The zero-inflated Conway-Maxwell-Poisson distribution: Bayesian inference, regression modeling and influence diagnostic

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic associations of visual scores with subsequent rebreeding and days to first calving in Nellore cattle

Records of Nellore animals born from 1990 to 2006 were used to estimate genetic correlations of visual scores at yearling (conformation, C; finishing precocity, P; and muscling, M) with primiparous subsequent rebreeding (SR) and days to first calving (DC), because the magnitude of these associations is still unknown. Genetic parameters were estimated by multiple-traits Bayesian analysis, using a nonlinear (threshold) animal models for visual scores and SR and a linear animal models for weaning weight (WW) and DC. WW was included in the analysis to account for the effects of sequential selection. The posterior means of heritabilities estimated for C, P, M, SR and DC were 0.24 +/- 0.01, 0.31 +/- 0.01, 0.30 +/- 0.01, 0.18 +/- 0.02 and 0.06 +/- 0.02, respectively. The posterior means of genetic correlations estimated between SR and visual scores were low and positive, with values of 0.09 +/- 0.02 (C), 0.19 +/- 0.03 (P) and 0.18 +/- 0.05 (M). on the other hand, negative genetic correlations were found between DC and C (-0.11 +/- 0.09), P (-0.19 +/- 0.09) and M (-0.16 +/- 0.09). The primiparous rebreeding trait has genetic variability in Nellore cattle. The genetic correlations between visual scores, and SR and DC were low and favourable. The genetic changes in C, P and M were 0.02, 0.03 and 0.03/year, respectively. For SR and DC, genetic trends were 0.01/year and -0.01 days/year, respectively, indicating that the increase in genetic merit for reproductive traits was small over time. Direct selection for visual scores together with female reproductive traits is recommended to increase the fertility of beef cows.

Comparison of different nonlinear functions to describe Nelore cattle growth

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estimação de parâmetros genéticos em caprinos leiteiros por meio de análise de regressão aleatória utilizando-se a Amostragem de Gibbs

Modelos de regressão aleatória foram utilizados neste estudo para estimar parâmetros genéticos da produção de leite no dia do controle (PLDC) em caprinos leiteiros da raça Alpina, por meio da metodologia Bayesiana. As estimativas geradas foram comparadas às obtidas com análise de regressão aleatória, utilizando-se o REML. As herdabilidades encontradas pela análise Bayesiana variaram de 0,18 a 0,37, enquanto, pelo REML, variaram de 0,09 a 0,32. As correlações genéticas entre dias de controle próximos se aproximaram da unidade, decrescendo gradualmente conforme a distância entre os dias de controle aumentou. Os resultados obtidos indicam que: a estrutura de covariâncias da PLDC em caprinos ao longo da lactação pode ser modelada adequadamente por meio da regressão aleatória; a predição de ganhos genéticos e a seleção de animais geneticamente superiores é viável ao longo de toda a trajetória da lactação; os resultados gerados pelas análises de regressão aleatória utilizando-se a Amostragem de Gibbs e o REML foram semelhantes, embora as estimativas das variâncias genéticas e das herdabilidades tenham sido levemente superiores na análise Bayesiana, utilizando-se a Amostragem de Gibbs.

Phylogeny of Triatoma sherlocki (Hemiptera: Reduviidae: Triatominae) Inferred from Two Mitochondrial Genes Suggests Its Location Within the Triatoma brasiliensis Complex

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

Population genetic relationships between Casearia sylvestris (Salicaceae) varieties occurring sympatrically and allopatrically in different ecosystems in south-east Brazil

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

Molecular systematics of the armored neotropical catfish subfamily Neoplecostominae (Siluriformes: Loricariidae)

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

Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal

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

Molecular tools and analytical approaches for the characterization of farm animal genetic diversity

Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation.

Segmentação de dados de perfilamento a laser em áreas urbanas utilizando uma abordagem Bayesiana

In this paper is presented a region-based methodology for Digital Elevation Model segmentation obtained from laser scanning data. The methodology is based on two sequential techniques, i.e., a recursive splitting technique using the quad tree structure followed by a region merging technique using the Markov Random Field model. The recursive splitting technique starts splitting the Digital Elevation Model into homogeneous regions. However, due to slight height differences in the Digital Elevation Model, region fragmentation can be relatively high. In order to minimize the fragmentation, a region merging technique based on the Markov Random Field model is applied to the previously segmented data. The resulting regions are firstly structured by using the so-called Region Adjacency Graph. Each node of the Region Adjacency Graph represents a region of the Digital Elevation Model segmented and two nodes have connectivity between them if corresponding regions share a common boundary. Next it is assumed that the random variable related to each node, follows the Markov Random Field model. This hypothesis allows the derivation of the posteriori probability distribution function whose solution is obtained by the Maximum a Posteriori estimation. Regions presenting high probability of similarity are merged. Experiments carried out with laser scanning data showed that the methodology allows to separate the objects in the Digital Elevation Model with a low amount of fragmentation.

Reinforcing and expanding the predictions of the disturbance vicariance hypothesis in Amazonian harlequin frogs: A molecular phylogenetic and climate envelope modelling approach

The disturbance vicariance hypothesis (DV) has been proposed to explain speciation in Amazonia, especially its edge regions, e. g. in eastern Guiana Shield harlequin frogs (Atelopus) which are suggested to have derived from a cool-adapted Andean ancestor. In concordance with DV predictions we studied that (i) these amphibians display a natural distribution gap in central Amazonia; (ii) east of this gap they constitute a monophyletic lineage which is nested within a pre-Andean/western clade; (iii) climate envelopes of Atelopus west and east of the distribution gap show some macroclimatic divergence due to a regional climate envelope shift; (iv) geographic distributions of climate envelopes of western and eastern Atelopus range into central Amazonia but with limited spatial overlap. We tested if presence and apparent absence data points of Atelopus were homogenously distributed with Ripley's K function. A molecular phylogeny (mitochondrial 16S rRNA gene) was reconstructed using Maximum Likelihood and Bayesian Inference to study if Guianan Atelopus constitute a clade nested within a larger genus phylogeny. We focused on climate envelope divergence and geographic distribution by computing climatic envelope models with MaxEnt based on macroscale bioclimatic parameters and testing them by using Schoener's index and modified Hellinger distance. We corroborated existing DV predictions and, for the first time, formulated new DV predictions aiming on species' climate envelope change. Our results suggest that cool-adapted Andean Atelopus ancestors had dispersed into the Amazon basin and further onto the eastern Guiana Shield where, under warm conditions, they were forced to change climate envelopes. © 2010 The Author(s).

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18. mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition, a statistically significant association was demonstrated between variation in cranial shape and genetic distances estimated from the mtDNA and nuclear loci. Notably, B. ephippium and B. garbeana that are predicted to be sister-species in the individual and concatenated gene trees and the BEST species tree share an evolutionary novelty, the hyperossified dorsal plate. © 2011 Elsevier Inc.

Comparação entre metodologias para avaliar a idade à primeira concepção em éguas puro-sangue inglês

In Brazil, due to the breeding season for Thoroughbred, the reproductive data are normally truncate, since the breeders try to get animals that were born at the beginning of the breeding season in order to take their competitive advantages (more developed, mature and trained animals) compared to animals born later in the same breeding season. To analyze these data suitable methods should be used. Then, this paper aims to compare three methodologies: the method of maximum restricted likelihood, using MTDFREML, bayesian analysis without censured data by software MTGSAM and bayesian analysis with censured data by software LMCD, to evaluate age at first conception in thoroughbred mares, in order to verify its impact on the choice of stallions during selection. The database contained 3509 records for age at first conception (months) for thoroughbred mares. The heritability estimates were 0.23, 0.30 and 0.0926 (log scale), for MTDF, MTGSAM and LMCD, respectively. Considering all animals in the pedigree (6713), ranking correlations varied from 0.91 to 0.99. When only stallions were considered (656), those varied from 0.48 to 0.99 (considering different percentages of selected males) between evalua-tion methods. The highest changes in the general classification were observed when LMCD was compared to the other two methods. As the linear censured model is the most suitable for trait analysis with censured data, it was observed that censure information would lead to the choice of different animals during the selection process, when compared to the two other methodologies.

Modelos estocásticos com heterocedasticidade: Uma abordagem Bayesiana para os retornos do Ibovespa

Current research compares the Bayesian estimates obtained for the parameters of processes of ARCH family with normal and Student's t distributions for the conditional distribution of the return series. A non-informative prior distribution was adopted and a reparameterization of models under analysis was taken into account to map parameters' space into real space. The procedure adopts a normal prior distribution for the transformed parameters. The posterior summaries were obtained by Monte Carlo Markov Chain (MCMC) simulation methods. The methodology was evaluated by a series of Bovespa Index returns and the predictive ordinate criterion was employed to select the best adjustment model to the data. Results show that, as a rule, the proposed Bayesian approach provides satisfactory estimates and that the GARCH process with Student's t distribution adjusted better to the data.

Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.