Michael Andrew Mccarthy

University of Melbourne | MSD · School of BioSciences

Information about species’ locations can influence what happens to them—from supporting habitat protection to exposing poaching targets. Debate about releasing locations when new species are found highlights the trade‐off between the risk of loss and the benefits of funding and public support. No research so far has collected data on how such decis...

1. While there has been substantial literature on the evaluation of predictions from single species distribution models, the topic of prediction has only recently begun to be addressed for joint species distribution models (JSDMs). These studies have covered only limited aspects of prediction: limited selection of models being compared, limited num...

Planned burning generates different types of pyrodiversity, however, experimental tests of how alternative spatial patterns of burning influence animal communities remain rare. Field tests are needed to understand the mechanisms through which spatial variation in planned fire affects fauna, and how fire can be applied to benefit biodiversity. We te...

Indirect surveillance methods, such as remote cameras and acoustic monitoring, are increasingly used in ecological surveys. The time to deploy these devices includes initial setup, possible maintenance, retrieval and then a potentially large investment in the processing of the collected data. Thus, costs will increase with both the number of sites...

No quantitative information exists on the movement patterns of Brolga, Antigone rubicunda (Gruidae) although the species is considered to undertake seasonal movements between breeding and non-breeding areas, and has been also described as both non-migratory and partly migratory. Information on this species’ movement behaviour is required to underst...

Surveys aimed at finding threatened and invasive species can be challenging due to individual rarity and low and variable individual detection rates. Detection rate in plant surveys typically varies due to differences among observers, among the individual plants being surveyed (targets), and across background environments. Interactions among these...

Fire has shaped Australia's diverse mammal fauna for millennia. However, ongoing changes to fire regimes threaten native mammal populations, and a significant conservation challenge is to understand and promote desirable forms of pyrodiversity (variation in fire regimes). A way forward is to quantify how different aspects of pyrodiversity influence...

1. The establishment of new botanic gardens in tropical regions highlights a need for weed risk assessment tools suitable for tropical ecosystems. The relevance of plant traits for invasion into tropical rainforests has not been well studied. 2. Working in and around four botanic gardens in Indonesia where 590 alien species have been planted, we es...

Line‐transect distance sampling is widely used to estimate population densities using distances of observed targets from transect lines to model detectability. When the target taxa are high density, the frequent measuring of distances may make the method seem impractical. We present a method that improves the efficiency of distance sampling when th...

Fire's growing impacts on ecosystems Fire has played a prominent role in the evolution of biodiversity and is a natural factor shaping many ecological communities. However, the incidence of fire has been exacerbated by human activity, and this is now affecting ecosystems and habitats that have never been fire prone or fire adapted. Kelly et al. rev...

Joint species distribution models (JSDMs) simultaneously model the distributions of multiple species, while accounting for residual co‐occurrence patterns. Despite increasing adoption of JSDMs in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. We define four different JSDM prediction types...

Conserving biodiversity and combating ecological hazards require cost‐effective allocation of limited resources among potential management projects. Project priorities, however, can change over time as underlying social‐ecological systems progress, novel priorities emerge, and management capabilities evolve. Thus, reallocation of ongoing investment...

Global biodiversity indices are used to measure environmental change and progress toward conservation goals, yet few indices have been evaluated comprehensively for their capacity to detect trends of interest, such as declines in threatened species or ecosystem function. Using a structured approach based on decision science, we qualitatively evalua...

Small mammals are commonly surveyed using live trapping but the influence of weather conditions on trap success is largely unknown. This information is required to design and implement more effective field surveys and monitoring. We tested the influence of weather and moon phase on capture rates of small mammals in the Murray Mallee region of semi-...

Habitat loss, degradation and fragmentation remain leading causes of amphibian declines across the globe. To mitigate these impacts, conservation managers may protect core habitats and pursue habitat creation or enhancement actions, including construction of artificial wetlands, manipulation of wetland hydroperiods, removal of invasive species or r...

Built infrastructure, such as wind farms and power lines, can impair wildlife movement. These barriers may displace individuals from important habitats due to direct mortality or disturbance. Understanding animal movement patterns can help avoid such impacts and manage population level effects. Avoiding impacts and implementing mitigation strategie...

Early warning signals (EWSs) offer the hope that patterns observed in data can predict the future states of ecological systems. While a large body of research identifies such signals prior to the collapse of populations, the prediction that such signals should also be present before a system’s recovery has thus far been overlooked. We assess whethe...

We developed a method to estimate population abundance from simultaneous counts of unmarked individuals over multiple sites. We considered that at each sampling occasion, individuals in a population could be detected at 1 of the survey sites or remain undetected and used either multinomial or binomial simultaneous‐count models to estimate abundance...

• In many animal populations, demographic parameters such as survival and recruitment vary markedly with age, as do parameters related to sampling, such as capture probability. Failing to account for such variation can result in biased estimates of population‐level rates. However, estimating age‐dependent survival rates can be challenging because a...

Joint species distribution models ( JSDM s) account for biotic interactions and missing environmental predictors in correlative species distribution models. Several different JSDM s have been proposed in the literature, but the use of different or conflicting nomenclature and statistical notation potentially obscures similarities and differences am...

Detecting exotic plant species is essential for invasive species management. By accounting for factors likely to affect species’ detection rates (e.g. survey conditions, observer experience), detectability models can help choose search methods and allocate search effort. Integrating information on species’ traits can refine detectability models, an...

Examples of used leaf photos for leaf area and leaf shape calculation of 25 detected exotic species. The photo ordered from smallest to the largest leaf shape (complexity) value. (TIF)

Line transect distance sampling lay out. Black circles represent individuals of exotic species and dashed arrows show their perpendicular distance to the transect. Surveys were conducted from the border of the botanic gardens towards the native rainforest interior. Only detections within 10 m of the transect line were recorded. The number of transe...

List of reference publications used for native species composition information data. (PDF)

Map of sampling locations: Cibodas, Kuningan, Baturraden and Eka Karya Bali. (TIF)

History plot of Markov chain Monte Carlo (MCMC) simulation based on the constructed detectability model. The plots demonstrate the converged chains in the model simulation for all variables (nodes) included (b0, bS, bS2, bH, bA, and bA2) (left part of the graph). The credible interval for all involved variables are not containing zero values except...

R code script for Bayesian analysis of the tested detection model in this study. (PDF)

Total data set used for the analysis. (CSV)

The increasing awareness that a fire regime that promotes biodiversity in one system can threaten biodiversity in another has resulted in a shift away from fire management based on vague notions of maximising pyrodiversity, towards determining the optimal fire regime based on the demonstrated requirements of target species. We utilised a long‐runni...

Australia has contributed a disproportionate number of the world's mammal extinctions over the past 200 years, with the greatest loss of species occurring through the continent's southern and central arid regions. Many taxonomically and ecologically similar species are now undergoing widespread decline across the northern Australian mainland, possi...

Understanding wildlife-vehicle collision risk is critical to mitigating its negative impacts on wildlife conservation, human health and economy. Research often focuses on collisions between wildlife and road vehicles, but collision risk factors for other types of vehicles, less examined in the literature, may also be informative. We studied spatial...

Biodiversity offsetting schemes permit habitat destruction provided that losses are compensated by gains elsewhere. While hundreds of offsetting schemes are used around the globe, the optimal timing of habitat creation in such projects is poorly understood. Here, we developed a spatially explicit metapopulation model for a single-species subject to...

Biodiversity indices are widely used to summarize changes in the distribution and abundance of multiple species and measure progress towards management targets. However, the sensitivity of biodiversity indices to the data, landscape classification and conservation values underpinning them are rarely interrogated. There are limited studies to help s...

Habitat loss and fragmentation are global threats to biodiversity and major research topics in ecology and conservation biology. We conducted a systematic review to assess where – the geographic locations and habitat types - and how – the study designs, conceptual underpinnings, landscape metrics and biodiversity measures - scientists have studied...

Invasive species managers must decide how best to allocate surveillance and control effort through space. Doing this requires the predicted location of the invasive species, and these predictions come with uncertainty. While optimal surveillance designs have been developed for many invasive species, few have considered uncertainty in species distri...

Urbanization causes major environmental changes globally, which can potentially homogenize biota across cities through the loss and gain of particular types of species. We examine whether urban environments consistently select for plants with particular traits and the implications of such changes on the functional composition of urban floras. We cl...

Deaths of animals in the wild are rarely observed directly, which often limits understanding of survival rates. Telemetry transmitters offer field ecologists the opportunity to observe mortality events in cases as the absence of animal movement. When observations of mortality are based on factors such as the absence of animal movement, live individ...

Fire is a global driver of ecosystem structure, function, and change. Problems common to fire scientists and managers worldwide include a limited knowledge of how multiple taxonomic groups within a given ecosystem respond to recurrent fires, and how interactions between fire regimes and environmental gradients influence biodiversity. We tested six...

The eradication of newly detected alien plant species is often prescribed, but rarely successful. Eradication programs fail for many reasons, however, for eradication to remain a cost-efficient management option it is clear that good decisions must be made at the outset. Here we re-frame the project prioritization protocol (PPP), a tool widely used...

Global change is threatening ecosystems and biodiversity world‐wide, creating a pressing need to understand how climate and disturbance regimes interact and influence the persistence of species. We quantify how three ecosystem drivers – rainfall, fire and herbivory – influence vital rates in the perennial resprouting graminoid, Triodia scariosa , a...

Adaptive management is widely advocated to improve environmental management. Derivations of optimal strategies for adaptive management, however, tend to be case specific and time consuming. In contrast, managers might seek relatively simple guidance, such as insight into when a new potential management action should be considered, and how much effo...

Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of “positi...

Aim To investigate whether feral cats influence the distribution of Australia's largest remnant population of the threatened brush‐tailed rabbit‐rat Conilurus penicillatus and examine whether they influenced the extinction probability of C. penicillatus over a 15‐year period (2000–2015). Location Melville Island, northern Australia. Methods In 20...

An influential concept in ecology commonly guides conservation decision makers: that environmental heterogeneity drives biodiversity (Stein et al. 2014). In the context of fire management for animal conservation, this concept has encouraged heterogeneity in fire regimes under the assumption that ‘pyrodiversity promotes biodiversity” (Martin & Sapsi...

Figure S2. Predicted relative likelihood of grey kangaroo presence across Australia.

Figure S1. Effects of predictors on relative likelihood of grey kangaroo occurrence.

Figure S3. Effects of predictor variables on traffic volume and speed.

Collisions of vehicles with wildlife kill and injure animals and are also a risk to vehicle occupants, but preventing these collisions is challenging. Surveys to identify problem areas are expensive and logistically difficult. Computer modeling has identified correlates of collisions, yet these can be difficult for managers to interpret in a way th...

A definitive list of invasive species traits remains elusive, perhaps due to inconsistent ways of identifying invasive species. Invasive species are typically identified using one or more of four demographic criteria (local abundance, geographic range, environmental range, spread rate), referred to here as the demographic dimensions of invasiveness...

Environmental DNA ( eDNA ) sampling can be a highly sensitive method for detecting aquatic taxa; however, the cost‐efficiency of this technique relative to traditional methods has not been rigorously assessed. We show how methods that account for imperfect and stochastic detection can be used to (i) determine the optimal allocation of survey effort...

Increased incidence of landscape fire and pollinator declines with co‐extinctions of dependent plant species are both globally significant. Fire can alter species distributions, but its effects on plant–pollinator interactions are poorly understood so its present and future role in coupled plant–pollinator declines cannot be assessed. We develop a...

Increasing the colonization rate of metapopulations can improve persistence, but can also increase exposure to threats. To make good decisions, managers must understand whether increased colonization is beneficial or detrimental to metapopulation persistence. While a number of studies have examined interactions between metapopulations, colonization...

The early detection of newly naturalised alien species is vital to ensuring the greatest chance of their successful eradication. Understanding where species naturalise most frequently is the first stage in allocating surveillance effort. Using Australia’s Virtual Herbarium, we compiled the collection records for all plant species in Australia. We c...

Previous studies that optimize allocation of surveillance resources over space have assumed that detection rates are constant over time and that travel or survey costs are the same for all sites. Other recent research explicitly accounts for stochastically varying detection rates and distinct travel costs but restricts attention to the optimal numb...

Adaptive management is a framework for resolving key uncertainties while managing complex ecological systems. Its use has been prominent in fisheries research and wildlife harvesting; however, its application to other areas of environmental management remains somewhat limited. Indeed, adaptive management has not been used to guide and inform metapo...

Adaptive management is a framework for resolving key uncertainties while managing complex ecological systems. Its use has been prominent in fi sheries research and wildlife harvesting; however, its application to other areas of environmental management remains somewhat limited. Indeed, adaptive management has not been used to guide and inform metap...

Practical conservation normally requires making decisions in the face of uncertainty. Our attitude toward that uncertainty, and the risks it entails, shape the way conservation decisions are made. Stochastic dominance (SD), a method more commonly used in economics, can be used to rank alternative conservation actions by comparing the probability di...

Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a tradit...

Ex-situ conservation strategies for threatened species often require long-term commitment and financial investment to achieve management objectives. Here, we interpret the decision to adopt ex-situ management for a target species as the end point of several linked decisions. Logically, one must first decide which specific management actions are mos...

There is a longstanding debate regarding the need for ecology to develop consistent terminology. On one hand, consistent terminology would aid in synthesizing results between studies and ease communication of results. On the other hand, there is no proof that standardizing terminology is necessary and it could limit the scope of research in certain...