The Amazon is a mosaic of ecosystems, accounting for 13% of all known species globally, and responsible for providing a variety of ecosystem services, including a key role in global climate regulation. However, 18% of the Amazon forest cover has been lost completely and a further 38% degraded, threatening biodiversity and millions of local livelihoods. Currently, little is known about how this impacts the functioning of ecological communities. Here, we combine an energetic approach with biodiversity metrics to quantify ecosystem functioning in mammal and bird food webs across Amazonia, along a gradient of forest degradation linked to road proximity. We show that even under relatively low disturbance, ecosystem functions shift: carnivory increases closer to roads, driven by generalist species that persist under these conditions, whereas herbivory declines mainly due to reduced herbivore biomass and species richness. This suggests that processes associated with forest degradation can alter energy flow even where biodiversity metrics remain relatively unchanged, highlighting energetic approaches as sensitive indicators of ecosystem disruption.

Conservation actions should account for species natural history and behavior related to differences between sexes. However, most studies have not taken into consideration non-independence of observations from the same individual. We used data from camera-trap surveys undertaken over six consecutive years to investigate habitat use by jaguar (Panthera onca) in varzea seasonally flooded forest. We used hierarchical modeling to assess sex differences in occurrence probability related to environmental factors, while accounting for individual and spatial autocorrelation. Specifically, we tested whether male and female jaguars responded differently to habitat type and anthropogenic influence. Our results do not support previous conclusions related to differences between sexes and indicate that, in the studied area, jaguars are habitat generalists, exploring all environments with similar probability during the low-water season. Human settlements also apparently have little effect on habitat use by jaguars in this area. The lack of avoidance of settlements might be due to the low levels of anthropogenic pressure in the area, which adds support to the effectiveness of sustainable-development reserves. The difference between our results and previous studies may be due to the fact that we took into account individual differences, or may be related to the unique environmental characteristics of the varzea of Mamiraua Sustainable Development Reserve in Central Amazonia.

Amazon forests are being degraded by myriad anthropogenic disturbances, altering ecosystem and climate function. We analyzed the effects of a range of land‐use and climate‐change disturbances on fine‐scale canopy structure using a large database of profiling canopy lidar collected from disturbed and mature Amazon forest plots. At most of the disturbed sites, surveys were conducted 10–30 years after disturbance, with many exhibiting signs of recovery. Structural impacts differed in magnitude more than in character among disturbance types, producing a gradient of impacts. Structural changes were highly coordinated in a manner consistent across disturbance types, indicating commonalities in regeneration pathways. At the most severely affected site – burned igapó (seasonally flooded forest) – no signs of canopy regeneration were observed, indicating a sustained alteration of microclimates and consequently greater vulnerability to transitioning to a more open‐canopy, savanna‐like state. Notably, disturbances rarely shifted forests beyond the natural background of structural variation within mature plots, highlighting the similarities between anthropogenic and natural disturbance regimes, and indicating a degree of resilience among Amazon forests. Studying diverse disturbance types within an integrated analytical framework builds capacity to predict the risk of degradation‐driven forest transitions.

The Amazon forest has the highest biodiversity on Earth. However, information on Amazonian vertebrate diversity is still deficient and scattered across the published, peer-reviewed, and gray literature and in unpublished raw data. Camera traps are an effective non-invasive method of surveying vertebrates, applicable to different scales of time and space. In this study, we organized and standardized camera trap records from different Amazon regions to compile the most extensive data set of inventories of mammal, bird, and reptile species ever assembled for the area. The complete data set comprises 154,123 records of 317 species (185 birds, 119 mammals, and 13 reptiles) gathered from surveys from the Amazonian portion of eight countries (Brazil, Bolivia, Colombia, Ecuador, French Guiana, Peru, Suriname, and Venezuela). The most frequently recorded species per taxa were: mammals: Cuniculus paca (11,907 records); birds: Pauxi tuberosa (3713 records); and reptiles: Tupinambis teguixin (716 records). The information detailed in this data paper opens up opportunities for new ecological studies at different spatial and temporal scales, allowing for a more accurate evaluation of the effects of habitat loss, fragmentation, climate change, and other human-mediated defaunation processes in one of the most important and threatened tropical environments in the world. The data set is not copyright restricted; please cite this data paper when using its data in publications and we also request that researchers and educators inform us of how they are using these data.

The rate of deforestation in the Amazon is increasing. Predictive models estimate that as a result of agricultural expansion 40% of these forests will be lost by 2050. As a consequence the habitat of forest-dwelling species such as the Endangered black-faced black spider monkeyAteles chamekis being lost, particularly along the arc of deforestation in the Brazilian Amazon. We used species distribution modelling to (1) define the distribution of this spider monkey, using environmental predictors, (2) calculate the area of this distribution covered by the protected area network, and (3) calculate the expected loss of the species' habitat under future scenarios of deforestation. We found that the species occupies only c. 28% of its extent of occurrence. Only 32% of the species' area of occupancy is legally protected, and the modelling suggests that 31-40% of the species' habitat will be lost by 2050. We highlight three unprotected regions with extensive forest cover that are predicted to become severely deforested by 2050 as priority regions for expanding the protected area network. We also propose landscape management and restoration in three human-modified regions. Our study provides an example of how species distribution modelling can be applied to assess threats to species and support decision makers in implementing conservation actions.

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species.

Amazonia forest plays a major role in providing ecosystem services for human and sanctuaries for wildlife. However, ongoing deforestation and habitat fragmentation in the Brazilian Amazon has threatened both. The ocelot is an ecologically important mesopredator and a potential conservation ambassador species, yet there are no previous studies on its habitat preference and spatial patterns in this biome. From 2010 to 2017, twelve sites were surveyed, totaling 899 camera trap stations, the largest known dataset for this species. Using occupancy modeling incorporating spatial autocorrelation, we assessed habitat use for ocelot populations across the Brazilian Amazon. Our results revealed a positive sigmoidal correlation between remote-sensing derived metrics of forest cover, disjunct core area density, elevation, distance to roads, distance to settlements and habitat use, and that habitat use by ocelots was negatively associated with slope and distance to river/lake. These findings shed light on the regional scale habitat use of ocelots and indicate important species-habitat relationships, thus providing valuable information for conservation management and land-use planning.

AbstractThe spatial distribution of biodiversity and related processes is the core of Biogeography. Amazonia is the world's most diverse rainforest and the primary source of diversity to several Neotropical regions. The origins of such diversity continue to be an unresolved question in evolutionary biology. Among many competing hypotheses to explain the evolution of the Amazonian biodiversity, one stands out as the most influential: the refugia hypothesis by Jürgen Haffer. Here, we provide a chronological overview on how the refugia hypothesis evolved over the decades and how the criticism from different fields affected its acceptance. We conclude that the refugia hypothesis alone cannot explain the diversification of the complex Amazonian diversity, and perhaps it was not the most important diversification mechanism. However, the debate provoked by refugia has produced a great amount of knowledge on Amazonian climatic, geological, and evolutionary processes, as well as on species distributions, movements, and history.

AbstractThe rate of deforestation in the Amazon is increasing. Predictive models estimate that as a result of agricultural expansion 40% of these forests will be lost by 2050. As a consequence the habitat of forest-dwelling species such as the Endangered black-faced black spider monkey Ateles chamek is being lost, particularly along the arc of deforestation in the Brazilian Amazon. We used species distribution modelling to (1) define the distribution of this spider monkey, using environmental predictors, (2) calculate the area of this distribution covered by the protected area network, and (3) calculate the expected loss of the species’ habitat under future scenarios of deforestation. We found that the species occupies only c. 28% of its extent of occurrence. Only 32% of the species’ area of occupancy is legally protected, and the modelling suggests that 31–40% of the species’ habitat will be lost by 2050. We highlight three unprotected regions with extensive forest cover that are predicted to become severely deforested by 2050 as priority regions for expanding the protected area network. We also propose landscape management and restoration in three human-modified regions. Our study provides an example of how species distribution modelling can be applied to assess threats to species and support decision makers in implementing conservation actions.

Várzea forests account for 17% of the Amazon basin and endure an annual inundation that can reach 14 m deep during 6-8 months. This flood pulse in combination with topography directly influences the várzea vegetation cover. Assemblages of several taxa differ significantly between unflooded terra firme and flooded várzea forests, but little is known about the distribution of medium and large sized terrestrial mammals in várzea habitats. Therefore, our goal was to understand how those habitats influence mammalian species distribution during the dry season. Specifically, we: (1) compared the species composition between a terra firme (Amanã Sustainable Development Reserve) and a várzea forest (Mamirauá Sustainable Development Reserve); and (2) tested the influence of the várzea habitat classes on the number of records, occurrence and species composition of mammalian assemblages. The sampling design in each reserve consisted of 50 baited camera trap stations, with an overall sampling effort of 5015 camera trap days. We used Non-Metric Multidimension Scaling (NMDS) to compare species composition between terra firme and várzea forests, and used Generalized Linear Models (GLM) to assess how habitat types and a habitat diversity index affect mammal distributions. We recorded 21 medium and large sized mammalian species, including 20 species in terra firme and only six in várzea (3443 records). Flood pulse and isolation in várzea forest drove the dissimilarity between these two forest types. In várzea forest, medium size mammals, in general, avoided habitats associated with long flooding periods, while jaguars (Panthera onca) appeared to prefer aquatic/terrestrial transition zones. Habitats that remain dry for longer periods showed more mammalian occurrence, suggesting that dispersion via soil is important even for semi-arboreal species. This is the first study to evaluate differential use of várzea habitats by terrestrial mammalian assemblages.

Ongoing deforestation in Southeast Asia is leading to increased fragmentation and reduction of habitat for the mainland clouded leopard (Neofelis nebulosa). Using the largest detection/non-detection camera trap survey dataset known for the species throughout its range, we investigated factors affecting clouded leopard habitat use across Peninsular Malaysia. Habitat use was modelled using fine scale covariates and recently developed analytical techniques to account for spatial autocorrelation. Clouded leopard habitat use increased with increasing distance from water bodies, higher numbers of discontinuous core areas per unit area and higher elevation. In addition, clouded leopard habitat use was higher in sites with higher average forest change values. After extrapolating the predicted habitat use of clouded leopards across the whole of Peninsular Malaysia, we assessed the suitability of proposed ecological linkages, and identified other suitable forest patches not within the current Central Forest Spine. Our findings are valuable for land use planning and management, in particular, for determining the suitability of forest remnants to support populations of clouded leopard and predicting how this species will respond in human-dominated landscapes.

The bush dog (Speothos venaticus) is a Neotropical canid with a wide geographic distribution. Although globally listed as Near Threatened, this species was listed as Vulnerable in a recent assessment by the Brazilian government. Few records of this mammal have been reported in the Brazilian Cerrado, and it is considered extinct in several localities as a result of human landscape fragmentation. The record presented here is the first evidence of bush dog presence in West Minas Gerais, Brazil, which augments the species distribution with expected occurrence for this region. The study site was a transitional area between the Cerrado and Atlantic Forest biomes, in the Triângulo Mineiro region, which is a highly fragmented landscape, dominated by cattle ranches with exotic pasture species and scattered natural patches. We only recorded a single bush dog individual in our survey (4,036 camera trap/night), but our sampling success was expected compared with that of other previous mammal surveys using the camera trapping method, in part, because of the species' elusive behavior and low natural densities. This record enhances knowledge of the S. venaticus distribution. Potentially, we confirm the presence of the bug dog in a region that was regarded being environmentally suitable for this species occurrence, but where it has never been reported. Moreover, our result elucidates the potential of the natural remnants to harbor threatened species in highly human-influenced and non-protected landscapes, which is the dominant scenario found in West Minas Gerais, Brasil. .

Ocelots (Leopardus pardalis) are presumed to be the most abundant of the wild cats throughout their distribution range and to play an important role in the dynamics of sympatric small-felid populations. However, ocelot ecological information is limited, particularly for the Amazon. We conducted three camera-trap surveys during three consecutive dry seasons to estimate ocelot density in Amanã Reserve, Central Amazonia, Brazil. We implemented a spatial capture-recapture (SCR) model that shared detection parameters among surveys. A total effort of 7020 camera-trap days resulted in 93 independent ocelot records. The estimate of ocelot density in Amanã Reserve (24.84 ± SE 6.27 ocelots per 100 km2) was lower than at other sites in the Amazon and also lower than that expected from a correlation of density with latitude and rainfall. We also discuss the importance of using common parameters for survey scenarios with low recapture rates. This is the first density estimate for ocelots in the Brazilian Amazon, which is an important stronghold for the species.

The bush dog (Speothos venaticus) is a small Neotropical canid. Although its distribution covers the entire Amazon basin, the occurrence of bush dogs in vast areas of the Amazon remains hypothetical. The records of bush dogs presented in this study reduce a large gap in the known distribution of the species in Central Amazonia and include the 1st documentation of the species from forest seasonally flooded by black water (Igapo).

Each kind of trap tends to be selective on species sampled, in a way that each one only reveals part of the abundance and species richness of the community sampled. In this way, in order to know the factors that affect the success of sampling methods is crucial for a better planning of experiments and data analysis. The aim of this study was to evaluate the factors that affect the success of pitfall traps in capturing small mammals, such as trap size, designs and use of bait. The study was carried out in two reserves inside the campus of the Universidade Federal de Lavras (UFLA), in South Minas Gerais State, Brazil. In total, 65 specimens belonging to 8 species were caught. Different types of trap design (Y-shaped and I-shaped) have not influenced the capture success of pitfalls. The same result was obtained for the different size of buckets, in exception for Oligoryzomys flavescens, in which larger buckets were more efficient. The use of baits was considered not necessary.

Each kind of trap tends to be selective on species sampled, in a way that each one only reveals part of the abundance and species richness of the community sampled. In this way, in order to know the factors that affect the success of sampling methods is crucial for a better planning of experiments and data analysis. The aim of this study was to evaluate the factors that affect the success of pitfall traps in capturing small mammals, such as trap size, designs and use of bait. The study was carried out in two reserves inside the campus of the Universidade Federal de Lavras (UFLA), in South Minas Gerais State, Brazil. In total, 65 specimens belonging to 8 species were caught. Different types of trap design (Y-shaped and I-shaped) have not influenced the capture success of pitfalls. The same result was obtained for the different size of buckets, in exception for Oligoryzomys flavescens, in which larger buckets were more efficient. The use of baits was considered not necessary.