群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。通过综述群体遗传结构的几种模式:陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。     

利用分子标记和形态学性状检测的陆地棉栽培品种遗传多样性

利用RAPD,ISSR和SSR3种分子标记方法和2年田间实验对国内外36个陆地棉栽培品种的遗传多样性进行了研究,以3种分子标记在36个品种之间扩增的282条多态性位点所赋值的0,1数据,采用Nei和Li的方法,计算的品种成对相似系数从0．5745到0．9291,其品种平均数从0．6547到0．7524,又以2年品种表现的性状平均数经正态标准化后,采用欧氏距离计算了成对品种的遗传距离。分别以相似系数和传距离矩阵,采用类平均法进行聚类分析,其聚类结果把供试品种大致分为国外品种,新疆品种,早熟类型品种和我国的中熟棉品种等几个类群,类内进一步分组表明,分子标记确定的传关系基本上与品种系谱的种质系统一致,但并不能按系谱或种植生态区域简单地归属,尽管分子标记数据计算的相似系数矩阵和表现型计算的遗传距离矩阵存在极显著的相关关系（r=-0.335),但以遗传距离进行聚类分析的类内分组的组间特征不明显,分子标记是检测类内品种间遗传差异的有效方法,研究结果为棉花育种亲本选配提供了理论依据。     

基于分子模拟的离子交换层析中静电相互作用研究

将分子模拟方法引入到蛋白质离子交换层析中的静电相互作用研究。选用蛋清溶菌酶和牛胰凝乳蛋白酶为模型蛋白质,阳离子交换吸附剂SP Sepharose FF等为模型层析介质。从蛋白质数据库(PDB)中获得蛋白质三维结构数据,分析了介质孔径和配基分布,以点电荷模拟离子交换层析介质的功能配基,构筑了蛋白质-介质配基模拟表面体系。采用MCCE、Delphi和GRASP等程序包进行了分子模拟计算,考察了作用方向、作用距离、盐浓度、pH等对蛋白质和模拟配基平面间静电相互作用的影响。结果表明,宏观的层析平衡常数与微观分子模拟计算的相互作用能量参数间存在良好的线性关系。     

应用混合遗传距离和基因型值遗传距离构建植物遗传资源核心子集

将连续性的基因型值数据和间断性的分子标记数据整合建立混合遗传距离,对比了应用混合遗传距离和单纯应用基因型遗传距离构建植物遗传资源核心子集的效果．应用混合线性模型中的调整无偏预测法（AUP）预测基因型值,结合不加权类平均法（UPGMA）逐步聚类构建遗传资源群体的核心子集,并检测一系列核心子集的代表性评价参数．采用包含8个农艺性状和60个SSR标记信息的水稻群体数据验证混合遗传距离的有效性．结果表明,采用混合数据构建的核心子集比单纯的基因型值数据构建的核心子集更有代表性．主成分分析结果验证了该结论的可知陛．     

葫芦科瓜类作物分子标记辅助育种研究进展

综述了几种常用分子标记在葫芦科瓜类作物遗传图谱构建、重要性状基因定位、遗传多样性及亲缘关系分析、分子标记辅助选择及在葫芦科遗传育种中的应用,对目前葫芦科遗传育种中应用分子标记技术存在的问题和解决方案进行了探讨,并对葫芦科分子标记辅助育种的前景做了展望。     

蛋白质序列的矩阵图谱表达

基于经典HP模型,利用蛋白质序列的矩阵图谱表达法(MGR)及数值刻画的思想提出了一种新的蛋白质序列的比对方法,通过观察蛋白质序列的数值刻画图及计算两蛋白质序列之间的欧氏距离d,对木聚糖酶两家族的蛋白质序列进行了相似性分析.发现被划分为同一木聚糖酶家族的蛋白质序列之间的相似性更大,而且蛋白质序列的相似性程度与分子大小、结构和分子进化相关.     

基于COI基因5′端与3′端序列田间常见粉虱的分子鉴定

【目的】粉虱种类繁多,个体微小,其种类识别与鉴定常需借助分子生物学技术。本研究旨在明确线粒体COI基因(mitochondrial cytochrome c oxidase subunit I gene) 5′端和3′端序列对常见种类粉虱识别鉴定的可行性。【方法】以我国田间常见的16种粉虱为对象,以COI基因5′端(641 bp)和3′端(738 bp)序列为靶标进行比对分析,以MEGA 5.10软件的K2-P模型计算种内与种间遗传距离,以邻接法(NJ法)构建进化树并进行系统发育分析。【结果】当以5′端为靶标时,16种粉虱的种内平均遗传距离为0.0015,种间平均遗传距离为0.2897,种间遗传距离为种内遗传距离的193.1倍;而且种内、种间遗传距离没有重叠区域。当以3′端为靶标时种内平均遗传距离为0.0007,种间平均遗传距离为0.2817,种间遗传距离为种内遗传距离的402.4倍;但桑粉虱Pealius mori与烟粉虱Bemisia tabaci Asia II 1的种内和种间遗传距离重叠。系统发育分析结果显示,以5′端为靶标时,16种粉虱可以形成独立的进化分支;以3′端为靶标时,除桑粉虱与传统分类学不一致外,其余种类均可形成独立的分支。【结论】结果表明,5′端序列更适用于基于DNA条形码技术的物种识别鉴定研究。     

内蒙古中东部草原区克氏针茅形态特征和RAPD遗传分化的相关性研究

以分布在内蒙古锡林郭勒盟东部草甸草原、中部典型草原和中西部荒漠化草原的4个克氏针茅种群为研究对象,采用形态学标记和RAPD分子标记相结合的方法进行遗传分化研究。结果表明：（1）无论是用形态学数据所得欧氏遗传距离矩阵还是用RAPD所得无偏差的Nei’s遗传距离矩阵,与种群分布的地理距离之间均不存在显著的相关关系,说明克氏针茅种群遗传分化受自然选择的影响。（2）种群之间存在显著的形态分化和遗传分化（p<0.05）。（3）对形态学数据所得欧氏遗传距离矩阵和RAPD所得Nei’s无偏差遗传距离矩阵进行Mantel检验所得结果不显著,表明对克氏针茅形态分化和遗传分化起主要作用的选择力是不完全相同的。     

一种研究蛋白质晶体中分子堆积的图形程序—PACKING

在蛋白质晶体结构研究中常需分析分子在晶胞内的堆积,本文介绍一种用于IRIS-4D计算机的图形软件,可显示分子在晶胞中的堆积图形、计算原子之间的距离和键角等,进行分子置换、模拟不同的分子堆积模型。     

江西新岗山森林昆虫种内遗传距离研究

DNA条形码目前广泛用于昆虫多样性研究。本研究采用DNA条形码（即线粒体细胞色素c氧化酶亚基I基因COI 5′端），通过比较所获分子分类操作单元（Molecular operational taxonomic units，MOTU）的种内遗传距离，探究DNA条形码在亚热带森林（位于我国江西省新岗山）不同昆虫类群中的物种鉴定和界定效用。数据分析中结合数据库比对信息，采用jMOTU、ABGD、bPTP、GMYC 这4种物种界定方法获得MOTU，从而开展种内遗传距离分析。本研究共挑选出479个昆虫样本，获得475条COI序列，经NCBI、BOLD在线数据库比对属于6个目，与形态初步划分一致；物种界定分析获得288个MOTU，其中鳞翅目最多，达85个，膜翅目、双翅目、半翅目、鞘翅目次之，分别为80、74、21和20个，直翅目最少，仅8个。膜翅目和双翅目的种内遗传距离均值及标准偏差较大（膜翅目：0.89%±0.87%；双翅目：0.73%±0.58%），鳞翅目的最小（0.28%±0.20%）。研究表明：不同昆虫类群的种内遗传距离虽然整体在一定范围，但仍然存在一定的差异，因此不能笼统地依靠遗传距离的距离阈值进行物种划分；现有数据库需要补充足够的昆虫物种信息，才能提升物种鉴定效率。本研究丰富了亚热带森林昆虫分子数据库，同时也为进一步探索基于分子分类学开展昆虫多样性研究提供了基础数据和参考。     

Microsatellite analysis of genetic structure in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae)

The level of genetic variation throughout the entire worldwide range of the mangrove species Avicennia marina (Forsk.) Vierh. was examined using microsatellite markers. Three microsatellite loci detected high levels of allelic diversity (70 alleles in total), essential for an accurate estimation of population genetic parameters. The informativeness of the microsatellite loci tended to increase with increasing average number of repeats. The levels of heterozygosity detected for each population, over all loci, ranged from 0.0 to 0.8, with an average of 0.407, indicating that some populations had little or no genetic variation, whereas others had a large amount. Populations at the extremes of the distribution range showed reduced levels of heterozygosity, and significant levels of inbreeding. This is not unexpected as these populations may be subject to founder effects and environmental constraints. The presence of genetic structure was tested in A. marina populations using three models: (i) a single panmictic model; (ii) the discrete subpopulation model; and (iii) the isolation by distance model. The discrete subpopulations model was supported by the overall measures of population differentiation based on the infinite alleles model (F-statistics), and the stepwise mutation model (R statistics). In addition, an analysis of molecular variance (AMOVA), using both theoretical models, found that most of the variation was between populations (41-71%), and within individuals in the total population (31-49%). There was little variation among individuals within populations (0-10%). There was no significant isolation by distance. The high levels of genetic differentiation observed among populations of A. marina may be due to environmental and ecological factors, particularly past sea level and climatic changes.     

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.     

Genetic Distances and Reconstruction of Phylogenetic Trees from Microsatellite DNA

Recently many investigators have used microsatellite DNA loci for studying the evolutionary relationships of closely related populations or species, and some authors proposed new genetic distance measures for this purpose. However, the efficiencies of these distance measures in obtaining the correct tree topology remains unclear. We therefore investigated the probability of obtaining the correct topology (P(C)) for these new distances as well as traditional distance measures by using computer simulation. We used both the infinite-allele model (IAM) and the stepwise mutation model (SMM), which seem to be appropriate for classical markers and microsatellite loci, respectively. The results show that in both the IAM and SMM CAVALLI-SFORZA and EDWARDS'' chord distance (D(C)) and NEI et al.''s D(A) distance generally show higher P(C) values than other distance measures, whether the bottleneck effect exists or not. For estimating evolutionary times, however, NEI''s standard distance and GOLDSTEIN et al.''s (δ μ)(2) are more appropriate than other distances. Microsatellite DNA seems to be very useful for clarifying the evolutionary relationships of closely related populations.     

Chromosome Rearrangements Recovered following Transformation of Neurospora Crassa

Analyses of evolution and maintenance of quantitative genetic variation depend on the mutation models assumed. Currently two polygenic mutation models have been used in theoretical analyses. One is the random walk mutation model and the other is the house-of-cards mutation model. Although in the short term the two models give similar results for the evolution of neutral genetic variation within and between populations, the predictions of the changes of the variation are qualitatively different in the long term. In this paper a more general mutation model, called the regression mutation model, is proposed to bridge the gap of the two models. The model regards the regression coefficient, γ, of the effect of an allele after mutation on the effect of the allele before mutation as a parameter. When γ = 1 or 0, the model becomes the random walk model or the house-of-cards model, respectively. The additive genetic variances within and between populations are formulated for this mutation model, and some insights are gained by looking at the changes of the genetic variances as γ changes. The effects of γ on the statistical test of selection for quantitative characters during macroevolution are also discussed. The results suggest that the random walk mutation model should not be interpreted as a null hypothesis of neutrality for testing against alternative hypotheses of selection during macroevolution because it can potentially allocate too much variation for the change of population means under neutrality.     

Evolutionary and statistical properties of three genetic distances

Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.     

Constraints on Allele Size at Microsatellite Loci: Implications for Genetic Differentiation

Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small populations. The evolution of selectively neutral markers is governed by the interaction of mutation and random genetic drift. Mutation pressure has the inherent tendency to shift different populations to the same distribution of alleles. Hence, mutation pressure is a homogenizing force, and population divergence is caused by random genetic drift. In case of allozymes or sequence data, the diversifying effect of drift is typically orders of magnitude larger than the homogenizing effect of mutation pressure. By a simple model, we demonstrate that the situation may be different for microsatellites where mutation rates are high and the range of alleles is limited. With the help of computer simulations, we investigate to what extent genetic distance measures applied to microsatellite data can nevertheless yield useful estimators for phylogenetic relationships or demographic parameters. We show that predictions based on microsatellite data are quite reliable in small populations, but that already in moderately sized populations the danger of misinterpretation is substantial.     

THE DIVERGENCE OF NEUTRAL QUANTITATIVE CHARACTERS AMONG PARTIALLY ISOLATED POPULATIONS

The neutral model of phenotypic evolution has yielded several simple predictions about the long-term rates of between-population divergence of polygenic traits and about the equilibrium level of within-population variance when mutation and random genetic drift are the sole evolutionary forces. These conclusions must be modified if populations are only partially isolated. A quantitative model is presented for the development of within- and between-population variance for neutral quantitative characters in pairs of populations with arbitrary effective sizes and migration rates. Both the variance in the base population and subsequent variance generated by mutation are considered, and several dynamical and equilibrium properties are shown to be adequately described by simple approximations. The resultant formulations provide some insight into the sensitivity of measures of morphological distance to gene flow, the necessity of isolation for the accumulation of variation between incipient species, and the consequences of gene flow into captive populations of endangered species.     

Relationship between heterozygosity and genetic distance in the three major races of man

In pairwise comparisons of gene frequency data from the three major races of man, the single locus measures of the heterozygosity within and the genetic distance between races are shown to be strongly correlated across the loci coding for red cell proteins and enzymes. The intercept of the regression line of genetic distance on heterozygosity in protein enzyme loci is statistically insignificant. These findings suggest that the genetic variability at the enzyme and protein loci in man is probably maintained by a balance of mutation and random genetic drift. At the blood group loci, however, the observed relationship between genetic distance and heterozygosity does not follow the expectation of the neutral mutation hypothesis. These observations are discussed in terms of the changes in probability of identical monomorphism in two populations during the process of gene differentiation.     

Measuring genetic distances between breeds: use of some distances in various short term evolution models

Many works demonstrate the benefits of using highly polymorphic markers such as microsatellites in order to measure the genetic diversity between closely related breeds. But it is sometimes difficult to decide which genetic distance should be used. In this paper we review the behaviour of the main distances encountered in the literature in various divergence models. In the first part, we consider that breeds are populations in which the assumption of equilibrium between drift and mutation is verified. In this case some interesting distances can be expressed as a function of divergence time, t, and therefore can be used to construct phylogenies. Distances based on allele size distribution (such as (δμ)² and derived distances), taking a mutation model of microsatellites, the Stepwise Mutation Model, specifically into account, exhibit large variance and therefore should not be used to accurately infer phylogeny of closely related breeds. In the last section, we will consider that breeds are small populations and that the divergence times between them are too small to consider that the observed diversity is due to mutations: divergence is mainly due to genetic drift. Expectation and variance of distances were calculated as a function of the Wright-Malécot inbreeding coefficient, F. Computer simulations performed under this divergence model show that the Reynolds distance [57]is the best method for very closely related breeds.     

Variance of genetic distance and correlation of heterozygosity between populations under the pressure of stepwise mutation

Using the stepwise mutation model of Ohta and Kimura (1973), formulas are developed for the correlation of heterozygosity and the variance of genetic distance between two finite populations. Studied in detail is the case where the sizes of the two descendant populations are equal to that of the ancestral population and the mutation rate is the same for all loci. Numerical computations are carried out by using the present formulas and those of Li and Nei (1975Genet. Res.25) for the infinite-allele model. The results are as follows: The correlation of heterozygosity decreases with time faster for the stepwise mutation model than for the infinite-allele model. However, the relationships between the correlation of heterozygosity and the normalized genetic identity for the two models are very similar, if the average heterozygosities of the two populations are around 0.20 or less. On the other hand, the variance of genetic distance for the stepwise mutation model may become considerably smaller than that for the infinite-allele model, if the average heterozygosities of the two populations are larger than 0.05. The ratio of the standard deviation to the mean is, however, very large for the stepwise mutation model as well as the infinite-allele model.