Estimativa dos impactos das mudanças climáticas na distribuição das espécies montanas do gênero Brachycephalus (Amphibia: anura) através da modelagem de nicho ecológico

The genus Brachycephalus is endemic to the Atlantic rainforest and is distributed mainly in the southeastern and southern Brazil. Currently, it has 17 recognized species, most of them, associated with mountainous habitats along the Serra do Mar and Serra da Mantiqueira ridges. Here we use an ecological niche modelling approach based on climatic variables, to assess the potential niche of the mountainous species of this genus. The model generated was then projected to future scenarios considering the last IPCC report, in order to estimate the impacts of climate changes on these species distribution. Results show a decrease in the total suitable area for the mountainous Brachycephalus species, as well as tendencies already observed for other organisms, such as, pole and upward migrations. A southern area on Planalto de Paranapiacaba increases in suitability for these species. We suggest special efforts on new surveys and conservation on the northern part of their distribution, once this seems to be the region more affected by climate changes on the projected scenarios

Proteomic analysis of the rare Uracoan rattlesnake Crotalus vegrandis venom: evidence of a broad arsenal of toxins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

In vitro antifungal susceptibility of candida albicans isolates from patients with chronic periodontitis and diabetes

Alterations that lead to deficiency of the immune system, such as diabetes mellitus, may promote proliferation of Candida albicans and selection of strains which have greater ability to adhere and to penetrate the host tissues. Recent studies indicate an increase of the antifungal resistance of C. albicans isolates in periodontal pockets, suggesting that the oral cavity could be a reservoir of resistant yeast to antifungal agents. Moreover, oral cavity can act as a reservoir of certain pathogens that may cause systemic infections. The periodontal pocket is an ecological niche suitable to host microorganisms that could act as opportunistic pathogens. The aim of this study is to contribute to the understanding of resistance to conventional antifungal against C. albicans isolates from patients with periodontitis and diabetes. The determination of the minimal inhibitory concentrations (MIC) was evaluated according to M27S3 of the CLSI (2008), with modifications. The results showed that 48.8% of the studied strains were resistant to one or more antifungals and 6.6% were resistant to fluconazole and voriconazole. These results suggest an increasing resistance to conventional antifungal agents among Candida species, suggesting that the oral cavity could host pathogen fungi.

Modeling the Potential Geographic Distribution of Black Pepper (Piper nigrum) in Asia Using GIS Tools

Known as the "king of spices", black pepper (Piper nigrum), a perennial crop of the tropics, is economically the most important and the most widely used spice crop in the world. To understand its suitable bioclimatic distribution, maximum entropy based on ecological niche modeling was used to model the bioclimatic niches of the species in its Asian range. Based on known occurrences, bioclimatic areas with higher probabilities are mainly located in the eastern and western coasts of the Indian Peninsula, the east of Sumatra Island, some areas in the Malay Archipelago, and the southeast coastal areas of China. Some undocumented places were also predicted as suitable areas. According to the jackknife procedure, the minimum temperature of the coldest month, the mean monthly temperature range, and the precipitation of the wettest month were identified as highly effective factors in the distribution of black pepper and could possibly account for the crop's distribution pattern. Such climatic requirements inhibited this species from dispersing and gaining a larger geographical range.

Desafios atuais da modelagem preditiva de distribuição de espécies

A modelagem preditiva tem sido aplicada para analisar a distribuição geográfica de espécies, a partir de extrapolações das características ambientais dos locais conhecidos de ocorrência. O interesse por esse tipo de modelagem deve-se à necessidade de respostas rápidas e fundamentadas para as ameaças que as espécies têm enfrentado, devido à perda de habitat, invasão de espécies exóticas, mudanças climáticas, entre outros. Este artigo oferece uma visão geral dos avanços recentes no campo da modelagem e visa incentivar a discussão e aplicação desse método, que pode auxiliar tanto na aquisição de conhecimento básico sobre a biologia das espécies, quanto na análise e formulação de políticas para sua conservação.

Rekonstruktion der eiszeitlichen Verbreitung und Artbildung vier alpiner Primeln durch Artenverbreitungsmodelle und Phylogeographie

Aim: Previous studies revealed that diversification events in the western clade of the alpine Primula sect. Auricula were concentrated in the Quaternary cold periods. This implies that allopatric speciation in isolated glacial refugia was the most common mode of speciation. In the first part of the present dissertation, this hypothesis is further investigated by locating refugial areas of two sister species, Primula marginata & P. latifolia during the last glacial maximum, 21,000 years ago. In the second part, the glacial and postglacial history of P. hirsuta and P. daonensis is investigated. Location: European Alps. Methods: Glacial refugia were located using species distribution models, which are projected to last glacial maximum climate. These refugia are validated with geographic distribution patterns of intra-specific genetic diversity, rarity and variation. Results 1) Speciation: Glacial refugia of the sister taxa Primula marginata and P. latifolia were largely separated, only a small overlapping zone at the southern margin of the former glacier in the Maritime Alps exists. This overlapping zone is too small to indicate sympatric speciation. The largely separated glacial distribution of both species rather confirms our hypothesis of allopatric speciation in isolated glacial refugia. Results 2) Glacial and postglacial history: Surprizingly, the modelled potential refugia of three out of four Primula species are situated within the former ice-shield, except for P. marginata. This indicates that peripheral and central nunataks played an important role for the glacial survival in P. latifolia, P. hirsuta and P. daonensis, while peripheral refugia outside the maximum extend of the glacier were crucial in P. marginata. In P. hirsuta and P. latifolia SDMs allowed to exclude several hypothetical refugial areas that overlap with today’s distribution as potential refugia for the species. In P. marginata, hypothetical refugial areas at the periphery of the former ice-shield that overlap with today’s distribution were confirmed by the models. The results from the SDMs are confirmed by population genetic patterns in three out of four species. P. daonensis represents an exception, where population genetic data contradict the SDMs. Main conclusions: Species distribution models provide species specific scenarios of glacial distribution and postglacial re-colonization, which can be validated using population genetic analyses. This combined approach is useful and helps to understand the complex processes that have lead to the genetic and floristic patterns of biodiversity that is found today in the Alps.

Analysis of coprolites from the extinct mountain goat Myotragus balearicus

Humans colonized the Balearic Islands 5-4 ka ago. They arrived in a uniquely adapted ecosystem with the Balearic mountain goat Myotragus balearicus (Bovidae, Antilopinae, Caprini) as the only large mammal. This mammal went extinct rapidly after human arrival. Several hypotheses have been proposed to explain the extinction of M. balearicus. For the present study ancient DNA analysis (Sanger sequencing, Roche-454, Ion Torrent), and pollen and macrofossil analyses were performed on preserved coprolites from M. balearicus, providing information on its diet and paleo-environment. The information retrieved shows that M. balearicus was heavily dependent on the Balearic box species Buxus balearica during at least part of the year, and that it was most probably a browser. Hindcast ecological niche modelling of B. balearica shows that local distribution of this plant species was affected by climate changes. This suggests that the extinction of M. balearicus can be related to the decline and regional extinction of a plant species that formed a major component of its diet. The vegetation change is thought to be caused by increased aridity occurring throughout the Mediterranean. Previous hypotheses relating the extinction of M. balearicus directly to the arrival of humans on the islands must therefore be adjusted. (C) 2013 University of Washington. Published by Elsevier Inn All rights reserved.

Mycobacterium ulcerans persistence at a village water source of Buruli ulcer patients

Buruli ulcer (BU), a neglected tropical disease of the skin and subcutaneous tissue, is caused by Mycobacterium ulcerans and is the third most common mycobacterial disease after tuberculosis and leprosy. While there is a strong association of the occurrence of the disease with stagnant or slow flowing water bodies, the exact mode of transmission of BU is not clear. M. ulcerans has emerged from the environmental fish pathogen M. marinum by acquisition of a virulence plasmid encoding the enzymes required for the production of the cytotoxic macrolide toxin mycolactone, which is a key factor in the pathogenesis of BU. Comparative genomic studies have further shown extensive pseudogene formation and downsizing of the M. ulcerans genome, indicative for an adaptation to a more stable ecological niche. This has raised the question whether this pathogen is still present in water-associated environmental reservoirs. Here we show persistence of M. ulcerans specific DNA sequences over a period of more than two years at a water contact location of BU patients in an endemic village of Cameroon. At defined positions in a shallow water hole used by the villagers for washing and bathing, detritus remained consistently positive for M. ulcerans DNA. The observed mean real-time PCR Ct difference of 1.45 between the insertion sequences IS2606 and IS2404 indicated that lineage 3 M. ulcerans, which cause human disease, persisted in this environment after successful treatment of all local patients. Underwater decaying organic matter may therefore represent a reservoir of M. ulcerans for direct infection of skin lesions or vector-associated transmission.

Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage.

Zoonoses, diseases affecting both humans and animals, can exert tremendous pressures on human and veterinary health systems, particularly in resource limited countries. Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria. Here we describe the genetic diversity of Bacillus anthracis in Nigeria and compare it to Chad, Cameroon and a broader global dataset based on the multiple locus variable number tandem repeat (MLVA-25) genetic typing system. Nigerian B. anthracis isolates had identical MLVA genotypes and could only be resolved by measuring highly mutable single nucleotide repeats (SNRs). The Nigerian MLVA genotype was identical or highly genetically similar to those in the neighboring countries, confirming the strains belong to this unique West African lineage. Interestingly, sequence data from a Nigerian isolate shares the anthrose deficient genotypes previously described for strains in this region, which may be associated with vaccine evasion. Strains in this study were isolated over six decades, indicating a high level of temporal strain stability regionally. Ecological niche models were used to predict the geographic distribution of the pathogen for all three countries. We describe a west-east habitat corridor through northern Nigeria extending into Chad and Cameroon. Ecological niche models and genetic results show B. anthracis to be ecologically established in Nigeria. These findings expand our understanding of the global B. anthracis population structure and can guide regional anthrax surveillance and control planning.

Gene sequences of the lichen Cetraria aculeata

Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large-scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on the DNA sequences from three loci for each symbiont, we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont data sets into three groups. An AMOVA shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and codispersal, we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of codispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled C. aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographical range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.

Nannofossil assemblages and flux rates during the late Oligocene-early Miocene

This study investigates abundance variations in Noelaerhabdaceae assemblages during the late Oligocene-early Miocene at three subtropical sites in the Atlantic and Pacific oceans (DSDP Sites 516, 608 and 588). At these three sites, nannofossil assemblages were characterized by the successive high proportion of Cyclicargolithus, Dictyococcites and Reticulofenestra. Local paleoceanographic changes, such as the input of nutrient-poor water masses, might explain shifts in ecological prominence within the Noelaerhabdaceae at DSDP Site 516 (South Atlantic). But the similar timing of a decline in Cyclicargolithus at the three studied sites more likely corresponds to a global process. Here, we explore possible causes for this long-term taxonomic turnover. A global change in climate, associated with early Miocene glaciations, could have triggered a decline in fitness of the taxon Cyclicargolithus. The ecological niche made vacant because of the decrease in Cyclicargolithus could then have been exploited by Dictyococcites and Reticulofenestra that became prominent in the assemblages after 20.5 Ma. Alternatively, this global turnover might reflect a gradual evolutionary succession and be the result of other selection pressures, such as increased competition between Cyclicargolithus and Dictyococcites/Reticulofenestra. A diversification within Dictyococcites/Reticulofenestra, indicated by an expansion in the size variation within this group since ~ 20.5 Ma, may have contributed to the decreased fitness of Cyclicargolithus.

Raster maps for 29 environmental variables in three geographical regions

Aim: Greater understanding of the processes underlying biological invasions is required to determine and predict invasion risk. Two subspecies of olive (Olea europaea subsp. europaea and Olea europaea subsp. cuspidata) have been introduced into Australia from the Mediterranean Basin and southern Africa during the 19th century. Our aim was to determine to what extent the native environmental niches of these two olive subspecies explain the current spatial segregation of the subspecies in their non-native range. We also assessed whether niche shifts had occurred in the non-native range, and examined whether invasion was associated with increased or decreased occupancy of niche space in the non-native range relative to the native range. Location: South-eastern Australia, Mediterranean Basin and southern Africa. Methods: Ecological niche models (ENMs) were used to quantify the similarity of native and non-native realized niches. Niche shifts were characterized by the relative contribution of niche expansion, stability and contraction based on the relative occupancy of environmental space by the native and non-native populations. Results: Native ENMs indicated that the spatial segregation of the two subspecies in their non-native range was partly determined by differences in their native niches. However, we found that environmentally suitable niches were less occupied in the non-native range relative to the native range, indicating that niche shifts had occurred through a contraction of the native niches after invasion, for both subspecies. Main conclusions: The mapping of environmental factors associated with niche expansion, stability or contraction allowed us to identify areas of greater invasion risk. This study provides an example of successful invasions that are associated with niche shifts, illustrating that introduced plant species are sometimes readily able to establish in novel environments. In these situations the assumption of niche stasis during invasion, which is implicitly assumed by ENMs, may be unreasonable.

Occurrence (presence-only) of living Lophelia pertusa reefs in the Irish continental margin

The present data set was used as a training set for a Habitat Suitability Model. It contains occurrence (presence-only) of living Lophelia pertusa reefs in the Irish continental margin, which were assembled from databases, cruise reports and publications. A total of 4423 records were inspected and quality assessed to ensure that they (1) represented confirmed living L. pertusa reefs (so excluding 2900 records of dead and isolated coral colony records); (2) were derived from sampling equipment that allows for accurate (<200 m) geo-referencing (so excluding 620 records derived mainly from trawling and dredging activities); and (3) were not duplicated. A total of 245 occurrences were retained for the analysis. Coral observations are highly clustered in regions targeted by research expeditions, which might lead to falsely inflated model evaluation measures (Veloz, 2009). Therefore, we coarsened the distribution data by deleting all but one record within grid cells of 0.02° resolution (Davies & Guinotte 2011). The remaining 53 points were subject to a spatial cross-validation process: a random presence point was chosen, grouped with its 12 closest neighbour presence points based on Euclidean distance and withheld from model training. This process was repeated for all records, resulting in 53 replicates of spatially non-overlapping sets of test (n=13) and training (n=40) data. The final 53 occurrence records were used for model training.

Forest connectivity restoration through reforestation: an integrated methodology for prioritizing agricultural lands and selecting reforestation species

Forest connectivity restoration is a major goal in natural resource planning. Given the high amount of abandoned cultivated lands, setting efficient methods for the reforestation of agricultural lands offers a good opportunity to face this issue. However, reforestations must be carefully planned, which poses two main challenges. In first place, to determine those agricultural lands that, once reforested, would meet more effectively the planning goals. As a further step, in order to grant the success of the activity, it is fairly advisable to select those tree species that are more adapted to each particular environment. Here we intend to give response to both requirements by proposing a sequential and integrated methodology that has been implemented in two Spanish forest districts, which are formed by several landscape types that were previously defined and characterized. Using the software Conefor Sensinode, a powerful tool for quantifying habitat availability that is based on graph theory concepts, we determined the landscapes where forest planning should have connectivity as a major concern and, afterwards, we detected the agricultural patches that would contribute most to enhance connectivity if they were reforested. The subsequent reforestation species assessment was performed within these priority patches. Using penalized logistic regressions we fitted ecological niche models for the Spanish native tree species. The models were trained with species distribution data from the Spanish Forest Map and used climatic and lithological variables as predictors. Model predictions were used to build ordered lists of suitable species for each priority patch. The lists include dominant and non dominant tree species and allow adding biodiversity goals to the reforestation planning. The result of this combined methodology is a map of agricultural patches that would contribute most to uphold forest connectivity if they were reforested and a list of suitable tree species for each patch ordered by occurrence probability. Therefore the proposed methodology may be useful for suitable and efficient forest planning and landscape designing.

Germination ecology of the perennial Centaurium somedanum, a specialist species of mountain springs

To improve understanding of how a rare endemic species of Centaurium adapts to a specialized ecological niche, we studied the germination ecology of the mountain spring specialist, C. somedanum, a perennial species restricted to an unusual habitat for this genus. We conducted laboratory experiments with fresh seeds collected from two populations for three consecutive years, to investigate: (1) the effect of temperature and light ongermination; (2) the existence of seed dormancy; and (3) inter-population and inter-annual variation in germinability. Germination occurred only in the light and at relatively low temperatures (15?228C) with no differences between constant and alternating regimes, and a significant decrease at high temperatures (258C and 308C). We found non-deep simple morphophysiological dormancy and variation in seed germinability depending on the year of seed collection. C. somedanum diverged from the common germination characteristics of the genus in: (1) its germination at lower temperatures, which contrasts with what is generally expected in wetland species but could be adaptive in the spring habitat; and (2) its morphophysiological dormancy, which we report here for the first time in the genus and which could be an adaptation to its mountain habitat.