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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 Borrelia burgdorferi. 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'.

Deforestation increases the odds of a species being threatened by extinction, and this effect is disproportionately strong in relatively intact landscapes, suggesting that efforts are needed to protect intact forest landscapes and prevent a new wave of extinctions. Pristine landscapes at highest risk of biodiversity loss Global efforts to reduce biodiversity loss must consider to what extent conservation efforts should focus on modified and fragmented landscapes where extinction threats are potentially greatest, versus landscapes that are largely intact. Matthew Betts and colleagues use International Union for Conservation of Nature (IUCN) data on species ranges and remote sensing data on forest cover to assess the effects of deforestation across intact and human-modified landscapes on the extinction risk of 19,432 vertebrate species worldwide. As expected, deforestation substantially increases the odds of a species being threatened with extinction. However, the strength of this relationship is disproportionately high in relatively intact landscapes. The authors estimate that under current rates of forest loss, 121–219 species will become threatened with extinction in Borneo, the central Amazon and the Congo Basin over the next 30 years. The findings suggest that large-scale efforts to reduce the degradation and loss of intact forest landscapes are needed to guard against an intensified wave of extinctions in the world's last wildernesses. Global biodiversity loss is a critical environmental crisis, yet the lack of spatial data on biodiversity threats has hindered conservation strategies 1 . 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%) 2 , 3 , 4 . Alternatively, recent evidence indicates that biodiversity is best conserved by minimizing human intrusion into intact and relatively unfragmented landscapes 5 . Here we use recently available forest loss data 6 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 7 , 8 are necessary to slow deforestation rates and to avert a new wave of global extinctions.

Changes to the community ecology of hosts for zoonotic pathogens, particularly rodents, are likely to influence the emergence and prevalence of zoonotic diseases worldwide. However, the complex interactions between abiotic factors, pathogens, vectors, hosts, and both food resources and predators of hosts are difficult to disentangle. Here we (1) use 19 yr of data from six large field plots in southeastern New York to compare the effects of hypothesized drivers of interannual variation in Lyme disease risk, including the abundance of acorns, rodents, and deer, as well as a series of climate variables; and (2) employ landscape epidemiology to explore how variation in predator community structure and forest cover influences spatial variation in the infection prevalence of ticks for the Lyme disease bacterium, Borrelia burgdorferi, and two other important tick-borne pathogens, Anaplasma phagocytophilum and Babesia microti. Acorn-driven increases in the abundance of mice were correlated with a lagged increase in the abundance of questing nymph-stage Ixodes scapularis ticks infected with Lyme disease bacteria. Abundance of white-tailed deer 2 yr prior also correlated with increased density of infected nymphal ticks, although the effect was weak. Density of rodents in the current year was a strong negative predictor of nymph density, apparently because high current abundance of these hosts can remove nymphs from the host-seeking population. Warm, dry spring or winter weather was associated with reduced density of infected nymphs. At the landscape scale, the presence of functionally diverse predator communities or of bobcats, the only obligate carnivore, was associated with reduced infection prevalence of I. scapularis nymphs with all three zoonotic pathogens. In the case of Lyme disease, infection prevalence increased where coyotes were present but smaller predators were displaced or otherwise absent. For all pathogens, infection prevalence was lowest when forest cover within a 1 km radius was high. Taken together, our results suggest that a food web perspective including bottom-up and top-down forcing is needed to understand drivers of tick-borne disease risk, a result that may also apply to other rodent-borne zoonoses. Prevention of exposure based on ecological indicators of heightened risk should help protect public health.

Society values landscapes that reliably provide many ecosystem functions. As the study of ecosystem functioning expands to include more locations, time spans, and functions, the functional importance of individual species is becoming more apparent. However, the functional importance of individual species does not necessarily translate to the functional importance of biodiversity measured in whole communities of interacting species. Furthermore, ecological diversity at scales larger than neighborhood species richness could also influence the provision of multiple functions over extended time scales. We created experimental landscapes based on whole communities from the world’s longest running biodiversity-functioning field experiment to investigate how local species richness (α diversity), distinctness among communities (β diversity), and larger scale species richness (γ diversity) affected eight ecosystem functions over 10 y. Using both threshold-based and unique multifunctionality metrics, we found that α diversity had strong positive effects on most individual functions and multifunctionality, and that positive effects of β and γ diversity emerged only when multiple functions were considered simultaneously. Higher β diversity also reduced the variability in multifunctionality. Thus, in addition to conserving important species, maintaining ecosystem multifunctionality will require diverse landscape mosaics of diverse communities.

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.

Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear rapid declines in Pd on soil, viable spores were harvested four months after inoculation. These results suggest that environmental substrates and guano can in general serve as infectious environmental reservoirs due to long-term persistence, and even growth, of live Pd. This should inform management interventions to sanitize or modify structures to reduce transmission risk as well early detection rapid response (EDRR) planning.

Due to the widespread eradication of large canids and felids, top predators in many terrestrial ecosystems are now medium-sized carnivores such as coyotes. Coyotes have been shown to increase songbird and rodent abundance and diversity by suppressing populations of small carnivores such as domestic cats and foxes. The restoration of gray wolves to many parts of North America, however, could alter this interaction chain. Here we use a 30-year time series of wolf, coyote, and fox relative abundance from the state of Minnesota, USA, to show that wolves suppress coyote populations, which in turn releases foxes from top-down control by coyotes. In contrast to mesopredator release theory, which has often considered the consequence of top predator removal in a three-species interaction chain (e.g., coyote-fox-prey), the presence of the top predator releases the smaller predator in a four-species interaction chain. Thus, heavy predation by abundant small predators might be more similar to the historical ecosystem before top-predator extirpation. The restructuring of predator communities due to the loss or restoration of top predators is likely to alter the size spectrum of heavily consumed prey with important implications for biodiversity and human health.

Protected areas are a key tool in the conservation of global biodiversity and carbon stores. We conducted a global test of the degree to which more than 18,000 terrestrial protected areas (totalling 5,293,217 km 2 ) reduce deforestation in relation to unprotected areas. We also derived indices that quantify how well countries’ forests are protected, both in terms of forested area protected and effectiveness of protected areas at reducing deforestation, in relation to vertebrate species richness, aboveground forest carbon biomass and background deforestation rates. Overall, protected areas did not eliminate deforestation, but reduced deforestation rates by 41%. Protected area deforestation rates were lowest in small reserves with low background deforestation rates. Critically, we found that after adjusting for effectiveness, only 6.5%—rather than 15.7%—of the world’s forests are protected, well below the Aichi Convention on Biological Diversity’s 2020 Target of 17%. We propose that global targets for protected areas should include quantitative goals for effectiveness in addition to spatial extent. A global analysis of deforestation rates in more than 18,000 terrestrial protected areas shows that, once protected area effectiveness is taken into account, only 6.5%—rather than 15.7%—of the world’s forests are protected, well below the Aichi Target of 17%.

Explaining the maintenance of tropical forest diversity under the countervailing forces of drift and competition poses a major challenge to ecological theory. Janzen–Connell effects, in which host-specific natural enemies restrict the recruitment of juveniles near conspecific adults, provide a potential mechanism. Janzen–Connell is strongly supported empirically, but existing theory does not address the stable coexistence of hundreds of species. Here we use high-performance computing and analytical models to demonstrate that tropical forest diversity can be maintained nearly indefinitely in a prolonged state of transient dynamics due to distance-responsive natural enemies. Further, we show that Janzen–Connell effects lead to community regulation of diversity by imposing a diversity-dependent cost to commonness and benefit to rarity. The resulting species–area and rank–abundance relationships are consistent with empirical results. Diversity maintenance over long time spans does not require dispersal from an external metacommunity, speciation, or resource niche partitioning, only a small zone around conspecific adults in which saplings fail to recruit. We conclude that the Janzen–Connell mechanism can explain the maintenance of tropical tree diversity while not precluding the operation of other niche-based mechanisms such as resource partitioning.

Although ungulates are the main prey of wolves (Canis lupus) throughout their range, substantial dietary diversity may allow wolves to persist even when ungulates are declining or rare. Alexander Archipelago wolves (Canis lupus ligoni) inhabit distinct mainland and island biogeographic units, each with a unique assemblage of available prey. We quantified biogeographic variability in wolf diets across the archipelago using DNA metabarcoding of prey in 860 wolf scats collected during 2010–2018 in 12 study sites. We hypothesized that wolves would increase their dietary diversity and niche breadth as the proportion of ungulate species in their diets decreased, but that this could be mediated by the availability of coastal resources. Application of DNA metabarcoding achieved fine taxonomic resolution of prey remains and identified 55 diet items representing species from 42 genera and 29 families, many previously undetected in coastal wolf diets. Overall, ungulates made up the largest proportion of wolf diets but were also most variable between study sites (occurrence per item index [O/I] = 0.130–0.851). On islands, Sitka black‐tailed deer (Odocoileus hemionus) were the most consumed ungulate species, whereas moose (Alces alces) and mountain goats (Oreamnos americanus) contributed more to mainland wolf diets. Wolves responded to biogeographical variation in availability of their primary prey by altering their foraging patterns. Wolves increased the number and diversity of species consumed and widened their dietary niche as the proportion of ungulates in their diet declined rather than prey switch to one or few individual diet items. Across all study sites combined, beaver (Castor canadensis; O/I = 0.125), marine mammals (O/I = 0.113), and black bears (Ursus americanus; O/I = 0.067) were important alternate prey. In areas where ungulates had become scarce, sea otters (Enhydra lutris) were particularly important, in one case even becoming the primary diet item suggesting that the ongoing expansion of sea otter populations postreintroduction restores an important food source for these cryptic predators. Here, we show extensive variation in the diet of wolves and elucidate regional consumer–resource interactions across an archipelagic landscape.