Hybridization and introgression across different ploidy levels in the Neotropical orchids Epidendrum fulgens and E-puniceoluteum (Orchidaceae)

The hypothesis of gene flow between species with large differences in chromosome numbers has rarely been tested in the wild, mainly because species of different ploidy are commonly assumed to be reproductively isolated from each other because of instantaneous and strong postzygotic barriers. In this study, a broad-scale survey of molecular variation was carried out between two orchid species with different ploidy levels: Epidendrum fulgens (2n = 2x = 24 chromosomes) and Epidendrum puniceoluteum (2n = 4x = 52 chromosomes). To test the strength of their reproductive barriers, we investigated the distribution of genetic variation in sympatric and allopatric populations of these two species and conducted crossing experiments. Nuclear and plastid microsatellite loci were used to genotype 463 individuals from eight populations across the geographical range of both species along the Brazilian coastal plain. All six sympatric populations analysed presented hybrid zones, indicating that hybridization between E. fulgens and E. puniceoluteum is a common phenomenon. Bayesian assignment analysis detected the presence of F(1) and F(2) individuals and also signs of introgression, demonstrating a high potential for interspecific gene flow. Introgression occurs preferentially from E. fulgens to E. puniceoluteum. Pure parental individuals of both species display strong genotype-habitat associations, indicating that environment-dependent selection could be acting in all hybrid zones. This study suggests that hybridization and introgression are evolutionary processes playing a role in the diversification of Epidendrum and indicates the importance of investigations of hybrid zones in understanding reproductive barriers and speciation processes in Neotropical orchid species.

On the Relationship between Zaprionus spinipilus Chassagnard & McEvey and Z. vittiger Coquillett, the Type Species of the Genus Zaprionus (Diptera: Drosophilidae)

Zaprionus vittiger Coquillett is the type species of the genus Zaprionus Coquillett. However, the species is only known from five old museum specimens collected from South Africa and Malawi. It has often been confused with many other Zaprionus species, especially with Z. spinipilus Chassagnard & McEvey, a widespread species in Africa known from Madagascar, Malawi, Ethiopia and Cameroon. We have recently collected flies from the type localities of both species (South Africa and Madagascar, respectively). This has prompted us to test the taxonomic boundaries of these two nominal species using molecular (the mitochondrial COII and the nuclear Amyrel genes), chromosomal, morphological (internal and external genitalia), and reproductive isolation analyses. The results suggest Z. spinipilus to be a junior synonym to Z. vittiger.

Biogeography of Glandulocaudinae (Teleostei : Characiformes : Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity

The biogeography of the Glandulocaudinae ( former Glandulocaudini) is reviewed. The major pattern of diversification presented by this group of freshwater fishes can be clearly associated to the main aspects of the tectonic evolution of the southern portion of the Cis-Andean South American Platform. The phylogenetic relationships within the group suggest that the clade represented by Lophiobrycon is the sister-group of the more derived clade represented by the genus Glandulocauda and Mimagoniates. Lophiobrycon and Glandulocauda occur in areas of the ancient crystalline shield of southeastern Brazil and their present allopatric distribution is probably due to relict survival and tectonic vicariant events. Populations of Glandulocauda melanogenys are found in contiguous drainages in presently isolated upper parts of the Tiete, Guaratuba, Itatinga, and Ribeira de Iguape basins and this pattern of distribution is probably the result of river capture caused by tectonic processes that affected a large area in eastern and southeastern Brazil. The species of Mimagoniates are predominantly distributed along the eastern and southeastern coastal areas, but M. microlepis is additionally found in the rio Iguacu and Tibagi basins. Mimagoniates barberi occurs in both SW margin of the upper rio Parana basin and the lower Paraguay and Mimagoniates sp. occurs in the upper Paraguay river basin. Tectonic activations of the Continental Rift of Southeastern Brazil along the eastern margin of the Upper Parana basin promoted population fragmentation responsible of the present day distribution presented by Glandulocauda melanogenys. We hypothesize that occurrence of Mimagoniates along the lowland area around the Parana basin was due to a single or a multiple fragmentation of populations along the W-SW border of the upper Parana Basin, probably due to the major tectonic origin of the Chaco-Pantanal wetland foreland basins since the Miocene as well as Cenozoic tectonic activity along the borders of the upper Parana basin, such as in the eastern Paraguay, in the Asuncion Rift. Distributional pattern of Mimagoniates suggests that its initial diversification may be related to the tectonic evolution of the Chaco-Pantanal foreland basin system and a minimum age of 2.5 M.Y are proposed for this monophyletic group. Previous hypotheses on sea level fluctuations of the late Quaternary as being the main causal mechanism promoting cladogenesis and speciation of the group are critically reviewed. Phylogeographic studies based on molecular data indicate significant differences among the isolated populations of M. microlepis. These findings suggest that a much longer period of time and a paleogeographic landscape configuration of the Brazilian southeastern coastal region explain the present observed phylogenetic and biogeographic patterns.

Checklist and morphometry of benthic cnidarians from the Fernando de Noronha Archipelago, Brazil

The Fernando de Noronha Archipelago (Pernambuco State, Brazil), a national marine park, is formed by 21 islands and islets of volcanic origin. An update of the checklist of the benthic cnidarians from some of the archipelago`s reef environments, as well as a study of their corals and calcified hydroids morphometry, was the major goal of this work. Fieldwork was undertaken in February 2005 and in April 2006 and observations were carried out at 13 stations during snorkeling and/or scuba diving up to 30 m deep. Thirty-four species of cnidarians were recorded, of which 17 are new occurrences for the studied area. When added to the species previously listed in the literature, the total number of benthic cnidarians recorded for the Archipelago increases to 57. Stephanocoenia michelini, a new occurrence of zooxanthellate coral, is worthy of mention, as well as the calcified hydroid Millepora braziliensis. Mussismilia hispida tenuisepta showed several variations among its skeletal characters that surpassed the limits of intraspecific morphological variation when compared to those of Mussismilia hispida.

Phylogenetic position of Dendropsophus gaucheri (Lescure and Marty 2000) highlights the need for an in-depth investigation of the phylogenetic relationships of Dendropsophus (Anura: Hylidae)

Dendropsophus gaucheri is a recently described species which inhabits open areas of the eastern part of the Guiana Shield and is currently assigned to the D. parviceps species group based on the presence of a subocular cream spot. Herein we investigate its phylogenetic position including material from the type locality and newly documented populations from Suriname and Brazil based on mtDNA sequences. The species, as well as D. riveroi which is assigned to the D. minimus species group, were recovered nested within the D. microcephalus species group which implies the paraphyly of the three Dendropsophus species groups. Such result, along with other evidences, highlights the need for a thorough revision of the genus. The genetic distances among D. gaucheri samples studied are low confirming their conspecificity and suggesting recent connections among populations from open areas currently isolated by rainforest in the lowlands of the Guiana Shield.

Assessing the impact of deforestation and climate change on the range size and environmental niche of bird species in the Atlantic forests, Brazil

Aim Habitat loss and climate change are two major drivers of biological diversity. Here we quantify how deforestation has already changed, and how future climate scenarios may change, environmental conditions within the highly disturbed Atlantic forests of Brazil. We also examine how environmental conditions have been altered within the range of selected bird species. Location Atlantic forests of south-eastern Brazil. Methods The historical distribution of 21 bird species was estimated using Maxent. After superimposing the present-day forest cover, we examined the environmental niches hypothesized to be occupied by these birds pre- and post-deforestation using environmental niche factor analysis (ENFA). ENFA was also used to compare conditions in the entire Atlantic forest ecosystem pre- and post-deforestation. The relative influence of land use and climate change on environmental conditions was examined using analysis of similarity and principal components analysis. Results Deforestation in the region has resulted in a decrease in suitable habitat of between 78% and 93% for the Atlantic forest birds included here. Further, Atlantic forest birds today experience generally wetter and less seasonal forest environments than they did historically. Models of future environmental conditions within forest remnants suggest generally warmer conditions and lower annual variation in rainfall due to greater precipitation in the driest quarter of the year. We found that deforestation resulted in a greater divergence of environmental conditions within Atlantic forests than that predicted by climate change. Main conclusions The changes in environmental conditions that have occurred with large-scale deforestation suggest that selective regimes may have shifted and, as a consequence, spatial patterns of intra-specific variation in morphology, behaviour and genes have probably been altered. Although the observed shifts in available environmental conditions resulting from deforestation are greater than those predicted by climate change, the latter will result in novel environments that exceed temperatures in any present-day climates and may lead to biotic attrition unless organisms can adapt to these warmer conditions. Conserving intra-specific diversity over the long term will require considering both how changes in the recent past have influenced contemporary populations and the impact of future environmental change.

Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest

The open vegetation corridor of South America is a region dominated by savanna biomes. It contains forests (i.e. riverine forests) that may act as corridors for rainforest specialists between the open vegetation corridor and its neighbouring biomes (i.e. the Amazonian and Atlantic forests). A prediction for this scenario is that populations of rainforest specialists in the open vegetation corridor and in the forested biomes show no significant genetic divergence. We addressed this hypothesis by studying plumage and genetic variation of the Planalto woodcreeper Dendrocolaptes platyrostris Spix (1824) (Aves: Furnariidae), a forest specialist that occurs in both open habitat and in the Atlantic forest. The study questions were: (1) is there any evidence of genetic continuity between populations of the open habitat and the Atlantic forest and (2) is plumage variation congruent with patterns of neutral genetic structure or with ecological factors related to habitat type? We used cytochrome b and mitochondrial DNA control region sequences to show that D. platyrostris is monophyletic and presents substantial intraspecific differentiation. We found two areas of plumage stability: one associated with Cerrado and the other associated with southern Atlantic Forest. Multiple Mantel tests showed that most of the plumage variation followed the transition of habitats but not phylogeographical gaps, suggesting that selection may be related to the evolution of the plumage of the species. The results were not compatible with the idea that forest specialists in the open vegetation corridor and in the Atlantic forest are linked at the population level because birds from each region were not part of the same genetic unit. Divergence in the presence of gene flow across the ecotone between both regions might explain our results. Also, our findings indicate that the southern Atlantic forest may have been significantly affected by Pleistocene climatic alteration, although such events did not cause local extinction of most taxa, as occurred in other regions of the globe where forests were significantly affected by global glaciations. Finally, our results neither support plumage stability areas, nor subspecies as full species. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103, 801-820.

An extinction-survival-type phase transition in the probabilistic cellular automaton p182-q200

We investigate the critical behaviour of a probabilistic mixture of cellular automata (CA) rules 182 and 200 (in Wolfram`s enumeration scheme) by mean-field analysis and Monte Carlo simulations. We found that as we switch off one CA and switch on the other by the variation of the single parameter of the model, the probabilistic CA (PCA) goes through an extinction-survival-type phase transition, and the numerical data indicate that it belongs to the directed percolation universality class of critical behaviour. The PCA displays a characteristic stationary density profile and a slow, diffusive dynamics close to the pure CA 200 point that we discuss briefly. Remarks on an interesting related stochastic lattice gas are addressed in the conclusions.

DFT study of the electronic, vibrational, and optical properties of SnO(2)

We report results on the electronic, vibrational, and optical properties of SnO(2) obtained using first-principles calculations performed within the density functional theory. All the calculated phonon frequencies, real and imaginary parts of complex dielectric function, the energy-loss spectrum, the refractive index, the extinction, and the absorption coefficients show good agreement with experimental results. Based on our calculations, the SnO(2) electron and hole effective masses were found to be strongly anisotropic. The lattice contribution to the low-frequency region of the SnO(2) dielectric function arising from optical phonons was also determined resulting the values of E > (1aSyen) (latt) (0) = 14.6 and E > (1ayen) (latt) (0) = 10.7 for directions perpendicular and parallel to the tetragonal c-axis, respectively. This is in excellent agreement with the available experimental data. After adding the electronic contribution to the lattice contribution, a total average value of E >(1)(0) = 18.2 is predicted for the static permittivity constant of SnO(2).

Ab initio study of the electronic and optical properties of sillimanite (Al(2)SiO(5)) crystal

Ab initio calculations based on the density functional theory (DFT) are used to investigate the electronic and optical properties of sillimanite. The geometrical parameters of the unit cell, which contain 32 atoms, have been fully optimized and are in good agreement with the experimental data. The electronic structure shows that sillimanite has an indirect band gap of 5.18 eV. The complex dielectric function and optical constants, such as extinction coefficient, refractive index, reflectivity and energy-loss spectrum, are calculated. The optical properties of sillimanite are discussed based on the band structure calculations. It is shown that the O-2p states and Al-3s, Si-3s states play the major role in optical transitions as initial and final states, respectively. (C) 2011 Elsevier B.V. All rights reserved.

Theoretical investigation of electronic and optical properties of andalusite within density functional theory

The electronic and optical properties of andalusite were studied by using quantum-mechanical calculations based on the density functional theory (DFT). The electronic structure shows that andalusite has a direct band gap of 5.01 eV. The complex dielectric function and optical constants, such as extinction coefficient, refractive index, reflectivity and energy-loss spectrum, are calculated. The optical properties of andalusite are discussed based on the band structure calculations. It is shown that the O-2p states and Al-3s states play a major role in optical transitions as initial and final states, respectively. (C) 2010 Elsevier Ltd. All rights reserved.

Electronic and optical properties of grossular garnet (Ca(3)Al(2)Si(3)O(12)): An ab initio study

The electronic and optical properties of grossular garnet are investigated using density functional theory (DFT) within generalized gradient approximation (GGA). The calculated lattice parameters are in good agreement with the experiment data. The electronic structure shows that grossular has a direct band gap of 5.22 eV. The dielectric functions, reflective index, extinction coefficient, reflectivity and energy-loss spectrum are calculated. The optical properties of grossular are discussed based on the band structure calculations. The O 2p states and Si 3s play a major role in these optical transitions as initial and final states, respectively. The absorption spectrum is localized in the ultraviolet range between 30 and 250 nm. Finally, we concluded that pure grossular crystal does not absorb radiation in the visible range. (c) 2009 Elsevier B.V. All rights reserved.

The electronic and optical properties of sodalite (Na(8)Al(6)Si(6)O(24)Cl(2)) from first principles

This study reports the results of ab initio electronic and optical calculations for pure socialite crystal using the linear augmented plane wave (LAPW) method within density functional theory (DFT). The calculated electronic structure revealed predominantly orbital characters of the valence band and the conduction band, and enabled us to determine the type and the value of the fundamental gap of the compound. The imaginary part of the dielectric tensor, extinction coefficient and refraction index were calculated as functions of the incident radiation wavelength. It is shown that the O 2p states and Na 3s states play the major role in optical transitions as initial and final states, respectively. The absorption spectrum is localized in the ultraviolet range between 40 and 250 nm. Furthermore, we concluded that the material does not absorb radiation in the visible range. (C) 2009 Elsevier Ltd. All rights reserved.

Analyzing Ru(III)-dmso and Ru(III)-dms motifs in compounds used in the synthesis of the antimetastatic agents

The chemistry of Ru(III) complexes containing dmso as a ligand has become an interesting area in the cancer treatment field. Because of this, structural knowledge and chemistry of the moiety Ru(III)-dmso have become important to cancer research. The crystal structures of the compounds mer-[RuCl(3)(dms)(3)] (1) and mer-[RuCl(3)(dms)(2)(dmso)]:mer-[RuCl(3)(dms)(3)] (2) were determined by X-ray crystallography and a speciation of the presence of intramolecular hydrogen bond in these structures has been studied. Compound (1) crystallizes in the orthorhombic space group, Pna2(1); a = 16.591(8) angstrom, b = 8.724(2) angstrom. c = 10.547(3) angstrom; Z = 12 and (2) crystallizes in the space group, P2(1)/C: a = 11.9930(2) angstrom, b = 7.9390(2) angstrom, c = 15.8700(3) angstrom, beta = 93.266(1)degrees, Z = 2. From the X-ray structures solved in this work, were possible to suggest an interpretation for the broad lines observed in the EPR spectra of the Ru(III) compounds explored here. Also, the exchange interactions detected by EPR spectroscopy in solid state and in solution, confirm the presence of van der Waals interactions such as C-H center dot center dot center dot Cl in the compounds (1), (2) and (3). The use of techniques such as IR, UV-vis, (1)H NMR and EPR Spectroscopy and Cyclic Voltammetry were applied in this work to analyze the behavior of these metallocompounds. (c) 2008 Elsevier B.V. All rights reserved.

Lead and aluminum bonding in Pb-Al metaphosphate glasses

The bonding properties of cations in phosphate glasses determine many short- and medium-range structural features in the glass network, hence influencing bulk properties. In this work, Pb-Al-metaphosphate glasses (1 - x)Pb-(PO(3))(2)center dot xAI(PO(3))(3) with 0 <= - x <= 1 were analyzed to determine the effect of the substitution of Pb by Al on the glass structure in the metaphosphate composition. The glass transition temperature and density were measured as a function of the Al concentration. The vibrational and structural properties were probed by Raman spectroscopy and nuclear magnetic resonance of (31)P, (27)Al, and (207)Pb. Aluminum incorporates homogeneously in the glass creating a stiffer and less packed network. The average coordination number for Al decreases from 5.9 to 5.0 as x increases from 0.1 to 1, indicating more covalent Al-O bonds. The coordination number of Pb in these glasses is greater than 8, showing an increasing ionic behavior for compositions richer in Al. A quantitative analysis of the phosphate speciation shows definite trends in the bonding of AlO(n) groups and phosphate tetrahedra. In glasses with x < 0.48, phosphate groups share preferentially only one nonbridging O corner with an AlO(n) coordination polyhedron. For x > 0.48 more than one nonbridging O can be linked to AlO(n) polyhedra. There is no corner sharing of O between AlO(n) and PbO(n) polyhedra nor between AlO(n) themselves throughout the compositional range. The PbO(n) coordination polyhedra show considerable nonbridging O sharing, with each O participating in the coordination sphere of at least two Pb. The bonding preferences determined for Al are consistent with the behavior observed in Na-Al and Ca-Al metaphosphates, indicating this may be a general behavior for ternary phosphate glasses.