A function-based typology for Earth's ecosystems.

As the United Nations develops a post-2020 global biodiversity framework for the Convention on Biological Diversity, attention is focusing on how new goals and targets for ecosystem conservation might serve its vision of 'living in harmony with nature'1,2. Advancing dual imperatives to conserve biodiversity and sustain ecosystem services requires reliable and resilient generalizations and predictions about ecosystem responses to environmental change and management3. Ecosystems vary in their biota4, service provision5 and relative exposure to risks6, yet there is no globally consistent classification of ecosystems that reflects functional responses to change and management. This hampers progress on developing conservation targets and sustainability goals. Here we present the International Union for Conservation of Nature (IUCN) Global Ecosystem Typology, a conceptually robust, scalable, spatially explicit approach for generalizations and predictions about functions, biota, risks and management remedies across the entire biosphere. The outcome of a major cross-disciplinary collaboration, this novel framework places all of Earth's ecosystems into a unifying theoretical context to guide the transformation of ecosystem policy and management from global to local scales. This new information infrastructure will support knowledge transfer for ecosystem-specific management and restoration, globally standardized ecosystem risk assessments, natural capital accounting and progress on the post-2020 global biodiversity framework.

Local and downstream cumulative effects of traditional meadow management on stream-water quality and multiple riparian taxa.

Water quality and riparian communities are among the most affected stream components by agriculture. However, little is known about the effects of riparian management for both aquatic and terrestrial taxa at different spatial scales. Here, we surveyed aquatic (diatoms) and terrestrial taxa (bryophytes, vascular plants, litter-dwelling snails, and ground and volant arthropods), to compare the abundance and richness of riparian taxa and chemical quality between reference and exposed sites in two stream reaches each of c. 3.5 km in northwestern Spain. Impacts in exposed sites were mainly due to traditional farming practices (TFPs), which included traditional meadow management, weirs built for now-unused water mills and sporadic timber harvesting. Therefore, we measured ten covariates and predictors related to the intensification of TFPs at local and within-stream scales and explored associations with riparian and water-quality measures to study the potential effects of TFPs in more detail. Reference and exposed sites did not differ significantly in water properties (diatom-biotic indices, conductivity, total organic carbon and nitrates), but exposed sites had less concentrations of soil metals Cd, Cu, Ni and Zn and less cover and richness of riparian trees, as inferred by the index QBR. Exposed sites had more volant insect decomposers and reference sites a greater abundance or richness of snails, ground predators and decomposers. Bryophyte richness was greater in reference sites. Our inferences may inform the joint cumulative downstream effects of weirs, meadow uses and riparian alterations but were generally consistent with most riparian taxa benefiting from having larger forested areas. Given the contrasting responses among taxa, we argue that land snails, terrestrial flies, and centipedes may be valuable additions to current riparian assessments mostly based on plants, beetles and spiders as indicator taxa. Our study also suggests caution when inferring farming impacts on streams from the surface area of pastoral land.

Integrated terrestrial-freshwater planning doubles conservation of tropical aquatic species.

Conservation initiatives overwhelmingly focus on terrestrial biodiversity, and little is known about the freshwater cobenefits of terrestrial conservation actions. We sampled more than 1500 terrestrial and freshwater species in the Amazon and simulated conservation for species from both realms. Prioritizations based on terrestrial species yielded on average just 22% of the freshwater benefits achieved through freshwater-focused conservation. However, by using integrated cross-realm planning, freshwater benefits could be increased by up to 600% for a 1% reduction in terrestrial benefits. Where freshwater biodiversity data are unavailable but aquatic connectivity is accounted for, freshwater benefits could still be doubled for negligible losses of terrestrial coverage. Conservation actions are urgently needed to improve the status of freshwater species globally. Our results suggest that such gains can be achieved without compromising terrestrial conservation goals.

FragSAD: A database of diversity and species abundance distributions from habitat fragments.

Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species' assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

Major determinants of the occurrence of a globally invasive parasite in riverine fish over large-scale environmental gradients.

The increased rate of outbreaks of infectious diseases in ecosystems is a dramatic consequence of global change, particularly when outbreaks affect important resources such as freshwater fish. However, the links between disease-inducing epizootics and widespread human impacts, including nutrient pollution and high water conductivity, in freshwater organisms are largely unexplored. We used data from extensive surveys in northeastern Spain (99,700 km2, 15 river catchments, n = 530 sites) to explore the environmental factors that singly, or in combination, are likely to influence the occurrence of the invasive parasite, Lernaea cyprinacea, after accounting for host fish characteristics. Smaller fish, lower altitudes, higher water conductivity and nutrient pollution were associated with higher probabilities of infection in 19 endemic and widely distributed fish species. We found no evidence that interactive effects among riverine stressors related to water and physical habitat quality better explained the probability of occurrence of L. cyprinacea in fish than did additive-stressor combinations. Nutrient pollution and high water conductivity were two of the major factors contributing to the increased occurrence of L. cyprinacea. Therefore, the improvement of wastewater treatment processes and agricultural practices probably would help to reduce the occurrence of this parasite among native fish.

Second rate or a second chance? Assessing biomass and biodiversity recovery in regenerating Amazonian forests.

Secondary forests (SFs) regenerating on previously deforested land account for large, expanding areas of tropical forest cover. Given that tropical forests rank among Earth's most important reservoirs of carbon and biodiversity, SFs play an increasingly pivotal role in the carbon cycle and as potential habitat for forest biota. Nevertheless, their capacity to regain the biotic attributes of undisturbed primary forests (UPFs) remains poorly understood. Here, we provide a comprehensive assessment of SF recovery, using extensive tropical biodiversity, biomass, and environmental datasets. These data, collected in 59 naturally regenerating SFs and 30 co-located UPFs in the eastern Amazon, cover >1,600 large- and small-stemmed plant, bird, and dung beetles species and a suite of forest structure, landscape context, and topoedaphic predictors. After up to 40 years of regeneration, the SFs we surveyed showed a high degree of biodiversity resilience, recovering, on average among taxa, 88% and 85% mean UPF species richness and composition, respectively. Across the first 20 years of succession, the period for which we have accurate SF age data, biomass recovered at 1.2% per year, equivalent to a carbon uptake rate of 2.25 Mg/ha per year, while, on average, species richness and composition recovered at 2.6% and 2.3% per year, respectively. For all taxonomic groups, biomass was strongly associated with SF species distributions. However, other variables describing habitat complexity-canopy cover and understory stem density-were equally important occurrence predictors for most taxa. Species responses to biomass revealed a successional transition at approximately 75 Mg/ha, marking the influx of high-conservation-value forest species. Overall, our results show that naturally regenerating SFs can accumulate substantial amounts of carbon and support many forest species. However, given that the surveyed SFs failed to return to a typical UPF state, SFs are not substitutes for UPFs.

Water-quality impacts in semi-arid regions: can natural 'green filters' mitigate adverse effects on fish assemblages?

The effective aridity in riparian areas is increasing from climate change and from human water consumption, which exacerbates the impacts of effluents from wastewater-treatment plants and from catchment run-off in rivers. The potential of natural riparian areas to act as 'green filters' has long been recognized, but the possible ecological benefits of natural riparian areas over large-scale environmental gradients on fish have not been explored in detail. Using an extensive data-set from northeastern Spain (99,700 km2, 15 catchments, 530 sites), ours is the first study to ask whether natural riparian vegetation can mitigate the effects of pollution on fish in rivers experiencing water scarcity. We used multimodel inference to explore the additive and interactive effects of riparian vegetation with nutrient pollution and water conductivity, which are among the world's worst river stressors, on multiple fish guilds, including widely distributed species and highly invasive alien fish species. Most models (54%) supported the additive effects of water-quality factors on fish, after having accounted for the influence of geography and hydrological alterations. Although many fewer models (7%) included riparian vegetation as an important predictor, riparian vegetation modulated the forms of the associations between fish and pollution. The relationship of nutrient pollution with native and alien fish richness changed from negative to positive with greater riparian structure or species richness. However, we found the opposite effect for the mean body size of sedentary fish, and only positive additive effects of riparian richness for the probability of occurrence of pelagic fish. Ammonium and nitrite concentrations adversely affected fish in these rivers up to 10 years after the enforcement of the implementation of the Water Framework Directive by the European Union. High conductivity also much affects fish, having negatives associations with migratory, pelagic, invertivorous and native fish, and positive associations with sedentary, benthic, omnivorous and alien fish. Therefore, the current status of natural riparian areas is unlikely to fully mitigate water-quality impacts on fish. The conservation of freshwater resources in semi-arid regions, such as north-eastern Spain, requires improved waste-water treatments and better agriculture practices.

Environmental correlates of food-chain length, mean trophic level and trophic level variance in invaded riverine fish assemblages.

Examining how the trophic structure of biotic assemblages is affected by human impacts, such as habitat degradation and the introduction of alien species, is important for understanding the consequences of such impacts on ecosystem functioning. We used general linear mixed models and hierarchical partitioning analyses of variance to examine for the first time the applicability of three hypotheses (ecosystem-size, productivity and disturbance) for explaining food-chain length (FCL) in invaded fish assemblages. We used Fishbase trophic level (TL) estimates for 16 native and 18 alien fish species in an extensive riverine system in north-eastern Spain (99,700 km2, 15 catchments, 530 sites). The FCL of assemblages ranged from 2.7 to 4.42. Ecosystem size-related variables (Strahler stream order, physical habitat diversity) and human-disturbance (conductivity) made the largest contribution to the explained variance in the FCL model after accounting for spatial confounding factors and collinearity among predictors. Within-assemblage TL also was positively associated with Strahler stream order, suggesting that large rivers have the highest trophic diversity. High conductivity was negatively associated with FCL, as did with the mean TL of fish assemblages. However, an inverse association was found between mean TL and Strahler stream order, possibly because the presence of fish species of high TL may be offset by larger numbers of alien species of lower TL in large rivers. Given that there may be trophic replacements among native and alien species, this inference needs to be addressed with detailed trophic studies. However, reducing water conductivity by improved wastewater treatment and better agricultural practices probably would help to conserve the fish species on the apices of aquatic food-webs.

Catchment land use predicts benthic vegetation in small estuaries.

Many estuaries are becoming increasingly eutrophic from human activities within their catchments. Nutrient loads often are used to assess risk of eutrophication to estuaries, but such data are expensive and time consuming to obtain. We compared the percent of fertilized land within a catchment, dissolved inorganic nitrogen loads, catchment to estuary area ratio and flushing time as predictors of the proportion of macroalgae to total vegetation within 14 estuaries in south-eastern Australia. The percent of fertilized land within the catchment was the best predictor of the proportion of macroalgae within the estuaries studied. There was a transition to a dominance of macroalgae once the proportion of fertilized land in the catchment exceeded 24%, highlighting the sensitivity of estuaries to catchment land use.

Institutional impediments to conservation of freshwater dependent ecosystems.

When freshwater resources become scarce there is a trade-off between human resource demands and environmental sustainability. The cost of conserving freshwater ecosystems can potentially be reduced by implementing institutional reforms that endow environmental water managers with a permanent water entitlement and the capacity to store, trade and release water. Australia's Murray Darling Basin Plan (MDBP) includes one of the world's most ambitious programs to recover water for the environment, supported by institutional reforms that allow environmental water managers to operate in water markets. One of the anticipated benefits of the Plan is to improve the health of flood-dependent forests, which are among the most endangered ecosystems globally because of river regulation and land clearance. However, periodic flooding to conserve floodplain ecosystems in the MDB creates losses to riparian landowners such as damage to fencing and temporary loss of access to flooded land. To reduce these losses reservoir operators restrict daily water release volumes. Using a model of optimal water management in Australia's southern MDB we estimate that current reservoir operating restrictions will substantially reduce the ecological benefits of investments made to recover water for the environment. The reduction in benefits is largest if floodplain forests decline rapidly without periodic inundation. In the latter circumstances, ecological losses cannot significantly be reduced by allowing environmental water managers to operate in water markets. Our findings demonstrate that the recovery of large volumes of water for environmental purposes and water market reforms are insufficient for conserving flood-dependent ecosystems without coordination and cooperation among multiple stakeholders responsible for water and land management.

The presence of non-native species is not associated with native fish sensitivity to water pollution in greatly hydrologically altered rivers.

There is a risk of 'ecological surprises' if multiple potentially interacting stressors are managed individually, which is a question attracting significant current interest. Habitat degradation and species introductions are major threats to global biodiversity, and riverine fish are among the most threatened taxa in the world. Our interest was whether the presence of non-native species can affect native fish sensitivity to water quality deterioration in a large region in northeastern Spain (99,700km2, 15 catchments, 530 sites). We used a 'base model' with geographical and hydro-morphological variables, which are the major shaping factors in rivers. We tested whether water pollution, non-native species, or their interaction provided an improved understanding of patterns of distributions and health measurements of the twelve most common native species. There was little evidence that variation in native species abundance, where they occurred, the presence of diseases and changes in mean fish length or body condition was affected by water deterioration, the presence of non-native species, or their interaction. The disease rate and occurrence of native species might be affected, to a minor degree, by water quality changes and the presence of non-native species. Environmental conditions between sites with and without non-native fish differed in the condition of riparian areas and in water quality. Based on presence-absence data and changes in abundances through weighted average equations we also derived potential safe levels of salinization, nutrient pollution, and pH for the native fish. Overall, additive effects of stressors prevail over interactions, and the restoration of natural hydro-morphology in rivers is likely to be the most effective management approach to improving the prospects for the native fish fauna.

Potential future scenarios for Australia's native biodiversity given on-going increases in human population.

Most natural assets, including native biodiversity (our focus), are under increasing threat from direct (loss of habitat, hunting) and indirect (climate change) human actions. Most human impacts arise from increasing human populations coupled with rises in per capita resource use. The rates of change of human actions generally outpace those to which the biota can respond or adapt. If we are to maintain native biodiversity, then we must develop ways to envisage how the biota may be affected over the next several decades to guide management and policy responses. We consider the future for Australia's native biodiversity in the context of two assumptions. First, the human population in Australia will be 40million by 2050, which has been mooted by federal government agencies. Second, greenhouse gas emissions will track the highest rates considered by the Intergovernmental Panel on Climate Change. The scenarios are based on major drivers of change, which were constructed from seven key drivers of change pertinent to native biodiversity. Five scenarios deal with differing distributions of the human population driven by uncertainties in climate change and in the human responses to climate change. Other scenarios are governed largely by global change and explore different rates of resource use, unprecedented rates of technological change, capabilities and societal values. A narrative for each scenario is provided. The set of scenarios spans a wide range of possible future paths for Australia, with different implications for the future of native biodiversity.

A method to identify drivers of societal change likely to affect natural assets in the future, illustrated with Australia's native biodiversity.

Human society has a profound adverse effect on natural assets as human populations increase and as global climate changes. We need to envisage different futures that encompass plausible human responses to threats and change, and become more mindful of their likely impacts on natural assets. We describe a method for developing a set of future scenarios for a natural asset at national scale under ongoing human population growth and climate change. The method involves expansive consideration of potential drivers of societal change, a reduction of these to form a small set of key drivers to which contrasting settings are assigned, which we use to develop a set of different scenarios. We use Australia's native biodiversity as the focus to illustrate the method.

Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation.

Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Pará. Catchments retaining more than 69­80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil's Forest Code, resulted in a 39­54% loss of conservation value: 96­171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Pará, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Pará's strictly protected areas is equivalent to the loss of 92,000­139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.

Idiosyncratic responses of Amazonian birds to primary forest disturbance.

As humans continue to alter tropical landscapes across the world, it is important to understand what environmental factors help determine the persistence of biodiversity in modified ecosystems. Studies on well-known taxonomic groups can offer critical insights as to the fate of biodiversity in these modified systems. Here we investigated species-specific responses of 44 forest-associated bird species with different behavioural traits to forest disturbance in 171 transects distributed across 31 landscapes in two regions of the eastern Brazilian Amazon. We investigated patterns of species occurrence in primary forests varyingly disturbed by selective-logging and fire and examined the relative importance of local, landscape and historical environmental variables in determining species occurrences. Within undisturbed and disturbed primary forest transects, we found that distance to forest edge and the biomass of large trees were the most important predictors driving the occurrence of individual species. However, we also found considerable variation in species responses to different environmental variables as well as inter-regional variation in the responses of the same species to the same environmental variables. We advocate the utility of using species-level analyses to complement community-wide responses in order to uncover highly variable and species-specific responses to environmental change that remain so poorly understood.

How pervasive is biotic homogenization in human-modified tropical forest landscapes?

Land-cover change and ecosystem degradation may lead to biotic homogenization, yet our understanding of this phenomenon over large spatial scales and different biotic groups remains weak. We used a multi-taxa dataset from 335 sites and 36 heterogeneous landscapes in the Brazilian Amazon to examine the potential for landscape-scale processes to modulate the cumulative effects of local disturbances. Biotic homogenization was high in production areas but much less in disturbed and regenerating forests, where high levels of among-site and among-landscape ß-diversity appeared to attenuate species loss at larger scales. We found consistently high levels of ß-diversity among landscapes for all land cover classes, providing support for landscape-scale divergence in species composition. Our findings support concerns that ß-diversity has been underestimated as a driver of biodiversity change and underscore the importance of maintaining a distributed network of reserves, including remaining areas of undisturbed primary forest, but also disturbed and regenerating forests, to conserve regional biota.

A bust but no boom: responses of floodplain bird assemblages during and after prolonged drought.

Climate change alters the frequency and severity of extreme events, such as drought. Such events will be increasingly important in shaping communities as climate change intensifies. The ability of species to withstand extreme events (resistance) and to recover once adverse conditions abate (resilience) will determine their persistence. We estimated the resistance and resilience of bird species during and after a 13-year drought (the 'Big Dry') in floodplain forests in south-eastern Australia. We conducted bird surveys at the beginning and end of the Big Dry, and after the abrupt end to the drought (the 'Big Wet'), to evaluate species-specific changes in reporting rates among the three periods. We assessed changes in bird-breeding activity before and after the Big Wet to estimate demographic resilience based on breeding. Between the start and the end of the Big Dry (1998 vs. 2009), 37 of 67 species declined substantially. Of those, only two had increased reporting rates after the Big Wet (2009 vs. 2013) that were equal to or larger than their declines, while three partially recovered. All other declining species showed low resilience: 25 showed no change in reporting rates and seven declined further. The number of breeding species and total breeding activity of all species declined after the Big Wet, and there was no change in the number of young produced. The Big Dry caused widespread declines in the floodplain avifauna. Despite the drought being broken by 2 years of well-above-average rainfall and subsequent near-average rainfall, most species showed low resilience and there was little indication that overall breeding had increased. The effects of drought appeared to be pervasive for much of the floodplain avifauna, regardless of species traits (species body mass, fecundity, mobility or diet). Ecosystems such as these are likely to require active management and restoration, including reinstatement of natural flooding regimes, to improve ecological condition, to enhance resistance and resilience to extreme climate events.

Thermodynamics predicts density-dependent energy use in organisms and ecological communities.

Linking our knowledge of organisms to our knowledge of ecological communities and ecosystems is a key challenge for ecology. Individual size distributions (ISDs) link the size of individual organisms to the structure of ecological communities, so that studying ISDs might provide insight into how organism functioning affects ecosystems. Similarly shaped ISDs among ecosystems, coupled with allometric links between organism size and resource use, suggest the possibility of emergent resource-use patterns in ecological communities. We drew on thermodynamics to develop a maximization principle that predicted both organism and community energy use. These predictions highlighted the importance of density-dependent metabolic rates and were able to explain nonlinear relationships between community energy use and community biomass. We analyzed data on fish community energy use and biomass and found evidence of nonlinear scaling, which was predicted by the thermodynamic principle developed here and is not explained by other theories of ISDs. Detailed measurements of organism energy use will clarify the role of density dependence in driving metabolic rates and will further test our derived thermodynamic principle. Importantly, our study highlights the potential for fundamental links between ecology and thermodynamics.

Regime shifts, thresholds and multiple stable states in freshwater ecosystems; a critical appraisal of the evidence.

The concepts of ecosystem regime shifts, thresholds and alternative or multiple stable states are used extensively in the ecological and environmental management literature. When applied to aquatic ecosystems, these terms are used inconsistently reflecting differing levels of supporting evidence among ecosystem types. Although many aquatic ecosystems around the world have become degraded, the magnitude and causes of changes, relative to the range of historical variability, are poorly known. A working group supported by the Australian Centre for Ecological Analysis and Synthesis (ACEAS) reviewed 135 papers on freshwater ecosystems to assess the evidence for pressure-induced non-linear changes in freshwater ecosystems; these papers used terms indicating sudden and non-linear change in their titles and key words, and so was a positively biased sample. We scrutinized papers for study context and methods, ecosystem characteristics and focus, types of pressures and ecological responses considered, and the type of change reported (i.e., gradual, non-linear, hysteretic or irreversible change). There was little empirical evidence for regime shifts and changes between multiple or alternative stable states in these studies although some shifts between turbid phytoplankton-dominated states and clear-water, macrophyte-dominated states were reported in shallow lakes in temperate climates. We found limited understanding of the subtleties of the relevant theoretical concepts and encountered few mechanistic studies that investigated or identified cause-and-effect relationships between ecological responses and nominal pressures. Our results mirror those of reviews for estuarine, nearshore and marine aquatic ecosystems, demonstrating that although the concepts of regime shifts and alternative stable states have become prominent in the scientific and management literature, their empirical underpinning is weak outside of a specific environmental setting. The application of these concepts in future research and management applications should include evidence on the mechanistic links between pressures and consequent ecological change. Explicit consideration should also be given to whether observed temporal dynamics represent variation along a continuum rather than categorically different states.