计算机模拟在野生动物种群遗传学研究中的应用

野生动物进化是遗传变异和环境变化相互作用的结果,其过程复杂、难以预测。进化过程包括基因突变、疾病、自然选择、空间扩散等自然因子,也包括驯化、栖息地破碎化、人工选择等人为干扰因子。计算机模拟能够揭示该复杂过程的历史特征,同时也能预测环境变化造成的遗传影响,正成为种群遗传学领域关注的研究方向。随着计算机模拟技术的发展,各种模拟软件层出不穷,功能全面且易操作,越来越多的计算机模拟软件被应用于野生动物的保护与管理。对计算机模拟应用于野生动物保护进行综述,总结了simu POP、ms、CDPOP、Sim Coal、Bayes SSC、DIYABC等近20种计算机模拟软件的功能,包括统计预测功能、统计推理功能和统计验证功能,并筛选了约20个典型的野生动物研究案例,展示了多达30个具体功能;同时,梳理了它们在推测生活史特征、推测进化历史特征、预测种群管理、预测遗传多样性受环境变化的影响、验证取样和验证统计方法等六大方面的适用性;从计算机模拟面临的挑战(准确率的监测)和机遇(多学科合作),对计算机模拟应用于未来野生动物保护提出了展望。     

常用统计软件在生物统计中的应用比较

生物统计分析方法通过对数据的科学分析从而排除误差,找出研究对象的内在联系以求获得正确的结论,在生物医学研究中具有不可替代的地位.随着21世纪"后基因组时代"的到来,以及系统生物学研究的兴起,海量的生物学数据愈来愈需要统计软件的辅助.本文结合相关分析实例就Excel、SPSS和SAS三种目前常用的统计软件的优缺点及其局限性进行综述.     

系统发育网络的构建与应用

系统发育网络目前主要应用于表达种上复杂的网状进化关系、种内个体及群体之间的关系以及相互矛盾数据集的系统发育分析结果3个方面。本文在综述网状进化现象的基础上,介绍了目前用于构建系统发育网络的几种常用方法,包括T-Rex软件包的网状图法,Tcs软件中的统计简约法,Splitstrees4的中间网法、二分裂法和邻接网法。     

定量古生物学软件PAST及其常用功能北大核心CSCD

近半个世纪以来,古生物学涉及越来越复杂的现象与过程,难以用传统的经验科学方法来解决。伴随着相关研究引入日益增多的定量分析,古生物学逐渐成为一门可定量分析的科学。作为最早的古生物学专用的免费统计软件包,PAST功能全面、易于使用,并在过去十几年中发展迅速,目前已在相关软件中占据重要地位。本文在简单介绍该软件基本操作方法的基础上,结合古生物学应用案例,解读最常用到的几类"常规统计分析"与"多元统计分析"的使用;同时,针对古生物学相关领域中的"多样性、丰度及居群结构","形态学"和"生物地层学"问题,给出具体分析实例。在相关案例的分析介绍中,详细梳理用PAST实现这些分析的具体步骤,因而具有较好的实用参考价值。受篇幅所限,文章对软件中其他不常用但相对重要的9个模块只进行简要介绍,以供读者在偶尔涉及该类分析时参考。PAST软件不仅功能强大,而且能够针对古生物学及地层学浮现出来的最新前沿问题不断进行调整、更新,值得在古生物学界推广使用。     

关于二次旋转组合设计共用统计方法的研究

本文改进 了二次旋转组合设计的统计方法,使其可为二次正交旋转组合设计和二次通用旋转组合设计所共用,计算简便,有利软件通用。     

生物技术软件介绍Ⅱ

生物技术软件介绍Ⅱ王槐春（军事医学科学院医学情报研究所北京１００８５０）本人在《生命科学》１９９２年第２期上介绍了六类生物技术数据库和软件。近一年多来,我们又引进和开发了一批新的生物技术软件,现综合简介如下。所介绍软件有些是我们自行设计,有些购自国外...     

医疗设备软件维修与调整

介绍了医疗设备软件维修必须具备的知识,DSA机与培养仪软件维修实例。同时还介绍了医疗设备的调整的方法,用于排除故障的经验。     

RAPD数据分析软件RAPDDIST V1.0的使用

介绍了RAPDDISTV1 0软件包中的 7个程序 ,并以已发表论文中的数据分析为例介绍了该软件程序的使用 ,目的是为使用此软件的同行提供一些帮助     

PCR引物设计及软件使用技巧

介绍了使用软件设计PCR引物的技巧。在PCR引物设计原则的基础上 ,详细介绍了两种常用引物设计软件的基本使用方法 ,并对其各自的优缺点进行了比较。一般性引物自动搜索可采用“PremierPrimer 5”软件 ,而引物的评价分析则可采用“Oli go6”软件。     

结构方程模型及其在生态学中的应用

基于多变量统计方法同时研究自然系统内多个因子之间的相互关系, 是阐释复杂的自然系统的一个重要手段。相比传统的多变量统计法, 结构方程模型基于研究者的先验知识预先设定系统内因子间的依赖关系, 不仅能够判别各因子之间的关系强度(路径系数), 还能对整体模型进行拟合和判断, 从而能更全面地了解自然系统。由于结构方程模型只在近年才被应用到生态学的数据分析中, 因此该文试图对其作一简略介绍, 包括结构方程模型的定义和变量类型, 结合事例研究展现结构方程模型分析的一般步骤、在生态学中的应用以及相关软件的介绍等。望能为相关研究人员提供直观的认识, 加强结构方程模型在生态学数据分析中的应用。     

Numerical approaches towards life cycle interpretation five examples

The ISO-standard for LCA distinguishes four phases, of which the last one, the interpretation, is the least elaborated. It can be regarded as containing procedural steps (like a completeness check) as well as numerical steps (like a sensitivity check). This paper provides five examples of techniques that can be used for the numerical steps. These are the contribution analysis, the perturbation analysis, the uncertainty analysis, the comparative analysis, and the discernibility analysis. All five techniques are described at a non-technical level with respect to basic concept, possibilities, tabular and graphical representation, restriction and warnings, and all are illustrated with a simple example.     

影响水稻光合日变化的酶和相关因素的分析

水稻叶片的最大光合速率出现在上午１０：００时,Ｒｕｂｉｓｃｏ初始活力也在此时达到最大,然后逐渐降低,下午１４：００时略上升后又下降．Ｒｕｂｉｓｃｏ初始活力与光合速率之间极显著相关,相关系数为 ０．９４７４．运用相关性分析、回归分析、通径分析,对晴（有时有云）天气水稻叶片的光合速度、光合关键酶及有关因素的日变化进行综合评估,结果发现中午光合下降主要来自气孔限制,同时Ｒｕｂｉｓｃｏ活性也下降;Ｒｕｂｉｓｃｏ活性是影响光合日变化的又一重要生化因子．体内Ｒｕｂｉｓｃｏ活性受Ｒｕｂｉｓｃｏ活化酶的调节．     

Discrimination of higher plant calluses based on embryogenic capacity and taxonomic classification by pyrolysis mass spectrometry

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum, and has been widely applied to the discrimination of closely related microbial strains. Minimally prepared samples of embryogenic and non-embryogenic calluses derived from various higher plants (sweet potato, morning glory, Korean ginseng, Siberian ginseng, and balloon flower) were subjected to PyMS for spectral fingerprinting. A dendrogram based on the unweighted pair group method, with arithmetic mean of pyrolysis mass spectra, divided the calluses into Siberian ginseng embryogenic callus and the others, which were subsequently divided into embryogenic and non-embryogenic callus groups, regardless of plant species from which the calluses were derived. In the non-embryogenic callus group, the dendrogram was in agreement with the known taxonomy of the plants. These results indicate that PyMS analysis could be applied for discriminating plant calluses based on embryogenic capacity and taxonomic classification.     

Intraspecific variation in Licuala glabra Griff. (Palmae) in Peninsular Malaysia– a morphometric analysis

We studied vegetative and reproductive characters of 74 herbarium specimens of Licuala glabra Griff. (Palmae) collected from 22 localities throughout Peninsular Malaysia. To test the null hypothesis that there are no distinct groups within the species, cluster analysis (nearest neighbour), principal coordinates and principal components analyses were performed on the set of 43 qualitative and quantitative characters. The results obtained suggested that: (1) there are three infraspeciflc groups within the species, viz., the two published varieties glabra and selangorensis as well as a possible third novel taxon; (2) there is clustering of individuals corresponding to their geographic localities; (3) clusters generated using only reproductive characters indicate a biogeographic distribution of populations correlated with the mountain ranges in the peninsula.     

Fish ecoregions of Kansas: stream fish assemblage patterns and associated environmental correlates

Synopsis Principal components analysis was performed on fish presence/absence data for 39 common fish species from 410 stream sites in Kansas. The analysis confirmed ten ecologically meaningful fish assemblages, based on species associations. Factor scores based on these assemblages were then clustered into six geographic areas or fish ecoregions. Canonical discriminant analysis identified environmental variables that distinguished the derived fish ecoregions. Mean annual runoff, mean annual growing season, and discharge appear most important. Mean width, mean depth, chloride concentration, water temperature, substrate type, gradient, and percent of pool habitat were less important. Correspondence exists between these fish ecoregions and the patterns of physiographic regions, river basins, geology, soil, and potential natural vegetation in Kansas. The multivariate statistical approach used to classify fish ecoregions should have considerable potential value for fish assessment and management purposes in areas other than the state of Kansas.     

Some remarks about the analysis of active control studies

In an active-controlled trial, the experimental treatment can be declared to be non-inferior to the control if the confidence interval for the difference excludes a fixed pre-specified margin. Recently, some articles have discussed an alternative method where the data from the current study and placebo-controlled studies for the active control are combined together into a single test statistic to test whether a fixed fraction of the effect of the active control is preserved. It has been shown that, conditional on nuisance parameters from the active-controlled study, a fixed margin can be defined that will be operationally equivalent to this latter method. In this article, we will discuss statistical properties associated with these approaches. Specifically, the interim monitoring boundaries and level of evidence will be considered.     

Normal Approximations of Exact Tests in Configural Frequency Analysis

The most common tests for types and antitypes in configural frequency analysis are normal approximations of exact tests. In the paper such statistics under the complete independence model and under the fixed margins model are discussed. It turns out that these test statistics are not acceptable when the number of simultaneously performed tests is large or when the expected frequencies are small. In these cases, the use of exact tests is advocated and some existing computer programs for such tests are indicated. A normal approximation based on the strong version of the De Moivre-Laplace limit theorem is also discussed. Empirical examples are given from longitudinal data describing psychological development of boys.     

Phenotypic evaluation of genetic variability and selection of yield contributing traits in chickpea recombinant inbred line population under high temperature stress

Heat is a major abiotic stress that drastically reduces chickpea yield. This study aimed to identify heat-responsive traits to sustain crop productivity by screening a recombinant inbred line (RILs) population at two locations in India (Ludhiana and Faridkot). The RIL population was derived from an inter-specific cross between heat-tolerant genotype GPF 2 (C. arietinum L.) and heat sensitive accession ILWC 292 (C. reticulatum). The pooled analysis of variance showed highly significant differences for all the traits in RILs and most of the traits were significantly affected by heat stress at both locations. High values of genotypic coefficient of variation (19.52–38.53%), phenotypic coefficient of variation (20.29–39.85%), heritability (92.50–93.90%), and genetic advance as a percentage of mean (38.68–76.74%) have been observed for plant height, number of pods per plant, biomass, yield, and hundred seed weight across the heat stress environments. Association studies and principal component analysis showed a significant positive correlation of plant height, number of pods per plant, biomass, hundred seed weight, harvest index, relative leaf water content, and pollen viability with yield under both timely-sown and late-sown conditions. Path analysis revealed that biomass followed by harvest index was the major contributor to yield among the environments. Both step-wise and multiple regression analyses concluded that number of pods per plant, biomass and harvest index consistently showed high level of contribution to the total variation in yield under both timely-sown and late-sown conditions. Thus, the holistic approach of these analyses illustrated that the promising traits provide a framework for developing heat-tolerant cultivars in chickpea.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-00977-5.     

分子水平的遗传多样性及其测量方法

遗传多样性水平是一项很重要的数据。目前从分子水平量化遗传多样性的方法以等位酶分析、ＲＦＬＰ分析和ＲＡＰＤ分析为代表。遗传变异在基因组中并非随机分布,所以取样方式对分析结果的影响不容忽视。本文叙述了遗传变异的产生和分布,并以此为基础比较了上述３种分析方法的理论与实践。     

凡纳滨对虾各月龄性状的主成分与判别分析

为了研究凡纳滨对虾各性状增长规律和判定最佳生长季节凡纳滨对虾的体格与月龄的关系,选择1～6月龄凡纳滨对虾各1000只,选择全长、体长、第一腹节背高、第三腹节背高、第一腹节背宽、头胸甲长和体重共7个性状,进行主成分与判别分析.结果表明:各月龄凡纳滨对虾性状之间均呈现显著的正相关(P<0.01), 其中以全长与体长的相关性最为明显,1月龄凡纳滨对虾体重与形态性状的相关系数较小.各月龄凡纳滨对虾的主成分有所不同,1～2月龄凡纳滨对虾的第一主成分为长度因子,第二主成分为宽度因子,第三主成分为高度因子;3月龄凡纳滨对虾的第一主成分与1～2月龄凡纳滨对虾一致,但第二主成分为高度因子,第三主成分为体重因子;4～6月龄凡纳滨对虾的第一主成分为体重因子,第二主成分为高度因子,第三主成分为宽度因子.1～3月龄凡纳滨对虾形态性状的增长优先于体重, 4～6月龄凡纳滨对虾体重优先于形态性状的增长.错过最佳生长季节的凡纳滨对虾的与体格大小相符的月龄可通过建立的判别式来判断,总的判别准确率为98.98%,其中2～4月龄凡纳滨对虾的判别准确率为100%.