The world's biodiversity is in peril. The major threats to biodiversity globally are habitat change, overexploitation, climate change, invasive species and pollution. Not only do these stressors impact free-living organisms, but they affect parasitic ones as well. Herein, this perspective examines the potential consequences of these anthropogenic perturbations on helminth populations and communities, with emphasis on significant developments over the past decade. Furthermore, several case studies are examined in more detail for each of these threats to biodiversity. While effects are widespread and diverse, for the most part all these environmental stressors have negative effects on parasite populations and communities. Those parasites with complex life cycles that are trophically transmitted are often more at risk, although larval parasites with a wide host spectrum, and directly transmitted ectoparasites, appear less threatened and may even benefit. However, differential effects on hosts and parasites, on parasite life cycle stages and on host–parasite interactions made specific predictions difficult and context-dependent. Experimental laboratory and mesocosm studies on specific parasites that test effects on the different life cycle stages, hosts and host–parasite interactions, permitting the determination of net effects of an environmental stressor, yield insightful and sometimes counterintuitive results, although they remain a simplification of real-world complexity. Recent advances in the use of parasites as bioindicators of effects also are discussed.

Over recent decades, Chinese giant salamanders Andrias spp. have declined dramatically across much of their range. Overexploitation and habitat degradation have been widely cited as the cause of these declines. To investigate the relative contribution of each of these factors in driving the declines, we carried out standardized ecological and questionnaire surveys at 98 sites across the range of giant salamanders in China. We did not find any statistically significant differences between water parameters (temperature, dissolved oxygen, ammonia, nitrite, nitrate, salinity, alkalinity, hardness and flow rate) recorded at sites where giant salamanders were detected by survey teams and/or had been recently seen by local respondents, and sites where they were not detected and/or from which they had recently been extirpated. Additionally, we found direct and indirect evidence that the extraction of giant salamanders from the wild is ongoing, including within protected areas. Our results support the hypothesis that the decline of giant salamanders across China has been primarily driven by overexploitation. Data on water parameters may be informative for the establishment of conservation breeding programmes, an initiative recommended for the conservation of these species.

A considerable variety of Indonesian avifauna is forced into the domestic and international pet trade, where the majority of individuals are caught in the wild. To monitor the volume and development of the trade and to evaluate the threat status of the traded species, bird market surveys are usually performed. The most commonly used monitoring technique is the “Direct Counting Method – DCM”, i.e. the counting of openly displayed individuals offered for sale. In this study, we evaluate the reliability of the outputs that DCM delivers by conducting regular long-term bird censuses at two of the main animal markets in Medan (Sumatra, Indonesia) involving 10 major local vendors specialising in the Sumatran Laughingthrush (Garrulax bicolor; SL), our target species. Both markets were visited from March to December 2015 with three different survey intervals (one, two and four visits per month). In total, according to DCM, we recorded up to 461 SL individuals offered for sale. However, a comparison of the monthly logs recorded directly by the vendors during the same period revealed that DCM only uncovered a negligible proportion of the total trade. Specifically, we detected only 4.6%, 8.1% and 16.1% of the traded SL individuals in relation to the set survey intervals. While the numbers of recorded SL individuals according to DCM and the three survey intervals were significantly interrelated, none of them correlated with the real numbers of traded birds provided by the vendors. Our results suggest that census-based market data are underestimated, and represent an unknown proportion of true trade volumes, regardless of the intensity of visits. In order to obtain reliable data and prevent the underestimation of the volume of trade, we recommend of undisclosed monitoring of markets and the engagement of trusted individuals with a past personal interest in this field or, if possible, the vendors themselves.

This study examines conservation effects of wildlife trade using demand and supply data from caged-bird markets in Sumatra, Indonesia. When consumers have a strong preference for species rarity, trade could result in wildlife overexploitation and species extinction. Results from a choice experiment show that buyers of caged birds indeed value species rarity. However, not all rare species are equally preferred. Species that are frequently traded lose their rarity value, even if rare in the wild. Analysis of time-series data collected from traders over a period of 20 months between 2013 and 2015 reveals an inelastic supply function for rare species, with market arrivals being insensitive to price changes. This may be due to a declining stock of rare species in the wild. Bird trade together with habitat loss can lead to extinction of a number of rare species in Indonesia. Several policy approaches on regulating caged-bird markets are discussed.

The Chinese giant salamander Andrias davidianus is endemic to China and is Critically Endangered, largely because of overexploitation for food. This species is an expensive delicacy in China, and a rapidly growing industry to farm the species has developed throughout much of the country, centred on the Qinling Mountain region of Shaanxi Province. During a 2010 workshop on Chinese giant salamander conservation, which involved a range of stakeholders from across China, it became clear that the conservation community knew little about the salamander farming industry and whether it posed actual or potential threats or opportunities for conservation of the Chinese giant salamander. We therefore conducted a series of investigations to understand the industry better. Our results indicate that although farming of Chinese giant salamanders has the potential to be a positive development for conservation by supplying market demand with farmed animals, it is currently more likely to threaten than support conservation of the species, with continued overexploitation and the potential added impacts of infectious disease and genetic pollution arising from farming practices such as movement of animals across the country and the release of untreated farm wastewater and farmed salamanders to the wild.

The processes that threaten 240 Indonesian threatened plants were identified and categorized based on a comprehensive review of the published literature and elicitation of information from experts. Intrinsic biological factors and habitat loss are the major causes of plant endangerment in Indonesia (affecting 83 and 82% of species respectively), followed by overexploitation (64%) and natural factors (6%). The dominant threats vary between major plant groups, with habitat loss being particularly important for palms and trees, and biological factors important for orchids. For all studied plant species three sets of inter-related threatening processes (threat syndromes) were identified that differed among the major plant groups. By identifying and evaluating the processes that threaten plants in Indonesia we provide knowledge to guide their future conservation.

Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action – ‘Water for Life’ – 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8% of the Earth's surface, yet this tiny fraction of global water supports at least 100000 species out of approximately 1.8 million – almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the ‘Water for Life’ decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as ‘receivers’ of land-use effluents, and the problems posed by endemism and thus non-substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and – in the case of migrating aquatic fauna – downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade-offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long-term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management – one that has been appropriately termed ‘reconciliation ecology’.

In the last 15 years new research findings have radically reshaped our understanding of human effects on ocean ecosystems. Here I describe five major shifts in perspective that reveal our impacts to be more severe and persistent than previously appreciated. Firstly, scientists have delved deep into the past and found that the global expansion of European nations across the planet caused the large-scale loss of marine megafauna. In the past century, expansion of industrial scale fishing has continued the process, massively reducing the biomass of exploited species. Secondly, once depleted we are finding that populations rarely rebound rapidly, contrary to a widespread belief in greater resilience of marine compared to terrestrial species. Thirdly, marine ecosystems are being shifted into alternative states that are less desirable from the human perspective and may be stable. It could be difficult, or impossible in some cases, to reverse impacts once inflicted. Fourthly, marine species are at risk of extinction. Loss of shallow water marine habitats is proceeding as rapidly as on land, many species have small geographic ranges, and many possess life history characteristics that leave them highly susceptible to overexploitation. Finally, the deep sea is not beyond harm. Depletion of shallow water fisheries and technological advances are opening up the deep to exploitation and its collateral impacts. If we are to reverse these negative trends we must establish large-scale networks of marine reserves that are off limits to damaging activities and fishing. Such reserves would protect biodiversity, and recover and sustain the world's fisheries productivity.