A checklist of attributes for effective monitoring of threatened species and threatened ecosystems

Panel-based assessment of ecosystem condition as a platform for adaptive and knowledge driven management

Ecosystems are subjected to increasing exposure to multiple anthropogenic drivers. This has led to the development of national and international accounting systems describing the condition of ecosystems, often based on few, highly aggregated indicators. Such accounting systems would benefit from a stronger theoretical and empirical underpinning of ecosystem dynamics. Operational tools for ecosystem management require understanding of natural ecosystem dynamics, consideration of uncertainty at all levels, means for quantifying driver-response relationships behind observed and anticipated future trajectories of change, and an efficient and transparent synthesis to inform knowledge-driven decision processes. There is hence a gap between highly aggregated indicator-based accounting tools and the need for explicit understanding and assessment of the links between multiple drivers and ecosystem condition as a foundation for informed and adaptive ecosystem management. We describe here an approach termed PAEC (Panel-based Assessment of Ecosystem Condition) for combining quantitative and qualitative elements of evidence and uncertainties into an integrated assessment of ecosystem condition at spatial scales relevant to management and monitoring. The PAEC protocol is founded on explicit predictions, termed phenomena, of how components of ecosystem structure and functions are changing as a result of acting drivers. The protocol tests these predictions with observations and combines these tests to assess the change in the condition of the ecosystem as a whole. PAEC includes explicit, quantitative or qualitative, assessments of uncertainty at different levels and integrates these in the final assessment. As proofs-of-concept we summarize the application of the PAEC protocol to a marine and a terrestrial ecosystem in Norway.

Genomic insights into the critically endangered King Island scrubtit

Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.

Six Steps towards a Spatial Design for Large-Scale Pollinator Surveillance Monitoring

Despite the importance of pollinators to ecosystem functioning and human food production, comprehensive pollinator monitoring data are still lacking across most regions of the world. Policy-makers have recently prioritised the development of large-scale monitoring programmes for pollinators to better understand how populations respond to land use, environmental change and restoration measures in the long term. Designing such a monitoring programme is challenging, partly because it requires both ecological knowledge and advanced knowledge in sampling design. This study aims to develop a conceptual framework to facilitate the spatial sampling design of large-scale surveillance monitoring. The system is designed to detect changes in pollinator species abundances and richness, focusing on temperate agroecosystems. The sampling design needs to be scientifically robust to address questions of agri-environmental policy at the scales of interest. To this end, we followed a six-step procedure as follows: (1) defining the spatial sampling units, (2) defining and delimiting the monitoring area, (3) deciding on the general sampling strategy, (4) determining the sample size, (5) specifying the sampling units per sampling interval, and (6) specifying the pollinator survey plots within each sampling unit. As a case study, we apply this framework to the "Wild bee monitoring in agricultural landscapes of Germany" programme. We suggest this six-step procedure as a conceptual guideline for the spatial sampling design of future large-scale pollinator monitoring initiatives.

Population trends in the vulnerable Grey-headed flying-fox, Pteropus poliocephalus; results from a long-term, range-wide study

Monitoring is necessary for the management of any threatened species if its predicament and status are to improve. Monitoring establishes baseline data for tracking trends in distribution and abundance and is a key tool for informing threatened species management. Across much of the Old World, bats in the genus Pteropus (Pteropodidae, Chiroptera) face significant threats from habitat loss, conflict with humans, and hunting. Despite conflict with humans and their threatened status, few Pteropus are being monitored. Often, this is because of difficulties associated with their high mobility, large and easily disturbed aggregations, and their use of unknown or remote habitat. Here we describe 10 years of results from the National Flying-fox Monitoring Program (NFFMP) for the grey-headed flying-fox, (Pteropus poliocephalus) in Australia. Range-wide quarterly surveys were conducted over a three-day period since November 2012 using standardized methods appropriate to conditions encountered at each roost. For our analysis of the population and its trend, we used a state-space model to account for the ecology of the grey-headed flying-fox and the errors associated with the surveying process. Despite the general perception that the species is in decline, our raw data and the modelled population trend suggest the grey-headed flying-fox population has remained stable during the NFFMP period, with the range also stable. These results indicate that the species' extreme mobility and broad diet bestow it with a high level of resilience to various disturbance events. Long-term, range-wide studies such as this one, are crucial for understanding relatively long-lived and highly nomadic species such as the grey-headed flying-fox. The outcomes of this study highlight the need for such systematic population monitoring of all threatened Pteropus species.

Designing a large-scale track-based monitoring program to detect changes in species distributions in arid Australia

Monitoring trends in animal populations in arid regions is challenging due to remoteness and low population densities. However, detecting species' tracks or signs is an effective survey technique for monitoring population trends across large spatial and temporal scales. In this study, we developed a simulation framework to evaluate the performance of alternative track-based monitoring designs at detecting change in species distributions in arid Australia. We collated presence-absence records from 550 2-ha track-based plots for 11 vertebrates over 13 years and fitted ensemble species distribution models to predict occupancy in 2018. We simulated plausible changes in species' distributions over the next 15 years and, with estimates of detectability, simulated monitoring to evaluate the statistical power of three alternative monitoring scenarios: (1) where surveys were restricted to existing 2-ha plots, (2) where surveys were optimized to target all species equally, and (3) where surveys were optimized to target two species of conservation concern. Across all monitoring designs and scenarios, we found that power was higher when detecting increasing occupancy trends compared to decreasing trends owing to the relatively low levels of initial occupancy. Our results suggest that surveying 200 of the existing plots annually (with a small subset resurveyed twice within a year) will have at least an 80% chance of detecting 30% declines in occupancy for four of the five invasive species modeled and one of the six native species. This increased to 10 of the 11 species assuming larger (50%) declines. When plots were positioned to target all species equally, power improved slightly for most compared to the existing survey network. When plots were positioned to target two species of conservation concern (crest-tailed mulgara and dusky hopping mouse), power to detect 30% declines increased by 29% and 31% for these species, respectively, at the cost of reduced power for the remaining species. The effect of varying survey frequency depended on its trade-off with the number of sites sampled and requires further consideration. Nonetheless, our research suggests that track-based surveying is an effective and logistically feasible approach to monitoring broad-scale occupancy trends in desert species with both widespread and restricted distributions.

Potential drivers of common brushtail possum (

Australia’s terrestrial mammalian fauna have experienced severe declines since European settlement. On the Murray–Darling floodplain in south-eastern Australia, common brushtail possums (Trichosurus vulpecula, ‘possums’), have contracted to riparian zones. Although an important possum refuge, little is known about possum population dynamics here. We examined possum population dynamics and potential drivers across two decades on the Murray River floodplain at Calperum Station. We related possum density to satellite derived fractional cover, (a measure of the proportion of green, non-green and bare ground cover), and contextualised these findings using tree condition and grazing pressure datasets. Possum surveys were conducted between 1998 and 2019 in riparian and non-riparian habitats and density was modelled in relation to fractional cover values of green, non-green, and bare ground. Possum density fluctuated between 1998 and 2008 but in 2018 and 2019, possums were undetectable. Possum density was negatively associated with bare ground and positively associated with non-green. Overgrazing by kangaroos likely reduced vegetation cover and diversity and contributed to possum decline, via a reduction in possum food resources and increased exposure to predation. Inconsistent monitoring meant that the population decline was not detected until after it had occurred, and management interventions were not triggered, highlighting the dilemma of allocating scarce monitoring resources.

Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan

Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity

Montane cloud forests are fragile biodiversity hotspots. To attain their conservation, disentangling diversity patterns at all levels of ecosystem organization is mandatory. Biotic communities are regularly structured by environmental factors even at small spatial scales. However, studies at this scale have received less attention with respect to larger macroscale explorations, hampering the robust view of ecosystem functioning. In this sense, fungal small-scale processes remain poorly understood in montane cloud forests, despite their relevance. Herein, we analyzed soil fungal diversity and ecological patterns at the small-scale (within a 10 m triangular transect) in a pristine montane cloud forest of Mexico, using ITS rRNA gene amplicon Illumina sequencing and biogeochemical profiling. We detected a taxonomically and functionally diverse fungal community, dominated by few taxa and a large majority of rare species (81%). Undefined saprotrophs represented the most abundant trophic guild. Moreover, soil biogeochemical data showed an environmentally heterogeneous setting with patchy clustering, where enzymatic activities suggest distinctive small-scale soil patterns. Our results revealed that in this system, deterministic processes largely drive the assemblage of fungal communities at the small-scale, through multifactorial environmental filtering.

Hare today, gone tomorrow: the role of interspecific competition in shaping riverine rabbit occurrence

Effective conservation, particularly of threatened species, requires an understanding of both abiotic and biotic drivers of distribution. In the case of one of Africa’s most endangered mammals, the riverine rabbit Bunolagus monticularis, only environmental covariates of presence have been used to provide coarse predictions of their distribution. Two potential competitors, namely scrub hare Lepus saxatilis and cape hare L. capensis, have significant (>90%) range overlap with the riverine rabbit, yet little is known about how these species interact. We used multi-species occupancy models, which model co-occurrence as a function of environmental variables, to assess the spatial response of riverine rabbits to both species of hare in Sanbona Wildlife Reserve, South Africa. We also examined temporal overlap between riverine rabbits and hares. Camera trapping data were collected from 150 camera traps distributed in clusters of 5 cameras at 30 independent sites, covering 223.24 km2. Contrary to prior studies, we found that riverine rabbits were not restricted to riparian habitat, and that their occurrence was conditional on hare absence and was negatively affected by terrain ruggedness. Whilst hare occurrence was independent of terrain ruggedness, it was negatively affected by rabbit presence. Activity patterns revealed high temporal overlap between hares and rabbits (Δ = 0.828, CI = 0.745-0.940); however, neither species co-occurred at any given site. Our results suggest that conservation management has greatly underestimated the importance of competition with other lagomorphs in understanding riverine rabbit occurrence.

Long-Term Empirical Studies Highlight Multiple Drivers of Temporal Change in Bird Fauna in the Wet Forests of Victoria, South-Eastern Australia

Birds are high profile elements of the vertebrate biota in almost all terrestrial ecosystems worldwide. Many studies have uncovered evidence of a decline in bird biodiversity, but temporal patterns of change vary among ecosystems and among bird species with different life history traits. Ecosystem-specific, long-term studies are critical for identifying patterns of temporal change in bird biodiversity and the drivers of that change. Here we present a case study of drivers of temporal change in the bird fauna of the Mountain Ash and Alpine Ash eucalypt forests of south-eastern Australia. Using insights from observational studies and experiments conducted over the past 18 years, we discuss the direct and interactive effects of fire and logging on birds. The extent and severity of wildfires have major negative effects on almost all bird species, and have persisted for more than a decade after the last major conflagration (in 2009). Logging has markedly different effects on birds than those quantified for fire, and may have resulted in elevated levels of site occupancy in remaining uncut areas in the landscape. Both fire and logging have led to marked losses in the extent of old growth forest in Mountain Ash and Alpine Ash ecosystems. This is a concern given the strong association of most species of birds with old forest relative to younger age cohorts. Based on an understanding of the effects of fire and logging as drivers of change, we propose a series of inter-related management actions designed to enhance the conservation of avifauna in Mountain Ash and Alpine Ash ecosystems. A particular focus of management must be on increasing the interval between fires and limiting the spatial extent of wildfires and, in turn, significantly expanding the extent of old growth forest. This is because old growth forest is where most bird species are most likely to occur, and in the event of future wildfires, where fire severity will be lowest. Expansion of the old growth estate will require commercial logging operations to be excluded from large parts of Mountain Ash and Alpine Ash forests.

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.

Effective number of white shark (Carcharodon carcharias, Linnaeus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand

Population size is a central parameter for conservation; however, monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data-poor presenting barriers to the evaluation of conservation management outcomes and the modeling of future solutions. Such is the case for the white shark (Carcharodon carcharias), a highly mobile apex predator for whom recent and substantial population declines have been recorded in many globally distributed populations. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle (Nb) to provide a snapshot of recent reproductive effort in an east Australian-New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, and 2013) using two genetic estimators (linkage disequilibrium; LD and sibship assignment; SA) based on genetic data derived from two types of genetic markers (single nucleotide polymorphisms; SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable; for example, the 2013 age cohort Nb(SA) was 289 (95% CI 200-461) and Nb(LD) was 208.5 (95% CI 116.4-712.7). We show that over the time period studied, Nb was stable and ranged between 206.1 (SD ± 45.9) and 252.0 (SD ± 46.7) per year using a combined estimate of Nb(LD+SA) from SNP loci. In addition, a simulation approach showed that in this population the effective population size (Ne) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data-poor species of conservation concern.