Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genomic signatures of evolutionary transitions from solitary to group living

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

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.

Signatures of doubly charged Higgs in the SU(3)(L) circle times U(1)(N) model at the CERN LHC

The scalar sector of the simplest version of the 3-3-1 electroweak model is constructed with three Higgs triplets only. We show that a relation involving two of the constants of the model, two vacuum expectation values of the neutral scalars, and the mass of the doubly charged Higgs boson leads to important information concerning the signals of this scalar particle.

Comparison of selection criteria for pre-weaning growth traits of Nelore cattle

Genetic parameters were estimated for pre-weaning average daily gain (ADG) and number of days to gain 160 kg from birth to weaning (D 160) of Nelore cattle. Ranks of animals were compared for these traits. Heritability estimates were 0.17 and 0.10 for ADG (direct and maternal), and 0.14 and 0.09, for D 160 (direct and maternal). Rank correlations between expected breeding values (EBV) were 0.97 and 0.95, for direct and maternal effects, respectively. Despite similar heritability estimates and high rank correlations, results showed that changes in rank could happen when choosing the best animals according to EBV for D 160 or ADG. There were evidences that sires selected using D 160 would produce progeny that achieve a specified market weight at an earlier age and would be more uniform, since this criterion is calculated as a harmonic mean function. (C) 2003 Elsevier B.V. All rights reserved.

Results of 23 years of selection for post-weaning weight in a Caracu beef herd

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Experimental paracoccidioidomycosis in high and low antibody responder mice of Selection IV-A

High (H) and low (L) responder mice were selected for their ability to produce antibodies against sheep and human erythrocytes (Selection IV-A). In this selection, the difference in antibody responsiveness between H and L lines (HIV-A and LIV-A mice, respectively) was shown to depend mainly on macrophage function. The more rapid catabolism of antigens by macrophages in L mice has been suggested as the main cause of the low antibody production. Due to this high macrophage activity, L animals have been described as more resistant than H animals to intracellular pathogens. These animals were utilized as an experimental model of paracoccidioidomycosis. HIV-A and LIV-A mice were infected with Paracoccidioides brasiliensis by the intravenous route. As expected, H mice were more susceptible to P. brasiliensis with a shorter survival time and higher levels of specific antibodies when compared to L mice. Contrasting with the survival time, the lungs, spleen and liver from H mice showed typical nodular granulomas containing epithelioid and giant cells and few fungi. on the other hand, in LN-A mice, the lesions of these organs were characterized by looser granulomas with irregular borders and the presence of a large number of fungi, However, the adrenal gland showed different lesion patterns. In H mice these lesions were extensive and characterized by loose granulomas with numerous fungi, while in LIV-A mice the lesions were small and limited to the cortex. Moreover the HIV-A mice presented higher levels of serum corticosterone when compared to LIV-A ones. The higher susceptibility of H mice could be attributed to the extensive lesions of the adrenal glands. These results suggest the use of the H line from the IV-A Selection as an experimental model for further studies of adrenal involvement in paracoccidioidomycosis.

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

kDNA gene signatures of Trypanosoma cruzi in blood and oesophageal mucosa from chronic chagasic patients

Trypanosoma cruzi presents a high degree of intraspecific variability, with possible implications for the pathogenesis of Chagas disease. The aim of this study was to evaluate T cruzi kDNA minicircle gene signatures using the low-stringency single-specific-primer PCR technique in both peripheral blood and oesophageal. mucosa from chronic chagasic patients, with or without megaesophagus, atone or in combination with cardiopathy and megacolon. It was not possible to identify a uniform pattern of shared bands between blood and oesophageal mucosa samples from individuals with the same clinical. form or mixed forms, suggesting multiple T. cruzi infections with differential tissue tropism. Thus, the results indicate that there is an intense intraspecific variability in the hypervariable regions of T cruzi kDNA, which has so far made it impossible to correlate the genetic profile of this structure with the clinical manifestations of Chagas disease. (C) 2008 Royal. Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. AIL rights reserved.

Search for Signatures of Extra Dimensions in the Diphoton Mass Spectrum at the Large Hadron Collider

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Signatures of primordial non-Gaussianities in the matter power-spectrum and bispectrum: the time-RG approach

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

The effect of hydrothermal alteration on the Sr and Nd isotopic signatures of the Barra do Itapirapua Carbonatite, Southern Brazil

The Cretaceous Barra do Itapirapua carbonatite in southern Brazil experienced extensive postmagmatic hydrothermal alteration. In this article, Sr and Nd isotope ratios of coexisting samples of hydrothermally overprinted and of preserved, nonoverprinted carbonatite are presented. Hydrothermal alteration caused strong REE enrichment, leading to the formation of minerals of the bastnaesite group. In the overprinted carbonatite, Nd contents reach 4000 ppm, two orders of magnitude higher than in the fresh carbonatite, but epsilon(Nd) varies only within a range of 3.4 units. In contrast, Sr was leached from the carbonatite during the postmagmatic alteration; hence values of around 10,000 ppm in the fresh carbonatite drop to about 1000 ppm in the overprinted samples. Leaching is accompanied by a variation of Sr isotopic composition toward more radiogenic values, resulting in an increase of 15 units in epsilon(Sr). Variation of Sr isotopic composition is related to postmagmatic alteration and is decoupled from the variation of Nd isotopic composition, ruling out heterogeneities in the mantle source as the main cause of isotopic variability in the data set. Furthermore, this cannot be explained by bulk crustal contamination. A two-step model is proposed in which (1) a REE-rich, carbonatite-derived hydrothermal fluid overprinted the pristine carbonatite, causing REE-enrichment with a relative small change of isotopic composition; and (2) crust-derived hydrothermal fluids percolated the cooling carbonatite, leaching the original Sr from the carbonatite and introducing a more radiogenic Sr isotopic signature. The amounts of carbonatite-derived Nd with primitive, carbonatite-like Nd isotope ratios introduced during the first stage of hydrothermal alteration are high enough to buffer the effect of crust-derived Nd on the Nd isotopic composition of the overprinted carbonatite.

Signatures of spontaneous breaking of R-parity in gluino cascade decays at LHC

We study the pattern of gluino cascade decays in a class of supersymmetric models where R-parity is spontaneously broken. We give a detailed discussion of the R-parity violating decays of the lightest neutralino, the second lightest neutralino and the lightest chargino. The multi-lepton and same-sign dilepton signal rates expected in these models are compared with those predicted in the Minimal Supersymmetric Standard Model. We show that these rates can be substantially enhanced in broken R-parity models. © 1997 Elsevier Science B.V.

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse. © 2013 Petersen et al.

Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle

The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (BTA) 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA), haplotype analysis, signatures of selection, runs of homozygosity (ROH), and identity by state (IBS) calculations were used to identify a 0.8 Mb (37.7-38.5 Mb) consensus region for the SLICK locus on BTA20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principal component analysis (PCA) and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.