Improving biodiversity monitoring

Influence of interactive effects on long-term population trajectories in multispecies reintroductions

Reintroduced populations are typically considered to progress through establishment, growth, and regulatory phases. However, most reintroduction programs do not monitor intensively enough to test this conceptual model. We studied population indices derived from track activity of 4 threatened species (greater bilby [Macrotis lagotis], burrowing bettong [Bettongia lesueur], greater stick-nest rat [Leporillus conditor], and Shark Bay bandicoot [Perameles bougainville]) over 23 years after multiple reintroductions of each species in arid Australia. We compared population trajectories among species and investigated the effect of time and environmental variables. All species bred immediately after release, and the growth phase lasted 3-16 years, varying markedly among but not within species. The end of the growth phase was characterized by an obvious peak in population density followed by either a catastrophic decline and sustained low density (bettongs), a slow decline to extirpation after 20 years (stick-nest rat), or a slight decline followed by irregular fluctuations (bilby and bandicoot). Minor fluctuations were related to environmental variables, including 12-month cumulative rainfall and lagged summer maximum temperatures. Three of the 4 species did not reach a regulation phase, even after 23 years, possibly due to interspecific competition and trophic cascades triggered by predator removal and multispecies reintroductions. Bilbies and bandicoots exhibited a second growth phase 18 years after reintroduction, likely caused by high rainfall and increased resources following the population crash of overabundant bettongs. Our results suggest that assemblages within multispecies reintroductions demonstrate high variability in population trajectories due to interactive effects. Intensive monitoring to assess population viability may require decades, particularly where multiple species are reintroduced, release sites are confined, and the climate is unpredictable. Intensive monitoring also allows for adaptive management to prevent precipitous population declines. Practitioners should not assume reintroduced species pass through predictable postrelease population phases or that viability is assured after a certain period.

Current extent and future opportunities for living shorelines in Australia

Living shorelines aim to enhance the resilience of coastlines to hazards while simultaneously delivering co-benefits such as carbon sequestration. Despite the potential ecological and socio-economic benefits of living shorelines over conventional engineered coastal protection structures, application is limited globally. Australia has a long and diverse coastline that provides prime opportunities for living shorelines using beaches and dunes, vegetation, and biogenic reefs, which may be either natural ('soft' approach) or with an engineered structural component ('hybrid' approach). Published scientific studies, however, have indicated limited use of living shorelines for coastal protection in Australia. In response, we combined a national survey and interviews of coastal practitioners and a grey and peer-reviewed literature search to (1) identify barriers to living shoreline implementation; and (2) create a database of living shoreline projects in Australia based on sources other than scientific literature. Projects included were those that had either a primary or secondary goal of protection of coastal assets from erosion and/or flooding. We identified 138 living shoreline projects in Australia through the means sampled starting in 1970; with the number of projects increasing through time particularly since 2000. Over half of the total projects (59 %) were considered to be successful according to their initial stated objective (i.e., reducing hazard risk) and 18 % of projects could not be assessed for their success based on the information available. Seventy percent of projects received formal or informal monitoring. Even in the absence of peer-reviewed support for living shoreline construction in Australia, we discovered local and regional increases in their use. This suggests that coastal practitioners are learning on-the-ground, however more generally it was stated that few examples of living shorelines are being made available, suggesting a barrier in information sharing among agencies at a broader scale. A database of living shoreline projects can increase knowledge among practitioners globally to develop best practice that informs technical guidelines for different approaches and helps focus attention on areas for further research.

Local Ecological Learning: Creating Place-based Knowledge through Collaborative Wildlife Research on Private Lands

Wildlife across all land tenures is under threat from anthropogenic drivers including climate change, invasive species, and habitat loss. This study focuses on private lands, where effective management for wildlife conservation requires locally relevant knowledge about wildlife populations, habitat condition, threatening ecological processes, and social drivers of and barriers to conservation. Collaborative socio-ecological research can inform wildlife management by integrating the place-based ecological and social knowledge of private landholders with the theoretical and applied knowledge of researchers and practitioners, including that of Traditional Owners. In privately-owned landscapes, landholders are often overlooked as a source of local ecological knowledge grounded in learning through continuous embodied interaction with their environment and community. Here we report on WildTracker, a transdisciplinary socio-ecological research collaboration involving 160 landholders in Tasmania, Australia. This wildlife-focused citizen science project generated and integrated local socio-ecological knowledge in the research process. The project gathered quantitative and qualitative data on wildlife ecology, land management practices, and landholder learning via wildlife cameras, sound recorders, workshops, questionnaires, and semi-structured interviews. Through this on-going collaboration, landholders, researchers, and conservation practitioners established relationships based on mutual learning, gathering and sharing knowledge, and insights about wildlife conservation. Our project documents how local ecological knowledge develops and changes through everyday processes of enquiry and interaction with other knowledge holders including researchers and conservation practitioners. Qualitative insights derived from the direct experience and citizen science practices of landholders were integrated with quantitative scientific assessments of wildlife populations and habitat condition to produce a novel model of collaborative conservation research.

Monitoring the fabric of nature: using allometric trophic network models and observations to assess policy effects on biodiversity

Species diversity underpins all ecosystem services that support life. Despite this recognition and the great advances in detecting biodiversity, exactly how many and which species co-occur and interact, directly or indirectly in any ecosystem is unknown. Biodiversity accounts are incomplete; taxonomically, size, habitat, mobility or rarity biased. In the ocean, the provisioning of fish, invertebrates and algae is a fundamental ecosystem service. This extracted biomass depends on a myriad of microscopic and macroscopic organisms that make up the fabric of nature and which are affected by management actions. Monitoring them all and attributing changes to management policies is daunting. Here we propose that dynamic quantitative models of species interactions can be used to link management policy and compliance with complex ecological networks. This allows managers to qualitatively identify 'interaction-indicator' species, which are highly impacted by management policies through propagation of complex ecological interactions. We ground the approach in intertidal kelp harvesting in Chile and fishers' compliance with policies. Results allow us to identify sets of species that respond to management policy and/or compliance, but which are often not included in standardized monitoring. The proposed approach aids in the design of biodiversity programmes that attempt to connect management with biodiversity change. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

River basin governance enabling pathways for sustainable management: A comparative study between Australia, Brazil, China and France

Successful river basin governance is challenged by actor engagement in the various stages of planning and management. A governance approach for determining priorities for actors for sustainable management was developed, based on a river basin diagnostic framework consisting of four social-institutional and four biophysical indicators. It was applied in river basins in Australia, Brazil, China and France. Actors diagnosed current and target capacity for these indicators, and estimated synergistic influences of interacting indicators. The results reveal different priorities and transformative pathways to achieve basin plan outcomes, specific to each basin and actor groups. Priorities include biodiversity for the Murray-Darling, local water management needs for the São Francisco and Yellow rivers, and improved decision-making for the Adour-Garonne. This novel approach challenges entrenched views about key issues and actor engagement roles in co-implementation of the basin plan under existing prevailing governance models, with implications for engagement and international collaboration on basin governance.

Novel microsatellites and investigation of faecal DNA as a non-invasive population monitoring tool for the banded hare-wallaby (

Monitoring programs for populations of small or medium-sized animals often use live-capture or photo-monitoring trapping methods to estimate population size. The banded hare-wallaby (Lagostrophus fasciatus), a small macropodiform marsupial, does not readily enter traps or have individually unique distinguishing physical features and is consequently difficult to monitor using these methods. Isolating DNA from faecal material to obtain individual genotypes is a promising monitoring technique and may present an alternative approach for this species. We developed novel species-specific microsatellite markers and undertook trials to assess faecal DNA degradation in ambient environmental conditions at two locations where this species has been translocated. The quality of DNA yielded from faecal pellets was evaluated through amplification failure and genotyping error rates of microsatellite markers. Error rates were compared for different treatments and exposure duration across multiple individuals. DNA was successfully obtained from all samples and error rates increased with exposure duration, peaking after 14–30 days depending on the site and treatment. The level of solar exposure was the most significant factor affecting degradation rate but both this and exposure duration had significant effects on amplification failure. Analysing DNA obtained from faecal pellets may represent a practical non-invasive method of deriving population estimates for this species and warrants further development.

A quantitative global review of species population monitoring

Species monitoring, defined here as the repeated, systematic collection of data to detect long-term changes in the populations of wild species, is a vital component of conservation practice and policy. We created a database of nearly 1200 schemes, ranging in start date from 1800 to 2018, to review spatial, temporal, taxonomic, and methodological patterns in global species monitoring. We identified monitoring schemes through standardized web searches, an online survey of stakeholders, in-depth national searches in a sample of countries, and a review of global biodiversity databases. We estimated the total global number of monitoring schemes operating at 3300-15,000. Since 2000, there has been a sharp increase in the number of new schemes being initiated in lower- and middle-income countries and in megadiverse countries, but a decrease in high-income countries. The total number of monitoring schemes in a country and its per capita gross domestic product were strongly, positively correlated. Schemes that were active in 2018 had been running for an average of 21 years in high-income countries, compared with 13 years in middle-income countries and 10 years in low-income countries. In high-income countries, over one-half of monitoring schemes received government funding, but this was less than one-quarter in low-income countries. Data collection was undertaken partly or wholly by volunteers in 37% of schemes, and such schemes covered significantly more sites and species than those undertaken by professionals alone. Birds were by far the most widely monitored taxonomic group, accounting for around half of all schemes, but this bias declined over time. Monitoring in most taxonomic groups remains sparse and uncoordinated, and most of the data generated are elusive and unlikely to feed into wider biodiversity conservation processes. These shortcomings could be addressed by, for example, creating an open global meta-database of biodiversity monitoring schemes and enhancing capacity for species monitoring in countries with high biodiversity. Article impact statement: Species population monitoring for conservation purposes remains strongly biased toward a few vertebrate taxa in wealthier countries.

Comparing detectability patterns of bird species using multi-method occupancy modelling

A robust knowledge of biodiversity distribution is essential for designing and developing effective conservation actions. The choice of a suitable sampling method is key to obtaining sufficiently accurate information of species distribution and consequently to improve biodiversity conservation. This study applies multi-method occupancy models to 36 common bird species associated with small ponds in the province of Murcia (south-eastern Spain), one of the most arid regions of Europe, in order to compare their effectiveness for detecting different bird species: direct observation, combined observation and video monitoring and mist netting captures. The results showed that the combined method and direct observation were similar and most effective than mist netting for detecting species occupancy, although detection rates ranged widely among bird groups, while some large species were poorly detected by all the methods used. Average detectability did not increase during the breeding period. The chosen approach is particularly applicable to both single- and multi-species bird monitoring programmes. However, we recommend evaluating the cost-effectiveness of all the available methods in order to reduce costs and improve the success of sampling designs.

Experimenting With the Past to Improve Environmental Monitoring

Long-term monitoring programs are a fundamental part of both understanding ecological systems and informing management decisions. However, there are many constraints which might prevent monitoring programs from being designed to consider statistical power, site selection, or the full costs and benefits of monitoring. Key considerations can be incorporated into the optimal design of a management program with simulations and experiments. Here, we advocate for the expanded use of a third approach: non-random resampling of previously-collected data. This approach conducts experiments with available data to understand the consequences of different monitoring approaches. We first illustrate non-random resampling in determining the optimal length and frequency of monitoring programs to assess species trends. We then apply the approach to a pair of additional case studies, from fisheries and agriculture. Non-random resampling of previously-collected data is underutilized, but has the potential to improve monitoring programs.

Patterns of decline of small mammal assemblages in vegetation communities of coastal south-east Australia: identification of habitat refuges

Since European settlement Australian native mammals have experienced significant extinctions and severe declines in the range and abundance of populations. Longitudinal studies are required to identify declines and activate timely management. Population studies of native small mammal communities were conducted across the eastern Otway Ranges during 1975–2007; however, their subsequent status was unknown. We aimed to: compare the current occurrence and abundance of species and communities (2013–18) to those in previous decades across major vegetation communities (heathy woodland, low forest, sand heathland, headland scrub, coastal dunes and estuarine wetland), and identify change characteristics and management priorities. Live trapping was employed to assess mammals at 30 sites across seven vegetation communities. In total, 67% of sites exhibited large to severe decreases in abundance and only 3% of sites had more than four species compared to 27% in earlier decades. Declines occurred following wildfire and drought, with drivers likely to be multifactorial. While regional declines were significant, higher mammal abundance (two- to six-fold) and native species richness were recorded at coastal dune sites, indicating that this community provides important mammal refuges. Identification of refuges across the landscape and their protection from inappropriate fire and predators should be management priorities.

Robust and simplified machine learning identification of pitfall trap-collected ground beetles at the continental scale

Insect populations are changing rapidly, and monitoring these changes is essential for understanding the causes and consequences of such shifts. However, large-scale insect identification projects are time-consuming and expensive when done solely by human identifiers. Machine learning offers a possible solution to help collect insect data quickly and efficiently.Here, we outline a methodology for training classification models to identify pitfall trap-collected insects from image data and then apply the method to identify ground beetles (Carabidae). All beetles were collected by the National Ecological Observatory Network (NEON), a continental scale ecological monitoring project with sites across the United States. We describe the procedures for image collection, image data extraction, data preparation, and model training, and compare the performance of five machine learning algorithms and two classification methods (hierarchical vs. single-level) identifying ground beetles from the species to subfamily level. All models were trained using pre-extracted feature vectors, not raw image data. Our methodology allows for data to be extracted from multiple individuals within the same image thus enhancing time efficiency, utilizes relatively simple models that allow for direct assessment of model performance, and can be performed on relatively small datasets.The best performing algorithm, linear discriminant analysis (LDA), reached an accuracy of 84.6% at the species level when naively identifying species, which was further increased to >95% when classifications were limited by known local species pools. Model performance was negatively correlated with taxonomic specificity, with the LDA model reaching an accuracy of ~99% at the subfamily level. When classifying carabid species not included in the training dataset at higher taxonomic levels species, the models performed significantly better than if classifications were made randomly. We also observed greater performance when classifications were made using the hierarchical classification method compared to the single-level classification method at higher taxonomic levels.The general methodology outlined here serves as a proof-of-concept for classifying pitfall trap-collected organisms using machine learning algorithms, and the image data extraction methodology may be used for nonmachine learning uses. We propose that integration of machine learning in large-scale identification pipelines will increase efficiency and lead to a greater flow of insect macroecological data, with the potential to be expanded for use with other noninsect taxa.

Effective ecosystem monitoring requires a multi-scaled approach

Ecosystem monitoring is fundamental to our understanding of how ecosystem change is impacting our natural resources and is vital for developing evidence-based policy and management. However, the different types of ecosystem monitoring, along with their recommended applications, are often poorly understood and contentious. Varying definitions and strict adherence to a specific monitoring type can inhibit effective ecosystem monitoring, leading to poor program development, implementation and outcomes. In an effort to develop a more consistent and clear understanding of ecosystem monitoring programs, we here review the main types of monitoring and recommend the widespread adoption of three classifications of monitoring, namely, targeted, surveillance and landscape monitoring. Landscape monitoring is conducted over large areas, provides spatial data, and enables questions relating to where and when ecosystem change is occurring to be addressed. Surveillance monitoring uses standardised field methods to inform on what is changing in our environments and the direction and magnitude of that change, whilst targeted monitoring is designed around testable hypotheses over defined areas and is the best approach for determining the causes of ecosystem change. The classification system is flexible and can incorporate different interests, objectives, targets and characteristics as well as different spatial scales and temporal frequencies, while also providing valuable structure and consistency across distinct ecosystem monitoring programs. To support our argument, we examine the ability of each monitoring type to inform on six key types of questions that are routinely posed for ecosystem monitoring programs, such as where and when change is occurring, what is the magnitude of change, and how can the change be managed? As we demonstrate, each type of ecosystem monitoring has its own strengths and weaknesses, which should be carefully considered relative to the desired results. Using this scheme, scientists and land managers can design programs best suited to their needs. Finally, we assert that for our most serious environmental challenges, it is essential that we include information from each of these monitoring scales to inform on all facets of ecosystem change, and this is best achieved through close collaboration between the scales. With a renewed understanding of the importance of each monitoring type, along with greater commitment to monitor cooperatively, we will be well placed to address some of our greatest environmental challenges.

DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species

DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.

The FrogID dataset: expert-validated occurrence records of Australia's frogs collected by citizen scientists

This dataset represents expert-validated occurrence records of calling frogs across Australia collected via the national citizen science project FrogID (http://www.frogid.net.au). FrogID relies on participants recording calling frogs using smartphone technology, after which point the frogs are identified by expert validators, resulting in a database of georeferenced frog species records. This dataset represents one full year of the project (10 November 2017-9 November 2018), including 54,864 records of 172 species, 71% of the known frog species in Australia. This is the first instalment of the dataset, and we anticipate providing updated datasets on an annual basis.

Persistence of the broad-toothed rat (Mastacomys fuscus) across Victoria is correlated with climate and elevation

Abstract ContextThe broad-toothed rat (Mastacomys fuscus; BTR) is distributed throughout south-eastern Australia, but its populations are restricted and dispersed. BTRs prefer cooler, wetter habitats and, as such, future climate change is projected to lead to further range reductions. However, recent changes in its distribution have not been well documented, and there is limited knowledge about the current occupancy and population size of the species in Victoria. AimsTo evaluate recent historical changes in the distribution of BTRs in Victoria, and to test whether changes in distribution are correlated with climate and elevation. MethodsWe obtained all documented records of BTRs in the state before 1990 and used field notes and verbal descriptions to geo-reference their historical localities. We then used a repeated sampling design to resurvey all historically occupied sites with a geographic coordinate uncertainty of 4km or less. We tested for the effects of climate and elevation on the persistence of BTRs. Key resultsWe detected BTRs at 32 of 68 historical sites surveyed. Consistent with climate model predictions, site persistence was more likely to occur at sites of higher elevation and precipitation and less likely to occur at sites with a higher temperature. Minimum temperature of the coldest month was the single best predictor of persistence. ConclusionsThese results demonstrated a substantial decline in the persistence of BTRs at historical sites across Victoria and provided a benchmark for future monitoring and management efforts. ImplicationsThe decline of BTRs from historically occupied sites across Victoria is consistent with their listing as endangered in the state, and climate correlations suggest further declines, with projected climate change compounding other threats to the species such as introduced predators, feral herbivores, fire and land use. However, the status of BTRs in Victoria and understanding of the threats to their persistence are based on sparse data, highlighting the critical need for more effective monitoring of the species.

Envisioning a national invasive species information framework

With a view toward creating a national Early Detection and Rapid Response Program (EDRR) program, the United States National Invasive Species Council Management Plan for 2016–2018 calls for a series of assessments of federal EDRR capacities, including the evaluation of “relevant federal information systems to provide the data and other information necessary for risk analyses/horizon scanning, rapid specimen identification, and rapid response planning.” This paper is a response to that directive. We provide an overview of information management needs for enacting EDRR and discuss challenges to meeting these needs. We then review the history of relevant US policy directives for advancing invasive species information systems and provide an overview of federal invasive species information system capacities, including current gaps and inconsistencies. We conclude with a summary of key principles and needs for establishing a national invasive species information framework. Our findings are consistent with earlier studies and, thus, emphasize the need to act on long-recognized needs. As a supplement to this paper, we have cataloged federal invasive species databases and information tools identified through this work.

The power to detect regional declines in common bird populations using continental monitoring data

Anthropogenic environmental change is driving the rapid loss of biodiversity. Large declines in the abundance of historically common species are now emerging as a major concern. Identifying declining populations through long-term biodiversity monitoring is vital for implementing timely conservation measures. It is, therefore, critical to evaluate the likelihood that persistent long-term population trends of a given size could be detected using existing monitoring data and methods. Here, we test the power to detect declines in Australia's common landbirds using long-term citizen science monitoring. We use spatially explicit simulations of occupancy dynamics and virtual sampling, designed to mimic bird monitoring in better-sampled regions of Australia, to assess likely power in these data to detect trends relevant for conservation. We predict the statistical power for 326 common species that meet minimum requirements for monitoring data across 10 regions of Australia, estimating the number of species for which we would have a high (≥80%) chance of detecting declines of different sizes. The power to detect declines of ≥30% per decade was predicted to be high for at least one-third of the common species in 7 of 10 regions, with a total of 103 (32% of 326) unique species sufficiently monitored in at least one region. These species spanned 12 taxonomic orders, four orders of magnitude in body mass, and a broad diversity of dietary guilds, suggesting the current species pool will likely serve as robust indicators for a broad range of environmental states and pressures. Power was strongly affected by species' detectability, and power to detect even large declines was negligible when species are detected on ≤50% of visits to an occupied site. Predicted power for many species fell just short of the 80% threshold in one or more regions, which suggests an increase in effort targeting these species could greatly enhance the species and regional representation of these data. Against the backdrop of unprecedented biodiversity losses, this study shows how critical evaluation of existing monitoring schemes is valuable both for assessing the contribution of citizen science schemes to biodiversity monitoring and for designing strategic monitoring to significantly improve the knowledge these schemes provide.

Occupancy and detectability modelling of vertebrates in northern Australia using multiple sampling methods

Understanding where species occur and how difficult they are to detect during surveys is crucial for designing and evaluating monitoring programs, and has broader applications for conservation planning and management. In this study, we modelled occupancy and the effectiveness of six sampling methods at detecting vertebrates across the Top End of northern Australia. We fitted occupancy-detection models to 136 species (83 birds, 33 reptiles, 20 mammals) of 242 recorded during surveys of 333 sites in eight conservation reserves between 2011 and 2016. For modelled species, mean occupancy was highly variable: birds and reptiles ranged from 0.01–0.81 and 0.01–0.49, respectively, whereas mammal occupancy was lower, ranging from 0.02–0.30. Of the 11 environmental covariates considered as potential predictors of occupancy, topographic ruggedness, elevation, maximum temperature, and fire frequency were retained more readily in the top models. Using these models, we predicted species occupancy across the Top End of northern Australia (293,017 km²) and generated species richness maps for each species group. For mammals and reptiles, high richness was associated with rugged terrain, while bird richness was highest in coastal lowland woodlands. On average, detectability of diurnal birds was higher per day of surveys (0.33 ± 0.09) compared with nocturnal birds per night of spotlighting (0.13 ± 0.06). Detectability of reptiles was similar per day/night of pit trapping (0.30 ± 0.09) as per night of spotlighting (0.29 ± 0.11). On average, mammals were highly detectable using motion-sensor cameras for a week (0.36 ± 0.06), with exception of smaller-bodied species. One night of Elliott trapping (0.20 ± 0.06) and spotlighting (0.19 ± 0.06) was more effective at detecting mammals than cage (0.08 ± 0.03) and pit trapping (0.05 ± 0.04). Our estimates of species occupancy and detectability will help inform decisions about how best to redesign a long-running vertebrate monitoring program in the Top End of northern Australia.

Effects of connectivity and watercourse distance on temporal coherence patterns in a tropical reservoir

Temporal coherence exists when environmental variables measured at different spatial locations vary synchronously over time. This is an important property to be analyzed because levels of coherence may indicate the role of regional and local processes in determining population and ecosystem dynamics. Also, studies on temporal coherence may guide the optimal allocation of sampling effort. We analyzed a dataset from a monitoring program undertaken at a tropical reservoir (Peixe Angical Reservoir, State of Tocantins, Brazil) to test three predictions. First, coherence should be a common pattern in the reservoir considering that sampling sites were distributed in a single water body and over a small spatial extent. Second, coherence was expected to decline with increasing watercourse distance and to increase with hydrological connectivity. Third, abiotic variables should exhibit higher coherence than biological variables. Twenty limnological variables were monitored at 14 sites and for 31 months. We found significant levels of coherence for all variables, supporting our first prediction. Watercourse distances, hydrological connectivity, or both were significant predictors of coherence for 17 environmental variables. In all these cases, the signs of the coefficients were in the direction predicted. Interestingly, for some environmental variables (color, turbidity, alkalinity, and total phosphorus), hydrological connectivity was even more important in predicting coherence than watercourse distance. The view that abiotic variables should exhibit higher coherence than biological variables was supported. Our analyses revealed that precipitation was an important factor inducing coherence of a key set of environmental variables, highlighting the role of regional processes in ecosystem dynamics.

Passive acoustic surveys for predicting species' distributions: Optimising detection probability

Surveying terrestrial species across diverse habitats is important for predicting species’ distributions and implementing conservation actions. For vocalising species, passive acoustic monitoring (PAM) is increasing in popularity; however, survey design rarely considers the factors influencing the timing and occurrence of vocalisations and in turn, how they may influence detectability of the species. Here, we use the koala (Phascolarctos cinereus) as a case study to show how PAM can be used to first examine the factors influencing vocalisations, and then use occupancy modelling to make recommendations on survey design for the species. We used automated recording units to monitor koala vocalisations at ten sites between August 2016 and January 2017. The timing of male koala vocalisations was linked to time of sunset with vocalisations increasing two hours prior to sunset and peaking at four hours after sunset. Vocalisations had a seasonal trend, increasing from the early to middle stage of the breeding season. Koala population density and stage of the breeding season had more influence on detection probability than daily sampling schedule. Where population density was low, and during the early stage of the breeding season, 7 survey nights (recording for 6 hours from 20:00h to 02:00h; i.e. the period of peak bellowing activity) were required to be 95% confident of a site-specific absence. Our study provides an approach for designing effective passive acoustic surveys for terrestrial species.

Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool

The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.

Evaluating the Contribution of North American Zoos and Aquariums to Endangered Species Recovery

The challenge of recovering threatened species necessitates collaboration among diverse conservation partners. Zoos and aquariums have long partnered with other conservation organizations and government agencies to help recover species through a range of in situ and ex situ conservation projects. These efforts tend to be conducted by individual facilities and for individual species, and thus the scope and magnitude of these actions at the national level are not well understood. Here we evaluate the means and extent to which North American zoos and aquariums contribute to the recovery of species listed under the U.S. Endangered Species Act (ESA), by synthesizing data from federal recovery plans for listed species and from annual surveys conducted by the Association of Zoos and Aquariums. We found that in addition to managing ex situ assurance populations, zoos frequently conduct conservation research and field-based population monitoring and assessments. Cooperatively managed populations in zoos tend to focus on species that are not listed on the ESA or on foreign listings, and thus it may be beneficial for zoos to manage more native threatened species. Our results highlight the existing contributions, but also identify additional opportunities for the zoo community to help recover threatened species.

A state-space modelling approach to wildlife monitoring with application to flying-fox abundance

Monitoring flying-foxes is challenging as their extreme mobility produces highly dynamic population processes, considerable logistic difficulty, and variability in estimated population size. We report on methods for inferring population trend for the population of the spectacled flying-fox (Pteropus conspicillatus) in Australia. Monthly monitoring is conducted at all known roost sites across the species’ range in the Wet Tropics Region. The proportion of animals in camps varies seasonally and stochastic environmental events appear to be influential. We develop a state-space model that incorporates these processes and enables inference on total population trends and uses early warning analysis to identify the causes of population dynamics. The model suggests that population growth rate is stable in the absence of cyclones, however, cyclones appear to impact on both survival and reproduction. The population recovered after two cyclones but declined after a third. The modelling estimates a population decline over 15 years of c. 75% (mean r = − 0.12yr⁻¹ and belief of negative trend is c. 83%) suggesting that conservation action is warranted. Our work shows that a state-space modelling approach is a significant improvement on inference from raw counts from surveys and demonstrates that this approach is a workable alternative to other methods.

Estimating population extinction thresholds with categorical classification trees for Louisiana black bears

Monitoring vulnerable species is critical for their conservation. Thresholds or tipping points are commonly used to indicate when populations become vulnerable to extinction and to trigger changes in conservation actions. However, quantitative methods to determine such thresholds have not been well explored. The Louisiana black bear (Ursus americanus luteolus) was removed from the list of threatened and endangered species under the U.S. Endangered Species Act in 2016 and our objectives were to determine the most appropriate parameters and thresholds for monitoring and management action. Capture mark recapture (CMR) data from 2006 to 2012 were used to estimate population parameters and variances. We used stochastic population simulations and conditional classification trees to identify demographic rates for monitoring that would be most indicative of heighted extinction risk. We then identified thresholds that would be reliable predictors of population viability. Conditional classification trees indicated that annual apparent survival rates for adult females averaged over 5 years ([Formula: see text]) was the best predictor of population persistence. Specifically, population persistence was estimated to be ≥95% over 100 years when [Formula: see text], suggesting that this statistic can be used as threshold to trigger management intervention. Our evaluation produced monitoring protocols that reliably predicted population persistence and was cost-effective. We conclude that population projections and conditional classification trees can be valuable tools for identifying extinction thresholds used in monitoring programs.

Barking up the right tree: comparative use of arboreal and terrestrial artificial refuges to survey reptiles in temperate eucalypt woodlands

Context Artificial refuges (cover boards) are a popular method to survey and monitor herpetofauna worldwide. However, one limitation of using artificial refuges in terrestrial environments is the low detection rates of arboreal species. Furthermore, destructive search techniques can damage critical microhabitat such as exfoliating rock or flaking bark of mature trees. Aim We tested a non-destructive, passive method of sampling arboreal reptiles in fragmented agricultural landscapes in south-eastern Australia. Methods We installed 84 artificial bark refuges consisting of strips of non-toxic, closed-cell foam attached to eucalypt trees in 13 patches of remnant vegetation. We used Bayesian statistics to compare differences in detection rates among artificial bark refuges, terrestrial artificial refuges and active searches of natural habitat over a 4-year period. Key results Active searches combined with terrestrial artificial refuges detected the highest number of reptile species, including several cryptic fossorial species. Artificial bark refuges detected, on average, 132 times more individuals of the arboreal southern marbled gecko, Christinus marmoratus, than did terrestrial refuges. Gecko abundance patterns were related to tree characteristics such as tree size, bark thickness and stand basal area, as well as survey year. Conclusions Traditional survey methods such as terrestrial cover boards, in combination with active searches of natural habitat, may significantly underestimate counts for arboreal gecko species. Implications Artificial bark refuges provide a cost-effective, non-destructive and durable method for surveying and monitoring arboreal reptiles in woodland environments over short to medium time frames. Foil-backed, closed-cell foam has broad application for use in spatial capture–recapture studies and long-term monitoring of arboreal reptiles. This method also may be effective for procuring records of threatened arboreal geckos or as a solution for providing temporary habitat in ecological restoration projects.

Logged peat swamp forest supports greater macrofungal biodiversity than large-scale oil palm plantations and smallholdings

Intensive land expansion of commercial oil palm agricultural lands results in reducing the size of peat swamp forests, particularly in Southeast Asia. The effect of this land conversion on macrofungal biodiversity is, however, understudied. We quantified macrofungal biodiversity by identifying mushroom sporocarps throughout four different habitats; logged peat swamp forest, large‐scale oil palm plantation, monoculture, and polyculture smallholdings. We recorded a total of 757 clusters of macrofungi belonging to 127 morphospecies and found that substrates for growing macrofungi were abundant in peat swamp forest; hence, morphospecies richness and macrofungal clusters were significantly greater in logged peat swamp forest than converted oil palm agriculture lands. Environmental factors that influence macrofungi in logged peat swamp forests such as air temperature, humidity, wind speed, soil pH, and soil moisture were different from those in oil palm plantations and smallholdings. We conclude that peat swamp forests are irreplaceable with respect to macrofungal biodiversity. They host much greater macrofungal biodiversity than any of the oil palm agricultural lands. It is imperative that further expansion of oil palm plantation into remaining peat swamp forests should be prohibited in palm oil producing countries. These results imply that macrofungal distribution reflects changes in microclimate between habitats and reduced macrofungal biodiversity may adversely affect decomposition in human‐modified landscapes.

Accounting for biodiversity in Australia

Purpose

This paper aims to respond to recent calls by Jones (2014) and Jones and Solomon (Accounting, Auditing & Accountability Journal, 2013) for more studies on biodiversity accounting and reporting. In particular, this paper explores biodiversity reporting of the Murray-Darling Basin Authority (MDBA), an Australian public sector enterprise.

Design/methodology/approach

The paper uses content analysis of MDBA’s published annual reports over the period of 15 years (1998-2012). Archival data (from different government departments) are also used to prepare natural inventory model.

Findings

The paper finds that although specific species, such as flora and fauna, and habitats-related disclosures have increased over the time, such information still allows only a partial construction of an inventory of natural assets, using Jones’ (1996, 2003) model. However, unlike prior studies that find lack of data availability to be the main impediment for operationalising biodiversity accounting, the abundance of biodiversity data in Australia makes it comparatively easier to produce such a statement.

Research limitations/implications

Informed by the environmental stewardship framework, the results of this paper suggest that the disclosures made by MDBA are constrained potentially due to its use of traditional accounting mechanisms of reporting that only allow tradable items to be reported to stakeholders. An alternative reporting format would be more relevant to stakeholder groups who are more interested in information regarding quality and availability of water, and loss of biodiversity in the basin area rather than the financial performance of the MDBA.

Originality/value

Although there are a growing number of studies exploring biodiversity reporting in Australia, this paper is one of the earlier attempts to operationalise biodiversity (particularly habitats, flora and fauna) within the context of an Australian public sector enterprise.

Falling apart? Insights and lessons from three recent studies documenting rapid and severe decline in terrestrial mammal assemblages of northern, south-eastern and south-western Australia

Context Since European settlement in 1788, much of the Australian terrestrial mammal fauna has declined or become extinct. The pattern of, and reason for, that decline was little documented, and is now difficult to decipher. Many mammal species are still declining, providing (an unfortunate) opportunity to better document the process, identify the causal factors and attempt to redress the problem. Aim We compare trends in mammal abundance reported in three recent longitudinal studies in conservation reserves in Australia. The studies were not established with the intention of documenting mammal decline, but marked simultaneous decline of co-existing species was the most striking feature of their results. Methods Long-term monitoring in Kakadu National Park, Northern Territory (2001–04 and 2007–09), the Upper Warren region of Western Australia (since 1974) and the Great Otway National Park, Victoria (since 1975) principally relied on trapping, but also some spotlighting and sand plots, to document changes and trends in abundance in their respective mammal assemblages. Key results Decline was reported in most mammal species, across taxonomic groups, diets and size classes, but mostly involved species <5500g. The studies differed in their monitoring protocols and varied in the degree to which potential causal factors were monitored, thereby constraining interpretation of the drivers of declines. Inappropriate fire regimes and predation by feral cats are likely contributing factors in at least two study areas, and periods of markedly below-average rainfall are implicated in two areas. Conclusions We conclude the following: (1) conservation reserves in Australia may be failing to maintain at least some elements of the biodiversity that they were established to protect, and substantially enhanced management is required to redress this problem; (2) with current threats, mammal assemblages in Australia may be highly unstable; (3) substantial increase in effective long-term biodiversity monitoring programs in an adaptive management framework is needed; and (4) such monitoring programs will be more insightful if they also monitor factors driving population change. Implications Native mammal species declines and community disassembly may be occurring elsewhere. Long-term monitoring is critical for assessing trends in biodiversity and if done well, it can guide more effective and efficient management to deliver better conservation outcomes.

Decline of the dasyurid marsupial Antechinus minimus maritimus in south-east Australia: implications for recovery and management under a drying climate

Our understanding of recent extinctions and declines of Australian mammals is poor, particularly where there is a paucity of data to quantify change. The swamp antechinus (A. m. maritimus) has a fragmented, coastal distribution in south-east Australia. Although long-term studies (1975–2007) of this vulnerable species were conducted in the eastern Otways, its current status was unclear. We assessed the success of live trapping and camera trapping (2013–17) at 42 sites, 19 where the species was trapped previously. Between 2013 and 2015 A. m. maritimus was recorded at only 6 sites (n = 8), but at none in 2016–17. Assessment of long-term changes found that high-density populations occurred after above-average rainfall, and both low- and high-density populations collapsed after wildfire, after low rainfall, and in fragmented habitat. The species may now be restricted to very small populations in refuges such as coastal dunes, and predicted low rainfall and increased burning frequency pose major threats to the species’ survival. Recovery is unlikely without targeted management, including predator control and protection from inappropriate fire regimes and habitat fragmentation. If similar declines have been experienced across the species’ range, prevention of extinction of the species will require similar management strategies.