DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras.

We assessed the presence of independent evolving lineages of the trahira, Hoplias malabaricus, one of the few freshwater fish species having wide distribution in the Neotropics which is the region with the highest global diversity of freshwater fish. To achieve that goal, 58 mitochondrial sequences of cytochrome c oxidase subunit I (COI; DNA barcoding) were generated from collected samples and 85 obtained from public databases, which were analyzed in comparison to chromosomal and geological data. The magnitude of genetic diversity found among different sampling sites was greater than 2%. Molecular species delimitation methods indicated the existence of a least four distinct lineages. The recognised cytotypes did not form monophyletic groups, suggesting that the karyotypic macrostructure could be a homoplastic character. The haplotype relationships suggested secondary contacts between the ecoregions of Northern and Northeastern Brazil that were shaped by coastal routes between adjacent watersheds during the Pleistocene epoch and probable exchanges of their ichthyofaunas. Our results indicated that multiple factors have driven the diversification of H. malabaricus, from ancient geological events linked to the reactivation of tectonic faults to more recent occurrences related to eustatic changes in ocean levels. Ultimately, the magnitude of its genetic diversity suggests the necessity of revising its taxonomic status.

Random regression models for the estimation of genetic and environmental covariance functions for growth traits in Santa Ines sheep.

Polynomial functions of different orders were used to model random effects associated with weight of Santa Ines sheep from birth to 196 days. Fixed effects included in the models were contemporary groups, age of ewe at lambing, and fourth-order Legendre polynomials for age to represent the average growth curve. In the random part, functions of different orders were included to model variances associated with direct additive and maternal genetic effects and with permanent environmental effects of the animal and mother. Residual variance was fitted by a sixth-order ordinary polynomial for age. The higher the order of the functions, the better the model fit the data. According to the Akaike information criterion and likelihood ratio test, a continuous function of order, five, five, seven, and three for direct additive genetic, maternal genetic, animal permanent environmental, and maternal permanent environmental effects (k = 5573), respectively, was sufficient to model changes in (co)variances with age. However, a more parsimonious model of order three, three, five, and three (k = 3353) was suggested based on Schwarz's Bayesian information criterion for the same effects. Since it was a more flexible model, model k = 5573 provided inconsistent genetic parameter estimates when compared to the biologically expected result. Predicted breeding values obtained with models k = 3353 and k = 5573 differed, especially at young ages. Model k = 3353 adequately fit changes in variances and covariances with time, and may be used to describe changes in variances with age in the Santa Ines sheep studied.

EXPANSION OF THE SHORT SYNDROME PHENOTYPE IN AN ADULT PATIENT WITH UNILATERAL BASAL GANGLIA CALCIFICATION.

SHORT syndrome is a rare autosomal dominant disorder whose acronym stands for short stature, hyperextensibility of joints and/or hernias, ocular depression, Rieger anomaly, and teething delay. Common clinical features include intrauterine and postnatal growth restriction, lipoatrophy, characteristic facial gestalt, anterior chamber defects and insulin resistance/diabetes. To date, the coexistence of SHORT syndrome and unilateral basal ganglia calcification has not been reported. Here, we describe a 27-year-old woman bom to healthy first-cousin Mexican parents who exhibited the SHORT syndrome phenotype and unilateral basal ganglia calcification. The current observation provides additional knowledge of the spectrum of anomalies that can occur in SHORT syndrome and further illustrates the clinical variability of this disorder. Therefore, basal ganglia calcification and other brain abnormalities should be specifically looked for in all affected patients in order to provide appropriate medical management and genetic counseling.

Genetic evaluation of milk yield in Alpine goats for the first four lactations using random regression models.

Random regression models have been used in evaluating test-day milk yield, providing accurate estimates of genetic values in animals. However, herd evaluation with only information from the first lactation may not be the best option from an economic perspective. Other factors should be taken into account, particularly other lactations. Our objective in this study was to analyze the genetic divergence between the first four lactations of Alpine goats. The RENPED software was used to perform descriptive statistics, check for errors in pedigree, recode the data, and for Pearson's and Spearman's correlations. The WOMBAT software was used to estimate the variance components and predict the breeding values. The CALC software was adopted to calculate the percentage of coincidence between the ranking of the animals and the animals kept in common at each lactation evaluation. The results show that selection using only the first lactation in small herds with a low degree of technology can be employed as a palliative measure, in view of the difficulty in evaluating all lactations. However, the selection of breeding goats and the production of catalogues should not be based only on the first lactation, because the results demonstrate inversions in the classification of the best breeders when other lactations are analyzed.

Effect of three pFSH doses on superovulation and embryo quality in goats during two breeding seasons in north-eastern mexico.

The aim of this research was to evaluate the effectiveness of three pFSH doses (80 mg; 145 mg and 215 mg) on ovarian response and on quantity and quality of transferable embryos of goats during the breeding and the non-breeding seasons. Ovary structures were exposed (laparatomy under general anaesthesia) and numbers of follicles and corpora lutea were registered. Surgical embryo flushing was conducted to count and classify embryos. There were more follicles (3.4 ± 1.1) in does administered 80 mg of pFSH (p < 0.05) than in goats administered 145 mg of pFSH (2.2 ± 1.1) and 215 mg of pFSH (0.9 ± 0.6). Numbers of corpora lutea, blastocysts, and recovered and transferable embryos of goats administered 145 mg pFSH (13.4 ± 3.7, 2.42 ± 1.0, 3.4 ± 1.2 and 3.2 ± 1.1, respectively) and those of goats administered 215 mg pFSH (11.6 ± 2.6, 3.2 ± 0.9, 5.7 ± 1.5, and 5.6 ± 1.5) were greater (p < 0.05) than values obtained from goats administered 80 mg pFSH (4.0 ± 1.5, 0.5 ± 0.3, 1.0 ± 0.5, and 0.8 ± 0.5). Numbers of morula of does administered 80 and 145 mg pFSH (0.4 ± 0.4 and 0.8 ± 0.3) were lower (p < 0.05) than those obtained from animals treated with 215 mg pFSH (2.4 ± 0.9). There was no effect of season upon the analyzed variables. In conclusion, under the prevalent conditions in north-eastern Mexico, administration of 145 or 215 mg pFSH in a decreasing dose schedule over 3.5 days to bred goats provided a satisfactory superovulatory result.

Genome scan for meat quality traits in Nelore beef cattle.

Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

Molecular taxonomy and evolutionary hypothesis concerning Astyanax fasciatus (Characiformes, Characidae) from Vila Velha State Park and Tibagi and Iguaçu Rivers.

A species complex hypothesis involving Astyanax fasciatus from southern Brazil was tested using 12S mtDNA sequences. Phylogenetic inferences were performed with maximum likelihood, maximum parsimony and Bayesian as phylogenetic methods and Hemigrammus bleheri as the outgroup. Besides 11 sequences from A. fasciatus, the data set was comprised of other partial 12S sequences including material from Astyanax altiparanae (two sequences) and Astyanax sp (four sequences), both from the Iguaçu River. The hypothesis of an A. fasciatus species complex was reinforced given the close relationship between A. altiparanae and Astyanax sp observed in the Bayesian tree. Consequently, a taxonomic revision is necessary for these species.

Factors that influence the test day milk yield and composition.

The objective of this research was to study the factors that influence the test day milk yield (TDMY) and percentages of protein, fat, lactose, and total dry extract obtained on test day. We evaluated 110,732 weekly milk production records from 1496 goats and 19,271 monthly milk constituent records from 1245 Alpine and Saanen goats, which were collected from 1997 to 2010 in the goat sector at Universidade Federal de Viçosa. To ensure greater record reliability, only lactation data with kidding order between 1 to 6, type of kidding data including 0 to 3 kids, milk control years after 1997, and genetic groupings other than types 7 or 9 were considered, due to the relative lack of information recorded for some classes of these factors. Data in which the reported milk days were less than 7 or greater than 315 were also eliminated. Goats aged greater than 300 days at calving and those aged less than 6 years at control were considered in this study. Milk production was higher in the dry season in comparison to the rainy season. Genetic grouping did not influence all traits in both breedings. The TDMY tended to increase along with increasing age of the goats at kidding, while the opposite trend was observed relative to kidding order. Factors that significantly influenced all of the studied traits varied, and the factors that significantly influenced each trait were altered between the relationship of Alpine and Saanen breeds. Thus, the analysis of factors that influence traits to be evaluated in the herd under study is critical for defining the best evaluation model.

Random regression models in the evaluation of the growth curve of Simbrasil beef cattle.

Random regression models were used to estimate the types and orders of random effects of (co)variance functions in the description of the growth trajectory of the Simbrasil cattle breed. Records for 7049 animals totaling 18,677 individual weighings were submitted to 15 models from the third to the fifth order including as fixed effects sex, contemporary group, feeding regimen, and type of reproduction and as random effects additive direct genetic effect, animal permanent environment, maternal additive genetic effect, and maternal permanent environment. The best-fit model presented order five to additive direct genetic effect, animal permanent environment, and maternal additive effect, with 6 classes of residual variances, and the maternal permanent environment effect was not significant, likely owing to the low average number of calves per cow. However, the model chosen for the growth curve presents three classes of residual variances, because even not showing the best fit it is more parsimonious, in addition to promoting a more realistic estimate of heritability.

Genetic evaluation of Alpine goats using different milk control intervals.

The objective of this study was to compare the results of genetic evaluations by using different milk control intervals to reduce the cost of milk yield controls without harming the quality of genetic evaluation of the animals. We analyzed test day milk yield data from the Goat Sector of Universidade Federal de Viçosa. After editing and checking for errors in the database, there were 20,710 records of test day milk yield for the 667 first lactations of Alpine goats, constituting the complete file, with 7-day control intervals. Information on specific weeks was excluded from the complete file to create files with data on control intervals of 15, 21, and 28 days. The RENPED program was used to recode the pedigree and data files and correct pedigree errors; the WOMBAT program was used for genetic evaluations of the 4 files. The following comparison criteria of analysis results were used: logarithm of the function of the restricted maximum likelihood, length of the analyses in seconds, Pearson and Spearman correlations, and common elimination percentage among the areas below the regression curve of the genetic values of the animals. Overall, it is recommended that a 7-day interval among milk controls should be used in breeding programs and farms with a high technical level. Intervals of 14 and 21 days can achieve satisfactory results combined with a lower data collection cost for farms with an average-to-low technical level, less effective size, and genetic variability that depend on external genetic material for genetic improvement.

Genetic evaluation using multi-trait and random regression models in Simmental beef cattle.

The Brazilian Association of Simmental and Simbrasil Cattle Farmers provided 29,510 records from 10,659 Simmental beef cattle; these were used to estimate (co)variance components and genetic parameters for weights in the growth trajectory, based on multi-trait (MTM) and random regression models (RRM). The (co)variance components and genetic parameters were estimated by restricted maximum likelihood. In the MTM analysis, the likelihood ratio test was used to determine the significance of random effects included in the model and to define the most appropriate model. All random effects were significant and included in the final model. In the RRM analysis, different adjustments of polynomial orders were compared for 5 different criteria to choose the best fit model. An RRM of third order for the direct additive genetic, direct permanent environmental, maternal additive genetic, and maternal permanent environment effects was sufficient to model variance structures in the growth trajectory of the animals. The (co)variance components were generally similar in MTM and RRM. Direct heritabilities of MTM were slightly lower than RRM and varied from 0.04 to 0.42 and 0.16 to 0.45, respectively. Additive direct correlations were mostly positive and of high magnitude, being highest at closest ages. Considering the results and that pre-adjustment of the weights to standard ages is not required, RRM is recommended for genetic evaluation of Simmental beef cattle in Brazil.

Evaluation of alternative schemes for recording body weights in meat-type quails by using random regression.

Data from 8759 meat-type quails from the UFV1 strain and 9128 from the UFV2 strain were used to assess the possibility of reducing the number of body weight records in genetic evaluations. The evaluated animals were weighed weekly since hatching to the 6th week of life, with up to 7 records of body weight for each bird. The data were evaluated by random regression models, with 9 alternative schemes of data recording, which included 4 records for each scheme and their covariance functions for additive and permanent environmental effects of order 3, fitting 4 intervals for residual variance, and a complete scheme, with 7 records, order of fit 6 for additive and permanent environmental effects and 7 intervals for residual variance. Estimates of heritability for body weight at the 6th week varied from 0.45 to 0.53 for the UFV1 strain and from 0.28 to 0.54 for UFV2 strain. The schemes that had more records in points at the final extreme of the age range showed better estimates, which was likely due to certain properties of polynomial regression that led to biased results in the final extreme of the age range when data are unbalanced. The reduction of the number of body weight records taken during the growth phase is feasible, with little change to breeding value estimates, when 4 body weight records are used in random regression models.

Random regression models using Legendre orthogonal polynomials to evaluate the milk production of Alpine goats.

The objective of this study was to identify the best random regression model using Legendre orthogonal polynomials to evaluate Alpine goats genetically and to estimate the parameters for test day milk yield. On the test day, we analyzed 20,710 records of milk yield of 667 goats from the Goat Sector of the Universidade Federal de Viçosa. The evaluated models had combinations of distinct fitting orders for polynomials (2-5), random genetic (1-7), and permanent environmental (1-7) fixed curves and a number of classes for residual variance (2, 4, 5, and 6). WOMBAT software was used for all genetic analyses. A random regression model using the best Legendre orthogonal polynomial for genetic evaluation of milk yield on the test day of Alpine goats considered a fixed curve of order 4, curve of genetic additive effects of order 2, curve of permanent environmental effects of order 7, and a minimum of 5 classes of residual variance because it was the most economical model among those that were equivalent to the complete model by the likelihood ratio test. Phenotypic variance and heritability were higher at the end of the lactation period, indicating that the length of lactation has more genetic components in relation to the production peak and persistence. It is very important that the evaluation utilizes the best combination of fixed, genetic additive and permanent environmental regressions, and number of classes of heterogeneous residual variance for genetic evaluation using random regression models, thereby enhancing the precision and accuracy of the estimates of parameters and prediction of genetic values.

Habitat monitoring and genotoxicity in Ucides cordatus (Crustacea: Ucididae), as tools to manage a mangrove reserve in southeastern Brazil.

In Brazil, the state of São Paulo contains both preserved areas (Juréia-Itatins Ecological Station) and extremely impacted ones (Cubatão Municipality). This study evaluated the concentrations of five metals (Cu, Cd, Cr, Pb, and Hg) in two mangroves with different levels of anthropogenic impact and the apparent genotoxicity to Ucides cordatus. Water and sediment samples were obtained, and metal concentrations were determined with an atomic absorption spectrophotometer. The genotoxic impact was quantified based on the number of micronucleated cells per 1,000 analyzed (MN‰), using hemolymph slides stained with Giemsa. Metal concentrations in water were below the detection limit, except for lead, although no significant difference was observed between the areas (P > 0.05). Sediment from Cubatão had higher concentrations of Cd, Pb, Cr, and Cu than sediment from Juréia-Itatins (P < 0.05), but no significant differences in metal concentrations were detected among depth strata of the sediment (P > 0.05). Crabs from Cubatão had a 2.6 times higher mean frequency of micronucleated cells (5.2 ± 1.8 MN‰) than those from Juréia-Itatins (2.0 ± 1.0 MN‰; P < 0.0001). The more-polluted conditions found in the mangrove sediments of Cubatão were reflected in the micronucleus assay, demonstrating their genotoxic effect; however, genetic damage should be attributed to a synergistic effect with other kinds of pollutants previously recorded in different environments of Cubatão. U. cordatus proved to be an excellent bioindicator of mangrove pollution. This study established, for the first time, the normal frequency of MN‰ in a population of this species within an ecological station.

Physiology and production of sugar-apple under water stress and application of proline.

The objective of this study was to evaluate the physiology and production of sugar-apple as a function of irrigation intervals and foliar application of proline under the conditions of Paraíba's semi-arid region. A randomized block design was laid out in a 4 × 2 factorial scheme, with treatments resulting from the combination of four irrigation intervals (1, 4, 8 and 12 days) and two concentrations of proline (0 and 10 mM), with four replicates, and the plot consisted of four usable plants. Increase in irrigation intervals reduced the gas exchange of sugar-apple plants at 298 days after transplanting. Exogenous application of proline at concentration of 10 mM increased contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids and fruit fresh mass in plants grown under 12-day irrigation intervals.

Mineral composition and production of guava under salt stress and salicylic acid.

The limitation in the quality of water sources for irrigation in the semi-arid region of northeastern Brazil is increasingly present, so it is necessary to use water with high concentrations of salts for agricultural production, which makes the use of elicitors essential to mitigate the harmful effects of salinity on plants. Given the above, the objective of this study was to evaluate the effects of foliar application of salicylic acid on the mineral composition and production of guava plants under salt stress conditions in the post-grafting phase. The experiment was carried out under greenhouse conditions, in a randomized block design, in a 2 × 4 factorial scheme, with two levels of electrical conductivity of irrigation water (0.6 and 3.2 dS m-1) and four concentrations of salicylic acid (0, 1.2, 2.4, and 3.6 mM), with three replicates. During the flowering stage of guava, N, P, and K contents accumulated in the leaves according to the following order of concentration: N > K > P. Foliar application of 1.2 mM of salicylic acid increases the leaf contents of N, P, and K in guava plants grown under irrigation with water of 0.6 dS m-1. Water salinity of 3.2 dS m-1 reduces the growth and production components of guava plants.

Milk yield persistency in Brazilian Gyr cattle based on a random regression model.

With the objective of evaluating measures of milk yield persistency, 27,000 test-day milk yield records from 3362 first lactations of Brazilian Gyr cows that calved between 1990 and 2007 were analyzed with a random regression model. Random, additive genetic and permanent environmental effects were modeled using Legendre polynomials of order 4 and 5, respectively. Residual variance was modeled using five classes. The average lactation curve was modeled using a fourth-order Legendre polynomial. Heritability estimates for measures of persistency ranged from 0.10 to 0.25. Genetic correlations between measures of persistency and 305-day milk yield (Y305) ranged from -0.52 to 0.03. At high selection intensities for persistency measures and Y305, few animals were selected in common. As the selection intensity for the two traits decreased, a higher percentage of animals were selected in common. The average predicted breeding values for Y305 according to year of birth of the cows had a substantial annual genetic gain. In contrast, no improvement in the average persistency breeding value was observed. We conclude that selection for total milk yield during lactation does not identify bulls or cows that are genetically superior in terms of milk yield persistency. A measure of persistency represented by the sum of deviations of estimated breeding value for days 31 to 280 in relation to estimated breeding value for day 30 should be preferred in genetic evaluations of this trait in the Gyr breed, since this measure showed a medium heritability and a genetic correlation with 305-day milk yield close to zero. In addition, this measure is more adequate at the time of peak lactation, which occurs between days 25 and 30 after calving in this breed.

Genetic and environmental factors that influence production and quality of milk of Alpine and Saanen goats.

Data from 1279 lactations of 783 Alpine and Saanen goats of the herd of our university in Minas Gerais, Brazil, were used to study environmental effects on and to estimate genetic parameters for milk production until 270 days of lactation (MP270) and for production and percentages of fat (PFAT and %FAT), protein (PPROT and %PROT), lactose (PLACT and %LACT), and total dry extract (PEXTR and %EXTR). Environmental effects were estimated by a statistical model that included contemporary group effect, type of kidding, genetic grouping, and kidding order. A multi-trait animal model with animal and permanent environment random effects was used to estimate genetic parameters and the significant environmental effects (fixed). Contemporary group influenced all traits; genetic grouping did not influence %LACT; type of kidding did not influence PFAT, %PROT or %LACT, and kidding order did not influence %FAT or %EXTR. Heritability and repeatability estimates were, respectively, 0.19 and 0.37 (MP270); 0.10 and 0.20 (PFAT); 0.12 and 0.24 (PPROT); 0.15 and 0.27 (PLACT); 0.13 and 0.24 (PEXTR); 0.21 and 0.34 (%FAT); 0.39 and 0.44 (%PROT); 0.17 and 0.29 (%LACT); 0.31 and 0.47 (%EXTR). Estimates of genetic correlations among MP270 and production of milk constituents were positive and high, but correlations between MP270 and %FAT, MP270 and %PROT, MP270 and %ESTR were moderate and negative. These heritability estimates show that satisfactory genetic gains can be obtained by selection, especially for milk constituents.

Reduced genetic diversity and the success of the invasive peacock bass (Cichliformes: Cichlidae).

Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960's, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.

Estimation of genetic parameters for milk yield in Murrah buffaloes by Bayesian inference.

Random regression models were used to estimate genetic parameters for test-day milk yield in Murrah buffaloes using Bayesian inference. Data comprised 17,935 test-day milk records from 1,433 buffaloes. Twelve models were tested using different combinations of third-, fourth-, fifth-, sixth-, and seventh-order orthogonal polynomials of weeks of lactation for additive genetic and permanent environmental effects. All models included the fixed effects of contemporary group, number of daily milkings and age of cow at calving as covariate (linear and quadratic effect). In addition, residual variances were considered to be heterogeneous with 6 classes of variance. Models were selected based on the residual mean square error, weighted average of residual variance estimates, and estimates of variance components, heritabilities, correlations, eigenvalues, and eigenfunctions. Results indicated that changes in the order of fit for additive genetic and permanent environmental random effects influenced the estimation of genetic parameters. Heritability estimates ranged from 0.19 to 0.31. Genetic correlation estimates were close to unity between adjacent test-day records, but decreased gradually as the interval between test-days increased. Results from mean squared error and weighted averages of residual variance estimates suggested that a model considering sixth- and seventh-order Legendre polynomials for additive and permanent environmental effects, respectively, and 6 classes for residual variances, provided the best fit. Nevertheless, this model presented the largest degree of complexity. A more parsimonious model, with fourth- and sixth-order polynomials, respectively, for these same effects, yielded very similar genetic parameter estimates. Therefore, this last model is recommended for routine applications.