Deforestation and threats to the biodiversity of Amazonia

Bird communities across different levels of human settlement: A comparative analysis from two northern Amazonian ecoregions

Urban ecosystems are increasingly dominating landscapes globally, so it is critical to understand the effects of human settlements on biodiversity. Bird communities are effective indicators because they are impacted by the size and expansion of human settlements, exemplified by changes in their habitat use, breeding and foraging behaviours, as well as patterns of richness and abundance. Existing studies on bird community responses to human settlements have mainly focused on single ecoregions and large cities, leaving a gap in comparative research on how differently sized human settlements affect bird communities across various ecoregions. To address this gap, we examine species richness, bird abundances and community composition in human settlements, which exhibit variable sizes, populations, landscape configurations, and overall intensity of settlement in two tropical ecoregions in Guyana, Amazonia: forest and savannah. In each ecoregion we explored how different groupings of urban tolerance in birds responded to human settlements of differing population size and building densities. Overall, we found significant differences in bird communities across the varying levels of human settlement intensity in both ecoregions, with greater differences in bird community composition in the forest ecoregion than the savannah region. In both ecoregions, species richness and abundance were highest at the medium level of settlement of human settlement. Our findings suggest that bird tolerance to human settlements varies based on ecoregion and site-level factors. In the savannah, built features may be benefitting birds from all urban tolerance levels, but they have a negative impact on less urban-tolerant species in the forest ecoregion. Our comparative analysis reveals for the first time that the impact of human settlements on avian communities in northern Amazonia varies among ecoregions, indicating that species evolved to live in a savannah may be more tolerant to human settlements than those more evolved to a forest system.

Drosophila nasuta (Diptera, Drosophilidae) in Brazil: a decade of invasion and occupation of more than half of the country

As a result of human activities and natural dispersal, exotic species can be brought to new areas, where they become established and spread, becoming invaders. These species are responsible for the loss of biodiversity and cause ecosystemic harm throughout the world. In this paper, we report the rapid, broad geographic expansion of the invasive fly Drosophila nasuta in Brazil. An 84% increase was found in its area of occupation in the country compared to previous studies. The present data reveal its arrival to the Pantanal wetlands in a location more than one thousand kilometers from the closest previous record in the Cerrado biome. We present the first record of D. nasuta in the Atlantic Forest in the states of Paraíba and Bahia. We report its introduction in the Amazon Forest in the state of Amazonas approximately 700 kilometers from previous records. The relative abundance of D. nasuta in this biome increased fivefold in comparison to a previous study. In the first decade of invasion in Brazil, D. nasuta has already colonized more than half of the country. The present data reveal its invasive potential and underscore the importance of following up the possible negative effects of this biological invasion.

Climate change and carnivores: shifts in the distribution and effectiveness of protected areas in the Amazon

Background

Carnivore mammals are animals vulnerable to human interference, such as climate change and deforestation. Their distribution and persistence are affected by such impacts, mainly in tropical regions such as the Amazon. Due to the importance of carnivores in the maintenance and functioning of the ecosystem, they are extremely important animals for conservation. We evaluated the impact of climate change on the geographic distribution of carnivores in the Amazon using Species Distribution Models (SDMs). Do we seek to answer the following questions: (1) What is the effect of climate change on the distribution of carnivores in the Amazon? (2) Will carnivore species lose or gain representation within the Protected Areas (PAs) of the Amazon in the future?

Methods

We evaluated the distribution area of 16 species of carnivores mammals in the Amazon, based on two future climate scenarios (RCP 4.5 and RCP 8.5) for the year 2070. For the construction of the SDMs we used bioclimatic and vegetation cover variables (land type). Based on these models, we calculated the area loss and climate suitability of the species, as well as the effectiveness of the protected areas inserted in the Amazon. We estimated the effectiveness of PAs on the individual persistence of carnivores in the future, for this, we used the SDMs to perform the gap analysis. Finally, we analyze the effectiveness of PAs in protecting taxonomic richness in future scenarios.

Results

The SDMs showed satisfactory predictive performance, with Jaccard values above 0.85 and AUC above 0.91 for all species. In the present and for the future climate scenarios, we observe a reduction of potencial distribution in both future scenarios (RCP4.5 and RCP8.5), where five species will be negatively affected by climate change in the RCP 4.5 future scenario and eight in the RCP 8.5 scenario. The remaining species stay stable in terms of total area. All species in the study showed a loss of climatic suitability. Some species lost almost all climatic suitability in the RCP 8.5 scenario. According to the GAP analysis, all species are protected within the PAs both in the current scenario and in both future climate scenarios. From the null models, we found that in all climate scenarios, the PAs are not efficient in protecting species richness.

First record of rainbow shrimp, exotic species Mierspenaeopsis sculptilis (Heller, 1862), in the Brazilian coastal amazon, validated by DNA barcode

BACKGROUND

This is the first record of the alien shrimp Mierspenaeopsis sculptilis in Brazil. The invasion was detected within Marine Extractive Reserves based on eight specimens accidentally caught by local fishermen using trawlnets focused on fisheries of native species. These specimens were transported to the Laboratory of Applied Genetics and morphologically identified as Mierspenaeopsis sculptilis (rainbow shrimp). The taxonomic status of analyzed samples was confirmed by DNA barcoding using a 627-bp fragment of the Cytochrome C Oxidase Subunit I (COI) gene.

RESULTS

A single haplotype was recovered from the eight specimens, being identical to a haplotype reported in India, where this species naturally occurs, and in Mozambique, where the rainbow shrimp is considered an invasive species. The present analyses indicated a putative invasive route (i.e., India-Mozambique-Brazil) mediated by shipping trade.

CONCLUSIONS

This study presents the first record of Mierspenaeopsis sculptilis in Brazil, in areas of extractive reserves on the Amazon coast. Notably exotic species can cause imbalance in the ecosystem, harming native species. In view of this, the registration of new invasions is essential as they contribute to the implementation of control plans.

Local working collections as the foundation for an integrated conservation of Theobroma cacao L. in Latin America

The intraspecific diversity of cacao has traditionally been preserved in genebanks. However, these establishments face various challenges, notably insufficient funding, accession redundancy, misidentification and lack of wild cacao population samples. In natural environments, it is expected that unknown varieties of cacao may still be found, but wild populations of cacao are increasingly threatened by climate change, deforestation, habitat loss, land use changes and poor knowledge. Farmers also retain diversity, but on-farm conservation is affected by geopolitical, economic, management and cultural issues, that are influenced at multiple scales, from the household to the international market. Taking separately, ex situ, in situ and on-farm conservation have not achieved adequate conservation fostering the inclusion of all stakeholders and the broad use of cacao diversity. We analyze the use of the traditional conservation strategies (ex situ, in situ and on-farm) and propose an integrated approach based on local working collections to secure cacao diversity in the long term. We argue that national conservation networks should be implemented in countries of origin to simultaneously maximize alpha (diversity held in any given working collection), beta (the change in diversity between working collections in different regions) and gamma diversity (overall diversity in a country).

The Effects of Environmental Changes on Plant Species and Forest Dependent Communities in the Amazon Region

We review the consequences of environmental changes caused by human activities on forest products and forest-dependent communities in the Amazon region—the vast Amazonas River basin and the Guiana Shield in South America. We used the 2018 and 2021 Intergovernmental Panel on Climate Change reports and recent scientific studies to present evidence and hypotheses for changes in the ecosystem productivity and geographical distribution of plants species. We have identified species associated with highly employed forest products exhibiting reducing populations, mainly linked with deforestation and selective logging. Changes in species composition along with a decline of valuable species have been observed in the eastern, central, and southern regions of the Brazilian Amazon, suggesting accelerated biodiversity loss. Over 1 billion native trees and palms are being lost every two years, causing economic losses estimated between US$1–17 billion. A decrease in native plant species can be abrupt and both temporary or persistent for over 20 years, leading to reduced economic opportunities for forest-dependent communities. Science and technology investments are considered promising in implementing agroforestry systems recovering deforested and degraded lands, which could engage companies that use forest products due to supply chain advantages.

Epidemiology, Biodiversity, and Technological Trajectories in the Brazilian Amazon: From Malaria to COVID-19

The Amazon biome is under severe threat due to increasing deforestation rates and loss of biodiversity and ecosystem services while sustaining a high burden of neglected tropical diseases. Approximately two thirds of this biome are located within Brazilian territory. There, socio-economic and environmental landscape transformations are linked to the regional agrarian economy dynamics, which has developed into six techno-productive trajectories (TTs). These TTs are the product of the historical interaction between Peasant and Farmer and Rancher practices, technologies and rationalities. This article investigates the distribution of the dominant Brazilian Amazon TTs and their association with environmental degradation and vulnerability to neglected tropical diseases. The goal is to provide a framework for the joint debate of the local economic, environmental and health dimensions. We calculated the dominant TT for each municipality in 2017. Peasant trajectories (TT1, TT2, and TT3) are dominant in ca. fifty percent of the Amazon territory, mostly concentrated in areas covered by continuous forest where malaria is an important morbidity and mortality cause. Cattle raising trajectories are associated with higher deforestation rates. Meanwhile, Farmer and Rancher economies are becoming dominant trajectories, comprising large scale cattle and grain production. These trajectories are associated with rapid biodiversity loss and a high prevalence of neglected tropical diseases, such as leishmaniasis, Aedes-borne diseases and Chagas disease. Overall, these results defy simplistic views that the dominant development trajectory for the Amazon will optimize economic, health and environmental indicators. This approach lays the groundwork for a more integrated narrative consistent with the economic history of the Brazilian Amazon.

Revisiting species and areas of interest for conserving global mammalian phylogenetic diversity

Various prioritisation strategies have been developed to cope with accelerating biodiversity loss and limited conservation resources. These strategies could become more engaging for decision-makers if they reflected the positive effects conservation can have on future projected biodiversity, by targeting net positive outcomes in future projected biodiversity, rather than reflecting the negative consequences of further biodiversity losses only. Hoping to inform the post-2020 biodiversity framework, we here apply this approach of targeting net positive outcomes in future projected biodiversity to phylogenetic diversity (PD) to re-identify species and areas of interest for conserving global mammalian PD. We identify priority species/areas as those whose protection would maximise gains in future projected PD. We also identify loss-significant species/areas as those whose/where extinction(s) would maximise losses in future projected PD. We show that our priority species/areas differ from loss-significant species/areas. While our priority species are mostly similar to those identified by the EDGE of Existence Programme, our priority areas generally differ from previously-identified ones for global mammal conservation. We further highlight that these newly-identified species/areas of interest currently lack protection and offer some guidance for their future management.

Saprophytic flies in impacted areas of the Belo Monte Dam, Pará, Brazil (Diptera: Mesembrinellidae, Neriidae, Ropalomeridae, and Sarcophagidae): community composition, abundance, and species richness

Abstract: The present study aims to document the community composition, abundance, and species richness of saprophytic fly species (Mesembrinellidae, Neriidae, Ropalomeridae, and Sarcophagidae) of the Volta Grande region of the Xingu River, a poorly sampled area impacted by the Belo Monte hydroelectric dam. Five collecting trips were carried out between 2014 and 2016, when traps baited with fermenting bananas were used. A total of 154 specimens, three genera, and six species were collected of Mesembrinellidae; 196 specimens, three genera, and seven species of Neriidae; 272 specimens, three genera, and six species of Ropalomeridae; and 624 specimens, 22 species and 10 genera of Sarcophagidae. Species accumulation curves for all families except Sarcophagidae demonstrated a strong tendency towards stabilization, showing that sampling efforts were sufficient to record most of the targeted species. Laneela perisi (Mariluis, 1987) (Mesembrinellidae) is a new record for the state of Pará. Among Ropalomeridae, Apophorhynchus amazonensisPrado, 1966, is a new record for Pará. Among Sarcophagidae, Helicobia aurescens (Townsend, 1927) is newly recorded from the Brazilian Amazon, and Ravinia effrenata (Walker, 1861) and Titanogrypa larvicida (Lopes, 1935) are new records for Pará.

Polycyclic aromatic hydrocarbons (PAHs) in sediments of the amazon coast: Evidence for localized sources in contrast to massive regional biomass burning

The Amazon coastal zone has become contaminated with organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs). However, information about their distribution and sources in this area is scarce, despite increasing deforestation and oil exploitation. Therefore, individual PAHs were analysed in the sediments of the Oyapock estuary, which is located in the Amazon coastal zone. This study provides information about the spatial and short-term temporal distributions of PAHs and discusses the major sources of PAHs to better understand the anthropogenic processes occurring in adjacent areas. The concentrations of all sixteen priority PAHs defined by the US EPA (United States Environmental Protection Agency, ∑₁₆PAHs) ranged from 10.9 to 138.8 ng g^-1 with a mean and standard deviation = 37.9 ± 20.5 and indicated that this estuary is not contaminated, while the mean levels were similar to those found in other Amazon regions and pristine areas along the coast of Brazil. No significant differences were found in the sedimentary PAHs levels between the wet and dry sampling campaigns, despite the different climatic conditions. Diagnostic ratios, positive matrix factorization (PMF) and cluster analysis have shown that the majority of the investigated PAHs were derived from combustion processes (at least 55.1%, as estimated by the PMF model). Localized source inputs from oil and its by-products concomitantly with natural/biogenic sources appear to be secondary sources. The PAH contribution from biomass and wood combustion was approximately 13.6% and was relatively lower than other regions of the Amazon that are undergoing massive biomass burning. As the first study of PAHs in this region, this study provides vital information on the healthy state of the estuary and can serve as a baseline for assessing the impacts of acute oil disasters or the chronic input of PAHs as a result of human settlements.

Assessing the effects of agricultural intensification on natural habitats and biodiversity in Southern Amazonia

The ongoing trend toward agricultural intensification in Southern Amazonia makes it essential to explore the future impacts of this development on the extent of natural habitats and biodiversity. This type of analysis requires information on future pathways of land-use and land-cover change (LULCC) under different socio-economic conditions and policy settings. For this purpose, the spatially explicit land-use change model LandSHIFT was applied to calculate a set of high-resolution land-use change scenarios for the Brazilian states Para and Mato Grosso. The period of the analysis were the years 2010-2030. The resulting land-use maps were combined with maps depicting vertebrate species diversity in order to examine the impact of natural habitat loss on species ranges as well as the overall LULCC-induced effect on vertebrate diversity as expressed by the Biodiversity Intactness Index (BII). The results of this study indicate a general decrease in biodiversity intactness in all investigated scenarios. However, agricultural intensification combined with diversified environmental protection policies show least impact of LULCC on vertebrate species richness and conservation of natural habitats compared to scenarios with low agricultural intensification or scenarios with less effective conservation policies.

Rapid Recent Deforestation Incursion in a Vulnerable Indigenous Land in the Brazilian Amazon and Fire-Driven Emissions of Fine Particulate Aerosol Pollutants

Deforestation in the Brazilian Amazon is related to the use of fire to remove natural vegetation and install crop cultures or pastures. In this study, we evaluated the relation between deforestation, land-use and land-cover (LULC) drivers and fire emissions in the Apyterewa Indigenous Land, Eastern Brazilian Amazon. In addition to the official Brazilian deforestation data, we used a geographic object-based image analysis (GEOBIA) approach to perform the LULC mapping in the Apyterewa Indigenous Land, and the Brazilian biomass burning emission model with fire radiative power (3BEM_FRP) to estimate emitted particulate matter with a diameter less than 2.5 µm (PM2.5), a primary human health risk. The GEOBIA approach showed a remarkable advancement of deforestation, agreeing with the official deforestation data, and, consequently, the conversion of primary forests to agriculture within the Apyterewa Indigenous Land in the past three years (200 km2), which is clearly associated with an increase in the PM2.5 emissions from fire. Between 2004 and 2016 the annual average emission of PM2.5 was estimated to be 3594 ton year−1, while the most recent interval of 2017–2019 had an average of 6258 ton year−1. This represented an increase of 58% in the annual average of PM2.5 associated with fires for the study period, contributing to respiratory health risks and the air quality crisis in Brazil in late 2019. These results expose an ongoing critical situation of intensifying forest degradation and potential forest collapse, including those due to a savannization forest-climate feedback, within “protected areas” in the Brazilian Amazon. To reverse this scenario, the implementation of sustainable agricultural practices and development of conservation policies to promote forest regrowth in degraded preserves are essential.

Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes

Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.

Arctiini Leach, [1815] (Lepidoptera, Erebidae, Arctiinae) of the Brazilian Amazon. IV - Subtribe Euchromiina Butler, 1876

Abstract: The Euchromiina moths comprise 735 species in the neotropics. Here we provide a list of Euchromiina species from the Brazilian Amazon. The list was produced from specimens deposited in the most important Brazilian collections and from literature data. Nearly 30% (219) of the neotropics Euchromiina species were recorded, including 13 new occurrences for the Brazilian Amazon. Santarém and Belém were the municipalities with the highest number of species records, with 96 and 74, respectively. Although the number of Euchromiina records is high in the Amazon, this value is underestimated because the fauna was never sampled in the vast majority of the biome. This is a worrying scenario because the Amazon has the world highest absolute rate of forest reduction. In order to suggest efficient conservation policies for the Amazon Arctiinae fauna, it is urgent to intensify the sampling effort in this biome.

Tiger-Moths in Savannas in Eastern Amazon: First Assessment of Diversity and Seasonal Aspects

Biodiversity knowledge on insects is urgently needed due to the ever growing demand for food and the consequent deforestation process and loss of natural habitats in many understudied tropical regions. In this paper, we describe the outcome of a biodiversity research on tiger moths performed for the first time in a poorly studied Amazonian landscape-the savanna. We sampled tiger moths monthly with UV automatic light traps for 12 consecutive months in two sampling points in an area of savanna in eastern Amazon, and we compared our results to previously available data for eastern Amazon. We found a total of 91 species of which 80 were identified to species level. The most species-rich subtribes were Phaegopterina and Euchromiina with 32 species each. Species richness and abundance did not differ among sampling sites, but in general the species richness was higher during the dry season while abundance was higher during the wet season. This seasonal diversity pattern differs from the most common patterns recorded for savannas in other parts of the world. The species composition also changed in wet and dry seasons and correlated significantly with temperature and relative humidity. Our results suggest that the alpha diversity of the Amazonian savannas in our sampling area is lower than that in nearby rain forests and similar to that in agriculturally disturbed areas surrounded by rain forests. However, the species composition differed considerably from natural and disturbed areas. These results highlight the need of basic biodiversity surveys of insects in Amazonian savannas.

The Roosevelt–Rondon expedition marmoset Mico marcai: unveiling the conservation status of a Data Deficient species

The Roosevelt–Rondon Expedition marmoset Mico marcai was first collected in 1914 and all information on this primate previously came from three skins brought back by this expedition. As a result, M. marcai is categorized as Data Deficient on the IUCN Red List. As the presumed range of M. marcai lies on the path of the advancing arc of deforestation in Brazil, the collection of relevant data to assess the conservation status of this Amazonian species is of some urgency. Here we present the first field data on the distribution and population size of, and threats to, M. marcai, to reassess the species’ conservation status. During 2012–2015 we surveyed the species in the Marmelos–Aripuanã interfluve, and estimated its density using distance sampling. We also used spatial predictive modelling to estimate forest loss within the species range under two deforestation scenarios. We found the marmoset in 13 localities and estimated its extent of occurrence to be 31,073 km2. We estimated the species’ density to be 8.31 individuals/km2 and extrapolated this to estimate a total population of 258,218 individuals (CI 150,705–441,860). Under a business-as-usual deforestation scenario, c. 10,000 km2 of forest, comprising 33% of the species’ range, would be lost in three marmoset generations (c. 18 years), and we, therefore, recommend that M. marcai be categorized as Vulnerable on the IUCN Red List based on criterion A3c. Other Amazonian marmosets require similar reassessment as their ranges also fall in the path of the arc of deforestation.

Illegal use of natural resources in federal protected areas of the Brazilian Amazon

Background

The Brazilian Amazon is the world’s largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive.

Methods

We evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon. We classified illegal activities into ten categories and used generalized additive models (GAMs) to evaluate the relationship between illegal use of natural resources inside PAs with management type, age of PAs, population density, and accessibility.

Results

We found 27 types of illegal use of natural resources that were grouped into 10 categories of illegal activities. Most infractions were related to suppression and degradation of vegetation (37.40%), followed by illegal fishing (27.30%) and hunting activities (18.20%). The explanatory power of the GAMs was low for all categories of illegal activity, with a maximum explained variation of 41.2% for illegal activities as a whole, and a minimum of 14.6% for hunting activities.

Discussion

These findings demonstrate that even though PAs are fundamental for nature conservation in the Brazilian Amazon, the pressures and threats posed by human activities include a broad range of illegal uses of natural resources. Population density up to 50 km from a PA is a key variable, influencing illegal activities. These threats endanger long-term conservation and many efforts are still needed to maintain PAs that are large enough and sufficiently intact to maintain ecosystem functions and protect biodiversity.

Butterflies of Amazon and Cerrado remnants of Maranhão, Northeast Brazil

Abstract Species inventories are important tools to evaluate biodiversity losses and contribute to the conservation of endangered areas. The Amazon and Cerrado are the largest Brazilian biomes and represent some of the most threatened regions of the country. Due to its location between these biomes, the state of Maranhão, Northeast Brazil, possesses a great variety of habitats and a high local diversity. Nonetheless, few faunistic inventories of diversified groups have been performed in the state. In the specific case of butterflies, a well-known biological indicator, no inventories have been published in the past years. This study aimed to expand the knowledge on the composition of butterflies in Amazon and Cerrado remnants of Maranhão. Butterflies were sampled between 2011 and 2015 across eight municipalities of the state. Captures were made through entomological nets and baited traps. In total, 189 species were sampled, of which 165 were captured in the Amazon, 65 in the Cerrado and 41 in both biomes. We sampled 167 species through entomological nets and 43 through baited traps, representing 12% of similarity in species composition between sampling methods. We estimate that the recorded species represent a small subset of the butterflies from Maranhão. Therefore, long-term researches in poorly studied areas of the state are recommended to identify novel and/or endemic taxa.

Effect of oil palm on the Plecoptera and Trichoptera (Insecta) assemblages in streams of eastern Amazon

The production of oil palm is expected to increase in the Amazon region. However, expansion of oil palm plantation leads to significant changes in the physical structure of aquatic ecosystems, mainly through the reduction of riparian vegetation that is essential for aquatic biodiversity. Here, we evaluated the effects of oil palm on the physical habitat structure of Amazonian stream environments and assemblages of Plecoptera and Trichoptera (PT), ​both found in these streams. We compared streams sampled in oil palm plantations (n = 13) with natural forest areas ("reference" streams, n = 8), located in the eastern Amazon, Brazil. Our results showed that oil palm streams were more likely to be in close proximity to roads, had higher pH values, and higher amounts of fine substrate deposited in the channel than reference streams. Further, these environmental changes had important effects on the aquatic invertebrate assemblages, reducing the abundance and richness of PT. Nevertheless, the genera composition of the assemblages did not differ between reference and oil palm (PERMANOVA, pseudo-F _(1,19) = 1.891; p = 0.111). We conclude that oil palm production has clear negative impacts on aquatic environments and PT assemblages in Amazonian streams. We recommend that oil palm producers invest more in planning of road networks to avoid the construction of roads near to the riparian vegetation. This planning can minimize impacts of oil palm production on aquatic systems in the Amazon.

Microgeographical structure in the major Neotropical malaria vector Anopheles darlingi using microsatellites and SNP markers

BACKGROUND

In recent decades, throughout the Amazon Basin, landscape modification contributing to profound ecological change has proceeded at an unprecedented rate. Deforestation that accompanies human activities can significantly change aspects of anopheline biology, though this may be site-specific. Such local changes in anopheline biology could have a great impact on malaria transmission. The aim of this study was to investigate population genetics of the main malaria vector in Brazil, Anopheles darlingi, from a microgeographical perspective.

METHODS

Microsatellites and ddRADseq-derived single nucleotide polymorphisms (SNPs) were used to assess levels of population genetic structuring among mosquito populations from two ecologically distinctive agricultural settlements (~60 km apart) and a population from a distant (~700 km) urban setting in the western Amazon region of Brazil.

RESULTS

Significant microgeographical population differentiation was observed among Anopheles darlingi populations via both model- and non-model-based analysis only with the SNP dataset. Microsatellites detected moderate differentiation at the greatest distances, but were unable to differentiate populations from the two agricultural settlements. Both markers showed low polymorphism levels in the most human impacted sites.

CONCLUSIONS

At a microgeographical scale, signatures of genetic heterogeneity and population divergence were evident in Anopheles darlingi, possibly related to local environmental anthropic modification. This divergence was observed only when using high coverage SNP markers.

Delimiting priority areas for the conservation of endemic and threatened Neotropical birds using a niche-based gap analysis

Knowledge of spatiotemporal distribution of biodiversity is still very incomplete in the tropics. This is one of the major problems preventing the assessment and effectiveness of conservation actions. Mega-diverse tropical regions are being exposed to fast and profound environmental changes, and the amount of resources available to describe the distribution of species is generally limited. Thus, the tropics is losing species at unprecedented rates, without a proper assessment of its biodiversity. Species distribution models (SDMs) can be used to fill such biogeographic gaps within a species' range and, when allied with systematic conservation planning (e.g. analyses of representativeness, gap analysis), help transcend such data shortage and support practical conservation actions. Within the Neotropics, eastern Amazon and northern Cerrado present a high variety of environments and are some of the most interesting ecotonal areas within South America, but are also among the most threatened biogeographic provinces in the world. Here, we test the effectiveness of the current system of Protected Areas (PAs), in protecting 24 threatened and endemic bird species using SDMs. We found that taxa with wider distributions are potentially as protected as taxa with smaller ranges, and larger PAs were more efficient than smaller PAs, while protecting these bird species. Nonetheless, Cerrado PAs are mostly misallocated. We suggest six priority areas for conservation of Neotropical birds. Finally, we highlight the importance of indigenous lands in the conservation of Neotropical biodiversity, and recommend the development of community management plans to conserve the biological resources of the region.

Discovery or Extinction of New Scleroderma Species in Amazonia?

The Amazon Forest is a hotspot of biodiversity harboring an unknown number of undescribed taxa. Inventory studies are urgent, mainly in the areas most endangered by human activities such as extensive dam construction, where species could be in risk of extinction before being described and named. In 2015, intensive studies performed in a few locations in the Brazilian Amazon rainforest revealed three new species of the genus Scleroderma: S. anomalosporum, S. camassuense and S. duckei. The two first species were located in one of the many areas flooded by construction of hydroelectric dams throughout the Amazon; and the third in the Reserva Florestal Adolpho Ducke, a protected reverse by the INPA. The species were identified through morphology and molecular analyses of barcoding sequences (Internal Transcribed Spacer nrDNA). Scleroderma anomalosporum is characterized mainly by the smooth spores under LM in mature basidiomata (under SEM with small, unevenly distributed granules, a characteristic not observed in other species of the genus), the large size of the basidiomata, up to 120 mm diameter, and the stelliform dehiscence; S. camassuense mainly by the irregular to stellate dehiscence, the subreticulated spores and the bright sulfur-yellow colour, and Scleroderma duckei mainly by the verrucose exoperidium, stelliform dehiscence, and verrucose spores. Description, illustration and affinities with other species of the genus are provided.

Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm

For half a century, the process of economic integration of the Amazon has been based on intensive use of renewable and nonrenewable natural resources, which has brought significant basin-wide environmental alterations. The rural development in the Amazonia pushed the agricultural frontier swiftly, resulting in widespread land-cover change, but agriculture in the Amazon has been of low productivity and unsustainable. The loss of biodiversity and continued deforestation will lead to high risks of irreversible change of its tropical forests. It has been established by modeling studies that the Amazon may have two "tipping points," namely, temperature increase of 4 °C or deforestation exceeding 40% of the forest area. If transgressed, large-scale "savannization" of mostly southern and eastern Amazon may take place. The region has warmed about 1 °C over the last 60 y, and total deforestation is reaching 20% of the forested area. The recent significant reductions in deforestation-80% reduction in the Brazilian Amazon in the last decade-opens up opportunities for a novel sustainable development paradigm for the future of the Amazon. We argue for a new development paradigm-away from only attempting to reconcile maximizing conservation versus intensification of traditional agriculture and expansion of hydropower capacity-in which we research, develop, and scale a high-tech innovation approach that sees the Amazon as a global public good of biological assets that can enable the creation of innovative high-value products, services, and platforms through combining advanced digital, biological, and material technologies of the Fourth Industrial Revolution in progress.

The effects of oil palm plantations on the functional diversity of Amazonian birds

Oil palm plantations are rapidly expanding in tropical areas, although the nature of the impacts on the functional roles of the different species in the ecosystem is poorly understood. The present study is the first assessment of how oil palm affects the functional diversity of birds in the Brazilian Amazon and tests the hypothesis that converting forest to oil palm decreases functional diversity of bird communities, selecting species more tolerant to environmental disturbances. We conducted point counts to survey bird communities in 16 plots in the eastern Amazon. We sampled 32 points in riparian forest, 128 in oil palm and 160 in forested habitats. To test whether the conversion of forest into oil palm plantations affects functional diversity of birds we calculated the FD (Functional Diversity) and FRic (Functional Richness) indices. To examine whether oil palm plantations select species functionally more similar than expected by chance we used a null model (SES.FD). FD was significantly higher in the forest plots in comparison with riparian forests and oil palm, and lower in oil palm when compared with riparian forests. FRic, in turn, was greater in forest plots than in oil palm and in riparian forest. These results show that the conversion of forested areas to oil palm represents a great loss of functional strategies. The SES values indicate that in forested habitats bird communities tend to be functionally clustered while in the oil palm they are functionally overdispersed. The functional traits most affected by oil palm were those associated with diet and foraging stratum. In short, oil palm plantations reduced functional diversity of birds, although the presence of riparian forests within the plantations and the fragments of forest adjacent are extremely important for the maintenance of ecosystem services.

Land use change emission scenarios: anticipating a forest transition process in the Brazilian Amazon

Following an intense occupation process that was initiated in the 1960s, deforestation rates in the Brazilian Amazon have decreased significantly since 2004, stabilizing around 6000 km(2) yr(-1) in the last 5 years. A convergence of conditions contributed to this, including the creation of protected areas, the use of effective monitoring systems, and credit restriction mechanisms. Nevertheless, other threats remain, including the rapidly expanding global markets for agricultural commodities, large-scale transportation and energy infrastructure projects, and weak institutions. We propose three updated qualitative and quantitative land-use scenarios for the Brazilian Amazon, including a normative 'Sustainability' scenario in which we envision major socio-economic, institutional, and environmental achievements in the region. We developed an innovative spatially explicit modelling approach capable of representing alternative pathways of the clear-cut deforestation, secondary vegetation dynamics, and the old-growth forest degradation. We use the computational models to estimate net deforestation-driven carbon emissions for the different scenarios. The region would become a sink of carbon after 2020 in a scenario of residual deforestation (~1000 km(2) yr(-1)) and a change in the current dynamics of the secondary vegetation - in a forest transition scenario. However, our results also show that the continuation of the current situation of relatively low deforestation rates and short life cycle of the secondary vegetation would maintain the region as a source of CO2 - even if a large portion of the deforested area is covered by secondary vegetation. In relation to the old-growth forest degradation process, we estimated average gross emission corresponding to 47% of the clear-cut deforestation from 2007 to 2013 (using the DEGRAD system data), although the aggregate effects of the postdisturbance regeneration can partially offset these emissions. Both processes (secondary vegetation and forest degradation) need to be better understood as they potentially will play a decisive role in the future regional carbon balance.

Status and challenges for conservation of small mammal assemblages in South America

South America spans about 44° latitude, covers almost 18 million km(2) , and is second only to Africa in continental mammal species richness. In spite of this richness, research on the status of this fauna and on the nature and magnitude of contemporary threats remains limited. Distilling threats to this diverse fauna at a continental scale is challenging, in part because of the limited availability of rigorous studies. Recognizing this constraint, we summarize key threats to small mammals in South America, emphasizing the roles of habitat loss and degradation, direct persecution, and the increasing threat of climate change. We focus on three regional 'case studies': the tropical Andes, Amazonia and adjacent lowland regions, and the southern temperate region. We close with a brief summary of recent findings at our long-term research site in north-central Chile as they pertain to projected threats to this fauna. Habitat alteration is a pervasive threat that has been magnified by market forces and globalization (e.g. extensive agricultural development in Amazonia), and threatens increasing numbers of populations and species. Climate change poses even greater threats, from changes in rainfall and runoff regimes and resulting changes in vegetative structure and composition to secondary influences on fire dynamics. It is likely that many changes have yet to be recognized, but existing threats suggest that the future may bring dramatic changes in the distribution of many mammal taxa, although it is not clear if key habitat elements (vegetation) will respond as rapidly as climatic factors, leading to substantial uncertainty. Climate change is likely to result in 'winners' and 'losers' but available information precludes detailed assessment of which species are likely to fall into which category. In the absence of long-term monitoring and applied research to characterize these threats more accurately, and to develop strategies to reduce their impacts, managers already are being faced with daunting challenges. As the line between 'pure' and 'applied' research blurs in the face of converging interests of scientists and society we hope that solutions to these critical issues will be incorporated in addressing anticipated conservation crises.

Antimicrobial activity of amazonian medicinal plants

Objectives

The aqueous extracts of currently utilized Amazonian medicinal plants were assayed in vitro searching for antimicrobial activity against human and animal pathogenic microorganisms.

Methods

Medium resuspended lyophilized aqueous extracts of different organs of Amazonian medicinal plants were assayed by in vitro screening for antimicrobial activity. ATCC and standardized microorganisms obtained from Oswaldo Cruz Foundation/Brazil were individually and homogeneously grown in agar plate, and holes previously perforated in the gel were filled with diluted plant aqueous extracts. Inhibition halos were evaluated and controlled by the use of the fluoroquinolone ciprofloxacin.

Results

The Amazonian medicinal plants, Hymenelobium petraeum showed inhibitory activity over Staphylococcus aureus, Enterococcus faecalis, Salmonella enterica serovar Typhi, Acinetobacter baumannii and Candida albicans, while Vatairea guianensis and Symphonia globulifera presented inhibitory activity exclusively for Staphylococcus aureus. Also, Ptychopetalum olacoides and Pentaclethra macroloba inhibited the growth of Klebsiella ozaenae and Acinetobacter baumannii.

Conclusion

The aqueous botanic extracts that showed activity against microroganisms of ATTC and Osvaldo Cruz strains had at least 40% of antimicrobial activity when compared to halo inhibition produced by the commercial antibiotic ciprofloxacin utilized as a control. Of all plants extracts assayed, the Hymenelobium petraeum had the best performance, sometimes exhibiting higher activity than ciprofloxacin. It is not well-defined by the physicians the exact indication of the majority of medicinal plants in the Amazon area in Brazil. Natives utilize the plants according to their symptoms, based on the traditional knowledge transmitted orally from generation to generation, among Amerindians, Afrodescendents and ethnic mixed populations. A significant number of Amazonian medicinal plants are totally unknown related to their medicinal properties including mechanism of action and therapeutic effects, as very few information is reported in the scientific literature. A tiny amount of data is presented, as the preliminary antimicrobial properties of the medicinal plants here accessed, under the urgent necessity of new antibiotics in the market and in face of the increased resistance of infectious microorganisms to antimicrobials.

Evaluation of Paracoccidioides brasiliensis infection by gp 43 intradermal test in rural settlements in Central-West Brazil

Epidemiological studies of paracoccidioidomycosis have been based on surveys achieved with intradermal tests, and paracoccidioidin is the most common antigen used in most cases. The glycoprotein of 43-kDa (gp43) has been used in intradermal tests. It is the most antigenic component of Paracoccidioides brasiliensis, and it provides greater specificity to evaluate infection for this fungus. In this study, the prevalence of P. brasiliensis infection was estimated with intradermal tests involving gp43 for 695 people in rural Central-West Brazil. The infection rate was 45.8 % (95 % CI = 42.1-49.5), and the average age of those infected was 45.8 ± 18.2 years. The prevalence did not show gender-based differences but increased with age. The results demonstrate the importance of P. brasiliensis infection in rural settlements and the early exposure of children in the region to the fungus. Despite the high antigenicity and specificity of gp43, its usage must be standardized, so that epidemiological surveys will be comparable and more accurately reflect P. brasiliensis infection in endemic areas.

Herpetofauna da área do Igarapé Esperança na Reserva Extrativista Riozinho da Liberdade, Acre - Brasil

A região do Alto Juruá localiza-se no estado do Acre (oeste da Amazônia brasileira) e é uma região conhecida por apresentar uma alta diversidade e também considerada prioritária para inventariamento e conservação da herpetofauna. Este trabalho foi realizado entre agosto de 2006 a junho de 2008 e apresenta a lista de espécies de anfíbios e répteis da área do Igarapé Esperança na Reserva Extrativista Riozinho da Liberdade, Acre. Quatro métodos amostrais foram empregados para inventariar a herpetofauna: procura limitada por tempo, armadilhas de interceptação e queda, registros auditivos e encontros ocasionais. Foram registradas 162 espécies, sendo 83 de anfíbios (80 anuros, dois gimnofionos e uma salamandra) e 79 de répteis (29 lagartos, 42 serpentes, um anfisbênio, quatro quelônios e três jacarés). Dessas espécies, onze (Adelphobates quinquevittatus, Hyalinobatrachium munozorum, Pristimantis academicus, P. aureolineatus, Syncope antenori, Alopoglossus buckleyi, Drymobius rhombifer, Liophis dorsocorallinus, L. taeniogaster, Umbrivaga pygmaea e Micrurus remotus) foram registradas pela primeira vez para o Acre, sendo que seis delas (H. munozorum, P. academicus, P. aureolineatus, S. antenori, A. buckleyi e L. dorsocorallinus) consistem também os primeiros registros para o Brasil. Salienta-se aqui a importância da forma do uso das florestas pelas populações tradicionais (indígenas, extrativistas e ribeirinhos) e das áreas protegidas na conservação da alta biodiversidade encontrada no Alto Juruá e também a necessidade de estudos sobre o uso de algumas espécies (especialmente de quelônios e crocodilianos) para analisar possíveis impactos sobre as populações desses animais.

Deforestation and avian infectious diseases

In this time of unprecedented global change, infectious diseases will impact humans and wildlife in novel and unknown ways. Climate change, the introduction of invasive species, urbanization, agricultural practices and the loss of biodiversity have all been implicated in increasing the spread of infectious pathogens. In many regards, deforestation supersedes these other global events in terms of its immediate potential global effects in both tropical and temperate regions. The effects of deforestation on the spread of pathogens in birds are largely unknown. Birds harbor many of the same types of pathogens as humans and in addition can spread infectious agents to humans and other wildlife. It is thought that avifauna have gone extinct due to infectious diseases and many are presently threatened, especially endemic island birds. It is clear that habitat degradation can pose a direct threat to many bird species but it is uncertain how these alterations will affect disease transmission and susceptibility to disease. The migration and dispersal of birds can also change with habitat degradation, and thus expose populations to novel pathogens. Some recent work has shown that the results of landscape transformation can have confounding effects on avian malaria, other haemosporidian parasites and viruses. Now with advances in many technologies, including mathematical and computer modeling, genomics and satellite tracking, scientists have tools to further research the disease ecology of deforestation. This research will be imperative to help predict and prevent outbreaks that could affect avifauna, humans and other wildlife worldwide.