Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA

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

The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless, our results argue against the indiscriminate use of molecular clock rates in evolutionary research and advocate the verification of the appropriateness of the traditional clock rate by means of independent calibrations in individual studies. (C) 2009 Elsevier Inc. All rights reserved.

Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales

Broad-scale phylogenetic analyses of the angiosperms and of the Asteridae have failed to confidently resolve relationships among the major lineages of the campanulid Asteridae (i.e., the euasterid II of APG II, 2003). To address this problem we assembled presently available sequences for a core set of 50 taxa, representing the diversity of the four largest lineages (Apiales, Aquifoliales, Asterales, Dipsacales) as well as the smaller ""unplaced"" groups (e.g., Bruniaceae, Paracryphiaceae, Columelliaceae). We constructed four data matrices for phylogenetic analysis: a chloroplast coding matrix (atpB, matK, ndhF, rbcL), a chloroplast non-coding matrix (rps16 intron, trnT-F region, trnV-atpE IGS), a combined chloroplast dataset (all seven chloroplast regions), and a combined genome matrix (seven chloroplast regions plus 18S and 26S rDNA). Bayesian analyses of these datasets using mixed substitution models produced often well-resolved and supported trees. Consistent with more weakly supported results from previous studies, our analyses support the monophyly of the four major clades and the relationships among them. Most importantly, Asterales are inferred to be sister to a clade containing Apiales and Dipsacales. Paracryphiaceae is consistently placed sister to the Dipsacales. However, the exact relationships of Bruniaceae, Columelliaceae, and an Escallonia clade depended upon the dataset. Areas of poor resolution in combined analyses may be partly explained by conflict between the coding and non-coding data partitions. We discuss the implications of these results for our understanding of campanulid phylogeny and evolution, paying special attention to how our findings bear on character evolution and biogeography in Dipsacales.

Contributions to the taxonomy of the Normanellidae (Copepoda, Harpacticoida): description of a new genus from the Brazilian continental shelf and re-assignment of Pseudocletodes vararensis Scott & Scott, 1893 (ex Nannopodidae)

A new genus and species of Normanellidae (Copepoda, Harpacticoida), Paranaiara inajae gen. et sp. nov., is described from the continental shelf off the northern coast of Sao Paulo State, Brazil. The new genus differs from the type genus Normanella Brady, 1880 and Sagamiella Lee & Huys, 1999 in its presence of lamelliform caudal rami, a maxillulary endopod represented by 2 setae, an unarmed maxillipedal syncoxa, and reduced setation on P2 enp-2 (without outer spine) and P3 enp-2 (with only 2 inner setae). All these apomorphic character states are shared with the genus Pseudocletodes Scott & Scott, 1893, formerly placed in the family Nannopodidae (ex Huntemanniidae) and here assigned to the Normanellidae. Pseudocletodes can be differentiated from Paranaiara by the loss of the P1 endopod and of the inner seta on P2-P4 enp-1, the presence of only 2 inner setae on P2 enp-2 (instead of 3) and only 1 inner seta on P4 exp-3 (instead of 2), the presence of a second inner seta on P4 enp-2 (instead of 1), the morphology of the fifth pair of legs which are not medially fused and have only 3 endopodal elements (instead of 4) in the male, and the well developed caudal ramus seta V (instead of rudimentary). It is postulated that prehensility of the P1 endopod was secondarily lost in the common ancestor of Paranaiara and Pseudocletodes. An updated family diagnosis of the Normanellidae and a dichotomous identification key to the 22 currently valid species are presented.

Selectivity in the mechanism of action of antimicrobial mastoparan peptide Polybia-MP1

Many potent antimicrobial peptides also present hemolytic activity, an undesired collateral effect for the therapeutic application. Unlike other mastoparan peptides, Polybia-MP1 (IDWKKLLDAAKQIL), obtained from the venom of the social wasp Polybia paulista, is highly selective of bacterial cells. The study of its mechanism of action demonstrated that it permeates vesicles at a greater rate of leakage on the anionic over the zwitterionic, impaired by the presence of cholesterol or cardiolipin; its lytic activity is characterized by a threshold peptide to lipid molar ratio that depends on the phospholipid composition of the vesicles. At these particular threshold concentrations, the apparent average pore number is distinctive between anionic and zwitterionic vesicles, suggesting that pores are similarly formed depending on the ionic character of the bilayer. To prospect the molecular reasons for the strengthened selectivity in Polybia-MP1 and its absence in Mastoparan-X, MD simulations were carried out. Both peptides presented amphipathic alpha-helical structures, as previously observed in Circular Dichroism spectra, with important differences in the extension and stability of the helix; their backbone solvation analysis also indicate a different profile, suggesting that the selectivity of Polybia-MP1 is a consequence of the distribution of the charged and polar residues along the peptide helix, and on how the solvent molecules orient themselves according to these electrostatic interactions. We suggest that the lack of hemolytic activity of Polybia-MP1 is due to the presence and position of Asp residues that enable the equilibrium of electrostatic interactions and favor the preference for the more hydrophilic environment.

The onset of flood basalt volcanism, Northern Parana Basin, Brazil: A precise U-Pb baddeleyite/zircon age for a Chapeco-type dacite

We report the first U-Pb baddeleyite/zircon date for a felsic volcanic rock from the Parana Large Igneous Province in south Brazil. The new date of 134.3 +/- 0.8 Ma for a hypocrystalline Chapeco-type dacite from Ourinhos (northern Parana basin) is an important regional time marker for the onset of flood basalt volcanism in the northern and western portion of the province. The dated dacite was erupted onto basement rocks and is overlain by a high-Ti basalt sequence, interpreted to be correlative with Pitanga basalts elsewhere. This new U-Pb date for the Ourinhos dacite is consistent with the local stratigraphy being slightly older than the few reliable step-heating (40)Ar/(39)Ar dates currently available for overlying high-Ti basalts (133.6-131.5 Ma). This indicates an similar to 3 Ma time span for the building of the voluminous high-Ti lava sequence of the Parana basin. On the other hand, it overlaps the (40)Ar/(39)Ar dates (134.8-134.1 Ma) available for the stratigraphically older low-Ti basalt (Gramado + Esmeralda types) and dacite-rhyolite (Palmas type) sequences from South Brazil, which is consistent with the short-lived character of this volcanism and its rapid succession by the high-Ti sequence. (C) 2010 Elsevier B.V. All rights reserved.

ON THE SUPERCRITICALITY OF THE FIRST HOPF BIFURCATION IN A DELAY BOUNDARY PROBLEM

The goal of this paper is to analyze the character of the first Hopf bifurcation (subcritical versus supercritical) that appears in a one-dimensional reaction-diffusion equation with nonlinear boundary conditions of logistic type with delay. We showed in the previous work [Arrieta et al., 2010] that if the delay is small, the unique non-negative equilibrium solution is asymptotically stable. We also showed that, as the delay increases and crosses certain critical value, this equilibrium becomes unstable and undergoes a Hopf bifurcation. This bifurcation is the first one of a cascade occurring as the delay goes to infinity. The structure of this cascade will depend on the parameters appearing in the equation. In this paper, we show that the first bifurcation that occurs is supercritical, that is, when the parameter is bigger than the delay bifurcation value, stable periodic orbits branch off from the constant equilibrium.

A three-state model for the photophysics of guanine

The nonadiabatic photochemistry of the guanine molecule (2-amino-6-oxopurine) and some of its tautomers has been studied by means of the high-level theoretical ab initio quantum chemistry methods CASSCF and CASPT2. Accurate computations, based by the first time on minimum energy reaction paths, states minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of the molecules lead to interpret the photochemistry of guanine and derivatives within a three-state model. As in the other purine DNA nucleobase, adenine, the ultrafast subpicosecond fluorescence decay measured in guanine is attributed to the barrierless character of the path leading from the initially populated (1)(pi pi* L-a) spectroscopic state of the molecule toward the low-lying methanamine-like conical intersection (gs/pi pi* L-a)(CI). On the contrary, other tautomers are shown to have a reaction energy barrier along the main relaxation profile. A second, slower decay is attributed to a path involving switches toward two other states, (1)(pi pi* L-b) and, in particular, (1)(n(o)pi*), ultimately leading to conical intersections with the ground state. A common framework for the ultrafast relaxation of the natural nucleobases is obtained in which the predominant role of a pi pi*-type state is confirmed.