新疆维吾尔族四个STR位点遗传多态性分析

研究新疆维吾尔族人群D16S539、D13S317、D7S820和D5S818的STR基因位点的基因及基因型分布,获得4个基因座的群体遗传学数据。采用PCR扩增技术和基因扫描技术进行样本STR遗传结构分析,并与其他种族、人群的等位基因频率进行比较。结果表明4个基因位点在新疆维吾尔族人群中均具有遗传多态性。4个基因座的基因型分布均符合Hardy-Weinberg平衡定律（P＞0.05）,不同人群基因频率分布存在一定的差异,所得到的等位基因频率等数据可为遗传学研究、法医个体畜产品识别及亲子鉴定提供依据。     

应用15个STRs揭示广西4个少数民族的遗传关系

为研究广西仫佬、毛南、苗和瑶族的15个短串联重复序列（STR）基因座的遗传多态性,探讨这4个民族群体的遗传差异和进化关系。通过PCR-STR及测序仪,检测了广西4个民族766例无关个体的15个STR位点基因频率的分布并比较各民族间的差异,计算遗传学参数、遗传距离和构建系统进化树。结果显示：仫佬、毛南、苗和瑶族的15个STR位点分别共检出135,134,148,145种等位基因和424,432,445,436种基因型;各民族的平均Ho〉0.7,累积DP,EPP和PIC均在0.99999以上;毛南族和苗族,瑶族和其他民族间在多数位点的基因频率分布上存在显著差异,而仫佬族和毛南族或苗族间在多数位点上不存在差异;4个民族在进化树上被分为两组,仫佬族和毛南族聚成一组,苗族和瑶族聚成另一组。说明广西仫佬、毛南、苗和瑶族的15个STR基因座具有高度的遗传多态性,实用价值较高,是一组可用于人类群体遗传学、法医学个体识别和亲子鉴定等研究的有力工具;4个民族STR的遗传差异性和遗传关系与他们的语言文化和民族历史基本一致。     

山西汉族17个Y-STR基因座遗传多态性及遗传关系

为了调查山西汉族群体17个Y-STR基因座的多态性分布,探讨其群体遗传学及法医学应用价值,文章应用Y-filer TM试剂盒检测222名山西汉族无关男性个体的17个Y-STR基因座,用ABI3130遗传分析仪进行基因分型,计算等位基因频率及单倍型多样性,并结合已公开发表的国内其他13个群体相关数据资料,分析山西汉族群体遗传距离和聚类关系。结果:山西汉族个体中共检出219种单倍型,单倍型多样性为0.9999;基因多样性GD值在0.3894(DYS391)~0.9755(DYS385a/b)。从遗传距离分析发现,山西汉族与吉黑汉族之间的遗传距离最近(?0.0001),与台湾群体(0.0152)之间的遗传距离相对较远。结果表明该17个Y-STR基因座在山西汉族群体中具有丰富的遗传多态性,对建立Y染色体STR数据库、研究群体遗传学和进行法医学应用有重要意义。     

性染色体微卫星标记在亲缘鉴定中的应用

性染色体短串联重复序列(short tandem repeat,STR),又称微卫星DNA(micro satellite DNA)作为一种特殊的遗传标记在法医学个体识别及亲缘鉴定中发挥着重要的作用。该文对亲子鉴定概念、原理和方法等基础知识以及性染色体STR的研究历史、特点以及局限性等进行综述,为性染色体STR在法医学、遗传学等方面的推广应用提供参考。     

用毛细管电泳技术对北京汉族人群9个STR基因座遗传多态性的研究

为对北京汉族D3S1358、vWA、FGA、D8S1179、D21S11、D18S51、D5S818、D13S317及D7S820等9个STR基因座的遗传多态性进行群体遗传学研究,利用荧光标记复合扩增及毛细管电泳自动荧光检测的方法,对236名无关个体获得9个STR基因座等位基因的分布频率,结果均符合Hardy-Weinberg平衡.计算了各基因座的杂合度（H）、个人识别能力（DP）、偶合率（PM）、非父排除率（EPP）和多态性信息总量（PIC）等群体遗传学数据.结果表明,这9个STR基因座多态性好,灵敏度高,可用于人类遗传分析及法医学中的亲子鉴定和个人识别.     

人类群体遗传结构的协方差阵主成分分析方法

目的:探讨基因频率矩阵的中心化(或均值化)协方差阵主成分分析方法在人类群体遗传结构研究中的适用性和合理性。方法:从基因频率矩阵的结构特征入手,分析中心化、均值化协方差阵主成分分析与标准化相关阵主成分分析在特征根、特征向量以及降维效果等方面的差异,并通过实例比较不同方法在解释群体遗传结构特征上合理性。结果:中心化(或均值化)协方差阵的主成分不仅反映了基因变异程度的“方差信息量权”,而且反映了基因间相互影响程度的“相关信息量权”;标准化相关阵的主成分反映的仅是“相关信息量权”,不包括“方差信息量权”。通过比较中国26个汉族人群HLA-A基因座中心化协方差阵和标准化相关阵2种主成分分析结果,证实中心化协方差阵主成分分析方法在特征根与特征向量、保留主成分的个数和对主成分的群体遗传学解释的合理性等方面均优于标准化相关阵主成分分析方法。结论:在对群体遗传结构进行主成分分析时,应使用中心化(或均值化)变换消除基因频率矩阵中量级的影响,然后在用其协方差阵提取主成分。     

植物分子群体遗传学研究动态

分子群体遗传学是当代进化生物学研究的支柱学科, 也是遗传育种和关于遗传关联作图和连锁分析的基础理论学科。分子群体遗传学是在经典群体遗传的基础上发展起来的, 它利用大分子主要是DNA序列的变异式样来研究群体的遗传结构及引起群体遗传变化的因素与群体遗传结构的关系, 从而使得遗传学家能够从数量上精确地推知群体的进化演变, 不仅克服了经典的群体遗传学通常只能研究群体遗传结构短期变化的局限性, 而且可检验以往关于长期进化或遗传系统稳定性推论的可靠程度。同时, 对群体中分子序列变异式样的研究也使人们开始重新审视达尔文的以“自然选择”为核心的进化学说。到目前为止, 分子群体遗传学已经取得长足的发展, 阐明了许多重要的科学问题, 如一些重要农作物的DNA多态性式样、连锁不平衡水平及其影响因素、种群的变迁历史、基因进化的遗传学动力等, 更为重要的是, 在分子群体遗传学基础上建立起来的新兴的学科如分子系统地理学等也得到了迅速的发展。文中综述了植物分子群体遗传研究的内容及最新成果。     

DXS6804/DXS9896/GATA144D04基因座在中国汉族群体中的遗传多态性及其法医学应用

为了调查X染色体上DXS6804、DXS9896和GATA144D04等3个STR基因座在中国汉族群体的遗传多态性及其法医学应用价值,来用PCR和聚丙烯酰胺凝胶电泳对X染色体3个STR基因座进行分型,并检验女性基因型频率分布是否符合Hardy Weinberg平衡,计算法医学常用各种概率。DXS6804、DXS9896和GATA144D04的非父排除率分别为0 5990、0 6220、0 4280,表明3个STR基因座在中国汉族群体均具有遗传多态性,χ2检验表明女性的基因型频率分布符合Hardy Weinberg平衡。X染色体上的基因座DXS6804、DXS9896和GATA144D04在中国汉族群体中具有较高的遗传多态性,可应用于法医学检验和群体遗传学分析。     

北京汉族群体39个短串联重复序列基因座多态性及其遗传关系

本文首次对北京地区汉族人群的13个CODIS(Combined DNA index system)和26个非CODIS系统STR基因座的遗传多态性进行了研究,建立了北京地区汉族人群39个STR基因座的群体遗传多态性数据库并对其法医学应用价值进行了评价。39个STR基因座的基因型分布均符合Hardy-Weinberg平衡且各基因座之间均不存在连锁现象,个体鉴别力(Power of discrimination, DP)在0.7740~0.9818之间,期望杂合度(Expected heterozygosity, He)在0.6000~0.9350之间,多态性信息含量(Polymorphism information content, PIC)在0.5317~0.9047之间,非父排除率(Power of exclusion, PE)在0.2909~0.8673之间,累积个体鉴别力(Cumulative probability of discrimination, CDP)为0.999999999999999999999999999999999999999964971,累积非父排除率(Cumulative probability of exclusion, CPE)为0.999999999973878。另外,结合已公开报道的国内其他11个群体相应基因座的遗传资料,根据等位基因频率计算遗传距离,构建了系统发生树。本研究可为中国法医DNA数据库和群体遗传学数据库提供重要的基础数据,对北京地区汉族人群开展法医学个体识别、亲权鉴定和遗传学研究具有重要的意义。     

中国汉族人群(西安)STR基因扫描与遗传结构

选择9种STR基因位点和Amelogenin基因位点,以测序为基础,研究我国汉族人群STR遗传结构.采用基因自动测序仪建立了10个位点基因分析方法,通过对汉族群体的基因扫描、基因分型和遗传结构分析,获得了STR基因传递特征的大量基因遗传数据,在汉族人群DP为1.05×10-0,EPP为0.9998,为建立我国不同民族STR基因数据库、基因资源研究与保护奠定了基础,为生物考古、基因诊断、性别鉴定、个人识别,司法审判、侦察破案提供有力的科学依据.     

DNA polymorphism in population genetics

In the review, the literature evidence on DNA polymorphism obtained in the last 10-15 years using various molecular-genetic methods is summarized. All main types of DNA variation are considered but attention is focused on those extensively used in population genetics. The areas of using DNA markers are outlined and the limitations of their potential in analyzing genetic processes in populations are discussed. Particular emphasis is placed on the relationship between the earlier developed biochemical genetics based on protein polymorphism analysis and modern molecular population genetics based on DNA polymorphism. The possible role of selection in maintaining DNA variation is considered.     

DNA Polymorphism in Population Genetics

In the review, the literature evidence on DNA polymorphism obtained in the last 10–15 years using various molecular-genetic methods is summarized. All main types of DNA variation are considered but attention is focused on those extensively used in population genetics. The areas of using DNA markers are outlined and the limitations of their potential in analyzing genetic processes in populations are discussed. Particular emphasis is placed on the relationship between the earlier developed biochemical genetics based on protein polymorphism analysis and modern molecular population genetics based on DNA polymorphism. The possible role of selection in maintaining DNA variation is considered.     

微卫星DNA标记及其在鱼类遗传多样性研究中的应用

微卫星DNA作为第二代分子遗传标记是高等真核生物基因组中种类多、分布广、具有高度的多态性和杂合度的分子标记,由于其具有多态性检出率高、信息含量大、共显性标记、实验操作简单、结果稳定可靠等优点,已经成为种群遗传学研究中被广泛应用的分子遗传标记。微卫星DNA标记技术在鱼类的群体遗传结构的分析、物种遗传多样性的鉴定以及遗传基因连锁图谱的构建等方面已初步得到应用。该文就微卫星技术的原理方法,在鱼类遗传多样性研究中的应用概况以及应用范围和注意事项等方面进行综述。为微卫星技术在鱼类遗传多样性研究中应用提供了理论参考。     

Genotyping-by-sequencing performance in selected livestock species

Application of next generation sequencing for large scale genotyping in livestock is limited by high costs and challenging data analysis process. However, available restriction enzyme-based enrichment techniques like e.g. genotyping-by-sequencing (GBS) are promising tools allowing reduction of financial outlies by a high sample multiplexing and narrowing down the sequenced genome areas to the randomly distributed read tags. In this study, we tested the performance of standard, PstI endonuclease-adapted GBS protocol for population genetics in cattle, horse and sheep with application of different, including low-depth sequencing setups. It was found that the detected SNPs display desirable polymorphism parameters and are evenly scattered across the whole genome including gene coding regions. It was also shown that the SNPs can be successfully applied in population genetics, revealing the genetic differentiation of the studied breeds. The GBS approach represents a cost-effective alternative to existing genotyping methods which may find adoption in various research applications.     

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.     

New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth

We present new methodology for calculating sampling distributions of single-nucleotide polymorphism (SNP) frequencies in populations with time-varying size. Our approach is based on deriving analytical expressions for frequencies of SNPs. Analytical expressions allow for computations that are faster and more accurate than Monte Carlo simulations. In contrast to other articles showing analytical formulas for frequencies of SNPs, we derive expressions that contain coefficients that do not explode when the genealogy size increases. We also provide analytical formulas to describe the way in which the ascertainment procedure modifies SNP distributions. Using our methods, we study the power to test the hypothesis of exponential population expansion vs. the hypothesis of evolution with constant population size. We also analyze some of the available SNP data and we compare our results of demographic parameters estimation to those obtained in previous studies in population genetics. The analyzed data seem consistent with the hypothesis of past population growth of modern humans. The analysis of the data also shows a very strong sensitivity of estimated demographic parameters to changes of the model of the ascertainment procedure.     

A worldwide analysis of AG molecular diversity inferred from serology.

Ten population samples from different geographic origins were tested serologically for the AG polymorphism of human beta-lipoproteins. Their haplotype frequencies were used with previously published data to perform a wide analysis of AG genetic differentiations throughout the world. Coancestry coefficients were computed from weighted F(ST)s among populations by using a matrix of molecular distances among AG haplotypes, which is here determined on the basis of DNA studies. Coancestry coefficients derived from unweighted F(ST)s and more classical Prevosti distances were computed on the same data and used for a comparison. In all cases a highly significant correlation was found between genetics and geography on a worldwide scale, while the significance of the correlation with linguistics differed. A test of significance of the pairwise F(ST)s among populations also gave different results depending on whether the molecular distance matrix among AG haplotypes was included. Globally, this study shows that in spite of being highly significantly correlated to each other, different genetic distance measures can lead to different interpretations of the same data set. Moreover, the elucidation of the molecular models related to the presently known serological polymorphisms may represent an additional tool for analyzing such polymorphisms in human population genetics studies.     

Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns

Biological invasions generally start from low initial population sizes, leading to reduced genetic variation in nuclear and especially mitochondrial DNA. Consequently, genetic approaches for the study of invasion history and population structure are difficult. An extreme example is the Mediterranean fruit fly, Ceratitis capitata (Medfly), for which successive invasions during this century have resulted in a loss of 60% of ancestral genetic variation in isozymes and 75% of variation in mitochondrial DNA. Using Medflies as an example, we present a new approach to invasion genetics that measures DNA sequence variation within introns from multiple nuclear loci. These loci are so variable that even relatively recently founded Medfly populations within California and Hawaii retain ample genetic diversity. Invading populations have only lost 35% of the ancestral genetic variation. Intron variation will allow high-resolution genetic characterization of invading populations in both natural and managed systems, although non-equilibrium methods of analysis may be necessary if the genetic diversity represents sorting ancestral polymorphism.     

基于简化基因组技术的云南蓝果树群体遗传分析

极小种群野生植物云南蓝果树是国家和云南省实施极小种群野生植物保护工程的代表性物种。为有效保护其遗传资源,本研究通过二代测序技术,对其进行简化基因组测序,开发一批特异性高的单核苷酸多态性标记,分析现存群体的遗传结构和遗传多样性。经过遗传变异检测,本次研究中共获得SNP位点98 498个,通过样品最低测序深度>2,样品缺失率<0.5,次要基因型频率（MAF）>0.05筛选以后,得到有效SNP位点6 309个。基于过滤后的SNP,运用生物信息学分析方法,对云南蓝果树完成了群体的遗传分析,其中：系统进化树分析将云南蓝果树划分为3大类,研究分析了云南蓝果树各分类的私人等位基因数目（Private）、平均观测杂合度（H_o）、平均期望杂合度（H_e）、核苷酸多样性（π）和平均近交系数（F_IS）5个遗传多样性参数;群体结构和主成分分析进一步证明了,云南蓝果树现存植株之间亲缘关系较远,遗传多样性差异较大,具有很高的遗传资源保存价值。本研究结果将为基于遗传管理的云南蓝果树就地保护、遗传资源保存和种群重建等保护工程提供科学依据。