The collapsing populations of large herbivores will have extensive ecological and social consequences.

To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha-and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.

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.

Tropical forests are the global cornerstone of biological diversity, and store 55% of the forest carbon stock globally, yet sustained provisioning of these forest ecosystem services may be threatened by hunting-induced extinctions of plant-animal mutualisms that maintain long-term forest dynamics. Large-bodied Atelinae primates and tapirs in particular offer nonredundant seed-dispersal services for many large-seeded Neotropical tree species, which on average have higher wood density than smaller-seeded and winddispersed trees. We used field data and models to project the spatial impact of hunting on large primates by ∼1 million rural households throughout the Brazilian Amazon. We then used a unique baseline dataset on 2,345 1-ha tree plots arrayed across the Brazilian Amazon to model changes in aboveground forest biomass under different scenarios of hunting-induced large-bodied frugivore extirpation. We project that defaunation of the most harvest-sensitive species will lead to losses in aboveground biomass of between 2.5-5.8% on average, with some losses as high as 26.5-37.8%. These findings highlight an urgent need to manage the sustainability of game hunting in both protected and unprotected tropical forests, and place full biodiversity integrity, including populations of large frugivorous vertebrates, firmly in the agenda of reducing emissions from deforestation and forest degradation (REDD+) programs. T ropical forests worldwide store >460 billion tons of carbonover half of the total atmospheric storage (1)-and tropical forest conversion and degradation account for as much as 20% of global anthropogenic greenhouse gas emissions (2). Tropical forests are also the most species-rich ecosystems on Earth, yet the role of species interactions in stabilizing tropical forest dynamics and maintaining the flow of natural ecosystem services, including long-term forest carbon pools, remains poorly understood. Over 80-96% of all woody plant species in tropical forests produce vertebrate-dispersed fleshy fruits (3, 4), yet many large-bodied frugivore populations in tropical forest regions have already been severely overhunted (5), resulting in functionally "empty" or "half-empty" forests with subsequent disruptions in seed dispersal mutualisms (6). Indeed, the total forest area degraded by unsustainable hunting in the largest remaining tropical forest regions may exceed the combined extent of deforestation, selective logging, and wildfires (7,8). Even formally decreed forest reserves in remote areas have succumbed to population declines and local extinctions of large vertebrates (9, 10), yet the consequences of this pervasive defaunation process to the persistence of tropical forest ecosystem services remains poorly explored.Overhunting can amplify dispersal limitation in many largeseeded plant species relying primarily or exclusively on harvestsensitive large-bodied frugivores. The causal mechanisms through which hunting leads to altered phytodemographics-recruitment bottlenecks resulting from replacement of seedlings f...

Global biodiversity loss is a critical environmental crisis, yet the lack of spatial data on biodiversity threats has hindered conservation strategies. Theory predicts that abrupt biodiversity declines are most likely to occur when habitat availability is reduced to very low levels in the landscape (10-30%). Alternatively, recent evidence indicates that biodiversity is best conserved by minimizing human intrusion into intact and relatively unfragmented landscapes. Here we use recently available forest loss data to test deforestation effects on International Union for Conservation of Nature Red List categories of extinction risk for 19,432 vertebrate species worldwide. As expected, deforestation substantially increased the odds of a species being listed as threatened, undergoing recent upgrading to a higher threat category and exhibiting declining populations. More importantly, we show that these risks were disproportionately high in relatively intact landscapes; even minimal deforestation has had severe consequences for vertebrate biodiversity. We found little support for the alternative hypothesis that forest loss is most detrimental in already fragmented landscapes. Spatial analysis revealed high-risk hot spots in Borneo, the central Amazon and the Congo Basin. In these regions, our model predicts that 121-219 species will become threatened under current rates of forest loss over the next 30 years. Given that only 17.9% of these high-risk areas are formally protected and only 8.9% have strict protection, new large-scale conservation efforts to protect intact forests are necessary to slow deforestation rates and to avert a new wave of global extinctions.

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats, (iv) reservoir competence of host species, and (v) pathogenicity for humans of different genotypes of Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host-vector-borne zoonotic disease.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

The authors note that on page 13064, right column, first full paragraph, lines 4-7, "Some of the climatic events linked to such concerns are the severe droughts experienced by the Amazon basin in 2005 and 2010, which reportedly reduced tropical forest NPP by 1.6 to 2.2 PgC/y and increased tree mortality (50, 51)" should instead appear as "Some of the climatic events linked to such concerns are the severe droughts experienced by the Amazon basin in 2005 and 2010, which reportedly reduced tropical forest NPP and increased tree mortality by a total biomass carbon loss of 1.6 to 2.2 PgC (50, 51)."On page 13064, right column, first full paragraph, lines 12-17, "Assuming that the large reductions of tropical NPP reported previously (50, 51) are realistic, the absence of marked variations of the global CO 2 growth rate after the 2005 and 2010 Amazon droughts may imply that the drought conditions also coincidently reduced tropical Rh along with NPP, resulting in (relatively) small NEE anomalies" should instead appear as "Assuming that the large reductions of tropical forest biomass reported previously (50, 51) are realistic, the absence of marked variations of the global CO 2 growth rate after the 2005 and 2010 Amazon droughts may imply that the drought conditions also coincidently reduced tropical Rh along with NPP, resulting in (relatively) small NEE anomalies."These changes do not affect the conclusions of the article.

Lyme disease is the most prevalent vector-borne disease in North America, and both the annual incidence and geographic range are increasing. The emergence of Lyme disease has been attributed to a century-long recovery of deer, an important reproductive host for adult ticks. However, a growing body of evidence suggests that Lyme disease risk may now be more dynamically linked to fluctuations in the abundance of small-mammal hosts that are thought to infect the majority of ticks. The continuing and rapid increase in Lyme disease over the past two decades, long after the recolonization of deer, suggests that other factors, including changes in the ecology of small-mammal hosts may be responsible for the continuing emergence of Lyme disease. We present a theoretical model that illustrates how reductions in small-mammal predators can sharply increase Lyme disease risk. We then show that increases in Lyme disease in the northeastern and midwestern United States over the past three decades are frequently uncorrelated with deer abundance and instead coincide with a range-wide decline of a key small-mammal predator, the red fox, likely due to expansion of coyote populations. Further, across four states we find poor spatial correlation between deer abundance and Lyme disease incidence, but coyote abundance and fox rarity effectively predict the spatial distribution of Lyme disease in New York. These results suggest that changes in predator communities may have cascading impacts that facilitate the emergence of zoonotic diseases, the vast majority of which rely on hosts that occupy low trophic levels.