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Conventional agriculture is a significant driver of ecosystem service loss. In contrast, agroforestry is a land use option that can restore ecosystem services, such as carbon sequestration. Using field data from small proprieties we aimed to quantify carbon sequestration and its potential economic impact in coffee agroforestry systems (CAS) in Brazil. Allometric equations were used to estimate carbon stock and tree biomass, while net present value (NPV), internal rate of return (IRR), and payback period were used as economic feasibility parameters in a 16-year modeled scenario. Discount rate and carbon price applied was 6% and US$ 5.1 Mg CO2e-1, respectively. Total mean carbon stock in two years old and 16 years old CAS were 1.38 ± 0.63 Mg C ha-1 and 59.69 ± 32.63 Mg C ha-1, respectively. All CAS presented payback periods of two years, with a mean NPV of US$ 50,585.91 and a mean IRR of 89.93%. Carbon revenue impact on NPV and IRR was US$ 148.80 and 0.24%, respectively. Our results indicate that carbon sequestration economic impact does not encourage the adoption of coffee agroforestry systems. However, these systems can be an economically viable land use option that sequester large amounts of carbon comparable to forest patches.

Jaguar (Panthera onca) populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.

The jaguar is the top predator of the Atlantic Forest (AF), which is a highly threatened biodiversity hotspot that occurs in Brazil, Paraguay and Argentina. By combining data sets from 14 research groups across the region, we determine the population status of the jaguar and propose a spatial prioritization for conservation actions. About 85% of the jaguar’s habitat in the AF has been lost and only 7% remains in good condition. Jaguars persist in around 2.8% of the region, and live in very low densities in most of the areas. The population of jaguars in the AF is probably lower than 300 individuals scattered in small sub-populations. We identified seven Jaguar Conservation Units (JCUs) and seven potential JCUs, and only three of these areas may have ≥50 individuals. A connectivity analysis shows that most of the JCUs are isolated. Habitat loss and fragmentation were the major causes for jaguar decline, but human induced mortality is the main threat for the remaining population. We classified areas according to their contribution to jaguar conservation and we recommend management actions for each of them. The methodology in this study could be used for conservation planning of other carnivore species.

Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of the effects of autocorrelation on home range estimation. We base our study on an extensive data set of GPS locations from 369 individuals representing 27 species distributed across five continents. We first assemble a broad array of home range estimators, including Kernel Density Estimation (KDE) with four bandwidth optimizers (Gaussian reference function, autocorrelated-Gaussian reference function [AKDE], Silverman's rule of thumb, and least squares cross-validation), Minimum Convex Polygon, and Local Convex Hull methods. Notably, all of these estimators except AKDE assume independent and identically distributed (IID) data. We then employ half-sample cross-validation to objectively quantify estimator performance, and the recently introduced effective sample size for home range area estimation (N̂area) to quantify the information content of each data set. We found that AKDE 95% area estimates were larger than conventional IID-based estimates by a mean factor of 2. The median number of cross-validated locations included in the hold-out sets by AKDE 95% (or 50%) estimates was 95.3% (or 50.1%), confirming the larger AKDE ranges were appropriately selective at the specified quantile. Conversely, conventional estimates exhibited negative bias that increased with decreasing N̂area. To contextualize our empirical results, we performed a detailed simulation study to tease apart how sampling frequency, sampling duration, and the focal animal's movement conspire to affect range estimates. Paralleling our empirical results, the simulation study demonstrated that AKDE was generally more accurate than conventional methods, particularly for small N̂area. While 72% of the 369 empirical data sets had >1,000 total observations, only 4% had an N̂area >1,000, where 30% had an N̂area <30. In this frequently encountered scenario of small N̂area, AKDE was the only estimator capable of producing an accurate home range estimate on autocorrelated data.

We used data from VHF and GPS radio-tagged jaguars, Panthera onca (Linnaeus, 1758) to quantify jaguar habitat selection and how adult individuals in the Upper Paraná River region selected among the available habitat types. We followed the framework in which animals make decisions about resource use at hierarchical stages, namely selection of home range within a study area (second-order selection) and selection of patches within a home range (third-order selection). We quantified habitat preferences at two orders of selection with respect to habitat types and to test the null hypothesis that habitat utilization by jaguars was random at both study sites. Using compositional analysis, we assessed habitat selection by jaguars at second- and third-orders of selection. Jaguars consistently preferred dense marshes and primary forests, and avoided human-dominated areas such as intensively managed open pastures. Although the avoidance of disturbed and developed habitat types by jaguars is not surprising, this is the first study to document it. If small protected areas, such as the ones already existing in the Upper Paraná region, are to sustain jaguar populations they, must include and protect as many primary forests and marshlands as possible, so that jaguars can disperse, hunt wild prey and take care of their cubs without being disturbed. What is urgently needed in these jaguar-protected areas is the creation of larger protected areas that can sustain jaguars in their favored habitat. [PUBLICATION ABSTRACT]

Agroforestry practices, such as Shaded Coffee and Homegardens, may provide habitat for forest butterflies and contribute to their conservation in fragmented agricultural landscapes. To determine the influence of agroforestry practices in an agricultural mosaic, the distribution of fruit-feeding butterflies was studied using a systematic approach that compared butterfly species richness in six land-use practices (Eucalyptus [ Eucalyptus spp.], Shaded Coffee, Homegardens, Secondary Growth, Pastures, and monocultures of Cassava [ Manihot esculenta ] and Sugarcane [ Saccharum officinarum ]), and in natural habitat (secondary Forest Edge and Interior) in two study areas (agricultural landscapes). In each study area, Van Someren-Rydon butterfly traps were placed as a grid every 150 m, creating quadrants of 2.2 and 2.4 km 2 that encompassed the different land-use practices. Land-use, plot area, number of traps and distance to the forest were set as covariates to compare species richness values. Butterfly species composition was compared using linear discriminant analysis (LDA). With the exception of Pastures, Cassava and Sugarcane, significant differences were not identified between the rest of the agricultural land-use practices and the forest habitats (edge and interior). The species composition in the agricultural practices was however, different to that found in forest habitats. Overall, Shaded Coffee practices that represent long-term mixed tree and crop stands have a better potential of conserving forest butterfly species compared to monoculture practices.

It is well recognized that commercial beef cattle production systems have a major impact on climate change, mainly due to the emission of enteric methane (CH4). The objective of this research was to evaluate if integrating animal + pasture + timber production in silvopastoral systems (SPS) would help neutralize the impact of enteric CH4 emission by facilitating carbon storage as soil organic carbon (SOC). This paper reports a study conducted in Brazil with a herd of 150 cows in 100 ha of Urochloa brizantha with Eucalyptus urograndis, on four tree configurations: SPS 1-clone GG-100 at 2 × 3 × 15 m spacing; SPS 2-clone i-144 at 2 × 3 × 15 m; SPS 3-clone GG-100 at 3 × 15 m; and SPS 4-clone i-144 at 3 × 15 m. Based on data collected through eight consecutive years, the gas balance was estimated. For all SPS treatments average, the carbon dioxide equivalent (CO2e) of additional C stock exceeded the emissions. Considering only C sequestration from trees, the average CO2e sequestration was − 26.27 Mg·CO2e ha−1, while the average emissions of CO2 e was 23.54 Mg·CO2e ha−1 for enteric CH4 + pasture + tree, giving a net balance of − 2.73 Mg·CO2e ha−1. The “loss” of CO2e analyzed was compensated by the soil C sequestration in long-lived SOC pools, enhancing the resilience of farming systems by increasing soil organic matter and soil fertility capacity, mitigating greenhouse gas emissions, therefore, providing benefits in livestock production and for environmental remediation.

Serum samples from 19 jaguars ( Panthera onca ), nine pumas ( Puma concolor ), and two ocelots ( Leopardus pardalis ) were collected between January 1999 and March of 2005 and tested for presence of canine distemper virus (CDV). All cats were free-ranging animals living in two protected areas in the Brazilian Atlantic Forest. In addition, 111 domestic dogs from nearby areas were sampled for CDV. Our results show the first evidence of CDV exposure in Brazilian free-ranging felids. From the 30 samples analyzed, six jaguars and one puma were tested seropositive for CDV. All seropositive large felids were from Ivinhema State Park, resulting in 31.5% of the sampled jaguars or 60% of the total jaguar population in Ivinhema State Park, and 11.28% of the sampled pumas. From the total 111 domestic dogs sampled, 45 were tested seropositive for CDV. At Morro do Diabo State Park, 34.6% of the dogs sampled were positive for CDV, and 100% at Ivinhema State Park. Canine distemper virus in wild felids seems to be related with home range use and in close association with domestic dogs living in nearby areas.

Most large carnivores are secretive and threatened, and these characteristics pose problems for research on, and monitoring of, these species across extensive areas. Participatory monitoring, however, can be a useful tool for obtaining long-term data across large areas. Pumas Puma concolor and jaguars Panthera onca are the largest predators in the threatened Upper Paraná Atlantic Forest. To survey the presence of these two species we established a participatory network of volunteers and a partnership with researchers in the three countries that share the Upper Paraná Atlantic Forest (Argentina, Brazil and Paraguay). We trained participants in simple methods of collecting faeces and track imprints of large felids. Between 2002 and 2008 > 100 volunteers helped with monitoring, obtaining 1,633 records identified as pumas or jaguars across c. 92,890 km2. We confirmed jaguar presence in a large section of the Misiones Green Corridor in Argentina and in the largest protected areas of Brazil and Paraguay. Pumas exhibited a wider distribution, being recorded throughout Misiones province in Argentina and in some areas of Brazil and Paraguay where jaguars were not detected. Both species, and especially jaguars, were detected mainly in the few remaining medium and large forest fragments in this Forest. Although these carnivores are often in conflict with local people, their charisma and cultural significance makes them flagship species that motivated the participation of volunteers and institutions. Participatory monitoring allowed coverage of a vast area at relatively low cost whilst enhancing collaborative management policies among people and institutions from three countries.

Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis), originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars), we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD) and Iguaçu Region (IR). Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883). Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE) revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i) larger effective population size of ocelots (relative to jaguars) in each fragment, implying a slower effect of drift-induced differentiation; and (ii) potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.