Michael P. Scroggie

Using presence-only and presence-absence data to estimate the current and potential distributions of established invasive species.

1.Predicting the current and potential distributions of established invasive species is critical for evaluating management options, but methods for differentiating these distributions have received little attention. In particular, there is uncertainty among invasive species managers about the value of information from incidental sightings compared to data from designed field surveys. This study compares the two approaches, and develops a unifying framework, using the case of invasive sambar deer Cervus unicolor in Victoria, Australia. 2.We first used 391 incidental sightings of sambar deer and 12 biophysical variables to construct a presence-only habitat suitability model using Maxent. We then used that model to stratify field sampling, with proportionately greater sampling of cells with high predicted habitat suitability. Field sampling, consisting of faecal pellet surveys, sign surveys and camera trapping, was conducted in 80 4-km2 grid cells. A Bayesian state-space occupancy model was used to predict probability of suitable habitat from the field data. 3.The Maxent and occupancy models predicted similar spatial distributions of habitat suitability for sambar deer in Victoria and there was a strong positive correlation between the rankings of cells by the two approaches. The congruence of the two models suggests that any spatial and detection biases in the presence-only data were relatively unimportant in our study. 4.We predicted the extent of suitable habitat from the occupancy model using a threshold that gave a false negative error rate of 0·05. The current distribution was the suitable habitat within a kernel that had a 99·5% chance of including the presence locations pooled from incidental sightings and field surveys: the potential distribution was suitable habitat outside that kernel. Several discrete areas of potential distribution were identified as priorities for surveillance monitoring with the aim of detecting and managing incursions of sambar deer. 5.Synthesis and applications.Our framework enables managers to robustly estimate the current and potential distributions of established invasive species using either presence-only and/or presence–absence data. Managers can then focus control and/or containment actions within the current distribution and establish surveillance monitoring to detect incursions within the potential distribution.

Modeling the Relationship Between Fecal Pellet Indices and Deer Density

Abstract Although fecal pellet counts have been widely used to index changes in deer abundance in forests, few studies have modeled the relationship between the indices and deer density. We examined the relationships between 3 fecal pellet indices (total pellets, pellet groups, and pellet frequency) and the density of deer (primarily red deer [Cervus elaphus scoticus]) in 20 enclosures in the North and South islands of New Zealand. In each enclosure we estimated the 3 indices on 30 randomly located 150-m transects, with each transect having 30 circular plots of 3.14 m2. We developed 4 candidate models (1 linear and 3 nonlinear) to describe the relationship between the indices and deer density. We used a Bayesian analysis to account for uncertainty in the estimates of deer abundance and to facilitate fitting models that included random transect effects. The 4 models explained the relationship between the 3 indices and deer density similarly well. The slopes of the linear relationships between the 3 indices and deer density were positive. Our results suggest that fecal pellet counts may be useful indices of deer abundance.

Assessing detection probabilities for the endangered growling grass frog (Litoria raniformis) in southern Victoria

Assessment of the efficacy of survey techniques for determining species occurrence is crucial for the validation of wildlife survey data. We analysed repeated site-survey data for adults and larvae of the growling grass frog (Litoria raniformis) in order to estimate probabilities of detection for the species using alternative survey techniques. The estimated probability of detecting adults of L. raniformis at occupied sites using diurnal searches was much less than 1.0 (0.107; 95% credible interval: 0.045, 0.192). The estimated probability of detecting adults using nocturnal spotlight searches was considerably higher, but still less than 1.0 (0.696; 95% credible interval: 0.585, 0.796). These results indicate that nocturnal searches are a much more efficient and reliable means of detecting the presence of adult L. raniformis than diurnal searches, but detection using either technique is less than certain. The probability of detecting tadpoles of L. raniformis using either funnel-trapping or dip-netting techniques was estimated at 0.350 (95% credible interval: 0.151, 0.567). Together, these results indicate that reliance on single-site visits during surveys for this species is likely to result in severe under-estimation of the proportion of sites that are actually occupied. We urge other workers to use repeated site-survey data and appropriate methods of data analysis to assess and report probabilities of detection when documenting the results of wildlife surveys.

Wetland characteristics influence disease risk for a threatened amphibian

Identifying determinants of the probability and intensity of infections is important for understanding the epidemiology of wildlife diseases, and for managing their impact on threatened species. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis, has decimated populations of some amphibians. However, recent studies have identified important environmental constraints on the disease, related to the pathogens physiological tolerances. In this study, we identified several intrinsic and extrinsic determinants of the probability and intensity of chytrid infections for the threatened growling grass frog (Litoria raniformis) in southeastern Australia, and used mark-recapture to estimate the effect of chytrid infections on the probability of survival of these frogs. Water temperature and salinity had negative effects on both the probability and intensity of chytrid infections. We coupled models of the infection process with a model of the effect of chytrid infections on the probability of survival to assess variation in the impact of chytridiomycosis between wetlands with differing temperature and salinity profiles. Our results suggest that warm, saline wetlands may be refuges from chytridiomycosis for L. raniformis, and should be priorities for protection. Our results also suggest that management actions that increase water temperature (e.g., reducing canopy shading) and salinity (e.g., complementing inflows with groundwater) could be trialed to reduce the impacts of chytridiomycosis on this species. This and other recent studies highlight the value of research on environmental risk factors for chytridiomycosis.

Refugia and connectivity sustain amphibian metapopulations afflicted by disease

Metapopulation persistence in fragmented landscapes depends on habitat patches that can support resilient local populations and sufficient connectivity between patches. Yet epidemiological theory for metapopulations has largely overlooked the capacity of particular patches to act as refuges from disease, and has suggested that connectivity can undermine persistence. Here, we show that relatively warm and saline wetlands are environmental refuges from chytridiomycosis for an endangered Australian frog, and act jointly with connectivity to sustain frog metapopulations. We coupled models of microclimate and infection probability to map chytrid prevalence, and demonstrate a strong negative relationship between chytrid prevalence and the persistence of frog populations. Simulations confirm that frog metapopulations are likely to go extinct when they lack environmental refuges from disease and lose connectivity between patches. This study demonstrates that environmental heterogeneity can mediate host-pathogen interactions in fragmented landscapes, and provides evidence that connectivity principally supports host metapopulations afflicted by facultative pathogens.

Habitat use by stream-breeding frogs in south-east Sulawesi, with some preliminary observations on community organization

The habitat associations of stream-breeding frogs were examined along a series of stream transects on Buton Island in south-east Sulawesi, Indonesia. Of the eight frog species located along streams, four were observed breeding in stream habitats. We examined spatial habitat partitioning among these species. Three of the four species were found to be associated with a non-random selection of the available perch sites. Strong partitioning between species in habitat associations was found; partitioning of the available habitat space was primarily associated with differences in proximity to stream features, and in the height of perch sites. General observations indicated that oviposition sites of most species were associated with the microhabitats in which the adult frogs were found. All four stream-breeding species appear to have synchronous breeding phenologies and the spatial relationships of these species within the habitat space appear to reflect partitioning of calling sites and oviposition sites. The stream-breeding frog community in this region of Sulawesi has much lower species richness and less specialized habitat use compared with other tropical stream-breeding frog communities in the region. Abstrakt (Bahasa Indonesia): Asosiasi habitat antara katak dengan lingkungan diteliti pada jenis-jenis amfibi riparia sepanjang transek sungai di pulau Buton, Sulawesi Tenggara, Indonesia. Dari delapan jenis katak yang ditemukan sepanjang sungai, empat jenis di antaranya berkembang biak pada waktu penelitian ini berlangsung. Telah diamati pula pola pemisahan habitat antar jenis-jenis yang diamati. Tiga dari empat jenis ditemukan secara acak pada semua macam tempat hinggap. Pemisahan habitat antar jenis mempunyai korekasi yang sangat kuat terhadap jarak dari sungai dan ketinggian tempat hinggap. Walaupun demikian tempat peneluran sangat erat berasosiasi dengan iklim mikro masing-masing jenis. Keempat jenis yang diamati, masing-masing mempunyai musim peneluran yang relatif sinkron dan mencerminkan pemisahan habitat sesuai dengan tempat melakukan panggilan kawin dan tempat bertelur. Pola yang diamati dibandingkan pula dengan data yang terdapat dari Borneo. Disimpulkan bahwa katak yang berkembang biak di sungai-sungai di Buton, Sulawesi mempunyai keanekaragaman jenis yang rendah dan juga relatif tidak terspesialisasi dalam penggunaan habitat.

Microhabitat preferences of the endangered Growling Grass Frog * Litoria raniformis in southern Victoria

We examined nocturnal microhabitat preferences of the endangered Growling Grass Frog Litoria raniformis in lotic and lentic environments in southern Victoria, Australia. Data were obtained during surveys of six wetland sites during the summer of 2003. At all sites the observed distribution of frogs amongst microhabitat categories differed from their availability, as assessed by sampling of random points. Frogs were located most often on bare soil, bare rock or leaf litter when on land, and on floating, submergent and emergent vegetation in aquatic situations. Non-metric multidimensional scaling and analysis of similarities (ANOSIM) were used to compare the structural attributes of microhabitats used by L. raniformis to those of random points. In both the riparian and aquatic zones of the study sites, microhabitats used by these frogs differed from random points in their degree of vertical structural complexity. Whilst our data may be biased by the observability of frogs in different microhabitats, this st...

Visible implant alphanumeric tags as an alternative to toe-clipping for marking amphibians - a case study.

The removal of toes in unique combinations (‘toe-clipping’) has historically been the most popular technique for individually marking amphibians. However, recent studies have questioned the utility and ethics of this technique, and provided impetus for research on the efficacy of alternative methods. In this study, the efficacy of Visible Implant Alphanumeric (VIA) tags for marking juvenile growling grass frogs (Litoria raniformis) was assessed with reference to the fundamental assumptions of the mark–recapture approach. Three questions were investigated: (1) What is the probability of tag loss? (2) What is the probability of tag misidentification, and does it vary between frogs or observers, or with observer experience? and (3) To what extent does tagging influence survival or growth? Laboratory and field trials demonstrated that the probability of tag loss for juvenile L. raniformis was ~0.07 (95% CI: 0.03–0.13) when tags where implanted on the dorsolateral region of the thorax, eight times lower than that estimated for tags implanted on the thigh (mean 0.59; 95% CI: 0.29–0.86). Tags were rarely misidentified by naive observers (mean probability of tag misidentification <0.01), but tag read accuracy varied amongst observers. In the laboratory, tagging did not adversely influence survival or growth of L. raniformis during the 12-week study period. Given that modification of the techniques used here may eliminate tag loss, and that variation in tag read accuracy between observers may be easily avoided, it is concluded that VIA tags represent a promising alternative to toe-clipping for marking L. raniformis and other amphibians.

Modelling the abundance of wildlife using field surveys and GIS: non-native sambar deer (Cervus unicolor) in the Yarra Ranges, south-eastern Australia

Combining abundance data collected in designed field surveys with biophysical data derived from geographic information systems is a powerful way to investigate predictors of spatial variation in the abundance of wildlife. We used such an approach to evaluate hypotheses about factors influencing the abundance of sambar deer (Cervus unicolour Kerr, 1792), a large non-native herbivore, in south-eastern Australia. We developed a spatial model for the abundance of sambar deer faecal pellets in a 3650-ha area in the Upper Yarra Ranges, Victoria. We counted the number of sambar deer faecal pellets along 100 randomly located transects and used a geographic information system to estimate biophysical variables around each transect. We formulated our hypotheses about how those variables might affect the abundance of sambar deer pellets into 22 candidate models and used the deviance information criterion to identify the ‘best’ model(s). Because five models had strong support we used model averaging to generate a predictive model. The three variables included in the predictive model were aspect (abundance of pellets declined with increasing ‘northerliness’ and increased with increasing ‘easterliness’), distance to water and elevation; the latter two variables were positively correlated and had a negative effect on the abundance of pellets. In contrast to previous models of sambar deer abundance in south-eastern Australia, our spatial predictions of the abundance of faecal pellets can be easily tested and updated. Our approach would be useful for modelling the abundances of other wildlife species at a range of spatial scales.

Experimental Examination of the Potential for Three Introduced Fish Species to Prey on Tadpoles of the Endangered Booroolong Frog, Litoria booroolongensis

Abstract Over the past three decades the Booroolong Frog (Litoria booroolongensis) has declined across the majority of its range, with predation from introduced fish hypothesized as contributing to this decline. In this study we undertook an experiment in artificial enclosures to test the propensity for three introduced fish species (European Carp, Cyprinus carpio; Redfin Perch, Perca fluviatilis; and Mosquito Fish, Gambusia holbrooki) to prey on L. booroolongensis tadpoles. We manipulated the presence–absence of refuge habitat and alternative prey to examine how these two factors may affect tadpole predation risk. All three fish species consumed L. booroolongensis tadpoles, with juvenile C. carpio consuming nearly all tadpoles in all treatments. The provision of rocks within enclosures did not reduce the proportion of tadpoles consumed for any of the fish species examined; however, there was a reduction in the proportion of tadpoles consumed by P. fluviatilis and G. holbrooki when alternative prey were present. Although L. booroolongensis currently persists in streams inhabited by these introduced fish, this study supports the likelihood that these species are having a negative impact on populations of this endangered frog.