Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.

Are tortoises important seed dispersers in Amazonian forests?

According to most studies on seed dispersal in tropical forests, mammals and birds are considered the main dispersal agents and the role played by other animal groups remains poorly explored. We investigate qualitative and quantitative components of the role played by the tortoise Chelonoidis denticulata in seed dispersal in southeastern Amazon, and the influence of seasonal variation in tortoise movement patterns on resulting seed shadows. Seed shadows produced by this tortoise were estimated by combining information on seed passage times through their digestive tract, which varied from 3 to 17 days, with a robust dataset on movements obtained from 18 adult C. denticulata monitored with radio transmitters and spoon-and-line tracking devices. A total of 4,206 seeds were found in 94 collected feces, belonging to 50 seed morphotypes of, at least, 25 plant genera. Very low rates of damage to the external structure of the ingested seeds were observed. Additionally, results of germination trials suggested that passage of seeds through C. denticulata`s digestive tract does not seem to negatively affect seed germination. The estimated seed shadows are likely to contribute significantly to the dispersal of seeds away from parent plants. During the dry season seeds were dispersed, on average, 174.1 m away from the location of fruit ingestion; during the rainy season, this mean dispersal distance increased to 276.7 m. Our results suggest that C. denticulata plays an important role in seed dispersal in Amazonian forests and highlight the influence of seasonal changes in movements on the resulting seed shadows.

Agribusiness Opportunity Costs and Environmental Legal Protection: Investigating Trade-Off on Hotspot Preservation in the State of So Paulo, Brazil

Prior to deforestation, So Paulo State had 79,000 km(2) covered by Cerrado (Brazilian savanna) physiognomies, but today less than 8.5% of this biodiversity hotspot remains, mostly in private lands. The global demand for agricultural goods has imposed strong pressure on natural areas, and the economic decisions of agribusiness managers are crucial to the fate of Cerrado domain remaining areas (CDRA) in Brazil. Our aim was to investigate the effectiveness of Brazilian private protected areas policy, and to propose a feasible alternative to promote CDRA protection. This article assessed the main agribusiness opportunity costs for natural areas preservation: the land use profitability and the arable land price. The CDRA percentage and the opportunity costs were estimated for 349 municipal districts of So Paulo State through secondary spatial data and profitability values of 38 main agricultural products. We found that Brazilian private protected areas policy fails to preserve CDRA, although the values of non-compliance fines were higher than average opportunity costs. The scenario with very restrictive laws on private protected areas and historical high interest rates allowed us to conceive a feasible cross compliance proposal to improve environmental and agricultural policies.

Balanced polymorphism in bottlenecked populations: The case of the CCR5 5 ` cis-regulatory region in Amazonian Amerindians

The 5` cis-regulatory region of the CCR5 gene exhibits a strong signature of balancing selection in several human populations. Here we analyze the polymorphism of this region in Amerindians from Amazonia, who have a complex demographic history, including recent bottlenecks that are known to reduce genetic variability. Amerindians show high nucleotide diversity (pi = 0.27%) and significantly positive Tajima`s D, and carry haplotypes associated with weak and strong gene expression. To evaluate whether these signatures of balancing selection could be explained by demography, we perform neutrality tests based on empiric and simulated data. The observed Tajima`s D was higher than that of other world populations: higher than that found for 18 noncoding regions of South Amerindians, and higher than 99.6% of simulated genealogies, which assume nonequilibrium conditions. Moreover, comparing Amerindians and Asians, the Fst for CCR5 cis-regulatory region was unusually low, in relation to neutral markers. These findings indicate that, despite their complex demographic history, South Amerindians carry a detectable signature of selection on the CCR5 cis-regulatory region. (C) 2010 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Nutrition in Transition: Dietary Patterns of Rural Amazonian Women During a Period of Economic Change

Objectives: The goal of this study was to understand the relationship between economic change (wage labor, retirement, and the Bolsa Familia program) and dietary patterns in the rural Amazon and to determine the extent to which these changes followed the pattern of the nutrition transition. Methods: The study was longitudinal. The weighed-inventory method and economic interviews were used to collect data on dietary intake and household economics in a sample of 30 and 52 women in 2002 and 2009, respectively. Twenty of the women participated in both years and make-up the longitudinal sub-sample. Comparative statistics were used to identify changes in dietary patterns over time and multiple linear regressions were used to explore the relationship between economics, subsistence strategies, and diet. Results: There was a significant decline in kcal (P < 0.01) and carbohydrate (P < 0.01) but no change in protein intake over time in both the larger and smaller, longitudinal subsample. The percent of energy, carbohydrate, protein, and fat purchased increased in the larger and longitudinal samples (P <= 0.02) and there was an increase in refined carbohydrate and processed, fatty-meat consumption over time. The abandonment of manioc gardens was associated with increased dependence on purchased food (P = 0.03) while receipt of the Bolsa Familia was associated with increased protein intake and adequacy (P = 0.02). Conclusions: The dietary changes observed are only in partial agreement with predictions of the nutrition transition literature. The relationship between the economic and diet changes was shaped by the local context which should be considered when implementing CCT programs, like the Bolsa Familia. Am. J. Hum. Biol. 23:458-469, 2011. (C) 2011 Wiley-Liss, Inc.

Taxon surrogates among Amazonian mammals: Can total species richness be predicted by single orders?

Limited financial sources and the difficulty in performing complete surveys, allied to the speed of habitat fragmentation and the urgent necessity in select conservation areas, create the necessity of using some methodologies which bypass these problems. One possibility is the use of surrogate taxa that might be used as indicator of others groups richness and even total richness of an area. We investigated if the use of surrogate taxon is useful among seven mammal orders in Amazon. We tested through Pearson`s correlation (Bonferroni`s adjusted) if (1) there was a correlation between richness of total species and some order; (2) there was a significant pair wise correlation between species richness of each order; and (3) the combination of two orders would give better results as a surrogate for the total richness. The correlations found, in general, were positive. It means that the increase in the richness of an order was followed by its increase in another order, as well as in the total species richness. Only Didelphimorphia was significantly correlated with the total species richness. In the pair wise analyses only one assembly, Primates and Artiodactyla, was significantly correlated with total richness. Since indicator species are more effective within taxonomic groups (life-history characteristics are likely to be more different among than within major taxonomic groups), we suggest that an indicator group might be chosen for each one. In this case, for mammals from Amazon, it would be Didelphimorphia. (C) 2008 Elsevier Ltd. All rights reserved.

Karyotypes of a Cryptic Diploid Form of the Unisexual Leposoma percarinatum (Squamata, Gymnophthalmidae) and the Bisexual Leposoma ferreirai from the Lower Rio Negro, Amazonian Brazil

Karyotypes of Leposoma show a clear differentiation between species of the scincoides group from Brazilian Atlantic Forest (2n = 52, without distinctive size groups of chromosomes) and those of the parietale group from the Amazon (2n = 44, with 20M + 24m). In a previous study, we found that in the parietale group the parthenoform Leposoma percarinatum from the state of Mato Grosso, Brazil, exhibited a triploid karyotype (3n = 66) with 30 macrochromosomes and 36 microchromosomes. It was suggested that this karyotype arose after hybridization between a bisexual species with N = 22 (10M + 12m) and a hypothetical unisexual cryptic diploid form of the L. percarinatum complex. Herein, we describe the karyotypes for two species of the parietale group occurring sympatrically in the Arquipelago das Anavilhanas, lower Rio Negro, in Amazonian Brazil. The first represents a distinctive diploid parthenogenetic clone of the L. percarinatum complex, and the other is the recently described Leposoma ferreirai. Both species have 44 biarmed chromosomes clearly represented by 20 macrochromosomes and 24 microchromosomes and present Ag-NORs in one pair of the smallest sized microchromosomes; heteromorphism of size for these regions was detected in L. percarinatum. C-banding revealed blocks of constitutive heterochromatin on the telomeric and pericentromeric regions of macrochromosomes and some microchromosomes. The description of a diploid karyotype (2n = 44, 20M + 24m) for the L. percarinatum complex and its sympatric congener L. ferreirai provides new insight for a better understanding of the origin of parthenogenesis in the L. percarinatum complex.

Immunocytochemical identification of adenohypophyseal cells in the pirarucu (Arapaima gigas), an Amazonian basal teleost

The adenohypophysis (AH) of juvenile pirarucu (Arapaima gigas), a representative species of the Osteoglossomorpha (bonytongue fishes, one of the oldest living groups of the teleosts), was studied using histochemical and immunocytochemical methods. The AH is comprised of the pars distalis (PD), without a clear distinction between rostral pars distalis (RPD) and proximal pars distalis (PPD), and the pars intermedia (PI). The neurohypophysis (NH) is positioned on top of the PD and penetrates and branches into the PI. In the most rostral dorsal portion of the PD, adrenocorticotropic cells and fusiform gonadotropic cells were found. In the central PD, scarce prolactin-producing cells and growth-hormone-producing cells were located mainly in the dorsal part, whereas round gonadotropic cells were abundant in the ventral portion of this region. Human thyrotropin immunoreactive cells were not found in the entire AH. In the PI, melanotropic, some adrenocorticotropic, and somatolactin-producing cells were located intermingled surrounding the neurohypophyseal branches. Our results showed that the A. gigas pituitary has some basal characteristics between the ancient Actinopterygii and the more derived teleosts.

Seroprevalence of orthopoxvirus in an Amazonian rural village, Acre, Brazil

Vaccinia virus strains from the family Poxviridae have been frequently isolated in Brazil and associated with outbreaks of exanthematic disease affecting cows and humans. An ELISA IgG was applied to evaluate the seroprevalence of orthopoxviruses in a community located in a rural settlement in the Amazon region, where no orthopoxvirus outbreaks have yet been reported. An overall seroprevalence of 27.89% was found, and it was 23.38% in the non-vaccinated population (smallpox vaccination). These results strongly suggest that orthopoxviruses circulate in this population, and it is the first finding of seropositivity for orthopoxviruses in a population without any previously reported outbreaks.

Comparison of two methods for collecting free-living ticks in the Amazonian forest

In the present study, we compared 2 methods for collecting ixodid ticks on the verges of animal trails in a primary Amazon forest area in northern Brazil. (i) Dragging: This method was based on passing a 1-m(2) white flannel over the vegetation and checking the flannel for the presence of caught ticks every 5-10 m. (ii) Visual search: This method consisted of looking for guesting ticks on the tips of leaves of the vegetation bordering animal trails in the forest. A total of 103 adult ticks belonging to 4 Amblyomma species were collected by the visual search method on 5 collecting dates, while only 44 adult ticks belonging to 3 Amblyomma species were collected by dragging on 5 other collecting dates. These values were statistically different (Mann-Whitney Test, P = 0.0472). On the other hand, dragging was more efficient for subadult ticks, since no larva or nymph was collected by visual search, whereas 18 nymphs and 7 larvae were collected by dragging. The visual search method proved to be suitable for collecting adult ticks in the Amazon forest: however, field studies should include a second method, such as dragging in order to maximize the collection of subadult ticks. Indeed, these 2 methods can be performed by a single investigator at the same time, while he/she walks on an animal trail in the forest. (C) 2010 Elsevier GmbH. All rights reserved.

Malaria on the Amazonian frontier: Transmission dynamics, risk factors, spatial distribution, and prospects for control

Little follow-up data on malaria transmission in communities originating from frontier settlements in Amazonia are available. Here we describe a cohort study in a frontier settlement in Acre, Brazil, where 509 subjects contributed 489.7 person-years of follow-up. The association between malaria morbidity during the follow-up and individual, household, and spatial covariates was explored with mixed-effects logistic regression models and spatial analysis. Incidence rates for Plasmodium vivax and Plasmodium falciparum malaria were 30.0/100 and 16.3/100 person-years at risk, respectively. Malaria morbidity was strongly associated with land clearing and farming, and decreased after five years of residence in the area, suggesting that clinical immunity develops among subjects exposed to low malaria endemicity. Significant spatial clustering of malaria was observed in the areas of most recent occupation, indicating that the continuous influx of nonimmune settlers to forest-fringe areas perpetuates the cycle of environmental change and colonization that favors malaria transmission in rural Amazonia.

The Rondonian-San Ignacio Province in the SW Amazonian Craton: An overview

The Rondonian-San Ignacio Province (1.56-1.30 Ga) is a composite orogen created through successive accretion of arcs, ocean basin closure and final oblique microcontinent-continent collision. The effects of the collision are well preserved mostly in the Paragua Terrane (Bolivia and Mato Grosso regions) and in the Alto Guapore Belt and the Rio Negro-Juruena Province (Rondonia region), considering that the province was affected by later collision-related deformation and metamorphism during the Sunsas Orogeny (1.25-1.00 Ga). The Rondonian-San Ignacio Province comprises: (1) the Jauru Terrane (1.78-1.42 Ga) that hosts Paleoproterozoic basement (1.78-1.72 Ga), and the Cachoeirinha (1.56-1.52 Ga) and the Santa Helena (1.48-1.42 Ga) accretionary orogens, both developed in an Andean-type magmatic arc; (2) the Paragua Terrane (1.74-1.32 Ga) that hosts pre-San Ignacio units (>1640 Ma: Chiquitania Gneiss Complex, San Ignacio Schist Group and Lomas Manechis Granulitic Complex) and the Pensamiento Granitoid Complex (1.37-1.34 Ga) developed in an Andean-type magmatic arc; (3) the Rio Alegre Terrane (1.51-1.38 Ga) that includes units generated in a mid-ocean ridge and an intra-oceanic magmatic arc environments; and (4) the Alto Guapore Belt (<1.42-1.34 Ga) that hosts units developed in passive marginal basin and intra-oceanic arc settings. The collisional stage (1.34-1.32 Ga) is characterized by deformation, high-grade metamorphism, and partial melting during the metamorphic peak, which affected primarily the Chiquitania Gneiss Complex and Lomas Manechis Granulitic Complex in the Paragua Terrane, and the Colorado Complex and the Nova Mamore Metamorphic Suite in the Alto Guapore Belt. The Paragua Block is here considered as a crustal fragment probably displaced from its Rio Negro-Juruena crustal counterpart between 1.50 and 1.40 Ga. This period is characterized by extensive A-type and intra-plate granite magmatism represented by the Rio Crespo Intrusive Suite (ca. 1.50 Ga), Santo Antonio Intrusive Suite (1.40-1.36 Ga), and the Teotonio Intrusive Suite (1.38 Ga). Magmatism of these types also occur at the end of the Rondonian-San Ignacio Orogeny, and are represented by the Alto Candeias Intrusive Suite (1.34-1.36 Ga), and the Sao Lourenco-Caripunas Intrusive Suite (1.31-1.30 Ga). The cratonization of the province occurred between 1.30 and 1.25 Ga. (C) 2009 Elsevier Ltd. All rights reserved.

A review of the tectonic evolution of the Sunsas belt, SW Amazonian Craton

The Sunsas-Aguapei province (1.20-0.95 Ga), SW Amazonian Craton, is a key area to study the heterogeneous effects of collisional events with Laurentia, which shows evidence of the Grenvillian and Sunsas orogens. The Sunsas orogen, characterized by an allochthonous collisional-type belt (1.11-1.00 Ga), is the youngest and southwestern most of the events recorded along the cratonic fringe. Its evolution occurred after a period of long quiescence and erosion of the already cratonized provinces (>1.30 Ga), that led to sedimentation of the Sunsas and Vibosi groups in a passive margin setting. The passive margin stage was roughly contemporary with intraplate tectonics that produced the Nova Brasilandia proto-oceanic basin (<1.21 Ga), the reactivation of the Ji-Parana shear zone network (1.18-1.12 Ga) and a system of aborted rifts that evolved to the Huanchaca-Aguapei basin (1.17-1.15 Ga). The Sunsas belt is comprised by the metamorphosed Sunsas and Vibosi sequences, the Rincon del Tigre mafic-ultramafic sill and granitic intrusive suites. The latter rocks yield epsilon(Nd(t)) signatures (-0.5 to -4.5) and geochemistry (S,1, A-types) suggesting their origin associated with a continental arc setting. The Sunsas belt evolution is marked by ""tectonic fronts"" with sinistral offsets that was active from c. 1.08 to 1.05 Ga, along the southern edge of the Paragua microcontinent where K/Ar ages (1.27-1.34 Ga) and the Huanchaca-Aguapei flat-lying cover attest to the earliest tectonic stability at the time of the orogen. The Sunsas dynamics is coeval with inboard crustal shortening, transpression and magmatism in the Nova Brasilandia belt (1.13-1.00 Ga). Conversely, the Aguapei aulacogen (0.96-0.91 Ga) and nearby shear zones (0.93-0.91 Ga) are the late tectonic offshoots over the cratonic margin. The post-tectonic to anorogenic stages took place after ca. 1.00 Ga, evidenced by the occurrences of intra-plate A-type granites, pegmatites, mafic dikes and sills, as well as of graben basins. Integrated interpretation of the available data related to the Sunsas orogen supports the idea that the main nucleus of Rodinia incorporated the terrains forming the SW corner of Amazonia and most of the Grenvillian margin, as a result of two independent collisional events, as indicated in the Amazon region by the Ji-Parana shear zone event and the Sunsas belt, respectively. (C) 2009 Elsevier Ltd. All rights reserved.

Trace element geochemistry and Sr-Nd characteristics of Mesoproterozoic mafic intrusive rocks from Rondonia, Brazil, SW Amazonian Craton: Petrogenetic and tectonic inferences

The Amazonian Craton comprises an Archean domain surrounded by four successively younger Proterozoic tectonic provinces. Within the Rio-Negro-Juruena province the Serra da Providencia Intrusive Suite (1.60 and 1.53 Ga) consists of A-type rapakivi granites, charnockites and mangerites genetically associated with diabase dikes, gabbros and amphibolites lites. The original mafic melts were derived from a depleted mantle source (epsilon(Nd(T)) + 2.5 to +2.8; epsilon(Sr(T)) - 12.1). Underplated mafic magma induced melting of a short-lived fielsic crust, thus originating coeval felsic-inafic magmatism in a continental intraplate setting. The Colorado Complex, assigned to the Rondonian-San Ignacio province, comprises 1.35-1.36 Ga intrusive bimodal magmatism represented by monzonite gneisses associated with amphibolite, gabbro and metadiabase dikes intercalated with metasediments with detrital zircon that yield U-Pb ages of 1.35 to 1.42 Ga. Mafic samples display juvenile signatures (epsilon(Nd(T)) 0.0 to +5.2; epsilon(Sr(T)) -5.0 to -30.7) and are less contaminated than the Serra da Previdencia and Nova Brasiladndia ones. The generation of the basaltic magma is related to the subduction of an oceanic slab below the peridotite wedge (intraoceanic arc setting). Fluids and/or small melts from the slab impregnated the mantle. The Nova Brasilandia Sequence (Sunsas-Aguapei province) comprises a metasedimentary sequence intruded by 1.10-1.02 Ga metadiabases, gabbros, meta-gabbros, and amphibolites associated with granitic plutons (bimodal magmatism). The original tholeiitic magmas, derived from a depleted source (epsilon(Nd(T)) = +3.1 to +5.0), in a proto-oceanic setting, underwent subsequent contamination by the host rocks, as indicated by the isotopic and trace element data.

The position of the Amazonian Craton in supercontinents

This paper examines the extensive regions of Proterozoic accretionary belts that either formed most of the Amazonian Craton, or are marginal to its southeastern border. Their overall geodynamic significance is considered taking into account the paleogeographic reconstruction of Columbia, Rodinia and Gondwana. Amazonia would be part of Columbia together With Laurentia, North China and Baltica, forming a continuous, continental landmass linked by the Paleo- to Mesoproterozoic mobile belts that constitute large portions of it. The Rodinia supercontinent was formed in the Mesoproterozoic by the agglutination of the existing cratonic fragments, such as Laurentia and Amazonia, during contemporary continental collisions worldwide. The available paleomagnetic data suggest that Laurentia and Amazonia remained attached until at least 600 Ma. Since all other cratonic units Surrounding Laurentia have already rifted away by that time, the separation between Amazonia and Laurentia marks the final break-up of Rodinia with the opening of the lapetus ocean. (C) 2009 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.