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.

Atmospheric versus vegetation controls of Amazonian tropical rain forest evapotranspiration: Are the wet and seasonally dry rain forests any different?

This study analyzes evapotranspiration data for three wet and two seasonally dry rain forest sites in Amazonia. The main environmental (net radiation, vapor pressure deficit, and aerodynamic conductance) and vegetation (surface conductance) controls of evapotranspiration are also assessed. Our research supports earlier studies that demonstrate that evapotranspiration in the dry season is higher than that in the wet season and that surface net radiation is the main controller of evapotranspiration in wet equatorial sites. However, our analyses also indicate that there are different factors controlling the seasonality of evapotranspiration in wet equatorial rain forest sites and southern seasonally dry rain forests. While the seasonality of evapotranspiration in wet equatorial forests is driven solely by environmental factors, in seasonally dry forests, it is also biotically controlled with the surface conductance varying between seasons by a factor of approximately 2. The identification of these different drivers of evapotranspiration is a major step forward in our understanding of the water dynamics of tropical forests and has significant implications for the future development of vegetation-atmosphere models and land use and conservation planning in the region.

Cloud condensation nuclei from biomass burning during the Amazonian dry-to-wet transition season

Aircraft measurements of cloud condensation nuclei (CCN) during the Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) were conducted over the Southwestern Amazon region in September-October 2002, to emphasize the dry-to-wet transition season. The CCN concentrations were measured for values within the range 0.1-1.0% of supersaturation. The CCN concentration inside the boundary layer revealed a general decreasing trend during the transition from the end of the dry season to the onset of the wet season. Clean and polluted areas showed large differences. The differences were not so strong at high levels in the troposphere and there was evidence supporting the semi-direct aerosol effect in suppressing convection through the evaporation of clouds by aerosol absorption. The measurements also showed a diurnal cycle following biomass burning activity. Although biomass burning was the most important source of CCN, it was seen as a source of relatively efficient CCN, since the increase was significant only at high supersaturations.

The impact of smoke from forest fires on the spectral dispersion of cloud droplet size distributions in the Amazonian region

In this paper, the main microphysical characteristics of clouds developing in polluted and clean conditions in the biomass-burning season of the Amazon region are examined, with special attention to the spectral dispersion of the cloud droplet size distribution and its potential impact on climate modeling applications. The dispersion effect has been shown to alter the climate cooling predicted by the so-called Twomey effect. In biomass-burning polluted conditions, high concentrations of low dispersed cloud droplets are found. Clean conditions revealed an opposite situation. The liquid water content (0.43 +/- 0.19 g m(-3)) is shown to be uncorrelated with the cloud drop number concentration, while the effective radius is found to be very much correlated with the relative dispersion of the size distribution (R(2) = 0.81). The results suggest that an increase in cloud condensation nuclei concentration from biomass-burning aerosols may lead to an additional effect caused by a decrease in relative dispersion. Since the dry season in the Amazonian region is vapor limiting, the dispersion effect of cloud droplet size distributions could be substantially larger than in other polluted regions.

Columbia revisited: Paleomagnetic results from the 1790 Ma colider volcanics (SW Amazonian Craton, Brazil)

In an attempt to improve our understanding of the Paleoproterozoic geodynamic evolution, a paleomagnetic study was performed on 10 sites of acid volcanic rocks of the Colider Suite, southwestern Amazonian Craton. These rocks have a well-dated zircon U-Pb mean age of 1789 +/- 7 Ma. Alternating field and thermal demagnetization revealed northern (southern) directions with moderate to high upward (downward) inclinations. Rock magnetism experiments and magnetic mineralogy show that this characteristic magnetization is carried by Ti-poor magnetite or by hematite that replaces magnetite by late-magmatic cleuteric alteration. Both magnetite and hematite carry the same characteristic component. The mean direction (Dm = 183.0 degrees, Im = 53.5 degrees, N = 10, alpha(95) = 9.8 degrees, K = 25.2) yielded a paleomagnetic pole located at 298.8 degrees E, 63.3 degrees S (alpha(95) = 10.2 degrees, K = 23.6), which is classified with a quality factor Q = 5. Paleogeographic reconstructions using this pole and other reliable Paleoproterozoic poles suggest that Laurentia, Baltica, North China Craton and Amazonian Craton were located in laterally contiguous positions forming a large continental mass at 1790 Ma ago. This is reinforced by geological evidence which support the existence of the supercontinent Columbia in Paleoproterozoic times. (C) 2008 Elsevier B.V. All rights reserved.

The role of carbohydrates in seed germination and seedling establishment of Himatanthus sucuuba, an Amazonian tree with populations adapted to flooded and non-flooded conditions

Background and Aims In the Amazonian floodplains plants withstand annual periods of flooding which can last 7 months. Under these conditions seedlings remain submerged in the dark for long periods since light penetration in the water is limited. Himatanthus sucuuba is a tree species found in the `varzea` (VZ) floodplains and adjacent non-flooded `terra-firme` (TF) forests. Biochemical traits which enhance flood tolerance and colonization success of H. sucuuba in periodically flooded environments were investigated. Methods Storage carbohydrates of seeds of VZ and TF populations were extracted and analysed by HPAEC/PAD. Starch was analysed by enzyme (glucoamylase) degradation followed by quantification of glucose oxidase. Carbohydrate composition of roots of VZ and TF seedlings was studied after experimental exposure to a 15-d period of submersion in light versus darkness. Key Results The endosperm contains a large proportion of the seed reserves, raffinose being the main nonstructural carbohydrate. Around 93% of the cell wall storage polysaccharides (percentage dry weight basis) in the endosperm of VZ seeds was composed of mannose, while soluble sugars accounted for 2.5%. In contrast, 74% of the endosperm in TF seeds was composed of galactomannans, while 22% of the endosperm was soluble sugars. This suggested a larger carbohydrate allocation to germination in TF populations whereas VZ populations allocate comparatively more to carbohydrates mobilized during seedling development. The concentration of root non-structural carbohydrates in non-flooded seedlings strongly decreased after a 15-d period of darkness, whereas flooded seedlings were less affected. These effects were more pronounced in TF seedlings, which showed significantly lower root non-structural carbohydrate concentrations. Conclusions There seem to be metabolic adjustments in VZ but not TF seedlings that lead to adaptation to the combined stresses of darkness and flooding. This seems to be important for the survival of the species in these contrasting environments, leading these populations to different directions during evolution.

Comparing species and measures of landscape structure as indicators of conservation importance

P>1. The use of indicators to identify areas of conservation importance has been challenged on several grounds, but nonetheless retains appeal as no more parsimonious approach exists. Among the many variants, two indicator strategies stand out: the use of indicator species and the use of metrics of landscape structure. While the first has been thoroughly studied, the same cannot be said about the latter. We aimed to contrast the relative efficacy of species-based and landscape-based indicators by: (i) comparing their ability to reflect changes in community integrity at regional and landscape spatial scales, (ii) assessing their sensitivity to changes in data resolution, and (iii) quantifying the degree to which indicators that are generated in one landscape or at one spatial scale can be transferred to additional landscapes or scales. 2. We used data from more than 7000 bird captures in 65 sites from six 10 000-ha landscapes with different proportions of forest cover in the Atlantic Forest of Brazil. Indicator species and landscape-based indicators were tested in terms of how effective they were in reflecting changes in community integrity, defined as deviations in bird community composition from control areas. 3. At the regional scale, indicator species provided more robust depictions of community integrity than landscape-based indicators. At the landscape scale, however, landscape-based indicators performed more effectively, more consistently and were also more transferable among landscapes. The effectiveness of high resolution landscape-based indicators was reduced by just 12% when these were used to explain patterns of community integrity in independent data sets. By contrast, the effectiveness of species-based indicators was reduced by 33%. 4. Synthesis and applications. The use of indicator species proved to be effective; however their results were variable and sensitive to changes in scale and resolution, and their application requires extensive and time-consuming field work. Landscape-based indicators were not only effective but were also much less context-dependent. The use of landscape-based indicators may allow the rapid identification of priority areas for conservation and restoration, and indicate which restoration strategies should be pursued, using remotely sensed imagery. We suggest that landscape-based indicators might often be a better, simpler, and cheaper strategy for informing decisions in conservation.

Effects of species turnover on reserve site selection in a fragmented landscape

Changes in species composition is an important process in many ecosystems but rarely considered in systematic reserve site selection. To test the influence of temporal variability in species composition on the establishment of a reserve network, we compared network configurations based on species data of small mammals and frogs sampled during two consecutive years in a fragmented Atlantic Forest landscape (SE Brazil). Site selection with simulated annealing was carried out with the datasets of each single year and after merging the datasets of both years. Site selection resulted in remarkably divergent network configurations. Differences are reflected in both the identity of the selected fragments and in the amount of flexibility and irreplaceability in network configuration. Networks selected when data for both years were merged did not include all sites that were irreplaceable in one of the 2 years. Results of species number estimation revealed that significant changes in the composition of the species community occurred. Hence, temporal variability of community composition should be routinely tested and considered in systematic reserve site selection in dynamic systems.

Rural property size drives patterns of upland and riparian forest retention in a tropical deforestation frontier

Deforestation in Brazilian Amazonia accounts for a disproportionate global scale fraction of both carbon emissions from biomass burning and biodiversity erosion through habitat loss. Here we use field- and remote-sensing data to examine the effects of private landholding size on the amount and type of forest cover retained within economically active rural properties in an aging southern Amazonian deforestation frontier. Data on both upland and riparian forest cover from a survey of 300 rural properties indicated that 49.4% (SD = 29.0%) of the total forest cover was maintained as of 2007. and that property size is a key regional-scale determinant of patterns of deforestation and land-use change. Small properties (<= 150 ha) retained a lower proportion of forest (20.7%, SD = 17.6) than did large properties (>150 ha; 55.6%, SD = 27.2). Generalized linear models showed that property size had a positive effect on remaining areas of both upland and total forest cover. Using a Landsat time-series, the age of first clear-cutting that could be mapped within the boundaries of each property had a negative effect on the proportion of upland, riparian, and total forest cover retained. Based on these data, we show contrasts in land-use strategies between smallholders and largeholders, as well as differences in compliance with legal requirements in relation to minimum forest cover set-asides within private landholdings. This suggests that property size structure must be explicitly considered in landscape-scale conservation planning initiatives guiding agro-pastoral frontier expansion into remaining areas of tropical forest. (C) 2010 Elsevier Ltd. All rights reserved.

Landscape perception by forest understory birds in the Atlantic Rainforest: black-and-white versus shades of grey

Even among forest specialists, species-specific responses to anthropogenic forest fragmentation may vary considerably. Some appear to be confined to forest interiors, and perceive a fragmented landscape as a mosaic of suitable fragments and hostile matrix. Others, however, are able to make use of matrix habitats and perceive the landscape in shades of grey rather than black-and-white. We analysed data of 42 Chiroxiphia caudata (Blue Manakin), 10 Pyriglena leucoptera (White-shouldered Fire-eye) and 19 Sclerurus scansor (Rufous-breasted Leaftosser) radio-tracked in the Atlantic Rainforest of Brazil between 2003 and 2005. We illustrate how habitat preferences may determine how species respond to or perceive the landscape structure. We compared available with used habitat to develop a species-specific preference index for each of six habitat classes. All three species preferred old forest, but relative use of other classes differed significantly. S. scansor perceived great contrast between old forest and matrix, whereas the other two species perceived greater habitat continuity. For conservation planning, our study offers three important messages: (1) some forest specialist species are able to persist in highly fragmented landscapes; (2) some forest species may be able to make use of different anthropogenic habitat types to various degrees; whereas (3) others are restricted to the remaining forest fragments. Our study suggests species most confined to forest interiors to be considered as potential umbrella species for landscape-scale conservation planning.

The impact of fragmentation and density regulation on forest succession in the Atlantic rain forest

The Atlantic Rain Forest, an important biodiversity hot spot, has faced severe habitat loss since the last century which has resulted in a highly fragmented landscape with a large number of small forest patches (<100 ha). For conservation planning it is essential to understand how current and future forest regeneration depends on ecological processes, fragment size and the connection to the regional seed pool. We have investigated the following questions by applying the forest growth simulation model FORMIND to the situation of the Atlantic Forest in the state of Sao Paulo, SE Brazil: (1) which set of parameters describing the local regeneration and level of density regulation can reproduce the biomass distribution and stem density of an old growth forest in a reserve? (2) Which additional processes apart from those describing the dynamics of an old growth forest, drive forest succession of small isolated fragments? (3) Which role does external seed input play during succession? Therefore, more than 300 tree species have been classified into nine plant functional types (PFTs), which are characterized by maximum potential height and shade tolerance. We differentiate between two seed dispersal modes: (i) local dispersal, i.e. all seedlings originated from fertile trees within the simulated area and (ii) external seed rain. Local seed dispersal has been parameterized following the pattern oriented approach, using biomass estimates of old growth forest. We have found that moderate density regulation is essential to achieve coexistence for a broad range of regeneration parameters. Considering the expected uncertainty and variability in the regeneration processes it is important that the forest dynamics are robust to variations in the regeneration parameters. Furthermore, edge effects such as increased mortality at the border and external seed rain have been necessary to reproduce the patterns for small isolated fragments. Overall, simulated biomass is much lower in the fragments compared to the continuous forest, whereas shade tolerant species are affected most strongly by fragmentation. Our simulations can supplement empirical studies by extrapolating local knowledge on edge effects of fragments to larger temporal and spatial scales. In particular our results show the importance of external seed rain and therefore highlight the importance of structural connectivity between regenerating fragments and mature forest stands. (C) 2009 Elsevier B.V. All rights reserved.

Study of the relationship between roads, relief, land use, and natural vegetation in the Ibiuna Plateau - SP, focusing on landscape ecology

Roads facilitate access by deforestation agents, being relevant in studies approaching conservationist matters in rainforests. It is important to understand the relationship between road distribution, relief, land use, and forest coverage in order to evaluate where forests are more vulnerable. This study aimed at: 1) understanding the relationship between relief and density and road connectivity in three moments in time; and 2) evaluating the relationship between distance from roads and forest coverage, farmlands and rural and urban facilities in a fragmented Atlantic Forest landscape in three moments in time. Maps of roads, altitude, and land use and coverage were used. Chi-square tests showed that: 1) density and road connectivity did not present significant relationship with the relief; and 2) forest areas occupy areas distant from the roads, while farmlands and rural and urban facilities occupy areas nearer the roads. Roads and land use, regardless of relief, influence forest coverage distribution. Thus, we suggest that roads are taken into account in conservationist strategies and environmental planning.

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.

Is bird incidence in Atlantic forest fragments influenced by landscape patterns at multiple scales?

The degree to which habitat fragmentation affects bird incidence is species specific and may depend on varying spatial scales. Selecting the correct scale of measurement is essential to appropriately assess the effects of habitat fragmentation on bird occurrence. Our objective was to determine which spatial scale of landscape measurement best describes the incidence of three bird species (Pyriglena leucoptera, Xiphorhynchus fuscus and Chiroxiphia caudata) in the fragmented Brazilian Atlantic forest and test if multi-scalar models perform better than single-scalar ones. Bird incidence was assessed in 80 forest fragments. The surrounding landscape structure was described with four indices measured at four spatial scales (400-, 600-, 800- and 1,000-m buffers around the sample points). The explanatory power of each scale in predicting bird incidence was assessed using logistic regression, bootstrapped with 1,000 repetitions. The best results varied between species (1,000-m radius for P. leucoptera; 800-m for X. fuscus and 600-m for C. caudata), probably due to their distinct feeding habits and foraging strategies. Multi-scale models always resulted in better predictions than single-scale models, suggesting that different aspects of the landscape structure are related to different ecological processes influencing bird incidence. In particular, our results suggest that local extinction and (re)colonisation processes might simultaneously act at different scales. Thus, single-scale models may not be good enough to properly describe complex pattern-process relationships. Selecting variables at multiple ecologically relevant scales is a reasonable procedure to optimise the accuracy of species incidence models.

Are corridors, fragment size and forest structure important for the conservation of leaf-litter lizards in a fragmented landscape?

To investigate the implications of forest fragmentation for conservation of leaf-litter lizards the importance of fragment size, corridors and forest structure was examined in 20 forest fragments and six localities within a continuous forest in the Atlantic Plateau of Sao Paulo state, Brazil. The fragments were 2-276 ha in area and had different degrees of connectivity depending on the presence or absence of corridors. Two species of lizards were dominant, Ecpleopus gaudichaudii and Enyalius perditus. Variation in forest structure among sites was important only in explaining the abundance of E. perditus. Regardless of variation in forest structure, lizard species composition, total lizard abundance, number of species and abundance of E. perditus were sensitive to fragmentation per se but not to fragment size or corridor linkage. The inhospitable matrix surrounding fragments is probably what determines the presence and abundance of E. perditus and the high er lizard richness in continuous forests. These conditions may have prevented lizard species from recolonizing the forest fragments. Our results emphasize that the conservation of this leaf-litter fauna depends on the maintenance of large tracts of continuous forests and not on the size of fragments or on the presence of forest connections. Strategies for conservation of leaf-litter lizards in such highly fragmented Atlantic Forest landscapes should consider the enlargement of landscape connectivity between fragments and continuous forest, allowing the latter areas to act as a source of individuals for fragments.