Analysis of culling probability in dairy buffalo using survival models

In order to contribute to the genetic breeding programs of buffaloes, this study aimed to determine the influence of environmental effects on the stayability (ST) of dairy female Murrah buffalo in the herd. Data from 1016 buffaloes were used. ST was defined as the ability of the female to remain in the herd for 1, 2, 3, 4, 5 or 6 years after the first calving. Environmental effects were studied by survival analysis, adjusted to the fixed effects of farm, year and season of birth, class of first-lactation milk yield and age at first calving. The data were analyzed using the LIFEREG procedure of the SAS program that fits parametric models to failure time data (culling or ST = 0), and estimates parameters by maximum likelihood estimation. Breeding farm, year of birth and first-lactation milk yield significantly influenced (P < 0.0001) the ST to the specific ages (1 to 6 years after the first calving). Buffaloes that were older at first calving presented higher probabilities of being culled 1 year after the first calving, without any effect on culling at older ages. Buffaloes with a higher milk yield at first calving presented a lower culling probability and remained for a longer period of time in the herd. The effects of breeding farm, year of birth and first-lactation milk yield should be included in models used for the analysis of ST in buffaloes. Copyright © The Animal Consortium 2010.

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).

The Poisson-exponential lifetime distribution

In this paper we proposed a new two-parameters lifetime distribution with increasing failure rate. The new distribution arises on a latent complementary risk problem base. The properties of the proposed distribution are discussed, including a formal proof of its probability density function and explicit algebraic formulae for its reliability and failure rate functions, quantiles and moments, including the mean and variance. A simple EM-type algorithm for iteratively computing maximum likelihood estimates is presented. The Fisher information matrix is derived analytically in order to obtaining the asymptotic covariance matrix. The methodology is illustrated on a real data set. © 2010 Elsevier B.V. All rights reserved.

Test-day model for milk yield of dairy buffaloes in colombia

The test-day model is the preferred method for genetic evaluations in dairy cattle. For this study, 28372 test-day records of 1220 lactations from 1997 to 2009 were used. The (co)variance components for milk in test-day were estimated using a Uni and multiple-traits repeated animal model with the Restricted Maximum Likelihood method (REML). The Contemporary Group (herd, year, and season of parity) and the age of parity (linear and quadratic) fixed effects, and the additive genetic, permanent environmental, and residual random effects were included in the model. The heritabilities ranged between 0.06 and 0.45 during lactation. The genetic correlations were greater than 0.93. In conclusion, the test-day model is appropriate for the genetic evaluation of dairy buffaloes in Colombia.

Análise temporal do uso do solo e comparação entre os índices de vegetação ndvi e savi no município de Santa Cruz do Rio Pardo - SP usando imagens landsat-5

This work aims to analyze the land use evolution in the city of Santa Cruz do Rio Pardo - SP through supervised classification of Landsat-5 TM satellite images according to the maximum likelihood (Maxlike), as well as verifying the mapping accuracy through Kappa index, comparing NDVI and SAVI vegetation indexes in different adjustment factors for the canopy substrate and determining the vegetal coverage percentage in all methods used on 2007, May 26 th; 2009, January 7 th and 2009, April 29 th. The Maxlike classification showed several spatial changes in land use over the study period. The most appropriated vegetation indexes were NDVI and SAVI - 0,25 factor, which showed similar values of vegetal coverage percentage, but discrepant from the inferred value for Maxlike classification.

Genetic (co)variance components for ratio of lamb weight to ewe metabolic weight as an indicator of ewe efficiency

Data from a multibreed commercial flock located at Mid-West of Brazil, supported by Programa de Melhoramento Genético de Caprinos e Ovinos de Corte (GENECOC), were used to estimate genetic parameters of traits related to ewe productivity by Average Information Restricted Maximum Likelihood method applied to an animal model. The analyzed traits were litter weight at birth (LWB) and at weaning (LWW), ewe weight at weaning (EW) and ewe production efficiency, estimated by WEE=LWW/EW 0.75. The heritabilities were 0.26±0.05, 0.32±0.06, 0.37±0.03 and 0.10±0.02 for LWB, LWW, EW and WEE, respectively. Significant effects for direct heterosis were observed for LWW and EW. Recombination losses were important for EW and WEE. Genetic correlations of LWB with LWW, EW and WEE were 0.68, 0.37 and 0.15, respectively; of LWW with EW and WEE were 0.30 and 0.34, respectively; and between EW and WEE was -0.25. Even though it is a low heritability trait, WEE can be indicated as a selection criteria for improving the ewe productivity without increasing the mature weight of animals due to its genetic correlations with LWW and other traits. © 2011 Elsevier B.V.

Genetic correlations between mature cow weight and productive and reproductive traits in Nellore cattle

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

Índice de seleção bioeconômico para fêmeas de corte da raça nelore

The reproductive efficiency of Nellore females was described on the basis of sexual precocity, staying productive in the herd (NP), maternal productivity (PM) and estimated cost for maintenance (CM). The combination of these traits resulted in the bioeconomic maternal revenue index (RMat) ensures reproductive efficiency. The index estimates the return in kilograms of live weight produced per cow per year. In addition, the composition of calf weight produced was considered, adding to the PM the information on the scores of conformation, muscling and early finishing at weaning, in order to input the calf biotype. The females considered precocious had their age at first calving before 30 months. The NP was expressed by the number of calving till 53 months of age. The CM was calculated according to the estimated feed intake of dry matter. The estimated average RMat was 62.02±24.12 kg/ cow/year. Estimates of additive genetic and residual variances for RMat, using restricted maximum likelihood under a single trait animal model was equal to 195.35 and 242.96, respectively. The heritability estimated was 0.45±0.02, indicating that RMat is inheritable and can be applied in the breeding program to improve reproductive efficiency. The NP was the main component of variation for RMat. Sires selected based on RMat tended to have more efficient daughters.

Análise Genética de Características Reprodutivas Na Raça Brahman

Aiming to establish selection criteria for the Brahman cattle in Brazil, the objective of this paper was to estimate genetic and environmental parameters for birth weight (BW), gestation length (GL) and scrotal circumference at 365 (SC365), 455 (SC455) and 550 (SC 550) days of age, and relative efficiency of indirect versus direct selection for these traits. Data were obtained from 15 851 animals belonging to 16 herds in six states, enrolled in a genetic breeding program. (Co)variance and heritability coefficients and genetic and environmental correlations between traits were estimated by restricted maximum likelihood (REML) under a multi trait animal model. The model included as fixed effects the contemporary group and the age of cow at calving as a covariate (linear and quadratic), and as random the direct genetic, the permanent environmental and residual effects. For BW and GL it was also considered the maternal genetic effect as random. Estimates of direct heritabilities were 0.36, 0.29, 0.55, 0.43 and 0.40 for BW, GL, SC365, SC455 and SC550, respectively. Genetic correlations between BW and GL, GL and SC365, GL and SC455, GL and SC550, SC365 and SC455, SC365 and SC550 and SC455 and SC550, were respectively 0.06, 0.13, 0.20, 0.13, 0.96, 0.98 and 0.99. The heritabilities estimates for all traits indicated these show enough additive genetic variability to respond favorably to selection. For sexual precocity, the best option would be SC365, due to the high value of heritability and to indirect selection at this age being more efficient than direct selection for PE455.

Genetic parameters for test-day milk yield, 305-day milk yield, and lactation length in Guzerat cows

Milk production in tropical environments requires the use of crossbreeding systems including breeds well adapted to harsh conditions, but with lower productivities when compared to specialized breeds. Besides the genetic improvement for milk production, lactation lengths also need to be studied for most of these breeds. Accordingly, genetic parameters were estimated for 305-day cumulative milk yield (MY305), test-day milk yield (TDMY), and lactation length (LL) using information from the first lactations of 2816 Guzerat cows selected for milk production in 28 herds in Brazil. Contemporary groups were defined as herd, year and season of the test for TDMY, and as herd, year and season of calving for MY305 and LL. Variance components were estimated with the restricted maximum likelihood method under a multi-trait animal model. Heritabilities estimated for TDMY ranged from 0.16 to 0.24, and were 0.24 and 0.12 for MY305 and LL, respectively. Genetic correlations were high and positive, ranging from 0.51 to 0.99 among TDMY records, from 0.81 to 0.98 between each TDMY and MY305, and from 0.71 to 0.94 between each TDMY and LL. Genetic parameters obtained in this study indicated the possibility of using test-day records for the prediction of breeding values for milk yield in this population of the Guzerat breed. The use of TDMY as selection criteria would result in indirect gains in MY305 and LL. However, the highest response to selection for MY305 would be obtained by direct selection for this trait. © 2012 Elsevier B.V.

Multivariate models for correlated count data

In this study, we deal with the problem of overdispersion beyond extra zeros for a collection of counts that can be correlated. Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial distributions have been considered. First, we propose a multivariate count model in which all counts follow the same distribution and are correlated. Then we extend this model in a sense that correlated counts may follow different distributions. To accommodate correlation among counts, we have considered correlated random effects for each individual in the mean structure, thus inducing dependency among common observations to an individual. The method is applied to real data to investigate variation in food resources use in a species of marsupial in a locality of the Brazilian Cerrado biome. © 2013 Copyright Taylor and Francis Group, LLC.

Improving methods in gap ecology: Revisiting size and shape distributions using a model selection approach

Questions: We assess gap size and shape distributions, two important descriptors of the forest disturbance regime, by asking: which statistical model best describes gap size distribution; can simple geometric forms adequately describe gap shape; does gap size or shape vary with forest type, gap age or the method used for gap delimitation; and how similar are the studied forests and other tropical and temperate forests? Location: Southeastern Atlantic Forest, Brazil. Methods: Analysing over 150 gaps in two distinct forest types (seasonal and rain forests), a model selection framework was used to select appropriate probability distributions and functions to describe gap size and gap shape. The first was described using univariate probability distributions, whereas the latter was assessed based on the gap area-perimeter relationship. Comparisons of gap size and shape between sites, as well as size and age classes were then made based on the likelihood of models having different assumptions for the values of their parameters. Results: The log-normal distribution was the best descriptor of gap size distribution, independently of the forest type or gap delimitation method. Because gaps became more irregular as they increased in size, all geometric forms (triangle, rectangle and ellipse) were poor descriptors of gap shape. Only when small and large gaps (> 100 or 400m2 depending on the delimitation method) were treated separately did the rectangle and isosceles triangle become accurate predictors of gap shape. Ellipsoidal shapes were poor descriptors. At both sites, gaps were at least 50% longer than they were wide, a finding with important implications for gap microclimate (e.g. light entrance regime) and, consequently, for gap regeneration. Conclusions: In addition to more appropriate descriptions of gap size and shape, the model selection framework used here efficiently provided a means by which to compare the patterns of two different types of forest. With this framework we were able to recommend the log-normal parameters μ and σ for future comparisons of gap size distribution, and to propose possible mechanisms related to random rates of gap expansion and closure. We also showed that gap shape varied highly and that no single geometric form was able to predict the shape of all gaps, the ellipse in particular should no longer be used as a standard gap shape. © 2012 International Association for Vegetation Science.

Estimativas de parâmetros genéticos para características de crescimento em ovinos da raça somalis brasileira

The aim of this study was to estimate genetic parameters for growth traits in Somalis Brasileira hair sheep breed. The data used in this study were from the flock of Embrapa Caprinos and Ovinos, located in the city of Sobral - CE, Brazil. Data contained records of 1,120 animals in the pedigree file. The analyzed traits were birth weight (PN), weaning weight (PD), weight gain from birth to weaning (GND) and adult weight (PA). Estimates of (co)variances and genetic parameters were obtained by Derivative Free Restricted Maximum Likelihood Method (DFREML) using the MTDFREML software. The heritabilities were low to moderate in univariate analysis. The maternal heritabilities were higher than direct heritabilities. The heritabilities in multivariate analysis exceeded those in univariate analysis. The values of genetic correlations varied widely.

Parâmetros genéticos de características de carcaça e de crescimento de bovinos da raça Nelore

The objectives of this study were to estimate genetic parameters involving yearling weight (Ps), carcass weight (Pc), hip height (Ag) and the scores of conformation (C), precocity (P) and musculature (M) and carcass yield (Rd) and finishing score (Ac) in Nellore cattle in order to define criteria for selection in this breed. The data of the 20 732 animals were obtained from Agrope-cuária Jacarezinho, SP. Data were analyzed by restricted maximum likelihood using animal model multi-trait analysis, which included fixed effects of contemporary groups (animals born at the same month and slaughtered on the same day) and the covariate age at slaughter (linear) for carcass traits, and contemporary groups (animals of the same farm, age, sex and management group at weaning and yearling) and yearling age (linear) for growth and as random, the additive effects and residual effects. Estimates ranged from 0.13 (Ac and Rd) to 0.36 (Ag) for heritability and from -0.59 ± 0.62 (Rd with Ac) to 0.71 ± 0.17 (Pc with C) for genetic correlations. Selection for Pc, C, P, M, Ag or Ps may be efficient because their heritability estimates are of magnitude moderate. Selection for Ps and C can favor heavier Pc, considering their positive and high genetic correlation.

Rubber tree early selection for yield stability in time and among locations

Rubber production in the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] can be expressed differently in different environments. Thus the objective of the present study was to select productive progenies, stable and responsive in time and among locations. Thirty progenies were assessed by early yield tests at three ages and in three locations. A randomized block design was used with three replications and ten plants per plot, in 3 × 3 m spacing. The procedure of the mixed linear Reml/Blup model-restricted maximum likelihood/best non-biased linear prediction was used in the genetic statistical analyses. In all the individual analyses, the values observed for the progeny average heritability (ĥpa 2) were greater than those of the additive effect based on single individuals (ĥa 2) and within plot additive (ĥad 2). In the joint analyses in time, there was genotype × test interaction in the three locations. When 20 % of the best progenies were selected the predicted genetic gains were: Colina GG = 24.63 %, Selvíria GG = 13.63 %, and Votuporanga GG = 25.39 %. Two progenies were among the best in the analyses in the time and between locations. In the joint analysis among locations there was only genotype × location interaction in the first early test. In this test, selecting 20 %, the general predicted genetic gain was GG = 25.10 %. Identifying progenies with high and stable yield over time and among locations contributes to the efficiency of the genetic breeding program. The relative performance of the progenies varies depending of the age of early selection test. © 2013 Springer Science+Business Media Dordrecht.