Rare canopy species in communities within the Atlantic Coastal Forest in Rio de Janeiro State, Brazil

Rare species are one of the principal components of the species richness and diversity encountered in Dense Ombrophilous Tropical Forests. This study sought to analyze the rare canopy species within the Atlantic Coastal Forest in Rio de Janeiro State, Brazil. Six different communities were examined: Dense Ombrophilous alluvial Forest; Dense sub-montane Ombrophilous Forest; Dense Montane Ombrophilous in Serra do Mar and Serra da Mantiqueira. In each area the vegetation was sampled within forty 10 x 25 m plots alternately distributed along a linear transect. All trees with DBH (1.3 m above ground level) a parts per thousand yen5 cm were sampled. The canopy was characterized using the allometric relationship between diameter and height, and included all trees with BDH a parts per thousand yen10 cm and height a parts per thousand yen10 m. A total of 64 families, 206 genera, and 542 species were sampled, of which 297 (54.8%) represented rare species (less than one individual per hectare). The percentage of rare species varied from 34 to 50% in each of the different communities sampled. A majority of these rare trees belonged to the Rosidae, and a smaller proportion to the Dilleniidae. It was concluded that there was no apparent pattern to rarity among families, that rarity was probably derived from a number of processes (such as gap formation), and that a great majority of the rare species sampled were consistently rare. This indicates that the restricted geographic distribution and high degree of endemism of many arboreal taxa justifies the conservation of even small fragments of Atlantic Forest.

Colonization and extinction of land planarians (Platyhelminthes, Tricladida) in a Brazilian Atlantic Forest regrowth remnant

Long-term assessments of species assemblages are valuable tools for detecting species ecological preferences and their dispersal tracks, as well as for assessing the possible effects of alien species on native communities. Here we report a 50-year-long study on population dynamics of the four species of land flatworms (Platyhelminthes, Tricladida, Terricola) that have colonized or become extinct in a 70-year-old Atlantic Forest regrowth remnant through the period 1955-2006. On the one hand, the two initially most abundant species, which are native to the study site, Notogynaphallia ernesti and Geoplana multicolor have declined over decades and at present do not exist in the forest remnant. The extinction of these species is most likely related with their preference for open vegetation areas, which presently do not exist in the forest remnant. On the other hand, the neotropical Geoplaninae 1 and the exotic Endeavouria septemlineata were detected in the forest only very recently. The long-term study allowed us to conclude that Geoplaninae 1 was introduced into the study area, although it is only known from the study site. Endeavouria septemlineata, an active predator of the exotic giant African snail, is originally known from Hawaii. This land flatworm species was observed repeatedly in Brazilian anthropogenic areas, and this is the first report of the species in relatively well preserved native forest, which may be evidence of an ongoing adaptive process. Monitoring of its geographic spread and its ecological role would be a good practice for preventing potential damaging effects, since it also feeds on native mollusk fauna, as we observed in lab conditions.

Assessment of groundwater recharge and water fluxes of the Guarani Aquifer System, Brazil

The groundwater recharge and water fluxes of the Guarani Aquifer System in the state of Sao Paulo in Brazil were assessed through a numeric model. The study area (6,748 km(2)) comprises Jacar,-Gua double dagger A(0) and Jacar,-Pepira River watersheds, tributaries of the Tiet River in the central region of the state. GIS based tools were used in the storage, processing and analysis of data. Main hydrologic phenomena were selected, leading to a groundwater conceptual model, taking into account the significant outcrops occurring in the study area. Six recharge zones were related to the geologic formation and structures of the semi-confined and phreatic aquifer. The model was calibrated against the baseflows and static water levels of the wells. The results emphasize the strong interaction of groundwater flows between watersheds and the groundwater inflow into the rivers. It has been concluded that lateral groundwater exchanges between basins, the deep discharges to the regional system, and well exploitation were not significant aquifer outflows when compared to the aquifer recharge. The results have shown that the inflows from the river into the aquifer are significant and have the utmost importance since the aquifer is potentially more vulnerable in these places.

A reference business process for ecological niche modelling

Ecological niche modelling combines species occurrence points with environmental raster layers in order to obtain models for describing the probabilistic distribution of species. The process to generate an ecological niche model is complex. It requires dealing with a large amount of data, use of different software packages for data conversion, for model generation and for different types of processing and analyses, among other functionalities. A software platform that integrates all requirements under a single and seamless interface would be very helpful for users. Furthermore, since biodiversity modelling is constantly evolving, new requirements are constantly being added in terms of functions, algorithms and data formats. This evolution must be accompanied by any software intended to be used in this area. In this scenario, a Service-Oriented Architecture (SOA) is an appropriate choice for designing such systems. According to SOA best practices and methodologies, the design of a reference business process must be performed prior to the architecture definition. The purpose is to understand the complexities of the process (business process in this context refers to the ecological niche modelling problem) and to design an architecture able to offer a comprehensive solution, called a reference architecture, that can be further detailed when implementing specific systems. This paper presents a reference business process for ecological niche modelling, as part of a major work focused on the definition of a reference architecture based on SOA concepts that will be used to evolve the openModeller software package for species modelling. The basic steps that are performed while developing a model are described, highlighting important aspects, based on the knowledge of modelling experts. In order to illustrate the steps defined for the process, an experiment was developed, modelling the distribution of Ouratea spectabilis (Mart.) Engl. (Ochnaceae) using openModeller. As a consequence of the knowledge gained with this work, many desirable improvements on the modelling software packages have been identified and are presented. Also, a discussion on the potential for large-scale experimentation in ecological niche modelling is provided, highlighting opportunities for research. The results obtained are very important for those involved in the development of modelling tools and systems, for requirement analysis and to provide insight on new features and trends for this category of systems. They can also be very helpful for beginners in modelling research, who can use the process and the experiment example as a guide to this complex activity. (c) 2008 Elsevier B.V. All rights reserved.

Floristic composition of seasonal riparian forests in Mato Grosso do Sul State, Brazil

(Floristic composition of seasonal riparian forests in Mato Grosso do Sit] State, Brazil). This Study aimed to characterize the floristic composition in two stretches of seasonal semideciduous forest associated with the Formoso River, Bonito, Mato Grosso do Sul State, and in three stretches of seasonal deciduous and semideciduous forests associated with the Salobra, Salobrinha and Perdido rivers in Bodoquena Plateau National Park (76,481 ha) - the only Federal Conservation unit with Integral Protection in the state of Mato Grosso do Sul. The floristic survey was carried out monthly from October/2004 to March/2006, where flowering and fruiting phanerogams were collected by the method of evaluation time. The floristic survey resulted in 56 families, 184 genera and 307 species. Of the total number of species, 68% were trees, 17% shrubs, 14% lianas and only 1% palms. The Fabaceae family (Leguminosae), represented by 51 (16.6%) species, was the most species-rich. These results increase our knowledge of the Mato Grosso do Sul flora and its geographic distribution, thus emphasizing the need for conservation of these riparian forests and providing subsidies for restoration projects of the degraded areas around the conservation unit and permanent protection areas (APPs) of regional rivers.

Morphological variation and reproductive incompatibility of three coconut-mite-associated populations of predatory mites identified as Neoseiulus paspalivorus (Acari: Phytoseiidae)

Predatory mites identified as Neoseiulus paspalivorus DeLeon (Phytoseiidae) have been considered as agents for classical biological control of the coconut mite, Aceria guerreronis Keifer (Eriophyidae), in Africa and elsewhere. Preliminary identification of geographically distinct populations as belonging to the same species (N. paspalivorus) was based on their morphological similarity. However, laboratory studies recently conducted have shown large differences in feeding behaviors and biological characteristics among individuals collected from three geographic origins: Brazil (South America), Benin and Ghana (West Africa). As morphologically similar specimens do not necessarily belong to the same species, we evaluated under laboratory conditions, reproductive compatibility between the specimens from three geographic locations to ascertain their conspecificity. Morphological measurements were also made to determine whether there is a means of discriminating between them. Inter-population crosses showed complete reproductive isolation between the three geographic populations, but interpopulation discontinuities in morphometric characters were absent. These results indicate that the tested specimens are distinct biological entities despite morphological similarity. Further molecular genetic studies are therefore proposed, including screening for endosymbionts and assessment of genetic differentiation, to determine the cause of reproductive incompatibility and to clarify the taxonomic relationship between those populations.

Definition of priority areas for forest conservation through the ordered weighted averaging method

The general objective of this study was to evaluate the ordered weighted averaging (OWA) method, integrated to a geographic information systems (GIS), in the definition of priority areas for forest conservation in a Brazilian river basin, aiming at to increase the regional biodiversity. We demonstrated how one could obtain a range of alternatives by applying OWA, including the one obtained by the weighted linear combination method and, also the use of the analytic hierarchy process (AHP) to structure the decision problem and to assign the importance to each criterion. The criteria considered important to this study were: proximity to forest patches; proximity among forest patches with larger core area; proximity to surface water; distance from roads: distance from urban areas; and vulnerability to erosion. OWA requires two sets of criteria weights: the weights of relative criterion importance and the order weights. Thus, Participatory Technique was used to define the criteria set and the criterion importance (based in AHP). In order to obtain the second set of weights we considered the influence of each criterion, as well as the importance of each one, on this decision-making process. The sensitivity analysis indicated coherence among the criterion importance weights, the order weights, and the solution. According to this analysis, only the proximity to surface water criterion is not important to identify priority areas for forest conservation. Finally, we can highlight that the OWA method is flexible, easy to be implemented and, mainly, it facilitates a better understanding of the alternative land-use suitability patterns. (C) 2008 Elsevier B.V. All rights reserved.

Genetic Diversity and a PCR-Based Method for Xanthomonas axonopodis Detection in Passion Fruit

Xanthomonas axonopodis pv. passiflorae causes bacterial spot in passion fruit. It attacks the purple and yellow passion fruit as well as the sweet passion fruit. The diversity of 87 isolates of pv. passiflorae collected from across 22 fruit orchards in Brazil was evaluated using molecular profiles and statistical procedures, including an unweighted pair-group method with arithmetical averages-based dendrogram, analysis of molecular variance (AMOVA), and an assigning test that provides information on genetic structure at the population level. Isolates from another eight pathovars were included in the molecular analyses and all were shown to have a distinct repetitive sequence-based polymerase chain reaction profile. Amplified fragment length polymorphism technique revealed considerable diversity among isolates of pv. passiflorae, and AMOVA showed that most of the variance (49.4%) was due to differences between localities. Cluster analysis revealed that most genotypic clusters were homogeneous and that variance was associated primarily with geographic origin. The disease adversely affects fruit production and may kill infected plants. A method for rapid diagnosis of the pathogen, even before the disease symptoms become evident, has value for producers. Here, a set of primers (Xapas) was designed by exploiting a single-nucleotide polymorphism between the sequences of the intergenic 16S-23S rRNA spacer region of the pathovars. Xapas was shown to effectively detect all pv. passiflorae isolates and is recommended for disease diagnosis in passion fruit orchards.

Macrogeographic Genetic Variation in Broad-Snouted Caiman (Caiman latirostris)

Broad-snouted caiman`s (Caiman latirostris) geographic distribution comprises one of the widest latitudinal ranges among all crocodilians. In this study we analyzed the relationship between geographic distance (along the species latitudinal range) and genetic differentiation using DNA microsatellite loci developed for C. latirostris and Alligator mississippiensis. The results suggest that there is a consistent relationship between geographic distance and genetic differentiation; however, other biogeographical factors seem to be relevant. The Atlantic Chain (Serra do Mar) seems to be an effective geographic barrier, as well as the relatively narrow (<= 1.5 km) sea channel between Cardoso Island and the continent. In addition, coastal populations seem to have been well connected in recent geological time (Pleistocene 16,000 years ago) all along the eastern Brazilian coast. Further studies should focus on the Sao Francisco River drainage, which is still poorly known for this species. J. Exp. Zool. 30.9A:628-636, 2008. (C) 2008 Wiley-Liss, Inc.

Overwintering of Sclerotium rolfsii and S-rolfsii var. delphinii in different latitudes of the United States

Previously known only from the southern United States, hosta petiole rot recently appeared in the northern United States. Sclerotium rolfsii var. delphinii is believed to be the predominant petiole rot pathogen in the northern United States, whereas S. rolfsii is most prevalent in the southern United States. In order to test the hypothesis that different tolerance to climate extremes affects the geographic distribution of these fungi, the survival of S. rolfsii and S. rolfsii var. delphinii in the northern and southeastern United States was investigated. At each of four locations, nylon screen bags containing sclerotia were placed on the surface of bare soil and at 20-cm depth. Sclerotia were recovered six times from November 2005 to July 2006 in North Dakota and Iowa, and from December 2005 to August 2006 in North Carolina and Georgia. Survival was estimated by quantifying percentage of sclerotium survival on carrot agar. Sclerotia of S. rolfsii var. delphinii survived until at least late July in all four states. In contrast, no S. rolfsii sclerotia survived until June in North Dakota or Iowa, whereas 18.5% survived until August in North Carolina and 10.3% survived in Georgia. The results suggest that inability to tolerate low temperature extremes limits the northern range of S. rolfsii.

Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and nucleotide sequencing of a fragment from the nucleocapsid gene

The variability of a fragment of the nucleocapsid gene of orchid fleck virus (OFV) was investigated by single-strand conformational polymorphism (SSCP) analysis and nucleotide sequencing. Forty-eight samples of 18 genera of orchids were collected from Brazil, Costa Rica and Australia. The SSCP analysis yielded six different band patterns, and phylogenetic analysis based on the nucleotide fragment sequence obtained in this work and six available in GenBank showed two different groups, one with isolates 023Germany and So-Japan, and other with the rest of the isolates. None of the analyses showed geographic correlation among the Brazilian strains. The data obtained in this study showed a low genetic variation in this region of the genome; the d(N)/d(S) ratio of 0.251-0.405 demonstrated a negative selective pressure that maintains the stability of the analyzed fragments.

Novel sequence types (STs) of Staphylococcus aureus isolates causing clinical and subclinical mastitis in flocks of sheep in the northeast of Brazil

Staphylococcus aureus is one of the most important infectious mastitis causative agents in small ruminants. In order to know the distribution of Staph. aureus strains associated with infectious mastitis in flocks of sheep in the northeast of Brazil and establish whether these clones are related to the strains distributed internationally, this study analysed the genetic diversity of Staph. aureus isolates from cases of clinical and subclinical mastitis in ewes by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this research, 135 ewes with mastitis from 31 sheep flocks distributed in 15 districts were examined. Staph. aureus was isolated from sheep milk in 9 (29%) out of 31 herds located in 47% of the districts surveyed. MLST analysis allowed the identification of four STs (ST750, ST1728, ST1729 and ST1730). The last three with their respective novel alleles (g/p-220; pta-182 and yqil-180) were recently reported in the Staph. aureus MLST database (http://www.mlst.net). Each novel allele showed only a nucleotide different from those already described. The occurrence of CC133 (ST750 and ST1729) in this study is in agreement with other reports that only a few clones of Staph. aureus seem to be responsible for most cases of mastitis in dairy farms and that some of these clones may have broad geographic distribution. However, the prevalence of CC5 (ST1728 and ST1730)-an important group related to cases of colonization or infection in humans-differs from previous studies by its widespread occurrence and may suggest human contamination followed by selective pressures of the allelic diversifications presented for these STs.

Elevated levels of selenium in the typical diet of Amazonian riverside populations

Selenium (Se) intake is generally from food, whose Se content depends on soil Se and plant accumulation. For humans, adequate Se intake is essential for several selenoenzymes. In the Lower Tapajos region of the Brazilian Amazon, Se status is elevated with large inter-community variability. Se intake in this region, where Hg exposure is among the highest in the world, may be important to counteract mercury (Hg) toxicity. The present study was conducted in 2006 with 155 persons from four communities of the Lower Tapajos. The objectives were: i) to evaluate Se content in their typical diet and drinking water; ii) to compare food Se concentrations with respect to geographic location; and iii) to examine the contribution of consumption of different food items to blood Se. More than 400 local foods and 40 drinking water samples were collected. Participants responded to an interview-administered food frequency questionnaire and provided blood samples. Food, water and blood Se levels were assessed by ICP-MS. Since Brazil nuts may also contain significant levels of barium (Ba) and strontium (Sr), these elements were likewise analyzed in nuts. The highest Se concentrations were found in Brazil nuts, but concentrations were highly variable (median: 13.9 mu g/g; range: 0.4-158.4 mu g/g). Chicken, game meat, eggs and beef also contained considerable levels of Se, with median concentrations from 0.3 to 1.4 mu g/g. There was no particular geographic distribution of food Se. Se concentration in drinking water was very low (<1.4 mu g/L). Blood Se covered a (103-1500 mu g/L), and was positively related to regular consumption of Brazil nuts, domestic chicken and game meat. Brazil nuts were found to contain highly variable and often very high concentrations of Ba (88.0 mu g/g, 1.9-1437 mu g/g) and Sr (38.7 mu g/g, 3.3-173 mu g/g). Further studies should address multiple nutrient/toxic interactions in the diet and related effects on health. (c) 2010 Elsevier B.V. All rights reserved.

Cytogenetic biomonitoring of inhabitants of a large uranium mineralization area: the municipalities of Monte Alegre, Prainha, and Alenquer, in the State of Para, Brazil

Uranium is a natural radioactive metallic element; its effect on the organism is cumulative, and chronic exposure to this element can induce carcinogenesis. Three cities of the Amazon region-Monte Alegre, Prainha, and Alenquer-in North Brazil, are located in one of the largest uranium mineralization areas of the world. Radon is a radioactive gas, part of uranium decay series and readily diffuses through rock. In Monte Alegre, most of the houses are built of rocks removed from the Earth`s crust in the forest, where the uranium reserves lie. The objective of the present work is to determine the presence or absence of genotoxicity and risk of carcinogenesis induced by natural exposure to uranium and radon in the populations of these three cities. The frequency of micronuclei (MN) and chromosomal aberrations (CA) showed no statistically significant differences between the control population and the three study populations (P > 0.05). MN was also analyzed using the fluorescence in situ hybridization (FISH) technique, with a centromere-specific probe. No clastogenic and/or aneugenic effects were found in the populations. Using FISH analysis, other carcinogenesis biomarkers were analyzed, but neither the presence of the IGH/BCL2 translocation nor an amplification of the MYC gene and 22q21 region was detected. Clastogenicity and DNA damage were also not found in the populations analyzed using the alkaline comet assay. The mitotic index showed no cytotoxicity in the analyzed individuals` lymphocytes. Once we do not have data concerning radiation doses from other sources, such as cosmic rays, potassium, thorium, or anthropogenic sources, it is hard to determine if uranium emissions in this geographic region where our study population lives are too low to cause significant DNA damage. Regardless, genetic analyses suggest that the radiation in our study area is not high enough to induce DNA alterations or to interfere with mitotic apparatus formation. It is also possible that damages caused by radiation doses undergo cellular repair.

Low Satellite DNA Variability in Natural Populations of Drosophila antonietae Involved in Different Evolutionary Events

Drosophila antonietae is a cactophilic species that is found in the mesophilic forest of the Parana`-Paraguay river basin and in the dunes of the South Atlantic coast of Brazil. Although the genetic structure of the Parana`-Paraguay river basin populations has already been established, the relationship between these populations and those on the Atlantic coast is controversial. In this study, we compared 33 repetitive units of pBuM-2 satellite DNA isolated from individuals from 8 populations of D. antonietae in these geographic regions, including some populations found within a contact zone with the closely related D. serido. The pBuM-2 sequences showed low interpopulational variability. This result was interpreted as a consequence of both gene flow among the populations and unequal crossing over promoting homogenization of the tandem arrays. The results presented here, together with those of previous studies, highlight the use of pBuM-2 for solving taxonomic conflicts within the D. buzzatii species cluster.