Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Data from: Patterns of mammalian population decline inform conservation action

1. Evaluations of wildlife population dynamics have the potential to convey valuable information on the type of pressure affecting a population and could help predict future changes in the population's trajectory. Greater understanding of different patterns of population declines could provide a useful mechanism for assessing decline severity in the wild and identifying those populations that are more likely to exhibit severe declines. 2. We identified 93 incidences of decline within 75 populations of mammalian species using a time-series analysis method. These included: linear, quadratic convex (accelerating) declines, exponential concave (decelerating) declines, and quadratic concave declines (representing recovering populations). Excluding linear declines left a dataset of 85 declines to model the relationship between each decline-curve type and a range of biological, anthropogenic, and time-series descriptor explanatory variables. 3. None of the decline-curve types were spatially or phylogenetically clustered. The only characteristic that could be consistently associated with any curve-type was the time at which they were more likely to occur within a time-series. Quadratic convex declines were more likely to occur at the start of the time-series, while recovering curve shapes (quadratic concave declines) were more likely at the end of the time-series. 4. Synthesis and applications: The ability to link certain factors with specific decline dynamics across a number of mammalian populations is useful for management purposes as it provides decision-makers with potential triggers upon which to base their conservation actions. We propose that the identification of quadratic convex declines could be used as an early-warning signal of potentially severe decline dynamics. For such populations, increased population monitoring effort should be deployed to diagnose the cause of its decline and avert possible extinctions. Conversely, the presence of a quadratic concave decline suggests that the population has already undergone a period of serious decline but is now in the process of recovery. Such populations will require different types of conservation actions, focussed on enhancing their chances of recovery

Patterns of mammalian population decline inform conservation action

Evaluations of wildlife population dynamics have the potential to convey valuable information on the type of pressure affecting a population and could help predict future changes in the population's trajectory. Greater understanding of different patterns of population declines could provide a useful mechanism for assessing decline severity in the wild and identifying those populations that are more likely to exhibit severe declines. We identified 93 incidences of decline within 75 populations of mammalian species using a time-series analysis method. These included linear, quadratic convex (accelerating) declines, exponential concave (decelerating) declines and quadratic concave declines (representing recovering populations). Excluding linear declines left a data set of 85 declines to model the relationship between each decline-curve type and a range of biological, anthropogenic and time-series descriptor explanatory variables. None of the decline-curve types were spatially or phylogenetically clustered. The only characteristic that could be consistently associated with any curve type was the time at which they were more likely to occur within a time series. Quadratic convex declines were more likely to occur at the start of the time series, while recovering curve shapes (quadratic concave declines) were more likely at the end of the time series. Synthesis and applications. The ability to link certain factors with specific decline dynamics across a number of mammalian populations is useful for management purposes as it provides decision-makers with potential triggers upon which to base their conservation actions. We propose that the identification of quadratic convex declines could be used as an early-warning signal of potentially severe decline dynamics. For such a population, increased population monitoring effort should be deployed to diagnose the cause of its decline and avert possible extinctions. Conversely, the presence of a quadratic concave decline suggests that the population has already undergone a period of serious decline but is now in the process of recovery. Such populations will require different types of conservation actions, focussing on enhancing their chances of recovery

Decline-curve data set for comparative analyses

Dataset used for generalized linear mixed modelling of decline curve-type. Please see the ReadMe file for further descriptions of each column title

Kalman-filtered time-series

The first column represents the years over which monitoring took place, and all subsequent columns represent the abundance of different population IDs, following the application of the Kalman filter (to account for potential sources of uncertainty arising from count errors)

Raw time-series data

75 high quality mammalian population time series, representing 33 species, spanning six orders, drawn from the Living Planet Index vertebrate population abundance data base. The first column represents the years over which monitoring took place, and all subsequent columns represent the abundance of different population IDs

Evaluating trade-offs between target persistence levels and numbers of species conserved

A focus of conservation planning is to maximize the probability of species persistence, but this may reduce the number of species that can be secured with a limited budget. Using a data set of 700 New Zealand species, we examine the trade-off between providing a high level of persistence for some species and a lower level of persistence for more species. We find that the target persistence level that delivers the highest conservation outcome is a function of the annual budget, such that lower budgets have lower optimal targets. However, it is never optimal to manage species below a 75% probability of persistence. We introduce a prioritization approach that maximizes biodiversity gains based on a flexible persistence target, and demonstrate how strategies with fixed high-persistence targets can be inefficient. We also illustrate the risks in spreading conservation resources too thinly by undertaking low levels of management on more species

Effect of risk aversion on prioritizing conservation projects

Conservation outcomes are uncertain. Agencies making decisions about what threat mitigation actions to take to save which species frequently face the dilemma of whether to invest in actions with high probability of success and guaranteed benefits or to choose projects with a greater risk of failure that might provide higher benefits if they succeed. The answer to this dilemma lies in the decision maker's aversion to risk—their unwillingness to accept uncertain outcomes. Little guidance exists on how risk preferences affect conservation investment priorities. Using a prioritization approach based on cost effectiveness, we compared 2 approaches: a conservative probability threshold approach that excludes investment in projects with a risk of management failure greater than a fixed level, and a variance-discounting heuristic used in economics that explicitly accounts for risk tolerance and the probabilities of management success and failure. We applied both approaches to prioritizing projects for 700 of New Zealand's threatened species across 8303 management actions. Both decision makers’ risk tolerance and our choice of approach to dealing with risk preferences drove the prioritization solution (i.e., the species selected for management). Use of a probability threshold minimized uncertainty, but more expensive projects were selected than with variance discounting, which maximized expected benefits by selecting the management of species with higher extinction risk and higher conservation value. Explicitly incorporating risk preferences within the decision making process reduced the number of species expected to be safe from extinction because lower risk tolerance resulted in more species being excluded from management, but the approach allowed decision makers to choose a level of acceptable risk that fit with their ability to accommodate failure. We argue for transparency in risk tolerance and recommend that decision makers accept risk in an adaptive management framework to maximize benefits and avoid potential extinctions due to inefficient allocation of limited resources

Balancing phylogenetic diversity and species numbers in conservation prioritization, using a case study of threatened species in New Zealand

Funding for managing threatened species is currently insufficient to assist recovery of all species, so management projects must be prioritized. In attempts to maximize phylogenetic diversity conserved, prioritization protocols for threatened species are increasingly weighting species using metrics that incorporate their evolutionary distinctiveness. In a case study using 700 of the most threatened species in New Zealand, we examined trade-offs between emphasis on species’ evolutionary distinctiveness weights, and the numbers of species prioritized, as well as costs and probabilities of success for recovery projects. Increasing emphasis on species’ evolutionary distinctiveness weights in the prioritization protocol led to greater per-species costs and higher risk of project failure. In a realistic, limited-budget scenario, this resulted in fewer species prioritized, which imposed limits on the total phylogenetic diversity that could be conserved. However, by systematically varying the emphasis on evolutionary distinctiveness weight in the prioritization protocol we were able to minimize trade-offs, and obtain species groups that were near-optimal for both species numbers and phylogenetic diversity conserved. Phylogenetic diversity may not equate perfectly with functional diversity or evolutionary potential, and conservation agencies may be reluctant to sacrifice species numbers. Thus, we recommend prioritizing species groups that achieve an effective balance between maximizing phylogenetic diversity and number of species conserved