Kirsten M. Parris

IMPROVING PRECISION AND REDUCING BIAS IN BIOLOGICAL SURVEYS: ESTIMATING FALSE-NEGATIVE ERROR RATES

The use of presence/absence data in wildlife management and biological surveys is widespread. There is a growing interest in quantifying the sources of error associated with these data. We show that false-negative errors (failure to record a species when in fact it is present) can have a significant impact on statistical estimation of habitat models using simulated data. Then we introduce an extension of logistic modeling, the zero-inflated binomial (ZIB) model that permits the estimation of the rate of false-negative errors and the correction of estimates of the probability of occurrence for false-negative errors by using repeated visits to the same site. Our simulations show that even relatively low rates of false negatives bias statistical estimates of habitat effects. The method with three repeated visits eliminates the bias, but estimates are relatively imprecise. Six repeated visits improve precision of estimates to levels comparable to that achieved with conventional statistics in the absence of false-negative errors. In general, when error rates are ≤50% greater efficiency is gained by adding more sites, whereas when error rates are >50% it is better to increase the number of repeated visits. We highlight the flexibility of the method with three case studies, clearly demonstrating the effect of false-negative errors for a range of commonly used survey methods.

Impacts of Traffic Noise and Traffic Volume on Birds of Roadside Habitats

Roadside habitats are important for a range of taxa including plants, insects, mammals, and birds, particularly in developed countries in which large expanses of native vegetation have been cleared for agriculture or urban development. Although roadside vegetation may provide suitable habitat for many species, resident animals can be exposed to high levels of traffic noise, visual disturbance from passing vehicles, and the risk of collision with cars and trucks. Traffic noise can reduce the distance over which acoustic signals such as song can be detected, an effect known as acoustic interference or masking. Studies from the northern hemisphere show that the singing behavior of birds changes in the presence of traffic noise. We investigated the impact of traffic noise and traffic volume on two species of birds, the Grey Shrike-thrush (Colluricincla harmonica) and the Grey Fantail (Rhipidura fuliginosa), at 58 roadside sites on the Mornington Peninsula, southeastern Australia. The lower singing Grey Shrike-thrush sang at a higher frequency in the presence of traffic noise, with a predicted increase in dominant frequency of 5.8 Hz/dB of traffic noise, and a total effect size of 209 Hz. In contrast, the higher singing Grey Fantail did not appear to change its song in traffic noise. The probability of detecting each species on a visit to a site declined substantially with increasing traffic noise and traffic volume, with several lines of evidence supporting a larger effect of traffic noise. Traffic noise could hamper detection of song by conspecifics, making it more difficult for birds to establish and maintain territories, attract mates and maintain pair bonds, and possibly leading to reduced breeding success in noisy roadside habitats. Closing key roads during the breeding season is a potential, but untested, management strategy to protect threatened bird species from traffic noise and collision with vehicles at the time of year when they are most vulnerable to their impacts. Other management options include reducing the speed and/or volume of traffic on such roads to an acceptably low level. Ours is the first study to investigate the effect of traffic noise on the singing behavior of birds in the southern hemisphere.

Frogs Call at a Higher Pitch in Traffic Noise

Male frogs call to attract females for mating and to defend territories from rival males. Female frogs of some species prefer lower-pitched calls, which indicate larger, more experienced males. Acoustic interference occurs when background noise reduces the active distance or the distance over which an acoustic signal can be detected. Birds are known to call at a higher pitch or frequency in urban noise, decreasing acoustic interference from low-frequency noise. Using Bayesian linear regression, we investigated the effect of traffic noise on the pitch of advertisement calls in two species of frogs, the southern brown tree frog (Litoria ewingii) and the common eastern froglet (Crinia signifera). We found evidence that L. ewingii calls at a higher pitch in traffic noise, with an average increase in dominant frequency of 4.1 Hz/dB of traffic noise, and a total effect size of 123 Hz. This frequency shift is smaller than that observed in birds, but is still large enough to be detected by conspecific frogs and confer a significant benefit to the caller. Mathematical modelling predicted a 24% increase in the active distance of a L. ewingii call in traffic noise with a frequency shift of this size. Crinia signifera may also call at a higher pitch in traffic noise, but more data are required to be confident of this effect. Because frog calls are innate rather than learned, the frequency shift demonstrated by L. ewingii may represent an evolutionary adaptation to noisy conditions. The phenomenon of frogs calling at a higher pitch in traffic noise could therefore constitute an intriguing trade-off between audibility and attractiveness to potential mates.

Understanding co‐occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

Summary A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species’ and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co-occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co-occurrence data into a SDM. JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co-occurrence patterns into components describing shared environmental responses and residual patterns of co-occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia. Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co-occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities. Environmental and residual correlations estimated from JSDMs can help indicate whether co-occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.

PRECISION AND BIAS OF METHODS FOR ESTIMATING POINT SURVEY DETECTION PROBABILITIES

Wildlife surveys often seek to determine the presence or absence of species at sites. Such data may be used in population monitoring, impact assessment, and species– habitat analyses. An implicit assumption of presence/absence surveys is that if a species is not detected in one or more visits to a site, it is absent from that site. However, it is rarely if ever possible to be completely sure that a species is absent, and false negative observation errors may arise when detection probabilities are less than 1. The detectability of species in wildlife surveys is one of the most important sources of uncertainty in determining the proportion of a landscape that is occupied by a species. Recent studies emphasize the need to acknowledge and incorporate false negative observation error rates in the analysis of site occupancy data, although a comparative study of the range of available methods for estimating detectability and occupancy is notably absent. The motivation for this study stems from the lack of guidan...

Geographically pervasive effects of urban noise on frequency and syllable rate of songs and calls in silvereyes (Zosterops lateralis)

Recent studies in the Northern Hemisphere have shown that songbirds living in noisy urban environments sing at higher frequencies than their rural counterparts. However, several aspects of this phenomenon remain poorly understood. These include the geographical scale over which such patterns occur (most studies have compared local populations), and whether they involve phenotypic plasticity or microevolutionary change. We conducted a field study of silvereye (Zosterops lateralis) vocalizations over more than 1 million km2 of urban and rural south-eastern Australia, and compared possible effects of urban noise on songs (which are learned) and contact calls (which are innate). Across 14 paired urban and rural populations, silvereyes consistently sang both songs and contact calls at higher frequencies in urban environments. Syllable rate (syllables per second) decreased in urban environments, consistent with the hypothesis that reflective structures degrade song and encourage longer intervals between syllables. This comprehensive study is, to our knowledge, the first to demonstrate varied adaptations of urban bird vocalizations over a vast geographical area, and to provide insight into the mechanism responsible for these changes.

HABITAT FRAGMENTATION, LANDSCAPE CONTEXT, AND MAMMALIAN ASSEMBLAGES IN SOUTHEASTERN AUSTRALIA

Abstract We examined relationships between mammalian assemblages and landscape context and habitat fragmentation in southeastern Australia. Data were gathered from spotlighting and hair sample surveys at 166 sites in 3 different spatial (landscape) contexts: remnant patches of native eucalypt forest surrounded by an extensive plantation of exotic radiata pine (Pinus radiata—86 sites), the radiata pine plantation (40 sites), and large areas of continuous native eucalypt forest that occurred at the margins of the plantation (40 sites). Continuous eucalypt forest supported more species than eucalypt patches, although some species were more common in the patch areas. All assemblages in the radiata pine sites were substantially impoverished. There was a significant patch size effect for the total mammalian assemblage and for terrestrial native mammals but not for arboreal marsupials. Bigger remnants supported an assemblage different from (and more species rich) that found in smaller remnants, particularly those <3 ha where many mammal species occurred less frequently. The landscape context and patch area effects recorded in this study have important implications for plantation design in southern Australia. Eucalypt remnants should be exempt from clearing during plantation development; larger remnants are the most important areas.

Identifying effects of toe clipping on anuran return rates: the importance of statistical power

Toe clipping is a common method of marking anurans for population studies. We re-analysed data from four published studies investigating the relationship between return rate and number of toes clipped for three anuran species: Bufo fowleri, Crinia signifera and Hyla labialis . Although these studies claimed contradictory results, a re-analysis of the data with proper attention to statistical power demonstrated a statistically significant decline of 6-18% in the probability of return for each toe removed after the first, in three of the four studies examined. The probability that the fourth study would detect a statistically significant effect of toe clipping was low unless the size of the effect was overwhelming. These results provide consistent evidence that toe clipping decreases the return rate of marked anurans, and demonstrates the importance of considering statistical power during data analysis. Use of toe clipping for mark-recapture studies may produce estimates of population parameters that are biased by the same magnitude as the return rates, unless researchers control for the effect of this marking method.

Detecting extinction risk from climate change by IUCN red list criteria

Anthropogenic climate change is a key threat to global biodiversity. To inform strategic actions aimed at conserving biodiversity as climate changes, conservation planners need early warning of the risks faced by different species. The IUCN Red List criteria for threatened species are widely acknowledged as useful risk assessment tools for informing conservation under constraints imposed by limited data. However, doubts have been expressed about the ability of the criteria to detect risks imposed by potentially slow-acting threats such as climate change, particularly because criteria addressing rates of population decline are assessed over time scales as short as 10 years. We used spatially explicit stochastic population models and dynamic species distribution models projected to future climates to determine how long before extinction a species would become eligible for listing as threatened based on the IUCN Red List criteria. We focused on a short-lived frog species (Assa darlingtoni) chosen specifically to represent potential weaknesses in the criteria to allow detailed consideration of the analytical issues and to develop an approach for wider application. The criteria were more sensitive to climate change than previously anticipated; lead times between initial listing in a threatened category and predicted extinction varied from 40 to 80 years, depending on data availability. We attributed this sensitivity primarily to the ensemble properties of the criteria that assess contrasting symptoms of extinction risk. Nevertheless, we recommend the robustness of the criteria warrants further investigation across species with contrasting life histories and patterns of decline. The adequacy of these lead times for early warning depends on practicalities of environmental policy and management, bureaucratic or political inertia, and the anticipated species response times to management actions.

More bang for your buck: the effect of caller position, habitat and chorus noise on the efficiency of calling in the spring peeper

Many animals use acoustic signals as a means of intra- and inter-specific communication. For example, male anuran amphibians produce advertisement calls to attract females for breeding, and as a territorial signal. The production of acoustic signals can be energetically costly, and the distance over which a signal is effective depends on a range of variables including the location of the caller and receiver, ambient conditions and the habitat through which the sound travels. This paper presents a spatially explicit model of the propagation of an anuran advertisement call across a landscape, using the example of the northern spring peeper Pseudacris crucifer crucifer. The model is used to investigate (a) the effect of habitat, caller position and chorus noise on the effective distance of a call with a frequency of approximately 3 kHz; and (b) the energetics and efficiency of calling at different intensities and from different locations in the landscape. Calling next to still water or from an elevated perch increases, while calling in a chorus decreases, the distance over which a female can distinguish an individual males call. For a given call intensity and calling rate, a male spring peeper will get the greatest “bang for its energetic buck” if it calls next to still water in the absence of chorus noise. However, when a chorus of spring peepers is gathered at a pond, calling from an elevated position away from the pond (and the chorus noise) will maximise the effective distance of an individual call, although this may entail other costs. The model presented here is the first realistic, interactive mathematical model of the propagation of animal sounds across a landscape, and uses a gis interface to display the effect of habitat and caller position on animal communication. It has applications for both research and teaching, and a copy can be obtained free of charge by contacting the author.