Bayes factors for detection of Quantitative Trait Loci

A fundamental issue in quantitative trait locus (QTL) mapping is to determine the plausibility of the presence of a QTL at a given genome location. Bayesian analysis offers an attractive way of testing alternative models (here, QTL vs. no-QTL) via the Bayes factor. There have been several numerical approaches to computing the Bayes factor, mostly based on Markov Chain Monte Carlo (MCMC), but these strategies are subject to numerical or stability problems. We propose a simple and stable approach to calculating the Bayes factor between nested models. The procedure is based on a reparameterization of a variance component model in terms of intra-class correlation. The Bayes factor can then be easily calculated from the output of a MCMC scheme by averaging conditional densities at the null intra-class correlation. We studied the performance of the method using simulation. We applied this approach to QTL analysis in an outbred population. We also compared it with the Likelihood Ratio Test and we analyzed its stability. Simulation results were very similar to the simulated parameters. The posterior probability of the QTL model increases as the QTL effect does. The location of the QTL was also correctly obtained. The use of meta-analysis is suggested from the properties of the Bayes factor.     

Bayesian predictive information criterion for the evaluation of hierarchical Bayesian and empirical Bayes models

The problem of evaluating the goodness of the predictive distributionsof hierarchical Bayesian and empirical Bayes models is investigated.A Bayesian predictive information criterion is proposed as anestimator of the posterior mean of the expected loglikelihoodof the predictive distribution when the specified family ofprobability distributions does not contain the true distribution.The proposed criterion is developed by correcting the asymptoticbias of the posterior mean of the loglikelihood as an estimatorof its expected loglikelihood. In the evaluation of hierarchicalBayesian models with random effects, regardless of our parametricfocus, the proposed criterion considers the bias correctionof the posterior mean of the marginal loglikelihood becauseit requires a consistent parameter estimator. The use of thebootstrap in model evaluation is also discussed.     

林分和景观水平因子对松材线虫病发生的影响——以山东威海地区松林为例

松材线虫病(Pine wilt disease)传入我国以来,造成了大面积松林枯死,严重威胁我国的林业和生态建设的发展,但目前分析林分和景观水平因子对松材线虫病综合影响的研究较少。本文基于松材线虫病危害后期的山东威海地区的松林,利用野外调查数据、森林资源二类调查数据和高分辨率遥感影像,获取了影响松材线虫病危害的林分水平和景观水平的各种因子,通过逐步回归分析、线性回归分析和建立广义线性模型(GLM),探讨了景观分析的最适尺度,分析不同因子在解释松材线虫病危害程度方面的作用和相对重要性,以期为松材线虫病的防控技术及宏观管理政策制定提供科学依据。结果显示,750 m尺度下景观格局指数对松材线虫病发病率的解释效果最好。景观因子中,距疫源地距离、景观分离度与距人为活动区域距离对发病率影响最显著（相对重要性值为1.00）,其中景观分离度和距疫源地距离与发病率呈负相关,距人为活动区域距离与发病率呈正相关;松林斑块连接度的相对重要性次之（相对重要性值为0.69）,与发病率呈正相关;斑块丰富度密度、相关外接圆指数的相对重要性值较低（0.33）。林分因子中,林分密度的相对重要性值最低（0.23）。综合分析林分因子和景观因子的作用发现,在威海地区松材线虫病暴发后期的林分中,相较于林分因子,景观因子起主导作用。研究结果有助于提高对松材线虫病发生的驱动机制的了解。     

Comparison of statistical models to analyse the genetic effect on within-litter variance in pigs

Genetics affects not only the weight of piglets at birth but also the variability of birth weight within litter. Previous studies on this topic assigned the sample standard deviation of piglet birth weights within litter as an observation to the sow. However, the contribution of the difference in mean birth weight per sex on the within-litter variance has been neglected so far. This work deals with the genetic effect on within-litter variance when different statistical models with different distributional assumptions are used and considers the sex effect and appropriate weights per trait. Traits were formed from the pooled sample variance of male and female birth weights within litter. A linear model approach was fitted to the logarithmized within-litter variance and the sample standard deviation. A generalized linear model with gamma-distributed residuals and log-link function was applied to the untransformed sample variance. Models were compared by analysing data from 9439 litters from Landrace and Large White of a commercial breeding programme. The estimates of heritability for different traits ranged from 7% to 11%. Although the generalized linear mixed model is preferred from a mathematical view, the rank correlations between breeding values of the linear mixed models and the generalized linear mixed model were relatively high, i.e. 94% to 98%. By residual diagnostics, a linear mixed model using the weighted and pooled within-litter standard deviation was identified as most suitable.     

沙棘木蠹蛾生殖系统形态学和组织学观察

沙棘木蠹蛾Holcocerus hippophaecolus Hua,Chou,Fang et Chen属鳞翅目(Lepidoptera)木蠹蛾科(Cossidae),是我国的特有种.2001年以来,沙棘木蠹蛾在我国大面积爆发,是屹今为止我国沙棘林最大的蛀干害虫,给我国的沙棘产业造成了巨大的损失.本论文从形态学和组织学2个方面确定了沙棘木蠹蛾雌、雄生殖系统的特征,同时,对比了雄性交尾前后生殖系统各部位的差异.未交尾雄蛾的生殖系统贮精囊、附腺管和射精管呈白色,其内包含大量的精子束待交尾,已交尾雄蛾的生殖系统呈透明或半透明状.除雄性附腺外,在交尾后的精巢、贮精囊和射精管中都能观察到真核精子束.通过上述对雄性生殖系统的形态学和组织学观察,尤其是对贮精囊和射精管中精子束观察,可判断精子束的填充状态,从而判断雄蛾交尾与否,能够检验性信息素引诱剂对沙棘木蠹蛾的防治效果,确立判断雄蛾交尾与否的标准对指导沙棘木蠹蛾防治具有重要意义.     

黄土高原森林枯落物储量、厚度分布规律及其影响因素

森林枯落物的储量(LM)和厚度(LD)等物理属性,能够表征森林植被的物种多样性以及水源涵养、物质循环等生态功能,然而目前对枯落物储量和厚度分布规律与影响因素的深入探讨较少。以黄土高原为研究区,通过系统取样获得该区主要森林群落枯落物的储量与厚度数据,利用Kruskal-Wallis秩和检验、线性混合效应模型(LME)、普通最小二乘回归等统计方法,分别对不同林型枯落物储量和厚度的差异、储量和厚度的影响因素以及二者之间的关系进行分析。结果表明:1)针叶林与针阔混交林的枯落物储量和厚度差异不显著,但二者都显著大于阔叶林的储量和厚度。2)在纬度方向上,除南部个别点外,枯落物储量和厚度存在单峰格局,如储量在35°—36°N之间存在峰值,而厚度峰值则出现在36°—37°N之间。3)在海拔方向上,储量分布规律并不明显,厚度除了高海拔(3000 m以上)个别点外总体呈现递减格局;LME模型显示,枯落物储量与气温年较差、非生长季降水、总干面积和立木密度呈显著正相关,与乔木层丰富度呈显著负相关,而枯落物厚度与最冷月均温、生长季降水、总干面积和立木密度呈显著正相关,与乔木层丰富度、非生长季降水和坡度呈显著负相关;枯落物储量与厚度具有显著正相关关系,特别是在阔叶林和针叶林中,而对于针阔混交林来说二者并无显著相关性。研究结果可为黄土高原乃至中国北方地区生态系统碳循环评估和水土保持实践提供参考依据。     

基于野外观测检验动物廊道选址模型的准确性——以白头叶猴为例

廊道构建是减少栖息地破碎化负面影响的重要策略之一。目前,已经有许多模型用于动物廊道的选址,而"选址模型是否能准确预测动物迁移的实际发生位置"一直是保护生物学最为关注的问题。最小成本路径模型（LCP）和条件最小成本廊道模型（CMTC）是两种较为常用的廊道选址模型。以白头叶猴（Trachypithecus leucocephalus）为目标物种,分别运用LCP和CMTC模拟生成白头叶猴迁移廊道,将模拟结果与野外观测廊道进行对比,检验两种方法的准确性。结果表明：与野外观测实际廊道相比,LCP模型模拟结果的完全准确率为46.7%,部分准确率为20%,完全不准确率为33.3%;CMTC模型模拟结果的完全准确率为26.7%,其余73.3%为部分准确,无完全不准确的结果;总体上看,CMTC廊道的准确率较LCP高,因而CMTC模型模拟白头叶猴实际迁移廊道位置的准确性优于LCP模型。输入"源"要素类型、阻力面栅格尺度设定、栖息地土地利用类型变化以及动物迁移行为复杂性4个因素是影响该模拟结果准确性的主要原因。     

生物发光法微生物快速检测试剂的性质及其影响因素研究

研究了ATP生物发光微生物快速检测试剂的反应动力学、反应最适温度、pH以及各种影响因素。在ATP生物发光反应中,测试系统中D-荧光素用量为40～50μg／mL时对反应已经足够;发光脉冲计数CPM值随反应时间的延长不断降低,开始的1min内,其CPM值下降最快,然后下降速度不断减缓;反应的最适温度为24℃～25℃;而体系的最佳pH为7．2-7．4。配制好的发光试剂溶液置于4℃保存45h,可以保持86％的活力。在25℃时保温1h,活力下降较少,随时间的增加,活力逐渐下降,到6．5h时,仅剩53．5％的活力,而在33℃时,随着保温时间的延长,酶活力下降较快,保温1．5h,活力剩下59．1％,因此保存温度对发光试剂活力的影响非常大。各种化学物质如酸、碱、盐及表面活性剂都会抑制ATP发光反应,当NaCl浓度达到1．5g／L时,即可以抑制52．5％的发光,TritonX-100及酸、碱对系统均有一定的影响,CTAB、SDS及TCA则严重抑制发光反应。