy and conditional occupancy for musk turtles in coastal wetlands of eastern Georgian Bay (Lake Huron) to identify threats to resident wetland habitat. Data collected from a synoptic survey of 58 coastal wetlands were used to create occupancy models, estimate detection probability, and to conduct a sensitivity analysis to determine model robustness. We had a 64-71% probability of detecting musk turtles, whenever present in the wetland, and an area under curve value of 0.82 confirmed high model accuracy. Coastal wetlands that supported musk turtles were associated with higher proportions of forest cover, lower densities of roads, buildings, and docks within 1 km of the wetland, and more-variable bathymetric slopes. High conditional occupancy across the majority of our study area indicates that, at present, habitat in eastern Georgian Bay is in good condition; however, land-use alterations and development should be limited to ensure the persistence of this population of musk turtles

Decades of Road Mortality Cause Severe Decline in a Common Snapping Turtle (Chelydra serpentina) Population from an Urbanized Wetland

Road networks threaten biodiversity and particularly herpetofauna, including common snapping turtles (Chelydra serpentina), which have an especially slow life history that prevents rapid recovery of populations subjected to road mortality. Cootes Drive is a 2.5-km 4-lane highway that bisects wetland habitat used for nesting and overwintering by snapping turtles. We hypothesized that turtle mortality from collisions with vehicles on Cootes Drive has caused a male bias and a decline in the population as turtles attempt to access habitat on both sides of the road. Capture-mark-recapture studies confirmed a dramatic decline in the turtle population from 941 individuals in 1985 to 177 individuals in 2002, a loss of 764 individuals in only 17 yrs. Using the same data, we also determined that the population has been significantly male-biased since 1985. Using 2009-2016 road mortality data obtained from the Dundas Turtle Watch (a citizen-science program), we completed a population viability analysis using the 2002 population size estimate to isolate the impact of road mortality. We found that this population is at risk of extirpation due to road mortality. The population range overlapped with the Cootes Drive and 7 of the 10 tracked turtles had individual home ranges that overlapped with the road. Our findings support the hypothesis that road mortality has contributed to the dramatic decline in the snapping turtle population in Cootes Paradise Marsh. This population is in jeopardy of extirpation; therefore, exclusion fencing must be installed for an extended distance along both sides of surrounding roads to prevent turtles from crossing the road and to promote their use of existing aquatic culverts