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Novel infectious diseases, particularly those caused by fungal pathogens, pose considerable risks to global biodiversity. The amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) has demonstrated the scale of the threat, having caused the greatest recorded loss of vertebrate biodiversity attributable to a pathogen. Despite catastrophic declines on several continents, many affected species have experienced population recoveries after epidemics. However, the potential ongoing threat of endemic Bd in these recovered or recovering populations is still poorly understood. We investigated the threat of endemic Bd to frog populations that recovered after initial precipitous declines, focusing on the endangered rainforest frog Mixophyes fleayi. We conducted extensive field surveys over 4 years at three independent sites in eastern Australia. First, we compared Bd infection prevalence and infection intensities within frog communities to reveal species‐specific infection patterns. Then, we analyzed mark‐recapture data of M. fleayi to estimate the impact of Bd infection intensity on apparent mortality rates and Bd infection dynamics. We found that M. fleayi had lower infection intensities than sympatric frogs across the three sites, and cleared infections at higher rates than they gained infections throughout the study period. By incorporating time‐varying individual infection intensities, we show that healthy M. fleayi populations persist despite increased apparent mortality associated with infrequent high Bd loads. Infection dynamics were influenced by environmental conditions, with Bd prevalence, infection intensity, and rates of gaining infection associated with lower temperatures and increased rainfall. However, mortality remained constant year‐round despite these fluctuations in Bd infections, suggesting major mortality events did not occur over the study period. Together, our results demonstrate that while Bd is still a potential threat to recovered populations of M. fleayi, high rates of clearing infections and generally low average infection loads likely minimize mortality caused by Bd. Our results are consistent with pathogen resistance contributing to the coexistence of M. fleayi with endemic Bd. We emphasize the importance of incorporating infection intensity into disease models rather than infection status alone. Similar population and infection dynamics likely exist within other recovered amphibian‐Bd systems around the globe, promising longer‐term persistence in the face of endemic chytridiomycosis. [ABSTRACT FROM AUTHOR]

Noninvasive genetic sampling (genetic tagging) of individuals is one of the most powerful and ethical tools for threatened species population monitoring. A recent review of the threats to Australia's rock-wallabies (Petrogale spp.) and the methods for their monitoring stated that noninvasive genetic sampling (faecal DNA analysis) is not viable for estimating population size and trends for species in this genus. We feel that it is important to respond as such statements have the potential to stifle the development and application of an important tool for threatened species monitoring and lead to lost opportunities for collection of high-quality data to inform conservation of these species. We take the opportunity to describe the breadth of successful application of noninvasive genetic sampling for monitoring rock wallabies and other mammal taxa, the research and development requirements for successful implementation of noninvasive DNA-based population monitoring and thoughts on why this powerful approach has not been implemented to its full potential in many jurisdictions. We need to be careful not to dismiss one of the most powerful and ethical threatened species monitoring tools due to lack of familiarity with the requirements for its implementation. [ABSTRACT FROM AUTHOR]

Woodland birds are a species assemblage of conservation concern, and their persistence in fragmented agricultural landscapes is dependent on both the preservation of existing woodland remnants and the implementation of restoration plantings. However, little is known about the habitat‐use and persistence of birds in fragmented agricultural landscapes. We present a detailed, population‐oriented study of woodland birds in temperate eucalypt woodland restoration plantings and remnant woodland patches in the South‐west Slopes bioregion of New South Wales, Australia. First, we undertook a 3‐yr mark–recapture project to assess annual survival and site fidelity in restoration plantings and woodland remnants. We supplemented our recapture efforts with resightings of color‐banded individuals. Second, we tracked individual birds of two species, Superb Fairywren (Malurus cyaneus) and Willie Wagtail (Rhipidura leucophrys), and documented snapshots of their home ranges and movement patterns during the breeding season. Annual survival in the woodland bird assemblage was lower than expected (51%). Home ranges of the Superb Fairywren were positively correlated with patch size, and were constrained by patch edges in linear sites. Superb Fairywrens and Willie Wagtails were more likely to travel longer distances between substrates while foraging in linear sites. Willie Wagtails engaged in significant gap‐crossing (up to 400 m) between adjacent habitat patches. Our findings indicate that (1) patch isolation and certain patch configurations place resident birds at an energetic disadvantage, and (2) in our study area, woodland bird populations are continuing to decline. We recommend landscape‐scale habitat restoration programs aim to address ongoing population declines. Studies such as ours conducted over longer time periods would provide a deeper understanding of habitat use and population processes of woodland birds in fragmented agricultural landscapes. [ABSTRACT FROM AUTHOR]

Large predators are particularly susceptible to population declines due to large area requirements, low population density, and conflict with humans. Their low density and secretive habits also make it difficult to know the spatial extent, size, and connectivity of populations; declines hence can go unnoticed. Here, we quantified decline in a large marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus gracilis), endemic to the Wet Tropics rainforest of northeast Australia. We compiled a large database of occurrence records and used species distributional modeling to estimate the distribution in four time periods (Pre-1956, 1956–1975, 1976–1995, 1996–2016) using climate layers and three human-use variables. The most supported variables in the distribution models were climatic, with highly suitable quoll habitat having relatively high precipitation, low temperatures, and a narrow annual range in temperature. Land-use type and road density also influenced quoll distribution in some time periods. The modeling revealed a significant decline in the distribution of D. m. gracilis over the last century, with contraction away from peripheral areas and from large areas of the Atherton Tablelands in the center of the distribution. Tests of the change in patch availability for populations of 20, 50, and 100 individuals revealed a substantial (17–32%) decline in available habitat for all population sizes, with a particular decline (31–40%) in core habitat (i.e. excluding edges). Six remaining populations were defined. Extrapolating capture–recapture density estimates derived from two populations in 2017 suggests these populations are small and range from about 10 to 160 individuals. Our total population estimate sums to 424 individuals, but we outline why this estimate is positively skewed and that the actual population size may be < 300 individuals. Continued decline and apparent absence in areas of highly suitable habitat suggests some threats are not being captured in our models. From our results, we provide management and research recommendations for this enigmatic predator. [ABSTRACT FROM AUTHOR]

Population monitoring is required to guide conservation programs. We conducted a capture–mark–recapture study of a population of the vulnerable green and golden bell frog (Litoria aurea) at the northern end of its range. Frogs were captured and marked over three breeding seasons (2015/16, 2016/17, 2017/18) in a large coastal lagoon. We aimed to: (1) produce annual estimates of population size to describe population trajectory, and (2) investigate monthly variation in abundance, capture probability, and temporary emigration to understand how these factors change at a finer temporal scale. Frog abundance varied across the three annual breeding seasons: 60–280 adult males, 120–190 adult females, and 90–420 subadults. We infer that the population is stable because adult abundance estimates were higher after 2015/16. Because our study sampled only half the available breeding habitat, the overall population may number 350–850 adults. Our modelling revealed >40 males but <20 females were detected in the sample area in our monthly samples. Estimates of temporary emigration were high (males: 0.54; females: 0.79), suggesting behaviour that made frogs unavailable for capture between months. Our results suggest that monitoring at greater than annual intervals should be adequate to monitor the future trend of this population. Population monitoring is required to guide conservation programs. We conducted a mark–recapture study of a population of the vulnerable green and golden bell frog in a large coastal lagoon in north-east New South Wales. We estimate that this population contains 350–850 adult frogs. Photo by D. Newell. [ABSTRACT FROM AUTHOR]

Passive integrated transponder (PIT) tag technology permits the "resighting" of animals tagged for ecological research without the need for physical re‐trapping. Whilst this is effective if animals pass within centimeters of tag readers, short‐distance detection capabilities have prevented the use of this technology with many species. To address this problem, we optimized a large (15 m long) flexible antenna system to provide a c. 8 m2 vertical detection plane for detecting animals in flight. We installed antennas at two roosting caves, including the primary maternity cave, of the critically endangered southern bent‐winged bat (Miniopterus orianae bassanii) in south‐eastern Australia. Testing of these systems indicated PIT‐tags could be detected up to 105 cm either side of the antenna plane. Over the course of a three‐year study, we subcutaneously PIT‐tagged 2,966 bats and logged over 1.4 million unique detections, with 97% of tagged bats detected at least once. The probability of encountering a tagged bat decreased with increasing environmental "noise" (unwanted signal) perceived by the system. During the study, we mitigated initial high noise levels by earthing both systems, which contributed to an increase in daily detection probability (based on the proportion of individuals known to be alive that were detected each day) from <0.2 (noise level ≥30%) to 0.7–0.8 (noise level 5%–15%). Conditional on a low (5%) noise level, model‐based estimates of daily encounter probability were highest (>0.8) during peak breeding season when both female and male southern bent‐winged bats congregate at the maternity cave. In this paper, we detail the methods employed and make methodological recommendations for future wildlife research using large antennas, including earthing systems as standard protocol and quantifying noise metrics as a covariate influencing the probability of detection in subsequent analyses. Our results demonstrate that large PIT antennas can be used successfully to detect small volant species, extending the scope of PIT technology and enabling a much broader range of wildlife species to be studied using this approach. [ABSTRACT FROM AUTHOR]

In response to a lack of data describing the population parameters of Turbinidae off south-eastern Australia, but a requirement for such information to support emerging harvest strategies, the growth of Lunella torquata was assessed from mark-recapture data using maximum likelihood and Bayesian approaches. Data for 564 tagged and recaptured L. torquata (29–90 mm shell lengths; SL) from 7658 tagged specimens were assessed in various competing models, but the final iteration (our 'best' model) comprised eight parameters for six characteristics, including growth at 40 and 80 mm SL, growth variability, measurement errors, outliers and seasonal variation—with the two seasonal growth parameters of most interest. This model was subsequently applied separately to data available for females and males. Growth rates at the selected indicator SLs of 40 and 80 mm were 17.4 and 4.0 mm year–1 for females and 19.1 and 4.9 mm year–1 for males. Regardless of sex, peak growth occurred in March, coinciding with the warmest water temperature. The results imply the smaller individuals would require 2+ years to reach a current minimum legal size of 75 mm SL. This growth rate, combined with the accessibility of the species to commercial and recreational fishers, might support a precautionary approach to management. [ABSTRACT FROM AUTHOR]

ABSTRACT An 8-year study of the foraging abundance of an Eretmochelys imbricata aggregation, found on 13 reefs (Howick Group) within the northern section of the Great Barrier Reef Marine Park was undertaken., A Cormack-Jolly-Seber method within program MARK was used to: (1) compare survival and recapture probabilities among age and sex classes of turtles; and (2) estimate survival and recapture rates for male and female adults and sub-adults from 665 capture-mark-recapture profiles of E. imbricata., Mean annual population density estimates were consistently greater for adult female E. imbricata (n = 333.7; SD = 135.6; R = 221-581) than for adult males (n = 32.4; SD = 33.4; R = 8-98), with both adult males and females displaying high survivorship rates (71.1%; 92.2%, respectively). This was also apparent in immature age-classes, with male and female turtles showing similarly high survivorship likelihoods (78.0%; 93.0%, respectively)., Both sexes exhibited a similar overall trend with a peak population density being displayed in the first two years of the study, followed by a general decline in the female stock and stable male population., These are the only reliable long-term abundance time-series data for a population that includes all age-classes of E. imbricata in the western Pacific and provide good baseline data for the detection of possible climate change induced trends., Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The article presents a study on the life and population of the black-flanked rock-wallaby in the Western Australian wheatbelt. The sample rock-wallabies were assessed at the Mt. Caroline Nature Reserve from 2007 to 2010 in terms of their body conditions based on various climates. Results showed that black-flanked rock-wallabies achieved their peak body conditions during the early summer while their breeding rates peaked to 90 percent per year except 2007, with most of the reproduction occurring in autumn and late winter or spring seasons.

Ecological specialization, such as major dependence upon a single-prey species, can render a predator taxon vulnerable to extinction. In such cases, understanding the population dynamics of that prey type is important for conserving the predator that relies upon it. In eastern Australia, the endangered broad-headed snake Hoplocephalus bungaroides feeds largely on velvet geckos ( Oedura lesueurii). We studied growth, longevity and reproduction in a population of velvet geckos in Morton National Park in south-eastern Australia. We marked 458 individual geckos over a 3-year period (1992–1995) and made yearly visits to field sites from 1995–2006 to recapture marked individuals. Female geckos grew larger than males, and produced their first clutch at age 4 years. Males can mature at 2 years, but male–male combat for females probably forces males to delay reproduction until age 3 years. Females lay a single clutch of two eggs in communal nests in November, and up to 22 females deposited eggs in a single nest. Egg hatching success was high (100%), and juveniles had high survival (76%) during their first 6 months of life. Velvet geckos are long-lived, and the mean age of marked animals recaptured after 1995 was 6.1 years (males) and 8.4 years (females). Older females (7.5–9.5 years) were all gravid when last recaptured. Like other temperate-climate gekkonids, O. lesueurii has a ‘slow’ life history, and population viability could be threatened by any factors that increase egg or adult mortality. Two such factors – the removal of ‘bush rocks’ for urban gardens, and the overgrowth of rock outcrops by vegetation – could render small gecko populations vulnerable to extinction. In turn, the reliance of predatory broad-headed snakes on this slow-growing lizard species may increase its vulnerability to extinction. [ABSTRACT FROM AUTHOR]

The article discusses a study which investigated annual recapture and survival rates of two non-breeding adult populations of Roseate terns (Sterna dougallii) captured on the Great Barrier Reef in Queensland. Estimates of their population sizes are also presented. It has been observed that the average annual survival rate for the birds from the Asian population is higher than that of the other population of unknown breeding origin. A full description of the study site in the Swain Reefs is also presented.

1. Precise estimates of demographic rates are key components of population models used to predict the effects of stochastic environmental processes, harvest scenarios and extinction probability. 2. We used a 12-year photographic identification library of whale sharks from Ningaloo Reef, Western Australia to construct Cormack–Jolly–Seber (CJS) model estimates of survival within a capture–mark–recapture (CMR) framework. Estimated survival rates, population structure and assumptions regarding age at maturity, longevity and reproduction frequency were combined in a series of age-classified Leslie matrices to infer the potential trajectory of the population. 3. Using data from 111 individuals, there was evidence for time variation in apparent survival (φ) and recapture probability ( p). The null model gave a @ of 0·825 (95% CI: 0·727–0·893) and &pcirc; = 0·184 (95% CI: 0·121–0·271). The model-averaged annual @ ranged from 0·737 to 0·890. There was little evidence for a sex effect on survival. 4. Using standardized total length as a covariate in the CMR models indicated a size bias in φ. Ignoring the effects of time, a 5-m shark has a @ = 0·59 and a 9 m shark has @ = 0·81. 5. Of the 16 model combinations considered, 10 (63%) indicated a decreasing population (λ < 1). For models based on age at first reproduction (α) of 13 years, the mean age of reproducing females at the stable age distribution (Ā) ranged from 15 to 23 years, which increased to 29–37 years when α was assumed to be 25. 6. All model scenarios had higher total elasticities for non-reproductive female survival [ E( s nr)] compared to those for reproductive female survival [ E( s r)]. 7. Assuming relatively slow, but biologically realistic, vital rates (α = 25 and biennial reproduction) and size-biased survival probabilities, our results suggest that the Ningaloo Reef population of whale sharks is declining, although more reproductive data are clearly needed to confirm this conclusion. Combining relatively precise survival estimates from CMR studies with realistic assumptions of other vital rates provides a useful heuristic framework for determining the vulnerability of large oceanic predators for which few direct data exist. [ABSTRACT FROM AUTHOR]

We applied genetic tagging (the identification of individuals by genetic markers) as part of a demographic and genetic analysis of a manipulative study of bush rats Rattus fuscipes in a fragmented landscape in south-eastern Australia. Our study comprised bush rat populations from 30 remnant patches embedded within an extensive exotic pine plantation. Genetic tagging was applied at 12 sites where eight or more animals were encountered in the initial census. Out of a total of 701 DNA samples, we determined (by genetic analysis at 11 microsatellite loci) that 588 bush rat individuals were sampled. Genetic tagging proved to be highly effective, with 97% of animals uniquely identified with three loci, and all animals identified by six loci. Mark–recapture distances moved by genetically tagged animals from the control sites and post-perturbation treatment samples were highly restricted, with a mean of 35 m (35.3±4.5, mean±se, max. 280 m, n=109). This mean distance moved appears to be lower than for other comparable studies of the species. Fragmentation and above-average densities of animals may partially explain this result. An analysis of the factors affecting mark–recapture distance indicated that there was a significant effect of trap layout on the maximum movement detected, but no significant difference in mark–recapture distance between the sexes. We have demonstrated that genetic tagging can facilitate traditional capture–mark–recapture studies in bush rats and pave the way for subsequent population genetic analyses that can offer additional insights not available from ecology alone. [ABSTRACT FROM AUTHOR]

Abstract: Adult western jewel butterflies Hypochrysops halyaetus Hewitson were studied in the Koondoola Regional Bushland Reserve on the northern outskirts of the Perth metropolitan area, Australia, in 1999. The butterfly is myrmecophilous, and the southern (Perth) form is considered to be ‘Vulnerable’. Butterfly dispersal, distribution, population size and habitat preferences were estimated using mark-recapture techniques. Butterflies were capable of moving large distances, and were widespread within the reserve but with a low density; however, one small physical area (80×20 m) contained a colony with large numbers of individuals. This colony, and an adjacent area of bush, was subject to a detailed microdistribution study: 1158 butterflies were marked within it over a 25-day period. The small size of the microdistribution study area compromised statistical independence assumptions: spatial autocorrelation was tested for and corrected, where appropriate, using a Markov-chain Monte-Carlo approach. Sex differences were evident in spatial autocorrelation: female data were not spatially autocorrelated, whilst male data was. The latter probably reflects the impact of the perching mode of mate location employed by males. Butterflies appeared to prefer rather degraded bush typical of a post fire/disturbance regime with high densities of the host plant Jacksonia sternbergiana. Males were positively correlated with the proportion of bare ground, again probably relating to preferred perching sites for mate location. Females were negatively correlated with Conospremum stoechadis probably indicating dense ground cover in degraded areas and Xanthorrhoea preissii probably an indicator at the site of more mature vegetation. Reserve management to improve vegetation quality may threaten the persistence of the butterfly within the reserve, whilst controlled burning to create even quite small new areas of habitat in an urban situation may be difficult to achieve. The creation of suitable habitat may be possible using mechanical means, provided the action of fire is not an essential component of habitat creation. As the western jewel appears to prefer degraded vegetation, it is possible that there may be opportunities for this species’ expansion within the urban environment provided that its mutualistic ant partner is also present. [Copyright &y& Elsevier]

Khan MT, Khan TA, Wilson ME. Habitat use and movement of river blackfish (Gadopsis marmoratusR.) in a highly modified Victorian stream, Australia.Ecology of Freshwater Fish 2004: 13: 285–293.© Blackwell Munksgaard, 2004Movement and habitat use of river blackfish (Gadopsis marmoratusR.) was studied in a highly modified central Victorian stream (Birch Creek), Australia, using radio telemetry (N = 10) and mark–recapture (N = 113) between October 2001 to May 2002, and November to December 2002 respectively. Blackfish had a small home range of 10–26 m with strong affinity to a pool. However, small movements within a pool were common which resulted in relatively large cumulative movements. At a diel scale there were no significant differences in blackfish movement between day and night (Kruskal–Wallis test,P = 0.95). Six of seven blackfish translocated 40 m upstream or downstream of their original positions returned within 48 h, suggesting strong affinity not only to a pool, but also to a small region within a pool. Blackfish utilised slow flowing (0–20 cm s−1) and deep waters (40–60 cm). Blackfish were strongly associated with the instream cover habitats of undercut banks and boulders. Significant differences were recorded in instream cover and water velocity used by blackfish between day and night (Kruskal–Wallis test,P = <0.01). At night blackfish used open areas with high water velocities whereas during the day blackfish used complex undercut banks with low water velocities. [ABSTRACT FROM AUTHOR]

The collection of reptiles for the pet trade is often cited as a potential problem for threatened species, but quantitative data on the effects of this trade on wild populations are lacking. In south-eastern Australia the decline of the threatened broad-headed snake Hoplocephalus bungaroides has been blamed on habitat destruction and the collection of snakes for pets, but there was little evidence to support the latter hypothesis. During 1992-2000 we studied one of the last extant southern populations of broad-headed snakes in Morton National Park, New South Wales, where <600 individuals remain on an isolated plateau. Analysis of 9 years of mark-recapture data reveal that the activities of snake collectors seriously endanger the viability of this species. The study population of H. bungaroides was stable over 1992-1996, but declined dramatically in 1997, coincident with evidence of illegal collecting, possibly stimulated by a government amnesty that allowed pet owners to obtain permits for illegally held reptiles. Survivorship analyses revealed that 85% of adult females disappeared from the population in 1997. There was no such effect on male survivorship, suggesting that snake collectors selectively removed adult females, which are the largest snakes in the population. Humans caused significant damage to fragile rock outcrops in three of the 9 years of the study, and a second bout of habitat disturbance in 1999 coincided with a second decline in the H. bungaroides population. We recommend that locked gates be placed on fire trails to protect existing populations of broad-headed snakes. [ABSTRACT FROM AUTHOR]

Accurate survival estimates are needed to construct robust population models, which are a powerful tool for understanding and predicting the fates of species under scenarios of environmental change. Microbats make up 17% of the global mammalian fauna, yet the processes that drive differences in demographics between species are poorly understood. We collected survival estimates for 44 microbat species from the literature and constructed a model to determine the effects of reproductive, feeding and demographic traits on survival. Our trait-based model indicated that bat species which produce more young per year exhibit lower apparent annual survival, as do males and juveniles compared with females and adults, respectively. Using 8 years of monitoring data for two Australian species, we demonstrate how knowledge about the effect of traits on survival can be incorporated into Bayesian survival analyses. This approach can be applied to any group and is not restricted to bats or even mammals. The incorporation of informative priors based on traits can allow for more timely construction of population models to support management decisions and actions., (© 2015 The Author(s).)