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Cutaneous Leishmaniasis (CL) is a vector-borne disease caused by a protozoan of the genus Leishmania and is considered one of the most important neglected tropical diseases. The Brazilian Amazon Forest harbors one of the highest diversity of Leishmania parasites and vectors and is one of the main focuses of the disease in the Americas. Previous studies showed that some types of anthropogenic disturbances have affected the abundance and distribution of CL vectors and hosts; however, few studies have thoroughly investigated the influence of different classes of land cover and land-use changes on the disease transmission risk. Here, we quantify the effect of land use and land-cover changes on the incidence of CL in all municipalities within the Brazilian Amazon Forest, from 2001 to 2017. We used a structured spatiotemporal Bayesian model to assess the effect of forest cover, agriculture, livestock, extractivism, and- deforestation on CL incidence, accounting for confounding variables such as population, climate, socioeconomic, and spatiotemporal random effects. We found that the increased risk of CL was associated with deforestation, especially modulated by a positive interaction between forest cover and livestock. Landscapes with ongoing deforestation for extensive cattle ranching are typically found in municipalities within the Amazon Frontier, where a high relative risk for CL was also identified. These findings provide valuable insights into developing effective public health policies and land-use planning to ensure healthier landscapes for people., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Biodiversity is declining globally, yet many biodiversity hotspots still lack comprehensive species conservation assessments. Using multiple International Union for Conservation of Nature (IUCN) Red List criteria to evaluate extinction risks and millions of herbarium and forest inventory records, we present automated conservation assessments for all tree species of the Atlantic Forest biodiversity hotspot, including ~1100 heretofore unassessed species. About 65% of all species and 82% of endemic species are classified as threatened. We rediscovered five species classified as Extinct on the IUCN Red List and identified 13 endemics as possibly extinct. Uncertainties in species information had little influence on the assessments, but using fewer Red List criteria severely underestimated threat levels. We suggest that the conservation status of tropical forests worldwide is worse than previously reported.

Trees structure the Earth's most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations 1-6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth's 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories 7 , we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world's most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees., (© 2024. The Author(s).)

Background: Vaccines developed between 2020 and 2021 against the SARS-CoV-2 virus were designed to diminish the severity and prevent deaths due to COVID-19. However, estimates of the effectiveness of vaccination campaigns in achieving these goals remain a methodological challenge. In this work, we developed a Bayesian statistical model to estimate the number of deaths and hospitalisations averted by vaccination of older adults (above 60 years old) in Brazil., Methods: We fit a linear model to predict the number of deaths and hospitalisations of older adults as a function of vaccination coverage in this group and casualties in younger adults. We used this model in a counterfactual analysis, simulating alternative scenarios without vaccination or with faster vaccination roll-out. We estimated the direct effects of COVID-19 vaccination by computing the difference between hypothetical and realised scenarios., Findings: We estimated that more than 165,000 individuals above 60 years of age were not hospitalised due to COVID-19 in the first seven months of the vaccination campaign. An additional contingent of 104,000 hospitalisations could have been averted if vaccination had started earlier. We also estimated that more than 58 thousand lives were saved by vaccinations in the period analysed for the same age group and that an additional 47 thousand lives could have been saved had the Brazilian government started the vaccination programme earlier., Interpretation: Our estimates provided a lower bound for vaccination impacts in Brazil, demonstrating the importance of preventing the suffering and loss of older Brazilian adults. Once vaccines were approved, an early vaccination roll-out could have saved many more lives, especially when facing a pandemic., Funding: The Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil (Finance Code 001 to F.M.D.M. and L.S.F.), Conselho Nacional de Desenvolvimento Científico e Tecnológico - Brazil (grant number: 315854/2020-0 to M.E.B., 141698/2018-7 to R.L.P.d.S., 313055/2020-3 to P.I.P., 311832/2017-2 to R.A.K.), Fundação de Amparo à Pesquisa do Estado de São Paulo - Brazil (contract number: 2016/01343-7 to R.A.K.), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - Brazil (grant number: E-26/201.277/2021 to L.S.B.) and Inova Fiocruz/Fundação Oswaldo Cruz - Brazil (grant number: 48401485034116) to L.S.B., O.G.C. and M.G.d.F.C. The funding agencies had no role in the conceptualization of the study., Competing Interests: The authors acknowledge the funding agencies: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (Finance Code 001 to FMDM and LSF), Conselho Nacional de Desenvolvimento Científico e Tecnológico – Brazil (grant number: 315854/2020-0 to MEB, 141698/2018-7 to RLPS, 313055/2020-3 to PIP, 311832/2017-2 to RAK), Fundação de Amparo à Pesquisa do Estado de São Paulo – Brazil (contract number: 2016/01343-7 to RAK), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro – Brazil (grant number: E-26/201.277/2021 to LSB) and Inova Fiocruz/Fundação Oswaldo Cruz – Brazil (grant number: VPPCB-005-FIO-20-2-50) to LSB, OGC and MGFC. The funding agencies had no role in the conceptualization of the study., (© 2022 The Author(s).)

We simulate the impact of school reopening during the COVID-19 pandemic in three major urban centers in Brazil to identify the epidemiological indicators and the best timing for the return of in-school activities and the effect of contact tracing as a mitigation measure. Our goal is to offer guidelines for evidence-based policymaking. We implement an extended SEIR model stratified by age and considering contact networks in different settings - school, home, work, and community, in which the infection transmission rate is affected by various intervention measures. After fitting epidemiological and demographic data, we simulate scenarios with increasing school transmission due to school reopening, and also estimate the number of hospitalization and deaths averted by the implementation of contact tracing. Reopening schools results in a non-linear increase in reported COVID-19 cases and deaths, which is highly dependent on infection and disease incidence at the time of reopening. When contact tracing and quarantining are restricted to school and home settings, a large number of daily tests is required to produce significant effects in reducing the total number of hospitalizations and deaths. Policymakers should carefully consider the epidemiological context and timing regarding the implementation of school closure and return of in-person school activities. While contact tracing strategies prevent new infections within school environments, they alone are not sufficient to avoid significant impacts on community transmission., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 Published by Elsevier Inc.)

The Pantanal wetland harbours the second largest population of jaguars in the world. Alongside climate and land-use changes, the recent mega-fires in the Pantanal may pose a threat to the jaguars' long-term survival. To put these growing threats into perspective, we addressed the reach and intensity of fires that have affected jaguar conservation in the Pantanal ecoregion over the last 16 years. The 2020 fires were the most severe in the annual series, burned 31% of the Pantanal and affected 45% of the estimated jaguar population (87% of these in Brazil); 79% of the home range areas, and 54% of the protected areas within home ranges. Fires consumed core habitats and injured several jaguars, the Pantanal's apex predator. Displacement, hunger, dehydration, territorial defence, and lower fecundity are among the impacts that may affect the abundance of the species. These impacts are likely to affect other less mobile species and, therefore, the ecological stability of the region. A solution to prevent the recurrence of mega-fires lies in combating the anthropogenic causes that intensify drought conditions, such as implementing actions to protect springs, increasing the number and area of protected areas, regulating fire use, and allocating fire brigades before dry seasons., (© 2022. The Author(s).)

Since the emergence of the novel coronavirus disease 2019 (COVID-19), mathematical modelling has become an important tool for planning strategies to combat the pandemic by supporting decision-making and public policies, as well as allowing an assessment of the effect of different intervention scenarios. A proliferation of compartmental models were developed by the mathematical modelling community in order to understand and make predictions about the spread of COVID-19. While compartmental models are suitable for simulating large populations, the underlying assumption of a well-mixed population might be problematic when considering non-pharmaceutical interventions (NPIs) which have a major impact on the connectivity between individuals in a population. Here we propose a modification to an extended age-structured SEIR (susceptible-exposed-infected-recovered) framework, with dynamic transmission modelled using contact matrices for various settings in Brazil. By assuming that the mitigation strategies for COVID-19 affect the connections among different households, network percolation theory predicts that the connectivity among all households decreases drastically above a certain threshold of removed connections. We incorporated this emergent effect at population level by modulating home contact matrices through a percolation correction function, with the few additional parameters fitted to hospitalisation and mortality data from the city of São Paulo. Our model with percolation effects was better supported by the data than the same model without such effects. By allowing a more reliable assessment of the impact of NPIs, our improved model provides a better description of the epidemiological dynamics and, consequently, better policy recommendations., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

It has been proposed that ecological theory develops in a pragmatic way. This implies that ecologists are free to decide what, from the knowledge available to them, they will use to build models and learn about phenomena. Because in fields that develop pragmatically knowledge generation is based on the decisions of individuals and not on a set of predefined axioms, the best way to produce theoretical synthesis in such fields is to assess what individuals are using to support scientific studies. Here, we present an approach for producing theoretical syntheses based on the propositions most frequently used to learn about a defined phenomenon. The approach consists of (i) defining a phenomenon of interest; (ii) defining a collective of scientists studying the phenomenon; (iii) surveying the scientific studies about the phenomenon published by this collective; (iv) identifying the most referred publications used in these studies; (v) identifying how the studies use the most referred publications to give support to their studies and learn about the phenomena; (vi) and from this, identifying general propositions on how the phenomenon is approached, viewed and described by the collective. We implemented the approach in a case study on the phenomenon of ecological succession, defining the collective as the scientists currently studying succession. We identified three propositions that synthesize the views of the defined collective about succession. The theoretical synthesis revealed that there is no clear division between "classical'' and "contemporary'' succession models, and that neutral models are being used to explain successional patterns alongside models based on niche assumptions. By implementing the pragmatic approach in a case study, we show that it can be successfully used to produce syntheses based on the actual activity of the scientific community studying the phenomenon. The connection between the resulting synthesis and research activity can be traced back through the methodological steps of the approach. This result can be used to understand how knowledge is being used in a field of study and can guide better informed decisions for future studies., Competing Interests: The authors have declared that no competing interests exist.

Background: The SARS-CoV-2 variant of concern (VOC) P.1 (Gamma variant) emerged in the Amazonas State, Brazil, in November 2020. The epidemiological consequences of its mutations have not been widely studied, despite detection of P.1 in 36 countries, with local transmission in at least 5 countries. A range of mutations are seen in P.1, ten of them in the spike protein. It shares mutations with VOCs previously detected in the United Kingdom (B.1.1.7, Alpha variant) and South Africa (B.1.351, Beta variant)., Methods: We estimated the transmissibility and reinfection of P.1 using a model-based approach, fitting data from the national health surveillance of hospitalized individuals and frequency of the P.1 variant in Manaus from December-2020 to February-2021., Results: Here we estimate that the new variant is about 2.6 times more transmissible (95% Confidence Interval: 2.4-2.8) than previous circulating variant(s). Manaus already had a high prevalence of individuals previously affected by the SARS-CoV-2 virus and our fitted model attributed 28% of Manaus cases in the period to reinfections by P.1, confirming the importance of reinfection by this variant. This value is in line with estimates from blood donors samples in Manaus city., Conclusions: Our estimates rank P.1 as one of the most transmissible among the SARS-CoV-2 VOCs currently identified, and potentially as transmissible as the posteriorly detected VOC B.1.617.2 (Delta variant), posing a serious threat and requiring measures to control its global spread., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2021.)

Although null hypothesis testing (NHT) is the primary method for analyzing data in many natural sciences, it has been increasingly criticized. Recently, approaches based on information theory (IT) have become popular and were held by many to be superior because it enables researchers to properly assess the strength of the evidence that data provide for competing hypotheses. Many studies have compared IT and NHT in the context of model selection and stepwise regression, but a systematic comparison of the most basic uses of statistics by ecologists is still lacking. We used computer simulations to compare how both approaches perform in four basic test designs (t-test, ANOVA, correlation tests, and multiple linear regression). Performance was measured by the proportion of simulated samples for which each method provided the correct conclusion (power), the proportion of detected effects with a wrong sign (S-error), and the mean ratio of the estimated effect to the true effect (M-error). We also checked if the p -value from significance tests correlated to a measure of strength of evidence, the Akaike weight. In general both methods performed equally well. The concordance is explained by the monotonic relationship between p -values and evidence weights in simple designs, which agree with analytic results. Our results show that researchers can agree on the conclusions drawn from a data set even when they are using different statistical approaches. By focusing on the practical consequences of inferences, such a pragmatic view of statistics can promote insightful dialogue among researchers on how to find a common ground from different pieces of evidence. A less dogmatic view of statistical inference can also help to broaden the debate about the role of statistics in science to the entire path that leads from a research hypothesis to a statistical hypothesis., Competing Interests: The authors declare that they have no competing interests., (© 2021 Castilho and Prado.)

This article discusses the epidemic situation of Covid-19 in Brazil, in the face of the emergence of a new strain called P.1, which is more transmissible and may be associated with reinfection. Given the collapse of hospital care in Manaus in January 2021 and the results of three recent preprints, each that reports increased transmissibility of the P.1 variant, we propose some urgent measures. Genomic surveillance based on multi-step diagnostics, starting with RT-PCR type tests and up to sequencing, should be established. Efforts to identify reinfections associated with this variant and the update of its definition in protocols should be prioritized, and studies on the efficacy of currently available vaccines in Brazil concerning the new variant should be conducted. We also propose improving the Brazilian health surveillance system such that genomic surveillance is coordinated and thereby better able to respond to future emergencies in a more timely fashion. We call on the public agents involved in health surveillance to share data and information regarding the epidemic in a clear, fast and transparent way. Finally, we propose a greater engagement in inter-institutional cooperation of all those involved in the response and production of knowledge about the pandemic in our country.

Tropical forests are being deforested worldwide, and the remaining fragments are suffering from biomass and biodiversity erosion. Quantifying this erosion is challenging because ground data on tropical biodiversity and biomass are often sparse. Here, we use an unprecedented dataset of 1819 field surveys covering the entire Atlantic Forest biodiversity hotspot. We show that 83-85% of the surveys presented losses in forest biomass and tree species richness, functional traits, and conservation value. On average, forest fragments have 25-32% less biomass, 23-31% fewer species, and 33, 36, and 42% fewer individuals of late-successional, large-seeded, and endemic species, respectively. Biodiversity and biomass erosion are lower inside strictly protected conservation units, particularly in large ones. We estimate that biomass erosion across the Atlantic Forest remnants is equivalent to the loss of 55-70 thousand km 2 of forests or US$2.3-2.6 billion in carbon credits. These figures have direct implications on mechanisms of climate change mitigation.

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data., (© 2020 The Authors. Ecology © 2020 The Ecological Society of America.)

Objective: To analyze the association between the transmission potential of SARS-CoV-2 and the decisions made by the municipal government of Florianópolis (Brazil) regarding social distancing., Methods: We analyzed new cases of COVID-19 identified in Florianópolis residents between February 1 and July 14, 2020, using a nowcasting approach. Decrees related to COVID-19 published in the Official Gazette of the Municipality between February 1 and July 14, 2020 were also analyzed. Based on the actions proposed in the decrees, whether they loosened social distancing measures, or increased or maintained existing restrictions, was analyzed, thus creating a Social Distancing Index. Time-dependent reproduction numbers (Rt) for a period of 14 days prior to each decree were calculated. A matrix was constructed associating the classification of each decree and the Rt values, analyzing the consonance or dissonance between the potential dissemination of SARS-CoV-2 and the actions of the decrees., Results: A total of 5,374 cases of COVID-19 and 26 decrees were analyzed. Nine decrees increased social distancing measures, nine maintained them, and eight loosened them. Of the 26 actions, 9 were consonant and 17 dissonant with the tendency indicated by the Rt. Dissonance was observed in all of the decrees that maintained the distance measures or loosened them. The fastest expansion in the number of new cases and the greatest amount of dissonant decrees was found in the last two months analyzed., Conclusion: There was an important divergence between municipal measures of social distancing with epidemiological indicators at the time of each political decision.

The foraging activity of diurnal bees often relies on flower availability, light intensity and temperature. We do not know how nocturnal bees, which fly at night and twilight, cope with these factors, especially as light levels vary considerably from night to day and from night to night due to moon phase and cloud cover. Given that bee apposition compound eyes function at their limits in dim light, we expect a strong dependence of foraging activity on light intensity in nocturnal bees. Besides being limited by minimum light levels to forage, nocturnal bees should also avoid foraging at brighter intensities, which bring increased competition with other bees. We investigated how five factors (light intensity, flower availability, temperature, humidity, and wind) affect flower visitation by Neotropical nocturnal bees in cambuci (Campomanesia phaea, Myrtaceae). We counted visits per minute over 30 nights in 33 cambuci trees. Light intensity was the main variable explaining flower visitation of nocturnal bees, which peaked at intermediate light levels occurring 25 min before sunrise. The minimum light intensity threshold to visit flowers was 0.00024 cd/m 2 . Our results highlight the dependence of these nocturnal insects on adequate light levels to explore resources.

Many authors have tried to explain the shape of the species abundance distribution (SAD). Some of them have suggested that sampling spatial scale is an important factor shaping SADs. These suggestions, however, did not consider the indirect and well-known effect of sample size, which increases as samples are combined to generate SADs at larger spatial scales. Here, we separate the effects of sample size and sampling scale on the shape of the SAD for three groups of organisms (trees, beetles and birds) sampled in the Brazilian Atlantic Forest. We compared the observed SADs at different sampling scales with simulated SADs having the same richness, relative abundances but comparable sample sizes, to show that the main effect shaping SADs is sample size and not sampling spatial scale. The effect of scale was minor and deviations between observed and simulated SADs were present only for beetles. For trees, the match between observed and simulated SADs was improved at all spatial scales when we accounted for conspecific aggregation, which was even more important than the sampling scale effect. We build on these results to propose a conceptual framework where observed SADs are shaped by three main factors, in decreasing order of importance: sample size, conspecific aggregation and beta diversity. Therefore, studies comparing SADs across sites or scales should use sampling and/or statistical approaches capable of disentangling these three effects on the shape of SADs., Competing Interests: The authors have declared that no competing interests exist.

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

In this work we analyze potential environmental drivers of malaria cases in Northwestern Argentina. We inspect causal links between malaria and climatic variables by means of the convergent cross mapping technique, which provides a causality criterion from the theory of dynamic systems. Analysis is based on 12 years of weekly malaria P. vivax cases in Tartagal, Salta, Argentina-at the southern fringe of malaria incidence in the Americas-together with humidity and temperature time-series spanning the same period. Our results show that there are causal links between malaria cases and both maximum temperature, with a delay of five weeks, and minimum temperature, with delays of zero and twenty two weeks. Humidity is also a driver of malaria cases, with thirteen weeks delay between cause and effect. Furthermore we also determined the sign and strength of the effects. Temperature has always a positive non-linear effect on cases, with maximum temperature effects more pronounced above 25°C and minimum above 17°C, while effects of humidity are more intricate: maximum humidity above 85% has a negative effect, whereas minimum humidity has a positive effect on cases. These results might be signaling processes operating at short (below 5 weeks) and long (over 12 weeks) time delays, corresponding to effects related to parasite cycle and mosquito population dynamics respectively. The non-linearities found for the strength of the effect of temperature on malaria cases make warmer areas more prone to higher increases in the disease incidence. Moreover, our results indicate that an increase of extreme weather events could enhance the risks of malaria spreading and re-emergence beyond the current distribution. Both situations, warmer climate and increase of extreme events, will be remarkably increased by the end of the century in this hot spot of climate change., Competing Interests: The authors have declared that no competing interests exist.

Trophic rewilding has been suggested as a restoration tool to restore ecological interactions and reverse defaunation and its cascading effects on ecosystem functioning. One of the ecological processes that has been jeopardized by defaunation is animal-mediated seed dispersal. Here, we propose an approach that combines joint species distribution models with occurrence data and species interaction records to quantify the potential to restore seed-dispersal interactions through rewilding and apply it to the Atlantic Forest, a global biodiversity hotspot. Using this approach, we identify areas that should benefit the most from trophic rewilding and candidate species that could contribute to cash the credit of seed-dispersal interactions in a given site. We found that sites within large fragments bearing a great diversity of trees may have about 20 times as many interactions to be cashed through rewilding as small fragments in regions where deforestation has been pervasive. We also ranked mammal and bird species according to their potential to restore seed-dispersal interactions if reintroduced while considering the biome as a whole and at finer scales. The suggested approach can aid future conservation efforts in rewilding projects in defaunated tropical rainforests.This article is part of the theme issue 'Trophic rewilding: consequences for ecosystems under global change'., (© 2018 The Author(s).)

The relation between rainfall and water accumulated in reservoirs comprises nonlinear feedbacks. Here we show that they may generate alternative equilibrium regimes, one of high water-volume, the other of low water-volume. Reservoirs can be seen as socio-environmental systems at risk of regime shifts, characteristic of tipping point transitions. We analyze data from stored water, rainfall, and water inflow and outflow in the main reservoir serving the metropolitan area of São Paulo, Brazil, by means of indicators of critical regime shifts, and find a strong signal of a transition. We furthermore build a mathematical model that gives a mechanistic view of the dynamics and demonstrates that alternative stable states are an expected property of water reservoirs. We also build a stochastic version of this model that fits well to the data. These results highlight the broader aspect that reservoir management must account for their intrinsic bistability, and should benefit from dynamical systems theory. Our case study illustrates the catastrophic consequences of failing to do so.

The stress gradient hypothesis (SGH) postulates how the balance between plant competition and facilitation shifts along environmental gradients. Early formulations of the SGH predicted that facilitation should increase monotonically with stress. However, a recent theoretical refinement of the SGH postulates stronger facilitation under moderate stress, followed by a decreasing role of facilitation in the most severe environments. We conducted field experiments along the most severe part of a coastal dune gradient in southeast Brazil to test the effect of stress on the intensity and importance of the net interactions between two tree species. First, we compared the performance of distinct life stages of Ternstroemia brasiliensis in the presence and absence of Guapira opposita adults along a beach-to-inland gradient, a gradient of environmental severity. To test the effect of one stress factor in particular, we also manipulated water availability, a limiting resource due to the sandy soils. At the most severe part of the coastal gradient (i.e. closest to the seashore), both intensity and importance of the interaction between G. opposita and T. brasiliensis were negatively related to stress, with a pattern consistent across distinct life stages of the target species. However, the sign of the net interaction depended on the life stage of the target species. Our results provide empirical evidence that the role of facilitation tends to wane, leading to neutral or even negative net interactions between species as stress reaches its maximum, as predicted by the recent refinements of the SGH.

Ecological science contributes to solving a broad range of environmental problems. However, lack of ecological literacy in practice often limits application of this knowledge. In this paper, we highlight a critical but often overlooked demand on ecological literacy: to enable professionals of various careers to apply scientific knowledge when faced with environmental problems. Current university courses on ecology often fail to persuade students that ecological science provides important tools for environmental problem solving. We propose problem-based learning to improve the understanding of ecological science and its usefulness for real-world environmental issues that professionals in careers as diverse as engineering, public health, architecture, social sciences, or management will address. Courses should set clear learning objectives for cognitive skills they expect students to acquire. Thus, professionals in different fields will be enabled to improve environmental decision-making processes and to participate effectively in multidisciplinary work groups charged with tackling environmental issues.

Empirical studies in salt marshes, arid, and alpine systems support the hypothesis that facilitation between plants is an important ecological process in severe or 'stressful' environments. Coastal dunes are both abiotically stressful and frequently disturbed systems. Facilitation has been documented, but the evidence to date has not been synthesized. We did a systematic review with meta-analysis to highlight general research gaps in the study of plant interactions in coastal dunes and examine if regional and local factors influence the magnitude of facilitation in these systems. The 32 studies included in the systematic review were done in coastal dunes located in 13 countries around the world but the majority was in the temperate zone (63%). Most of the studies adopt only an observational approach to make inferences about facilitative interactions, whereas only 28% of the studies used both observational and experimental approaches. Among the factors we tested, only geographic region mediates the occurrence of facilitation more broadly in coastal dune systems. The presence of a neighbor positively influenced growth and survival in the tropics, whereas in temperate and subartic regions the effect was neutral for both response variables. We found no evidence that climatic and local factors, such as life-form and life stage of interacting plants, affect the magnitude of facilitation in coastal dunes. Overall, conclusions about plant facilitation in coastal dunes depend on the response variable measured and, more broadly, on the geographic region examined. However, the high variability and the limited number of studies, especially in tropical region, indicate we need to be cautious in the generalization of the conclusions. Anyway, coastal dunes provide an important means to explore topical issues in facilitation research including context dependency, local versus regional drivers of community structure, and the importance of gradients in shaping the outcome of net interactions.

Resource specialisation, although a fundamental component of ecological theory, is employed in disparate ways. Most definitions derive from simple counts of resource species. We build on recent advances in ecophylogenetics and null model analysis to propose a concept of specialisation that comprises affinities among resources as well as their co-occurrence with consumers. In the distance-based specialisation index (DSI), specialisation is measured as relatedness (phylogenetic or otherwise) of resources, scaled by the null expectation of random use of locally available resources. Thus, specialists use significantly clustered sets of resources, whereas generalists use over-dispersed resources. Intermediate species are classed as indiscriminate consumers. The effectiveness of this approach was assessed with differentially restricted null models, applied to a data set of 168 herbivorous insect species and their hosts. Incorporation of plant relatedness and relative abundance greatly improved specialisation measures compared to taxon counts or simpler null models, which overestimate the fraction of specialists, a problem compounded by insufficient sampling effort. This framework disambiguates the concept of specialisation with an explicit measure applicable to any mode of affinity among resource classes, and is also linked to ecological and evolutionary processes. This will enable a more rigorous deployment of ecological specialisation in empirical and theoretical studies., (© 2014 John Wiley & Sons Ltd/CNRS.)

The proximity of adult neighbors often increases the performance of woody seedlings under harsh environmental conditions but this nurse plant effect becomes less intense when abiotic stress is alleviated, as predicted by the stress gradient hypothesis (SGH). Although some studies have tested how the net nurse effect is changed by stress, few studies have tested how the mechanism that drives the facilitative effect of nurse responds to changes in stress. We conducted field experiments in a subtropical coastal dune to test if shading drives the known nurse effect of adults of the tree Guapira opposita on seedling performance of another tree species, Ternstroemia brasiliensis. We transplanted T. brasiliensis seedlings to three neighbor environments: under a G. opposita crown, under artificial shade and without neighbor as a control. Furthermore, assuming that proximity to the seashore correlates with stress intensity, we tested if the potential shade-driven facilitation became less intense as stress decreased. Regardless of the proximity to the seashore, after a year, the survival of T. brasiliensis seedlings was twice as high when the seedlings were under G. opposita or under artificial shade compared to the control, indicating that the nurse effect is driven by shade and that this facilitation mechanism is constant along the stress gradient. However, G. opposita and artificial shade had a negative effect on seedlings growth. Overall, our results showed that the facilitation mechanism behind the nurse effect did not wane as the stress was reduced. Furthermore, in spite of the potential costs in terms of biomass production, our study highlights the potential of nurse plants and artificial shade as techniques to improve the survival of transplanted seedlings used in the restoration of degraded shrubland coastal dunes.

Background: Plasmodium vivax is a widely distributed, neglected parasite that can cause malaria and death in tropical areas. It is associated with an estimated 80-300 million cases of malaria worldwide. Brazilian tropical rain forests encompass host- and vector-rich communities, in which two hypothetical mechanisms could play a role in the dynamics of malaria transmission. The first mechanism is the dilution effect caused by presence of wild warm-blooded animals, which can act as dead-end hosts to Plasmodium parasites. The second is diffuse mosquito vector competition, in which vector and non-vector mosquito species compete for blood feeding upon a defensive host. Considering that the World Health Organization Malaria Eradication Research Agenda calls for novel strategies to eliminate malaria transmission locally, we used mathematical modeling to assess those two mechanisms in a pristine tropical rain forest, where the primary vector is present but malaria is absent., Methodology/principal Findings: The Ross-Macdonald model and a biodiversity-oriented model were parameterized using newly collected data and data from the literature. The basic reproduction number ([Formula: see text]) estimated employing Ross-Macdonald model indicated that malaria cases occur in the study location. However, no malaria cases have been reported since 1980. In contrast, the biodiversity-oriented model corroborated the absence of malaria transmission. In addition, the diffuse competition mechanism was negatively correlated with the risk of malaria transmission, which suggests a protective effect provided by the forest ecosystem. There is a non-linear, unimodal correlation between the mechanism of dead-end transmission of parasites and the risk of malaria transmission, suggesting a protective effect only under certain circumstances (e.g., a high abundance of wild warm-blooded animals)., Conclusions/significance: To achieve biological conservation and to eliminate Plasmodium parasites in human populations, the World Health Organization Malaria Eradication Research Agenda should take biodiversity issues into consideration.

Theoretical and empirical studies demonstrate that the total amount of forest and the size and connectivity of fragments have nonlinear effects on species survival. We tested how habitat amount and configuration affect understory bird species richness and abundance. We used mist nets (almost 34,000 net hours) to sample birds in 53 Atlantic Forest fragments in southeastern Brazil. Fragments were distributed among 3 10,800-ha landscapes. The remaining forest in these landscapes was below (10% forest cover), similar to (30%), and above (50%) the theoretical fragmentation threshold (approximately 30%) below which the effects of fragmentation should be intensified. Species-richness estimates were significantly higher (F= 3715, p = 0.00) where 50% of the forest remained, which suggests a species occurrence threshold of 30-50% forest, which is higher than usually occurs (<30%). Relations between forest cover and species richness differed depending on species sensitivity to forest conversion and fragmentation. For less sensitive species, species richness decreased as forest cover increased, whereas for highly sensitive species the opposite occurred. For sensitive species, species richness and the amount of forest cover were positively related, particularly when forest cover was 30-50%. Fragment size and connectivity were related to species richness and abundance in all landscapes, not just below the 30% threshold. Where 10% of the forest remained, fragment size was more related to species richness and abundance than connectivity. However, the relation between connectivity and species richness and abundance was stronger where 30% of the landscape was forested. Where 50% of the landscape was forested, fragment size and connectivity were both related to species richness and abundance. Our results demonstrated a rapid loss of species at relatively high levels of forest cover (30-50%). Highly sensitive species were 3-4 times more common above the 30-50% threshold than below it; however, our results do not support a unique fragmentation threshold., (©2012 Society for Conservation Biology.)

The high dependence of herbivorous insects on their host plants implies that plant invaders can affect these insects directly, by not providing a suitable habitat, or indirectly, by altering host plant availability. In this study, we sampled Asteraceae flower heads in cerrado remnants with varying levels of exotic grass invasion to evaluate whether invasive grasses have a direct effect on herbivore richness independent of the current disturbance level and host plant richness. By classifying herbivores according to the degree of host plant specialization, we also investigated whether invasive grasses reduce the uniqueness of the herbivorous assemblages. Herbivorous insect richness showed a unimodal relationship with invasive grass cover that was significantly explained only by way of the variation in host plant richness. The same result was found for polyphagous and oligophagous insects, but monophages showed a significant negative response to the intensity of the grass invasion that was independent of host plant richness. Our findings lend support to the hypothesis that the aggregate effect of invasive plants on herbivores tends to mirror the effects of invasive plants on host plants. In addition, exotic plants affect specialist insects differently from generalist insects; thus exotic plants affect not only the size but also the structural profile of herbivorous insect assemblages.

Background: Simple models inspired by processes shaping consumer-resource interactions have helped to establish the primary processes underlying the organization of food webs, networks of trophic interactions among species. Because other ecological interactions such as mutualisms between plants and their pollinators and seed dispersers are inherently based in consumer-resource relationships we hypothesize that processes shaping food webs should organize mutualistic relationships as well., Methodology/principal Findings: We used a likelihood-based model selection approach to compare the performance of food web models and that of a model designed for mutualisms, in reproducing the structure of networks depicting mutualistic relationships. Our results show that these food web models are able to reproduce the structure of most of the mutualistic networks and even the simplest among the food web models, the cascade model, often reproduce overall structural properties of real mutualistic networks., Conclusions/significance: Based on our results we hypothesize that processes leading to feeding hierarchy, which is a characteristic shared by all food web models, might be a fundamental aspect in the assembly of mutualisms. These findings suggest that similar underlying ecological processes might be important in organizing different types of interactions.

Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andrén proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions--that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework, providing a powerful tool for analysing the potential effectiveness of management interventions.

Anthropogenic changes in the landscape result in an environmental mosaic with serious consequences for biodiversity. The aim of the present study was to assess the effects of the anthropogenic changes on Asteraceae richness and abundance, and to evaluate the consequences for the richness of Tephritidae assemblages in five sampling sites, with three sampled habitats in each: cerrado (Brazilian savanna), eucalyptus stands and pasture. Sampling was carried out in 15 random transects (cerrados and one pasture) and in 30 transects (eucalyptus stands and the remaining pastures). Composition, species richness and insect abundance in each habitat type was estimated by sampling the flower heads for each species of host plant, collected by four people for 1h. Differences in mean abundance of plant population between habitats and sites were tested by two-way ANOVA. Differences in plant species richness between habitats and sites and effects of habitat, site and host plant richness on insect richness were tested using a generalized linear model with Poisson errors. Within each sampling site, cerrados showed higher species richness of Asteraceae than pastures and eucalyptus stands. There were also significant differences in plant richness among sites. Mean population abundance values were significantly different among habitats, but not among sites. Increased host plant richness led to significant insect species richness. There were no additional significant effects of habitat on insect richness. Therefore, anthropogenic alterations in landscape determined the impoverishment of plant assemblages and therefore of insect assemblages, because of the positive relationship between host plant richness and insect richness.

Most amphibian species have biphasic life histories and undergo an ontogenetic shift from aquatic to terrestrial habitats. In deforested landscapes, streams and forest fragments are frequently disjunct, jeopardizing the life cycle of forest-associated amphibians with aquatic larvae. We tested the impact of habitat split--defined as human-induced disconnection between habitats used by different life-history stages of a species--on four forest-associated amphibian species in a severely fragmented landscape of the Brazilian Atlantic Forest. We surveyed amphibians in forest fragments with and without streams (referred to as wet and dry fragments, respectively), including the adjacent grass-field matrix. Our comparison of capture rates in dry fragments and nearby streams in the matrix allowed us to evaluate the number of individuals that engaged in high-risk migrations through nonforested habitats. Adult amphibians moved from dry fragments to matrix streams at the beginning of the rainy season, reproduced, and returned at the end of the breeding period. Juveniles of the year moved to dry fragments along with adults. These risky reproductive migrations through nonforested habitats that expose individuals to dehydration, predation, and other hazards may cause population declines in dry fragments. Indeed, capture rates were significantly lower in dry fragments compared with wet fragments. Declining amphibians would strongly benefit from investments in the conservation and restoration of riparian vegetation and corridors linking breeding and nonbreeding areas.

The worldwide decline in amphibians has been attributed to several causes, especially habitat loss and disease. We identified a further factor, namely "habitat split"-defined as human-induced disconnection between habitats used by different life history stages of a species-which forces forest-associated amphibians with aquatic larvae to make risky breeding migrations between suitable aquatic and terrestrial habitats. In the Brazilian Atlantic Forest, we found that habitat split negatively affects the richness of species with aquatic larvae but not the richness of species with terrestrial development (the latter can complete their life cycle inside forest remnants). This mechanism helps to explain why species with aquatic larvae have the highest incidence of population decline. These findings reinforce the need for the conservation and restoration of riparian vegetation.

Contamination of recreational waters and public water supplies by Escherichia coli represents a risk for public health, since some strains can be pathogenic or propagated with other pathogenic microorganisms. In this study, two reservoirs, Billings and Guarapiranga (São Paulo metropolitan area, Brazil), were investigated in order to assess E. coli diversity. Genetic typing using rep-PCR completely differentiated all strains and enabled the determination of their genetic variability. Although the same level of genetic variability was observed for strains originating from both reservoirs, randomization procedures showed that isolates from the same reservoir were more closely related to each other. Phylogenetic group frequencies in each reservoir suggested that contamination in the Billings reservoir was mostly from humans, whereas contamination in the Guarapiranga reservoir was mostly from animals. Colony blot experiments using probes from several virulence factor genes showed that both reservoirs contained potential pathogenic strains and may represent a risk to recreational or household usage of these water resources.

A survey of the endophagous insects fauna associated to Asteraceae capitula was carried out from 2000 to 2002 in eight cerrado sensu stricto sites located in the Brazilian state of Sdo Paulo. Sixty-four endophagous species of Diptera and Lepidoptera were recorded from 49 asteracean host plants. Approximately half of the species were obtained from a single locality, with a large proportion emerging from a single sample (unicates). Thirty percent of the species were singletons (i.e. only one individual was recorded). The large proportion of rare species suggests a high species turnover among localities. Lepidopteran species were recorded on more host species than dipterans, confirming their more polyphagous food habit, also observed in other Brazilian biomes and in Europe. We conclude that the studied cerrado localities, all within São Paulo State, are isolated with its invertebrate fauna composed of many rare and exclusive species. We suggest that the maintenance of Asteraceae biodiversity and their endophagous insects depend on the conservation of all cerrado remnants in the state.

Herbivorous insects are abundant and diverse and insect-host plant associations tend to be specialized and evolutionarily conserved. Some authors suggested that generalist insect lineages tend to become specialists, with host specialization leading to an evolutionary dead-end for the parasite species. In this paper, we have examined this tendency using a phylogenetic tree of Tomoplagia (Diptera: Tephritidae), a parasite of asteracean plants. We have tested the trend towards specialization in different hierarchical degrees of host specialization. The topology of the tree, the inference of ancestral hosts, and the lack of directional evolution indicated that specialization does not correspond to a phylogenetic dead-end. Although most Tomoplagia species are restricted to a single host genus, specialization does not seem to limit further host range evolution. This work emphasizes the advantages of the use of different levels of specialization and the inclusion of occasional hosts to establish a more detailed scenario for the evolution of this kind of ecological association.

Phylogenetic and statistical analyses of 16S rRNA gene libraries were used for the investigation of actinobacterial communities present in two tropical estuarine sediments (Santos-São Vicente estuary, Brazil). The libraries were constructed from samples collected at the brackish end of the estuary, highly hydrocarbon-contaminated, and at the marine end, uncontaminated. Clones from the marine end of the estuary were all related to sequences from non-cultured Actinobacteria and unidentified bacteria recovered from a wide range of environmental samples, whereas clones from the brackish end were mainly related to sequences from cultured Actinobacteria. Statistical analyses showed that the community recovered from the hydrocarbon-contaminated sediment sample, at the brackish end, was less diverse than the uncontaminated one, at the marine end, and that the communities from the two libraries were differently structured, suggesting that these may have not originated from the same community. The recognition of the spatial pattern of actinobacterial distribution in a natural environment is a first step towards understanding the way these communities are organized, providing valuable data for further investigations of their taxonomic and functional diversity.

Restriction fragment length polymorphism (RFLP) and sequence analyses of the PCR-amplified 16S-23S rDNA intergenic spacer (ITS) were used for differentiating Acidithiobacillus thiooxidans strains from other related acidithiobacilli, including A. ferrooxidans and A. caldus. RFLP fingerprints obtained with AluI, DdeI, HaeIII, HinfI and MspI enabled the differentiation of all Acidithiobacillus reference strains into species groups. The A. thiooxidans strains investigated (metal mine isolates) yielded identical RFLP patterns to the A. thiooxidans type strain (ATCC 19377(T)), except for strain DAMS, which had a distinct pattern for all enzymes tested. Fourteen A. ferrooxidans mine strains were assigned to 3 RFLP groups, the majority of which were grouped with A. ferrooxidans ATCC 23270(T). The spacer region of one representative strain from each of the RFLP groups obtained was subjected to sequence analysis, in addition to eleven additional A. thiooxidans strains isolated from sediment and water samples, and A. caldus DSM 8584(T). The tRNA(IIe) and tRNA(Ala) genes, present in all strains analyzed, showed high sequence similarity. Phylogenetic analysis of the ITS sequences differentiated all three Acidithiobacillus species. Inter- and infraspecific genetic variations detected were mainly due to the size and sequence polymorphism of the ITS3 region. Mantel tests showed no significant correlation between ITS sequence similarity and the geographical origin of strains. The results showed that the 16S-23S rDNA spacer region is a useful target for the development of molecular-based methods aimed at the detection, rapid differentiation and identification of acidithiobacilli.