The effect of random and density‐dependent variation in sampling efficiency on variance of abundance estimates from fishery surveys

Abundance indices (AIs) provide information on population abundance and trends over time, while AI variance (AIV) provides information on reliability or quality of the AI. AIV is an important output from surveys and is commonly used in formal assessments of survey quality, in survey comparison studies, and in stock assessments. However, uncertainty in AIV estimates is poorly understood and studies on the precision and bias in survey AIV estimates are lacking. Typically, AIV estimates are “design based” and are derived from sampling theory under some aspect of randomized samples. Inference on population density in these cases can be confounded by unaccounted process errors such as those due to variable sampling efficiency (q). Here, we simulated fish distribution and surveys to assess the effect of q and variance in q on design‐based estimates of AIV. Simulation results show that the bias and precision of AIV depend on the mean q and variance in q. We conclude that to fully evaluate the reliability of AI, both observation error and variability in q must be accounted for when estimating AIV. A decrease in mean q and an increase in the variance in q results in increased bias and decreased precision in survey AIV estimates. These effects are likely small in surveys with mean q ≥ 1. However, for surveys where q ≤ 0.5, these effects can be large. Regardless of the survey type, AIV estimates can be improved with knowledge of q and variance in q.     

Adjusting for heterogeneity of variance for carcass traits affects single and multiple trait selections in genetic evaluation of Japanese Black cattle

Heterogeneity of variance among subclasses of an effect is a potential source of bias in genetic evaluation. Degrees of the heterogeneity of variance among farm‐market‐year‐sex (FMYS) subclasses for carcass weight, beef marbling standard number, rib‐eye area, rib thickness and subcutaneous fat thickness were investigated in Japanese Black cattle. Consequences of adjusting for the heterogeneity on the predicted breeding values (PBVs) or on the genetic indexes derived from the PBVs of the five carcass traits were assessed. A total of 57 461 records were collected between 1997 and 2002 from steers and heifers fattened at farms across Japan. These records were grouped into 1591 FMYS subclasses. Bartlett's test showed that the degree of the heterogeneity of variance among the FMYS subclasses was sizeable in all traits (P < 0.0001). By applying a two‐step adjustment procedure it was possible to reduce the standard deviation, the coefficient of variation and the Gini coefficient of the phenotypic variances by 67.5% to 75.0% in the different traits. The applied adjustment caused a substantial re‐ranking of elite dams in the PBV for each trait as well as in the genetic index. This study provided evidence that the applied adjustment reduces the bias in the PBVs due to heterogeneous variances and increases the accuracy of bull‐dam selection.     

Genetic parameters for semen production traits in Swiss dairy bulls

Variance components (VC) were estimated for the semen production trait ejaculate volume, sperm concentration and sperm motility in the Swiss cattle breeds Brown Swiss (BS), Original Braunvieh (OB), Holstein (HO), Red‐Factor‐Carrier (RF), Red Holstein (RH), Swiss Fleckvieh (SF) and Simmental (SI). For this purpose, semen production traits from 2,617 bulls with 124,492 records were used. The data were collected in the years 2000–2012. The model for genetic parameter estimation across all breeds included the fixed effects age of bull at collection, year of collection, month of collection, number of collection per bull and day, interval between consecutive collections, semen collector, bull breed as well as a random additive genetic component and a permanent environmental effect. The same model without a fixed breed effect was used to estimate VC and repeatabilities separately for each of the breeds BS, HO, RH, SF and SI. Estimated heritabilities across all breeds were 0.42, 0.25 and 0.09 for ejaculate volume, sperm concentration and sperm motility, respectively. Different heritabilities were estimated for ejaculate volume (0.42; 0.45; 0.49; 0.40; 0.10), sperm concentration (0.34; 0.30; 0.20; 0.07; 0.23) and number of semen portions (0.18; 0.30; 0.04; 0.14; 0.04) in BS, HO, RH, SF and SI breed, respectively. The phenotypic and genetic correlations across all breeds between ejaculate volume and sperm concentration were negative (?0.28; ?0.56). The other correlations across all breeds were positive. The phenotypic and genetic correlations were 0.01 and 0.19 between sperm motility and ejaculate volume, respectively. Between sperm motility and sperm concentration, the phenotypic and genetic correlations were 0.20 and 0.36, respectively. The results are consistent with other analyses and show that genetic improvement through selection is possible in bull semen production traits.     

The influence of topography and fire in controlling landscape composition and structure in Sierra de Gredos (Central Spain)

Mediterranean landscapes are dynamic systems that undergo temporal changes in composition and structure in response to disturbances, such as fire. Neither landscape patterns nor driving factors that affect them are evenly distributed in space. Accordingly, disturbances and biophysical factors interact in space through time. The aim of this paper is to assess the relative influence of topography and fire on the landscape patterns of a large forested area located in Sierra de Gredos (Central Spain) through time. A series of Landsat MSS images from 1975 to 1990, and a digital elevation model (DEM) were used to map fires, assess topographical complexity and evaluate changes in landscape composition and structure. Functional regions across the entire landscape were identified using different classification criteria (i.e., percentage burned area and topographic properties) to model topographic and fire impacts at regional scales. A canonical variance partition method, with a time series split-plot design, quantified the relative influence and co-variation of topography and fire on land cover patterns through time. Main results indicated that analyzing portions of the landscape under similar environmental conditions and fire histories, the effects of different fire regimes on the spatio-temporal dynamics of main land covers can be highlighted. However, the impact of fire on landscape patterns was high variable among regions due to the different regeneration abilities of main land covers, the topographic constraints and the fire histories of each region. Hence, broad patterns of fire related variance and co-variation with topography emerged across the entire area due to the different conditions of each landscape portion in which this large Mediterranean landscape was divided. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of particle size on the quality attributes of reconstituted whole-wheat flour and tortillas made from it

The objective of this study was to examine the effects of whole-wheat flour (WWF) particle size on the quality attributes of WWF tortillas. WWF samples of different particle size distributions from commercial U.S. hard white (median diameters: 175.7, 128.6, 120.0, 108.5 and 102.4 μm), hard red winter (median diameters: 173.7, 133.6, 124.3, 110.8 and 104.2 μm) and hard red spring (median diameters: 173.7, 132.1, 124.7, 112.9, 106.3 μm) wheat classes were obtained by fine grinding of bran and shorts and re-combining with the rest of fractions. For all three wheat classes, as WWF median particle size decreased, the L* (lightness) value decreased but the adjusted damaged starch, polyphenol oxidase activity, and a* and b* values increased. Mixolab data showed that development time decreased as WWF particle size was reduced, while stability time and starch retrogradation increased. As for WWF tortilla quality, the breaking force and extensibility increased with decreasing particle size from ∼175 to 129–134 μm, but diameter and thickness were not significantly affected. The results indicated that reducing the median particle sizes of WWFs from ∼175 μm to ∼130 μm would significantly improve the WWF tortilla quality.     

A mixed model analysis of 10 years of oat evaluation data: use of agronomic information to explain genotype by environment interaction

The versatility of mixed model procedures in investigating large, unbalanced sets of genotype by environment data is illustrated on an historic set of yields from a South Australian oat evaluation program. Information on specific genotypic traits is included in the analysis in order to isolate unexplained genotype by environment interaction.     

Methods for Comparing the Yield Stability of Cropping Systems

The stability of yield is an important characteristic to be considered when judging the value of a cropping system relative to others. In the context of agricultural research, the analysis of yield stability has been largely confined to multienvironment trials of crop cultivars. This review emphasizes that methods for comparing the stability of cultivars can also be used for comparing different agronomic treatments in general, of which cultivars are but a special case. Throughout the paper, different agronomic treatments are referred to as cropping systems. Some of the methods useful for stability analysis of cropping systems are discussed and a brief review of applications of these methods is given. The paper puts different stability measures into a unifying mixed model perspective.     

质量—数量性状的遗传分析 Ⅲ.受三倍体遗传控制的胚乳性状

将二倍体质量—数量性状的遗传分析方法推广应用于受三倍体遗传控制的胚乳性状。给出了加性—显性模型下有关胚乳世代的平均数和遗传方差的分量。以稻米胚乳的糊化温度（以碱扩散值表示,简记为ASV）为例演示了分析程序。结果表明被研究组合ASV的遗传涉及一个主基因和基干微基因。根据分离世代中胚乳ASV的株平均数和方差,可     

不同栽杉代数29年生林分生产力变化

对一代、二代及三代杉木人工林林分生产力变化的比较分析结果表明：随着杉木栽植代数增加,林分生产力明显下降,不同代数间胸径、树高和蓄积量差异均达到极显著水平,但多重比较显示一代与二代平均胸径、二代和三代平均树高差异不显著．利用调查数据建立的立地指数与立地指数衰退量数学模型,能较好反映了连栽后杉木生长的实际情况．     

栽培大豆×半野生大豆主要农艺性状的遗传变异及回交改良

对６个栽培大豆与半野生大豆杂交组合及９个回交组合进行了分析。结果表明：大豆品种间杂种优势是普遍存在的,而且主要表现在产量性状上,百粒重的杂种优势及超亲优势为负值,超亲优势的表现与杂种优势的表现基本相同。杂种后代植株高、分枝多、籽粒小是半野生大豆在育种工作中利用的障碍。以有限性品种做回交亲本对种间杂种后代降低株高效果最佳,亚有限品种次之,无限品种效果最差。为克服杂种后代的小粒性,必须用大粒亲本进行回交并进行定向选择。在蛋白质含量上用高蛋白品种进行连续回交,可逐年提高杂种后代蛋白质含量