Responses of transplanted native tree species to invasive alien grass removals in an abandoned cattle pasture in the Lacandon region, Mexico

We tested the early performance of 16 native early-, mid-, and late-successional tree species in response to four intensities of grass removal in an abandoned cattle pasture dominated by the introduced, invasive African grass, Cynodon plectostachyus, within the Lacandon rainforest region, southeast Mexico. The increase in grass removals significantly improved the performance of many species, especially of early-and mid-successional species, while performance of late-successional species was relatively poor and did not differ significantly among treatments. Good site preparation and at least one additional grass removal four months after seedling transplant were found to be essential; additional grass removals led to improved significantly performance of saplings in most cases. In order to evaluate the potential of transplanting tree seedlings successfully in abandoned tropical pastures, we developed a "planting risk index", combining field performance measurements and plantation cost estimations. Our results showed a great potential for establishing restoration plantings with many early-and mid-successional species. Although planting risk of late-successional species was considered high, certain species showed some possibilities of acclimation after 18 months and should be considered in future plantation arrangements in view of their long-term contributions to biodiversity maintenance and also to human welfare through delivery of ecosystem services. Conducting a planting risk analysis can help avoid failure of restoration strategies involving simultaneous planting of early-, mid-, and late-successional tree species. This in turn will improve cost-effectiveness of initial interventions in large-scale, long-term restoration programs.

Improving Planting Stocks for the Brazilian Atlantic Forest Restoration through Community-Based Seed Harvesting Strategies

High-diversity reforestation can help jumpstart tropical forest restoration, but obtaining viable seedlings is a major constraint: if nurseries do not offer them, it is hard to plant all the species one would like. From 2007 to 2009, we investigated five different seed acquisition strategies employed by a well-established tree nursery in southeastern Brazil, namely (1) in-house seed harvesters; (2) hiring a professional harvester; (3) amateur seed harvesters; or (4) a seed production cooperative, as well as (5) participating in a seed exchange program. In addition, we evaluated two strategies not dependent on seeds: harvesting seedlings from native tree species found regenerating under Eucalyptus plantations, and in a native forest remnant. A total of 344 native tree and shrub species were collected as seeds or seedlings, including 2,465 seed lots. Among these, a subset of 120 species was obtained through seed harvesting in each year. Overall, combining several strategies for obtaining planting stocks was an effective way to increase species richness, representation of some functional groups (dispersal syndromes, planting group, and shade tolerance), and genetic diversity of seedlings produced in forest tree nurseries. Such outcomes are greatly desirable to support high-diversity reforestation as part of tropical forest restoration. In addition, community-based seed harvesting strategies fostered greater socioeconomic integration of traditional communities in restoration projects and programs, which is an important bottleneck for the advance of ecological restoration, especially in developing countries. Finally, we discuss some of the limitations of the various strategies for obtaining planting stocks and the way forward for their improvement.

Yield mapping, soil fertility and tree gaps in an orange orchard

The current high competition on Citrus industry demands from growers new management technologies for superior efficiency and sustainability. In this context, precision agriculture (PA) has developed techniques based on yield mapping and management systems that recognize field spatial variability, which contribute to increase profitability of commercial crops. Because spatial variability is often not perceived the orange orchards are still managed as uniform and adoption of PA technology on citrus farms is low. Thus, the objective of the present study was to characterize the spatial variability of three factors: fruit yield, soil fertility and occurrence of plant gaps caused by either citrus blight or huanglongbing (HLB) in a commercial Valencia orchard in Brotas, São Paulo State, Brazil. Data from volume, geographic coordinates and representative area of the bags used on harvest were recorded to generate yield points that were then interpolated to produce the yield map. Soil chemical characteristics were studied by analyzing samples collected along planting rows and inter-rows in 24 points distributed in the field. A map of density of tree gaps was produced by georeferencing individual gaps and later by counting the number of gaps within 500 m² cells. Data were submitted to statistical and geostatistical analyses. A t test was used to compare means of soil chemical characteristics between sampling regions. High variation on yield and density of tree gaps was observed from the maps. It was also demonstrated overlapping regions of high density of plant absence and low fruit yield. Soil fertility varied depending on the sampling region in the orchard. The spatial variability found on yield, soil fertility and on disease occurrence demonstrated the importance to adopt site specific nutrient management and disease control as tools to guarantee efficiency of fruit production.

Tree height integrated into pantropical forest biomass estimates

Aboveground tropical tree biomass and carbon storage estimates commonly ignore tree height (H). We estimate the effect of incorporating H on tropics-wide forest biomass estimates in 327 plots across four continents using 42 656 H and diameter measurements and harvested trees from 20 sites to answer the following questions: 1. What is the best H-model form and geographic unit to include in biomass models to minimise site-level uncertainty in estimates of destructive biomass? 2. To what extent does including H estimates derived in (1) reduce uncertainty in biomass estimates across all 327 plots? 3. What effect does accounting for H have on plot- and continental-scale forest biomass estimates? The mean relative error in biomass estimates of destructively harvested trees when including H (mean 0.06), was half that when excluding H (mean 0.13). Power- and Weibull-H models provided the greatest reduction in uncertainty, with regional Weibull-H models preferred because they reduce uncertainty in smaller-diameter classes (< 40 cm D) that store about one-third of biomass per hectare in most forests. Propagating the relationships from destructively harvested tree biomass to each of the 327 plots from across the tropics shows that including H reduces errors from 41.8 Mg ha(-1) (range 6.6 to 112.4) to 8.0 Mg ha(-1) (-2.5 to 23.0).

Genetic characterization of fig tree mutants with molecular markers

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes.

CHARACTERIZATION OF THE MICRO-SITE CONDITIONS FROM RESTORED AREAS WITH DIFFERENT AGES

Regeneration microsites are characterized by diverse combinations of attributes which assure the best conditions for seed germination and seedling establishment. By understanding these attributes, we can contribute to determining better management methodologies for reestablishing ecological process in sites under restoration. Thus, we sought to characterize and differentiate the micro-site conditions of restoration plantings to indentify likely physical-chemical limitations for the establishment of native tree species in the forest understory. This study was carried out in reforestation plantings with different ages (10, 22 and 55 years). The physical-chemical characterization of the micro-site of regeneration of the study areas was carried out by evaluating the soil compression level, porosity, humidity, organic matter and nutrients content and granulometry, as well as litter dry mass and canopy cover. An increase on the canopy cover and soil porosity, humidity, clay and organic matter content were observed in the oldest restored areas, as well as a decrease in soil compression. Thus, these findings demonstrated that the evaluated microsite properties are in process of restoration. Therefore, microsite conditions for seedling establishment become even more similar to reference ecosystems as restoration planting evolve.

PHENOLOGY AND FRUIT TRAITS OF ARCHONTOPHOENIX CUNNINGHAMIANA, AN INVASIVE PALM TREE IN THE ATLANTIC FOREST OF BRAZIL

The Australian palm Archontophoenix cunninghamiana was introduced into Brazil as an ornamental species, and became a dangerous invader of remnant Atlantic forest patches, demanding urgent management actions that require careful planning. Its fruits are greatly appreciated by generalist birds and its sudden eradication could be as harmful as its permanence in the native community. Our hypothesis was that A. cunninghamiana phenology and fruit traits would have facilitated the invasion process. Hence the aim of the study was to characterize the reproductive phenology of the palm by registering flowering and fruiting events, estimating fruit production, and evaluating fruit nutritional levels. Phenological observations were carried out over 12 months and analyzed statistically. Fruit traits and production were estimated. Pulp nutritional levels were determined by analyzing proteins, lipids, and carbohydrates. Results showed constant flowering and fruiting throughout the year with a weak reproductive seasonality. On average, 3651 fruits were produced per bunch mainly in the summer. Fruit analysis revealed low nutrient contents, especially of proteins and lipids compared with other Brazilian native palm species. We concluded that the abundant fruit production all year round, and fruit attractivity mainly due to size and color, :may act positively on the reproductive performance and effective dispersion of A. cunninghamiana. As a management procedure which would add quality to frugivore food resources we suggest the replacement of A. cunninghamiana by the native palm Euterpe edulis, especially in gardens and parks near to Atlantic forest fragments.

CONTEXT TREE SELECTION AND LINGUISTIC RHYTHM RETRIEVAL FROM WRITTEN TEXTS

The starting point of this article is the question "How to retrieve fingerprints of rhythm in written texts?" We address this problem in the case of Brazilian and European Portuguese. These two dialects of Modern Portuguese share the same lexicon and most of the sentences they produce are superficially identical. Yet they are conjectured, on linguistic grounds, to implement different rhythms. We show that this linguistic question can be formulated as a problem of model selection in the class of variable length Markov chains. To carry on this approach, we compare texts from European and Brazilian Portuguese. These texts are previously encoded according to some basic rhythmic features of the sentences which can be automatically retrieved. This is an entirely new approach from the linguistic point of view. Our statistical contribution is the introduction of the smallest maximizer criterion which is a constant free procedure for model selection. As a by-product, this provides a solution for the problem of optimal choice of the penalty constant when using the BIC to select a variable length Markov chain. Besides proving the consistency of the smallest maximizer criterion when the sample size diverges, we also make a simulation study comparing our approach with both the standard BIC selection and the Peres-Shields order estimation. Applied to the linguistic sample constituted for our case study, the smallest maximizer criterion assigns different context-tree models to the two dialects of Portuguese. The features of the selected models are compatible with current conjectures discussed in the linguistic literature.

A survey of evolutionary algorithms for decision-tree induction

This paper presents a survey of evolutionary algorithms that are designed for decision-tree induction. In this context, most of the paper focuses on approaches that evolve decision trees as an alternate heuristics to the traditional top-down divide-and-conquer approach. Additionally, we present some alternative methods that make use of evolutionary algorithms to improve particular components of decision-tree classifiers. The paper's original contributions are the following. First, it provides an up-to-date overview that is fully focused on evolutionary algorithms and decision trees and does not concentrate on any specific evolutionary approach. Second, it provides a taxonomy, which addresses works that evolve decision trees and works that design decision-tree components by the use of evolutionary algorithms. Finally, a number of references are provided that describe applications of evolutionary algorithms for decision-tree induction in different domains. At the end of this paper, we address some important issues and open questions that can be the subject of future research.

Two new species of marsupial tree-frogs genus Gastrotheca Fitzinger, 1843 (Anura, Hemiphractidae) from the Brazilian Atlantic Forest

Two new species of Gastrotheca are described from northeastern Minas Gerais and southern Bahia, in the Atlantic Forest of Brazil. Data on morphology, calls, mitochondrial, and nuclear DNA are provided. Allied to G. fissipes and G. megacephala, the new taxa provide evidence for a higher diversity of species of Gastrotheca than previously thought at the Atlantic Forest. The data also suggest that G. pulchra, another Atlantic Forest taxon, is more closely related to non-Atlantic Forest species than to the remaining analyzed Brazilian Gastrotheca species. This implies that the Gastrotheca at the Brazilian coastal forests have at least two independent origins.

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Background: This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results: The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. Conclusions: We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor.

Detection of isometric, dsRNA-containing viral particles in Colletotrichum gloeosporioides isolated from cashew tree

Fungi are disease-causing agents in plants and affect crops of economic importance. One control method is to induce resistance in the host by using biological control with hypovirulent phytopathogenic fungi. Here, we report the detection of a mycovirus in a strain of Colletotrichum gloeosporioides causing anthracnose of cashew tree. The strain C. gloeosporioides URM 4903 was isolated from a cashew tree (Anacardium occidentale) in Igarassu, PE, Brazil. After nucleic acid extraction and electrophoresis, the band corresponding to a possible double-stranded RNA (dsRNA) was purified by cellulose column chromatography. Nine extrachromosomal bands were obtained. Enzymatic digestion with DNAse I and Nuclease S1 had no effect on these bands, indicating their dsRNA nature. Transmission electron microscopic examination of extracts from this strain showed the presence of isometric particles (30-35 nm in diameter). These data strongly suggest the infection of this C. gloeosporioides strain by a dsRNA mycovirus. Once the hypovirulence of this strain is confirmed, the strain may be used for the biological control of cashew anthracnose.

Mating system parameters at hierarchical levels of fruits, individuals and populations in the Brazilian insect-pollinated tropical tree, Tabebuia roseo-alba (Bignoniaceae)

For many tree species, mating system analyses have indicated potential variations in the selfing rate and paternity correlation among fruits within individuals, among individuals within populations, among populations, and from one flowering event to another. In this study, we used eight microsatellite markers to investigate mating systems at two hierarchical levels (fruits within individuals and individuals within populations) for the insect pollinated Neotropical tree Tabebuia roseo-alba. We found that T. roseo-alba has a mixed mating system with predominantly outcrossed mating. The outcrossing rates at the population level were similar across two T. roseo-alba populations; however, the rates varied considerably among individuals within populations. The correlated paternity results at different hierarchical levels showed that there is a high probability of shared paternal parentage when comparing seeds within fruits and among fruits within plants and full-sibs occur in much higher proportion within fruits than among fruits. Significant levels of fixation index were found in both populations and biparental inbreeding is believed to be the main cause of the observed inbreeding. The number of pollen donors contributing to mating was low. Furthermore, open-pollinated seeds varied according to relatedness, including half-sibs, full-sibs, self-sibs and self- half-sibs. In both populations, the effective population size within a family (seed-tree and its offspring) was lower than expected for panmictic populations. Thus, seeds for ex situ conservation genetics, progeny tests and reforestation must be collected from a large number of seed-trees to guarantee an adequate effective population in the sample.

Production and carbon allocation in monocultures and mixed-species plantations of Eucalyptus grandis and Acacia mangium in Brazil

Introducing nitrogen-fixing tree species in fast-growing eucalypt plantations has the potential to improve soil nitrogen availability compared with eucalypt monocultures. Whether or not the changes in soil nutrient status and stand structure will lead to mixtures that out-yield monocultures depends on the balance between positive interactions and the negative effects of interspecific competition, and on their effect on carbon (C) uptake and partitioning. We used a C budget approach to quantify growth, C uptake and C partitioning in monocultures of Eucalyptus grandis (W. Hill ex Maiden) and Acacia mangium (Willd.) (treatments E100 and A100, respectively), and in a mixture at the same stocking density with the two species at a proportion of 1 : 1 (treatment MS). Allometric relationships established over the whole rotation, and measurements of soil CO2 efflux and aboveground litterfall for ages 4-6 years after planting were used to estimate aboveground net primary production (ANPP), total belowground carbon flux (TBCF) and gross primary production (GPP). We tested the hypotheses that (i) species differences for wood production between E. grandis and A. mangium monocultures were partly explained by different C partitioning strategies, and (ii) the observed lower wood production in the mixture compared with eucalypt monoculture was mostly explained by a lower partitioning aboveground. At the end of the rotation, total aboveground biomass was lowest in A100 (10.5 kg DM m(-2)), intermediate in MS (12.2 kg DM m(-2)) and highest in E100 (13.9 kg DM m(-2)). The results did not support our first hypothesis of contrasting C partitioning strategies between E. grandis and A. mangium monocultures: the 21% lower growth (delta B-w) in A100 compared with E100 was almost entirely explained by a 23% lower GPP, with little or no species difference in ratios such as TBCF/GPP, ANPP/TBCF, delta B-w/ANPP and delta B-w/GPP. In contrast, the 28% lower delta B-w in MS than in E100 was explained both by a 15% lower GPP and by a 15% lower fraction of GPP allocated to wood growth, thus partially supporting our second hypothesis: mixing the two species led to shifts in C allocations from above- to belowground, and from growth to litter production, for both species.

Classification and regression tree (CART) model to predict pulmonary tuberculosis in hospitalized patients

Background: Tuberculosis (TB) remains a public health issue worldwide. The lack of specific clinical symptoms to diagnose TB makes the correct decision to admit patients to respiratory isolation a difficult task for the clinician. Isolation of patients without the disease is common and increases health costs. Decision models for the diagnosis of TB in patients attending hospitals can increase the quality of care and decrease costs, without the risk of hospital transmission. We present a predictive model for predicting pulmonary TB in hospitalized patients in a high prevalence area in order to contribute to a more rational use of isolation rooms without increasing the risk of transmission. Methods: Cross sectional study of patients admitted to CFFH from March 2003 to December 2004. A classification and regression tree (CART) model was generated and validated. The area under the ROC curve (AUC), sensitivity, specificity, positive and negative predictive values were used to evaluate the performance of model. Validation of the model was performed with a different sample of patients admitted to the same hospital from January to December 2005. Results: We studied 290 patients admitted with clinical suspicion of TB. Diagnosis was confirmed in 26.5% of them. Pulmonary TB was present in 83.7% of the patients with TB (62.3% with positive sputum smear) and HIV/AIDS was present in 56.9% of patients. The validated CART model showed sensitivity, specificity, positive predictive value and negative predictive value of 60.00%, 76.16%, 33.33%, and 90.55%, respectively. The AUC was 79.70%. Conclusions: The CART model developed for these hospitalized patients with clinical suspicion of TB had fair to good predictive performance for pulmonary TB. The most important variable for prediction of TB diagnosis was chest radiograph results. Prospective validation is still necessary, but our model offer an alternative for decision making in whether to isolate patients with clinical suspicion of TB in tertiary health facilities in countries with limited resources.