Phylogenetic relationships among genera Eucalyptus and Corymbia species based on rnDNA internal transcribed spacers sequences

Phylogenetio relationships between Eucalyptus species, subgenus Symphyomyrtus (sections Adnataria, Exsertaria, Maldenaria, and Transversaria), and Corymbia species (sections Politaria and Ocharia) were established based on the sequence of Internal transcribed rDNA spacers (ITS1 and ITS2). The species analyzed were obtained from a collection kept in Brazil. Fragments obtained using primers ITS1 and ITS2 were sequenced and part of the sequence of ITS1 and ITS2 and the complete sequence of 5.8S rDNA were used in the analysis. ITSs and 5.8S rDNA sequences from E. globulus ssp. globulus and A. bakeri (Genus Angophora) were downloaded from the Genbank database and included in the analysis. Psidlum guajava was the selected outgroup used. The sequence alignment and a Neighbor-joining tree were obtained using Clustal X. Few variations were detected in the 5.8S rDNA sequences obtained, occurring mainly between Eucalyptus and Corymbia, thus defining these genera. Variations in ITS sequences occurred in all investigated species. Phylogenetic analysis showed a clear separation between the genera Corymbia and Eucalyptus. A bakeri was more closely related to species belonging to genus Corymbia. Regarding the subgenus Symphyomyrtus (Genus Eucalyptus), only species from section Maidenaria grouped together according to their common section. This could have been caused by the removal of natural reproductive barriers when these species were introduced In Brazil, with a consequent Increase in the rate of interspecific crossings and Introgression events.

Phylogeography of Hypostomus strigaticeps (Siluriformes: Loricariidae) inferred by mitochondrial DNA reveals its distribution in the upper Paraná River basin

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural and Phylogenetic Studies with MjTX-I Reveal a Multi-Oligomeric Toxin - a Novel Feature in Lys49-PLA2s Protein Class

The mortality caused by snakebites is more damaging than many tropical diseases, such as dengue haemorrhagic fever, cholera, leishmaniasis, schistosomiasis and Chagas disease. For this reason, snakebite envenoming adversely affects health services of tropical and subtropical countries and is recognized as a neglected disease by the World Health Organization. One of the main components of snake venoms is the Lys49-phospholipases A2, which is catalytically inactive but possesses other toxic and pharmacological activities. Preliminary studies with MjTX-I from Bothrops moojeni snake venom revealed intriguing new structural and functional characteristics compared to other bothropic Lys49-PLA2s. We present in this article a comprehensive study with MjTX-I using several techniques, including crystallography, small angle X-ray scattering, analytical size-exclusion chromatography, dynamic light scattering, myographic studies, bioinformatics and molecular phylogenetic analyses.Based in all these experiments we demonstrated that MjTX-I is probably a unique Lys49-PLA2, which may adopt different oligomeric forms depending on the physical-chemical environment. Furthermore, we showed that its myotoxic activity is dramatically low compared to other Lys49-PLA2s, probably due to the novel oligomeric conformations and important mutations in the C-terminal region of the protein. The phylogenetic analysis also showed that this toxin is clearly distinct from other bothropic Lys49-PLA2s, in conformity with the peculiar oligomeric characteristics of MjTX-I and possible emergence of new functionalities inresponse to environmental changes and adaptation to new preys. © 2013 Salvador et al.

An assessment approach for application of spermatic data in phylogenetic analyses: Within the genus Moenkhausia Eigenmann, 1903 (Characiformes: Characidae)

Spermiogenesis and sperm ultrastructure from 21 species of Moenkhausia and others related genera are described. To evaluate the phylogenetic signals, 18 unordered characters were utilized in implied weighting analysis through the program TNT 1.1. Four variations of spermiogenesis were found. In the earliest spermatids, the nucleus can be positioned lateral, eccentric, strongly eccentric or nearly medial in relation to the distal centriole. The nuclear rotation can be present or absent. These spermiogenesis processes are related or intermediate to Type I and Type III. Taking into account the degrees of nuclear rotation during the spermiogenesis and other characteristics, distinct forms of spermatozoa are observed among the species analyzed. The phylogenetic analysis yielded a single most parsimonious tree with fit value 2.70000 and the topology obtained founds Moenkhausia as non-monophyletic. However, some hypothesis of relationships previously proposed viz the clade 20, which contains the type species Moenkhausia xinguensis, is recovered herein. This clade is supported by five synapomorphies, and it allows the supposition that these species constitute a monophyletic group. The whole topology is presented and discussed. © 2012 The Authors. Acta Zoologica © 2012 The Royal Swedish Academy of Sciences.

Description and phylogenetic relationships of a new species of treefrog of the Dendropsophus leucophyllatus group (Anura: Hylidae) from the Amazon basin of Colombia and with an exceptional color pattern

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A Bayesian view of the Higgs sector with higher dimensional operators

We investigate the possibilities of New Physics affecting the Standard Model (SM) Higgs sector. An effective Lagrangian with dimension-six operators is used to capture the effect of New Physics. We carry out a global Bayesian inference analysis, considering the recent LHC data set including all available correlations, as well as results from Tevatron. Trilinear gauge boson couplings and electroweak precision observables are also taken into account. The case of weak bosons tensorial couplings is closely examined and NLO QCD corrections are taken into account in the deviations we predict. We consider two scenarios, one where the coefficients of all the dimension-six operators are essentially unconstrained, and one where a certain subset is loop suppressed. In both scenarios, we find that large deviations from some of the SM Higgs couplings can still be present, assuming New Physics arising at 3 TeV. In particular, we find that a significantly reduced coupling of the Higgs to the top quark is possible and slightly favored by searches on Higgs production in association with top quark pairs. The total width of the Higgs boson is only weakly constrained and can vary between 0.7 and 2.7 times the Standard Model value within 95% Bayesian credible interval (BCI). We also observe sizeable effects induced by New Physics contributions to tensorial couplings. In particular, the Higgs boson decay width into Zγ can be enhanced by up to a factor 12 within 95% BCI. © 2013 SISSA.

Analysis of inteins in the Candida parapsilosis complex for simple and accurate species identification

Inteins are coding sequences that are transcribed and translated with flanking sequences and then are excised by an autocatalytic process. There are two types of inteins in fungi, mini-inteins and full-length inteins, both of which present a splicing domain containing well-conserved amino acid sequences. Full-length inteins also present a homing endonuclease domain that makes the intein a mobile genetic element. These parasitic genetic elements are located in highly conserved genes and may allow for the differentiation of closely related species of the Candida parapsilosis (psilosis) complex. The correct identification of the three psilosis complex species C. parapsilosis, Candida metapsilosis, and Candida orthopsilosis is very important in the clinical setting for improving antifungal therapy and patient care. In this work, we analyzed inteins that are present in the vacuolar ATPase gene VMA and in the threonyl-tRNA synthetase gene ThrRS in 85 strains of the Candida psilosis complex (46 C. parapsilosis, 17 C. metapsilosis, and 22 C. orthopsilosis). Here, we describe an accessible and accurate technique based on a single PCR that is able to differentiate the psilosis complex based on the VMA intein. Although the ThrRS intein does not distinguish the three species of the psilosis complex by PCR product size, it can differentiate them by sequencing and phylogenetic analysis. Furthermore, this intein is unusually present as both mini- and full-length forms in C. orthopsilosis. Additional population studies should be performed to address whether this represents a common intraspecific variability or the presence of subspecies within C. orthopsilosis. Copyright © 2013, American Society for Microbiology. All Rights Reserved.

Análise das relações filogenéticas entre espécies da subfamília Bryconinae (Ostariophysi: Characiformes: Characidae) utiliando sequeências de DNA mitocrondrial e nuclear

Pós-graduação em Ciências Biológicas (Zoologia) - IBB

Cryptic Genetic Diversity Is Paramount in Small-Bodied Amphibians of the Genus Euparkerella (Anura: Craugastoridae) Endemic to the Brazilian Atlantic Forest

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic Parameters for Reproductive Traits of Crossbred Buffaloes from Brazil, Estimated by Bayesian Inference

The objective of the study was to estimate heritability for calving interval (CI) and age at first calving (AFC) and also calculate repeatability for CI in buffaloes using Bayesian inference. The Brazilian Buffaloes Genetic Improvement Program provided the database. Data consists on information from 628 females and four different herds, born between 1980 and 2003. In order to estimate the variance, univariate analyses were performed employing Gibbs sampler procedure included in the MTGSAM software. The model for CI included the random effects direct additive and permanent environment factors, and the fixed effects of contemporary groups and calving orders. The model for AFC included the direct additive random effect and contemporary groups as a fixed effect. The convergence diagnosis was obtained using Geweke that was implemented through the Bayesian Output Analysis package in R software. The estimated averages were 433.2 days and 36.7months for CI and AFC, respectively. The means, medians and modes for the calculated heritability coefficients were similar. The heritability coefficients were 0.10 and 0.42 for CI and AFC respectively, with a posteriori marginal density that follows a normal distribution for both traits. The repeatability for CI was 0.13. The low heritability estimated for CI indicates that the variation in this trait is, to a large extent, influenced by environmental factors such as herd management policies. The age at first calving has clear potential for yield improvement through direct selection in these animals.

Genetic Correlation for Pre-Weaning and Post-Weaning Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

The aim of this study was to estimate genetic, environmental and phenotypic correlation between birth weight (BW) and weight at 205 days age (W205), BW and weight at 365 days age (W365) and W205-W365, using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data that included 3,883 observations from Mediterranean breed buffaloes. With the purpose to estimate variance and covariance, bivariate analyses were performed using Gibbs sampler that is included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, maternal environmental random effect and contemporary group as fixed effect. The convergence diagnosis was achieved using Geweke, a method that uses an algorithm implemented in R software through the package Bayesian Output Analysis. The calculated direct genetic correlations were 0.34 (BW-W205), 0.25 (BW-W365) and 0.74 (W205-W365). The environmental correlations were 0.12, 0.11 and 0.72 between BW-W205, BW-W365 and W205-W365, respectively. The phenotypic correlations were low for BW-W205 (0.01) and BW-W365 (0.04), differently than the obtained for W205-W365 with a value of 0.67. The results indicate that BW trait have low genetic, environmental and phenotypic association with the two others traits. The genetic correlation between W205 and W365 was high and suggests that the selection for weight at around 205 days could be beneficial to accelerate the genetic gain.

Genetic Parameters for Growth Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

Quantitative analysis of growth genetic parameters is not available for many breeds of buffaloes making selection and breeding decisions an empirical process that lacks robustness. The objective of this study was to estimate heritability for birth weight (BW), weight at 205 days (W205) and 365 days (W365) of age using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data. For the traits BW, W205 and W365 of Brazilian Mediterranean buffaloes 5169, 3792 and 3883 observations have been employed for the analysis, respectively. In order to obtain the estimates of variance, univariate analyses were conducted using the Gibbs sampler included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, random maternal permanent environmental effect and contemporary group that was treated as a fixed effect. The convergence diagnosis was performed employing Geweke, a method that uses an algorithm from the Bayesian Output Analysis package that was implemented using R software environment. The average values for weight traits were 37.6 +/- 4.7 kg for BW, 192.7 +/- 40.3 kg for W205 and 298.6 +/- 67.4 kg for W365. The heritability posterior distributions for direct and maternal effects were symmetric and close to those expected in a normal distribution. Direct heritability estimates obtained using the modes were 0.30 (BW), 0.52 (W205) and 0.54 (W365). The maternal heritability coefficient estimates were 0.31, 0.19 and 0.21 for BW, W205 and W365, respectively. Our data suggests that all growth traits and mainly W205 and W365, have clear potential for yield improvement through direct genetic selection.

Genetic Parameters for Milk Yield and Lactation Length of Crossbred Buffaloes from Brazil by Bayesian Inference

The objective of the study was to estimate heritability and repeatability for milk yield (MY) and lactation length (LL) in buffaloes using Bayesian inference. The Brazilian genetic improvement program of buffalo provided the data that included 628 females, from four herds, born between 1980 and 2003. In order to obtain the estimates of variance, univariate analyses were performed with the Gibbs sampler, using the MTGSAM software. The model for MY and LL included direct genetic additive and permanent environment as random effects, and contemporary groups, milking frequency and calving number as fixed effects. The convergence diagnosis was performed with the Geweke method using an algorithm implemented in R software through the package Bayesian Output Analysis. Average for milk yield and lactation length was 1,546.1 +/- 483.8 kg and 252.3 +/- 42.5 days, respectively. The heritability coefficients were 0.31 (mode), 0.35 (mean) and 0.34 (median) for MY and 0.11 (mode), 0.10 (mean) and 0.10 (median) for LL. The repeatability coefficient (mode) were 0.50 and 0.15 for MY and LL, respectively. Milk yield is the only trait with clear potential for genetic improvement by direct genetic selection. The repeatability for MY indicates that selection based on the first lactation could contribute for an improvement in this trait.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Background: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

Molecular and phylogenetic characterization based on the complete genome of a virulent pathotype of Newcastle disease virus isolated in the 1970s in Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)