Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.

Mangrove habitat partitioning by Ucides cordatus (Ucididae): Effects of the degree of tidal flooding and tree-species composition during its life cycle

Environmental factors strongly affect mangrove crabs, and some factors modulate population structure and habitat partitioning during the crabs' life cycle. However, the effect of these environmental factors on habitat selection by mangrove crabs is still unknown. We evaluated habitat selection by the mangrove crab Ucides cordatus in mangrove forests with different degrees of predominance of Rhizophora mangle, Laguncularia racemosa or Avicennia schaueriana, two tidal flooding levels (less- and more-flooded), and two biological periods (breeding and non-breeding seasons). Sampling was conducted in four mangrove forests with different influences of these biotic and abiotic parameters. We used the data for sex ratio to explain environmental partitioning by this species. Females predominated in R. mangle mangroves, independently of the biological period (breeding or non-breeding seasons), and males predominated only in the less-flooded L. racemosa mangroves. The flooding level affected the sex ratio of U. cordatus, with a predominance of males in less-flooded mangroves, independently of the biological period; and a gender balance in the more-flooded mangroves only during the breeding season. Outside the breeding season, the largest specimens were recorded in the R. mangle mangroves, but in the breeding season, the largest crabs were recorded in the L. racemosa mangroves with a higher level of flooding. These results suggest that tree-species composition and tidal flooding level can have a significant effect on the habitat partitioning of sexes and sizes of the mangrove crab U. cordatus both during and outside the breeding season. © 2012 Springer-Verlag and AWI.

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3′UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.Genes and Immunity advance online publication, 3 October 2013; doi:10.1038/gene.2013.47.

Population structure of Lutjanus purpureus (Lutjanidae - Perciformes) on the Brazilian coast: further existence evidence of a single species of red snapper in the western Atlantic

ABSTRACT: The present study focus on the mitochondrial control region to investigate phylogeographic patterns and population structure in Lutjanus purpureus, and to evaluate the genetic similarity between L. purpureus and L. campechanus. For the initial analysis, 810 base pairs sequence from control region were obtained from 239 specimens of L. purpureus collected from four localities off the Brazilian coast. The results revealed the presence of a single panmictic population characterized by high values of genetic diversity. The 299 base pairs hypervariable portion were used for the combined analysis of L. purpureus and L. campechanus, being 275 haplotypes identified in the 414 specimens. Phylogenetic tree and haplotype network did not indicate phylogeographic substructuring between the two species, but rather an intense intermingling of individuals. Considering their marked morphological similarity, the molecular data presented here indicatethat only one species of red snapper exists in the western Atlantic.

The Usefulness of the Sting Apparatus in Phylogenetic Reconstructions in Vespids, with Emphasis on the Epiponini: More Support for the Single Origin of Eusociality in the Vespidae

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

A genome-wide scan for selection signatures in Nellore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Single nucleotide polymorphisms in candidate genes associated with gastrointestinal nematode infection in goats

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

Análise de marcadores culturais no par de obras Relato de um certo oriente e The tree of the seventh heaven

This paper presents some results of a study on culturally marked terms in a corpus composed by the Brazilian novel Relato de um certo oriente (1989), by Milton Hatoum, and its translation into English The tree of the seventh heaven, by Ellen Watson. For the analysis of culturally marked terms, we followed the interdisciplinary approach proposed by Camargo (2005, 2007) involving corpus-based translation studies (BAKER, 1993, 1995, 1996, 2000), and the investigations of cultural domains (NIDA, 1945; AUBERT, 1981, 2006). The methodology adopted in the present research required the software WordSmith Tools (SCOTT, 2007), which provides the necessary resources for the collection of data in a corpus of translated texts. The software tool called WordList was used for the selection of the most frequent words in the texts and also for the identification of the culturally marked terms. For the analysis of the culturally marked terms in both texts we used the software tool Concord. The results revealed that most of the culturally marked terms are inserted in the ecological domain, and the other terms are distributed in the domains of material, social and ideological culture, which reflects the theme of the book.

Cladistic analysis of self-grooming indicates a single origin of eusociality in corbiculate bees (Hymenoptera: Apidae)

Behavioural traits have been used extensively in recent years as an important character source for making phylogenetic inferences. The phylogenetic positions of the members of the Apini subtribe are increasingly being debated, and new characters must be examined. We analysed the presence and absence of certain behavioural patterns, as well as the sequences of some of these patterns, to generate 79 characters. Eleven species comprised the ingroup, and Xylocopini comprised the outgroup. Parsimony analysis showed that the most parsimonious tree was (Euglossina(Bombina(Apina+Meliponina))). This topology is consistent with most studies that use morphological data and the few that use behavioural data, which suggests that advanced eusociality arose only once in a common ancestor of the clade Apina plus Meliponina; however, this hypothesis is inconsistent with our molecular data. Thus we considered behavioural, molecular, and morphological data and recovered the same topology, in which eusociality has a single origin in corbiculate bees.

Alterações epigenéticas e do número de cópias do gene SFN em carcinomas mamários

Pós-graduação em Ciências Biológicas (Genética) - IBB

Genetic gain in the selection by multi-effects index in open-pollinated progenies of Eucalyptus grandis Hill ex Maiden

In Brazil, Eucalyptus grandis Hill ex Maiden is widely used for commercial reforestation, especially for production of pulp, paper and energy. Its genetic variability is being explored in tree improvement programs for over 30 years. The objective of this work was to estimate genetic parameters and compare genetic gains by multi-effects index in a breeding population of E. grandis. Progeny tests were established using open-pollinated seeds from ten provenances ranging from 153 to 160 progenies established in a completely randomized block design in four sites of Sao Paulo State (Anhembi, Avere Itarare e Pratania). At 24 months of age the traits diameter at breast height (DBH), height (ALT) and volume (VOL) were measured. The individual site analyses indicated significant genetic differences among progenies, height genetic variability and the mean progeny heritability (> 0.70). For joint analyses of sites, significant differences in genotype x environmental interaction effects were detected, showing differences of performance of the progenies in different sites. The Itarare site gave high genetic gains, effective size and genetic diversity. The genetic diversity and low effective size are unviable factors; considering that the progeny tests studied should retain adequate levels of genetic variability in order to be transformed in future seedling seed orchards.

Measurement of the W boson helicity in events with a single reconstructed top quark in p p collisions at root s=8 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genomic data as the hitchhiker's guide to cattle adaptation: tracking the milestones of past selection in the bovine genome

The bovine species have witnessed and played a major role in the drastic socio-economical changes that shaped our culture over the last 10,000 years. During this journey, cattle hitchhiked on human development and colonized the world, facing strong selective pressures such as dramatic environmental changes and disease challenge. Consequently, hundreds of specialized cattle breeds emerged and spread around the globe, making up a rich spectrum of genomic resources. Their DNA still carry the scars left from adapting to this wide range of conditions, and we are now empowered with data and analytical tools to track the milestones of past selection in their genomes. In this review paper, we provide a summary of the reconstructed demographic events that shaped cattle diversity, offer a critical synthesis of popular methodologies applied to the search for signatures of selection (SS) in genomic data, and give examples of recent SS studies in cattle. Then, we outline the potential and challenges of the application of SS analysis in cattle, and discuss the future directions in this field.

Aircraft selection with DEA's triple index: an approach for sustainability

The objective of this paper is to present a benefit-cost ranking of 127 civil transport aircraft; this ranking was determined considering a new data envelopment analysis (DEA) approach, called triple index, which combines three assessment methods: 1) standard frontier, 2) inverted index; 3) cross-multiplicative index. The analysis used the following inputs: a) market price; b) direct operating costs; and as outputs: a) payload, b) cruise speed; c) maximum rate of climb with a single engine. To ensure the homogeneity of the units, the aircrafts were divided according to the propulsion system (jet and turboprop) and size (regional, narrow-body and wide-body); they were also evaluated according to different ranges in order to identify the aircraft with the best cost-benefit relationship for each option.

EC28-36 Spraying Tree Fruits (Revised March 1932)

The production of sound, clean fruit is unquestionably one of the major problems facing the modern fruit grower. Culture may be neglected and pruning delayed for a time but the omission of sprays for even a single season demonstrates their absolute necessity. This applies equally to the commercial grower and to the farmer or gardener who has only a few trees. Spray materials, equipment, management, schedules, insect pests and orchard diseases are discussed in this 1928 extension circular.