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Wildfire dynamics are changing around the world and understanding their effects on ecological communities and landscapes is urgent and important. We report detailed food webs for unburned, low-to-moderate and high severity burned habitats three years post-fire in the Eldorado National Forest, California. The cumulative cross-habitat food web contains 3,084 ontogenetic stages (nodes) or plant parts comprising 849 species (including 107 primary producers, 634 invertebrates, 94 vertebrates). There were 178,655 trophic interactions between these nodes. We provide information on taxonomy, body size, biomass density and trophic interactions under each of the three burn conditions. We detail 19 sampling methods deployed across 27 sites (nine in each burn condition) used to estimate the richness, body size, abundance and biomass density estimates in the node lists. We provide the R code and raw data to estimate summarized node densities and assign trophic links.

Detailed metabarcoding methods, tree construction, and supplementary tables and figures

Main text analyses using a 0.2% RRA threshold for filtering

Predator–prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ15N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator–prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.

Main text analyses using a 99% similarity threshold for clustering

Modeling mosquito abundance

We used partial least squares structural equation models (PLS-SEM) to analyze links between putative drivers and disease burden, but a more traditional approach is panel analysis. This document presents the results of a panel analysis conducted in parallel with the PLS-SEM presented in the main text. The consistency in results between the two methods highlights the robustness of our findings.

In our analysis, two diseases declined in burden in response to increasing population density over time, even though these diseases are expected to be transmitted in a density-dependent manner (i.e., measles, varicella). In this document, we compare these unexpected results to those of an earlier paper (Morand et al. 2014).

The 60 countries used in our analysis (in red). From an initial group of 192 nations, countries were excluded if: (i) area was greater than 1.5 million km2 or less than 625 km2 (in blue), (ii) less than 10% of area was forested in 1990 (according to satellite-derived metrics of forest cover, in yellow), (iii) population, GNI, or climate data were unavailable (in orange). Map courtesy of Maggie Klope.

Meta-data for dataset assembled to test potential drivers of country-level human infectious disease burden. Dataset available in xls, txt, and csv formats as Supplementary Material 1.

In geographic studies, replicates (e.g., countries) may be non-independent due to their proximity, a problem termed spatial autocorrelation. This non-independence is problematic because it can inflate Type I error. Here, we describe our approach to addressing spatial autocorrelation in our analysis.

Terrestrial mammals are experiencing a massive collapse in their population sizes and geographical ranges around the world, but many of the drivers, patterns and consequences of this decline remain poorly understood. Here we provide an analysis showing that bushmeat hunting for mostly food and medicinal products is driving a global crisis whereby 301 terrestrial mammal species are threatened with extinction. Nearly all of these threatened species occur in developing countries where major coexisting threats include deforestation, agricultural expansion, human encroachment and competition with livestock. The unrelenting decline of mammals suggests many vital ecological and socio-economic services that these species provide will be lost, potentially changing ecosystems irrevocably. We discuss options and current obstacles to achieving effective conservation, alongside consequences of failure to stem such anthropogenic mammalian extirpation. We propose a multi-pronged conservation strategy to help save threatened mammals from immediate extinction and avoid a collapse of food security for hundreds of millions of people.

Terrestrial mammals are experiencing a massive collapse in their population sizes and geographical ranges around the world, but many of the drivers, patterns and consequences of this decline remain poorly understood. Here we provide an analysis showing that hunting for mostly food and medicinal products is driving a global crisis whereby 301 terrestrial mammal species are threatened with extinction. Nearly all of these threatened species occur in developing countries where major coexisting threats include deforestation, agricultural expansion, human encroachment and competition with livestock. The unrelenting decline of mammals suggests many vital ecological and socio-economic services that these species provide will be lost, potentially changing ecosystems irrevocably. We discuss options and current obstacles to achieving effective conservation, alongside consequences of failure to stem such anthropogenic mammalian extirpation. We propose a multi-pronged conservation strategy to help save threatened mammals from immediate extinction and avoid a collapse of food security for hundreds of millions of people.

Terrestrial mammals are experiencing a massive collapse in their population sizes and geographical ranges around the world, but many of the drivers, patterns and consequences of this decline remain poorly understood. Here we provide an analysis showing that bushmeat hunting for mostly food and medicinal products is driving a global crisis whereby 301 terrestrial mammal species are threatened with extinction. Nearly all of these threatened species occur in developing countries where major coexisting threats include deforestation, agricultural expansion, human encroachment and competition with livestock. The unrelenting decline of mammals suggests many vital ecological and socio-economic services that these species provide will be lost, potentially changing ecosystems irrevocably. We discuss options and current obstacles to achieving effective conservation, alongside consequences of failure to stem such anthropogenic mammalian extirpation. We propose a multi-pronged conservation strategy to help save threatened mammals from immediate extinction and avoid a collapse of food security for hundreds of millions of people.

© 2015 by the Ecological Society of America. Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large-wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife declines on other animals in a community, we examined the effects of three common forms of largewildlife loss (removal without replacement [using fences], removal followed by replacement with domestic stock, and removal accompanied by crop agricultural use) on small-mammal abundance, diversity, and community composition, in landscapes that varied in several abiotic attributes (rainfall, soil fertility, land-use intensity) in central Kenya. We found that smallmammal communities were indeed heavily impacted by all forms of large-wildlife decline, showing, on average: (1) higher densities, (2) lower species richness per site, and (3) different species assemblages in sites from which large wildlife were removed. However, the nature and magnitude of these effects were strongly context dependent. Rainfall, type of land-use change, and the interaction of these two factors were key predictors of both the magnitude and type of responses of small mammals. The strongest effects, particularly abundance responses, tended to be observed in low-rainfall areas. Whereas isolated wildlife removal primarily led to increased small-mammal abundance, wildlife removal associated with secondary uses (agriculture, domestic stock) had much more variable effects on abundance and stronger impacts on diversity and composition. Collectively, these results (1) highlight the importance of context in determining the impacts of large-wildlife decline on small-mammal communities, (2) emphasize the challenges in extrapolating results from controlled experimental studies to predict the effects of wildlife declines that are accompanied by secondary land-uses, and (3) suggest that, because of the context-dependent nature of the responses to large-wildlife decline, large-wildlife status alone cannot be reliably used to predict small-mammal community changes.

Remote areas harbor some of the world's most undisturbed ecosystems. Major conservation gains can be made by effectively protecting nature in these remote zones. Conducting conservation work in remote settings presents both unique challenges and promising opportunities. We discuss how five commonly used approaches for conservation (buy and protect conservation; conservation motivated by the intrinsic values of nature; ecosystem service based conservation; ecotourism driven conservation; and conservation enabled by community planning) can be optimally applied to protect ecosystems in these special settings. In this discussion we draw examples from two model remote sites: Palmyra and Tabuaeran Atolls. Spatial analyses conducted using population density as a proxy for remoteness indicate that many existing recognized protected areas already include remote regions, but that the vast majority of the overall remote zones on the planet are not yet formally protected. Initiating discussions that directly consider both the roadblocks and opportunities for conservation in remote areas will help increase our odds of successfully protecting biodiversity in these unique and strategically important contexts. © 2013 Elsevier Ltd.

Tables S1-S4 and Figures S1-S6

Both large-wildlife loss and climatic changes can independently influence the prevalence and distribution of zoonotic disease. Given growing evidence that wildlife loss often has stronger community-level effects in low-productivity areas, we hypothesized that these perturbations would have interactive effects on disease risk. We experimentally tested this hypothesis by measuring tick abundance and the prevalence of tick-borne pathogens (Coxiella burnetii and Rickettsia spp.) within long-term, size-selective, large-herbivore exclosures replicated across a precipitation gradient in East Africa. Total wildlife exclusion increased total tick abundance by 130% (mesic sites) to 225% (dry, low-productivity sites), demonstrating a significant interaction of defaunation and aridity on tick abundance. When differing degrees of exclusion were tested for a subset of months, total tick abundance increased from 170% (only mega-herbivores excluded) to 360% (all large wildlife excluded). Wildlife exclusion differentially affected the abundance of the three dominant tick species, and this effect varied strongly over time, likely due to differences among species in their host associations, seasonality and other ecological characteristics. Pathogen prevalence did not differ across wildlife exclusion treatments, rainfall levels or tick species, suggesting that exposure risk will respond to defaunation and climate change in proportion to total tick abundance. These findings demonstrate interacting effects of defaunation and aridity that increase disease risk, and they highlight the need to incorporate ecological context when predicting effects of wildlife loss on zoonotic disease dynamics.

Modeling mosquito abundance

Sample locations

Tables S1-S4 and Figures S1-S6

Sample locations

Researcher surveys

Researcher surveys

Both large-wildlife loss and climatic changes can independently influence the prevalence and distribution of zoonotic disease. Given growing evidence that wildlife loss often has stronger community-level effects in low-productivity areas, we hypothesized that these perturbations would have interactive effects on disease risk. We experimentally tested this hypothesis by measuring tick abundance and the prevalence of tick-borne pathogens (Coxiella burnetii and Rickettsia spp.) within long-term, size-selective, large-herbivore exclosures replicated across a precipitation gradient in East Africa. Total wildlife exclusion increased total tick abundance by 130% (mesic sites) to 225% (dry, low-productivity sites), demonstrating a significant interaction of defaunation and aridity on tick abundance. When differing degrees of exclusion were tested for a subset of months, total tick abundance increased from 170% (only mega-herbivores excluded) to 360% (all large wildlife excluded). Wildlife exclusion differentially affected the abundance of the three dominant tick species, and this effect varied strongly over time, likely due to differences among species in their host associations, seasonality and other ecological characteristics. Pathogen prevalence did not differ across wildlife exclusion treatments, rainfall levels or tick species, suggesting that exposure risk will respond to defaunation and climate change in proportion to total tick abundance. These findings demonstrate interacting effects of defaunation and aridity that increase disease risk, and they highlight the need to incorporate ecological context when predicting effects of wildlife loss on zoonotic disease dynamics.

Most prominent theories of food web dynamics imply the simultaneous action of bottom-up and top-down forces. However, transient bottom-up effects resulting from resource pulses can lead to sequential shifts in the strength of top-down predator effects. We used a large-scale field experiment (32 small islands sampled over 5years) to probe how the frequency and magnitude of pulsed seaweed inputs drives temporal variation in the top-down effects of lizard predators. Short-term weakening of lizard effects on spiders and plants (the latter via a trophic cascade) were associated with lizard diet shifts, and were more pronounced with larger seaweed inputs. Long-term strengthening of lizard effects was associated with lizard numerical responses and plant fertilisation. Increased pulse frequency reinforced the strengthening of lizard effects on spiders and plants. These results underscore the temporally variable nature of top-down effects and highlight the role of resource pulses in driving this variation.