群体遗传学研究中STR数据的统计方法应用

STR作为遗传多态性较高的标记, 被广泛地运用于群体遗传学的研究。对于STR分型产生的基因型频率及等位基因频率数据, 文章总结了各种参数指标的计算及分析方法。其中参数指标包括杂合度、多态信息量、连锁不平衡系数、近交系数、遗传距离以及固定指数等; 分析方法包括主成分分析、系统发生树、分子方差分析、R矩阵、地理信息系统以及空间自相关分析。通过这些参数指标及分析方法的使用, 可以既直观又科学地揭示群体遗传结构、群体间遗传分化以及人类起源与进化等群体遗传学中研究的关键问题。     

等位基因多态性群体遗传结构的多元非线性分析方法

长期以来,对于多维基因多态性数据的多元统计分析,如计算遗传距离时昕用的聚类分析、分析群体遗传结构时所用的主成分分析、因子分析和典型相关分析等,一直应用为无约束条件数据而设计的经典多元线性分析方法,并没有注意基因多态性数据的“闭合效应”所带来的问题。从分析基因多态性数据的分布和结构特征入手,文中指出了基因多态性分布具有“闭合数据”的特点,分析了由于“闭合效应”的影响,经典多元线性方法用于群体遗传结构分析昕面临的困难。根据成分数据统计分析的理论和方法,提出了基因多态性群体遗传结构的多元非线性分析基本方法。并以主成分分析为例,通过实例比较和分析了经典线性主成分分析和“对数比”非线性主成分分析的结果,证明“对数比”非线性主成分分析方法是研究基因多态性群体遗传结构的良好方法,具有特异、灵敏等优点,其结果符合群体遗传学规律。     

植物数量性状方差协方差分量精度的估计

一、引言传统的方差协方差分析技术尽管在数量遗传研究中获得了广泛的应用,但仍有很大的局限性。特别是随着电子计算机的应用和多元统计技术的发展,这种局限性日益暴露出来.其一是估算误差较大;其二是遗传协差阵与遗传相关阵有时非正定或接近奇异而出现所谓“病态”;其三是根据于方差协方差成分的有些估计最难于进行显著性检验。这些均给多元遗传分析和生物学解释带来根本性困难.因此,对传统分析技术进行新的评审很有     

种子与花粉的随机迁移对植物群体遗传结构分化的影响

将Ｗｒｉｇｈｔ的经典岛屿模型拓广到植物群体上,同时考虑了含有花粉和种子随机迁移的影响。并给出了３种不同遗传方式的基因（双亲遗传,父本和母本遗传）频率的期望均值和方差。理论结果证明花粉或种子的随机迁移可增加基因频率方差,其幅度取决于迁移率和迁移基因频率的方差。同绝对迁移率一样,花粉和种子的迁移率方差及迁移基因频率的方差对群体遗传结构的分化有着同样的重要。一个重要结论就是花粉或种子的随机迁移率和随机迁     

人类群体遗传空间结构对应分析中的“蹄型效应”及其遗传学解释

探讨了人类群体遗传结构对应分析中“蹄型效应”的产生机制及其遗传学解释。从分析基因频率矩阵的结构特点入手,以实例验证和比较了对应分析中散点图的结构特征。发现当基因频率矩阵的结构不同时,其对应分析中散点图的分布模式不同;当基因频率矩阵中存在稀有基因时,其对应分析的散点图则呈现明显的“蹄型效应”。“蹄型效应”经常会歪曲潜在遗传结构的真实形态,其产生主要是因为对应分析中的c2距离不相似测度高估了稀有基因的作用。在人类群体遗传结构对应分析中,当出现“蹄型效应”效应时,需认真分析基因频率矩阵的结构,寻找“蹄型效应”产生原因并给出合理的遗传学解释,以免做出错误结论。     

基于两种主成分分析方法分析石斛化学成分差异

探索相关性矩阵和协方差矩阵两种算法的主成分分析方法的差异。本文采用两种主成分分析方法分别计算色谱技术检测得到的石斛化学成分并进行聚类讨论。结果表明在16种石斛植物中得到的11种化学成分含量差异明显,通过相关性矩阵和协方差矩阵两种算法提取得到的主成分及其次序有一定差异,结合聚类分析表明两种聚类结果也存在差异。因此,在对近缘种植物天然产物成分进行差异分析或化学成分聚类,甚至在药材类真伪品鉴别的研究中,建立高效、精准的检测手段与选择适当的数据分析方法同等重要。     

用主成分分析法分析金翅夜蛾亚科各性状对分类的重要性和性状变异方向

本文在“金翅夜蛾亚科的数值分类研究”的基础上用主成分分析的结果对金翅夜蛾亚科分类的性状做进一步分析,说明各性状对分类的重要性和性状的变异方向,并对用协方差矩阵和相关矩阵进行的主成分分析结果进行比较,说明对本问题（分类指标全是定性指标）适宜用协方差矩阵做主成分分析。     

笋瓜节间长发育逆转及其遗传模型研究

分别以短蔓型和长蔓型笋瓜材料为亲本构建6世代群体,测量各群体不同节位节间长的变化,对节间长性状进行遗传规律分析。研究结果表明:节间长性状受核基因控制,F1群体的节间长性状在生长过程中存在发育逆转现象,逆转时期发生在6~15节位之间。遗传模型分析结果显示,在幼苗期和逆转期,笋瓜的节间长受到2对主效基因控制,符合E1模型,主基因方差能解释F2群体方差的70%以上;生长后期则受到主效单基因控制,符合D4模型,但主效基因效应不强,只能解释F2群体方差的10%,且环境因素对植株生长后期节间长具有明显影响。     

人类群体遗传空间结构的"克立格"模型

通过将“克立格”技术应用于人类群体遗传学领域,构建了人类群体遗传空间结构的“克立格”模型,并论述了其原理和计算方法。以HLA-A基因座为例,应用“克立格”模型,定量分析了中国人群HLA-A基因座的空间遗传异质性;对HLA-A基因频率的空间数据矩阵进行了主成分分析,进而定义了人类群体遗传结构的综合遗传测度(SPC),绘制了综合遗传测度和主成分(PC)的“克立格”地图,分析了其群体遗传空间结构特性。与其他空间插值或平滑方法相比,人类群体遗传空间结构的“克立格”模型具有明显优点：1)“克立格”估计以空间遗传变异函数模型为基础,在绘制空间遗传结构地图之前,可利用变异函数模型定量分析所研究基因座(或多基因座)的空间遗传异质性;2)“克立格”插值方法是真正意义上的无偏估计模型,它利用待估区域周围的已知群体遗传调查点数据,并充分考虑调查点的空间影响范围,给出待估区域的最优估计值;3)“克立格”模型允许估计插值误差,这种插值误差既可用于评价空间估计效果,又可通过绘制误差地图指导在误差过高的地点增加新的群体遗传调查样本点,以优化估计效果。然而,人类群体遗传空间结构的“克立格”模型也存在一定缺点：1)若不能用任何理论遗传变异函数模型拟合观察遗传变异函数值,则不能建立“克立格”模型;2)若理论遗传变异函数的拟合优度很低,则据此建立的“克立格”模型的估计标准差在整个空间范围内会很大,此时“克立格”模型不适用于估计群体遗传空间结构。出现上述两种情形时,应选用不考虑空间相关性的空间随机插值方法绘制群体遗传结构地图,如基因绘图软件中的Cavalli-Sforza方法,反向距离加权法和条样函数插值法等。     

应用混合分布模型研究水稻株高的遗传

用质量－数量性状的混合分布遗传模型对２个水稻矮秆×高秆的Ｆ_２群体（组合１：Ｈ３５９／Ａｃｃ８５１８;组合 ２：Ｈ３５９／Ａｃｃ８５５８）的株高遗传进行了研究．结果表明：１）存在 １对主基因的分离,高秆对矮秆完全显性; ２）这对主基因的效应大小在两个组合中非常相近,说明这对主基因在不同遗传背景中效应稳定,与微基因之间无明显互作,这对于育种应用是有利的;３）两组合中由微基因分离引起的遗传方差大小相近,微基因的平均显性效应皆是减效方向,且数值上也相近,而平均加性效应则皆呈增效方向,但数值上相差很大,说明两组合中发生分离的微基因的数目可能相似,但微基因在双亲间的分布情况却大不相同;４）亲本表型方差（亦即环境方差）与亲本均值呈明显正相关关系,高秆的环境方差要比矮秆大得多,因而在不同主基因型中,微基因的遗传力表现不同,这在育种实践中应引起注意．     

客家人起源的遗传学分析

客家人是南方讲客家话的特殊汉族民系,其来源学术界有一定争议。该研究对福建长汀的148个客家男子做了遗传分析。从父系遗传的Y染色体SNP的主成分分析看,客家人与中原汉族最近,又偏向于苗瑶语族群中的畲族,不同于其他南方汉族偏向于侗台语族群。混合分析发现客家人数据结构中汉族结构占80．2％,类畲族结构13％,类侗族结构6．8％。各族M7个体Y-STR单倍型的网络结构分析发现客家人中类苗瑶结构有两个来源,其一来自湖北,其一来自广东。客家人之类侗族结构应来自江西土著干越。客家人母系遗传的线粒体Region V区段9bp缺失频率为19．7％,与畲族很近,不同于中原汉族。客家人的主要成分应是中原汉人,畲族是对客家人影响最大的外来因素。与客家话中的苗瑶语特征相印证,客家人可能是古代荆蛮族的核心成分不断加上中原汉人移民形成的。客家话等南方汉语方言最初也可能是南方原住民语言在中原汉语不断影响下逐渐形成的。     

Modeling the evolution of genetic architecture: A continuum of alleles model with pairwise AxA epistasis

A continuum of alleles model with pair-wise AxA epistasis is proposed and its transmission genetic, and variational properties are analysed. The basic idea is that genes control the values of underlying variables, which affect the genotypic value of phenotypic characters proportional to a "scaling factor". Epistasis is the influence of one gene on the average effect of another gene. In this model, epistasis is introduced as a mutational effect of one gene on the scaling factors of another gene. In accordance with empirical results, the model assumes that the average direct effect of mutations is zero, as is the average epistatic effect. The model predicts that, on average, a mutation at one locus increases the expected mutational variance of mutations at another interacting locus. The increase in mutational variance is predicted to be equal to the variance of the pair-wise epistatic effects. This result is consistent with the observation that mutant phenotypes tend to be more variable than the wildtype phenotype. Another generic result of this model is that the frequency of canalizing mutations can at most be equal to the frequency of de-canalizing mutations. Furthermore, it is predicted that the mutational variance of a character increases at least linearly with the size of the character; hence this model is scale variant. In the case of two characters it is shown that the dimensionality of the locus-specific mutational effect distribution is invariant, i.e. the rank of the mutational covariance matrix M is invariant. While in additive models the mutational covariance matrix is always and entirely invariant, the invariance in the case of epistatic models is unexpected. Epistatic interactions can change the magnitude of the mutational (co)variances at a locus and can thus influence the structure of the mutational covariance matrix. However, in the present model the dimensionality of the mutational effect distribution remains the same. A consequence of this result is that, in this model, the genetic architecture of a set of characters is always evolvable i.e. no hard constraints can evolve.     

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

Patterns of phenotypic covariation and correlation in modern humans as viewed from morphological integration

Proportionality of phenotypic and genetic distance is of crucial importance to adequately focus on population history and structure, and it depends on the proportionality of genetic and phenotypic covariance. Constancy of phenotypic covariances is unlikely without constancy of genetic covariation if the latter is a substantial component of the former. If phenotypic patterns are found to be relatively stable, the most probable explanation is that genetic covariance matrices are also stable. Factors like morphological integration account for such stability. Morphological integration can be studied by analyzing the relationships among morphological traits. We present here a comparison of phenotypic correlation and covariance structure among worldwide human populations. Correlation and covariance matrices between 47 cranial traits were obtained for 28 populations, and compared with design matrices representing functional and developmental constraints. Among-population differences in patterns of correlation and covariation were tested for association with matrices of genetic distances (obtained after an examination of 10 Alu-insertions) and with Mahalanobis distances (computed after craniometrical traits). All matrix correlations were estimated by means of Mantel tests. Results indicate that correlation and covariance structure in our species is stable, and that among-group correlation/covariance similarity is not related to genetic or phenotypic distance. Conversely, genetic and morphological distance matrices were highly correlated. Correlation and covariation patterns were largely associated with functional and developmental factors, which probably account for the stability of covariance patterns.     

Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.     

THE COVARIANCE STRUCTURE OF LIFE-HISTORY CHARACTERS IN DAPHNIA PULEX

The genetic covariance structure for life-history characters in two populations of cyclically parthenogenetic Daphnia pulex indicates considerable positive correlation among important fitness components, apparently at odds with the expectation if antagonistic pleiotropy is the dominant cause of the maintanence of genetic variation. Although there is no genetic correlation between offspring size and offspring number, present growth and present reproduction are both strongly positively correlated genetically with future reproduction, and early maturity is genetically correlated with larger clutch size. Although the ubiquity of antagonistic pleiotropy has been recently questioned, there are peculiarities of cyclical parthenogenesis that could lead to positive life-history covariance even when negative covariance would be expected in a similar sexual species. These include the influence of nonadditive gene action on evolution in clonally reproducing organisms, and the periodic release of hidden genetic variance within populations of cyclical parthenogens. Examination of matrix similarity, using the bootstrap for distribution-free hypothesis testing, reveals no evidence to suggest that the genetic covariance matrices differ between the populations. However, there is considerable evidence that the phenotypic and environmental covariance matrices differ between populations. These results indicate approximate stability of the genetic covariance matrix within species, an important assumption of many phenotypic evolution models, but should caution against the use of phenotypic in place of genetic covariance matrices.     

云南泸西汉族17个Y-STR基因座多态性及遗传关系分析

调查云南泸西县汉族群体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。应用AmpF?STR?Yfiler荧光标记复合扩增系统扩增156名汉族无关男性个体的17个Y-STR基因座, 用ABI3100遗传分析仪进行基因检测, 计算等位基因及单倍型频率, 并结合已公开发表的国内外其他16个群体的遗传学资料, 分析各群体间的遗传距离。云南泸西汉族男性群体中, 共观察到154种单倍型, 其中152种为仅观察到1次的单倍型, 2种单倍型观察到2次, 单倍型多样性(HD)值为0.9998, 基因多样性(GD)值在0.3901(DYS437)—0.9632(DYS385a/b)。17个群体遗传距离分析提示, 国内人群云南泸西汉族与湖南汉族的遗传距离最小(0.005), 与闽南汉族的遗传距离最大(0.035); 在中国周边群体中,云南泸西汉族与新加坡华人的遗传距离最小(0.015), 与日本人和马来西亚印度人群的遗传距离最大(0.060)。结果表明, 17个Y-STR基因座在云南泸西汉族中具有较高的遗传多态性, 适用当地的法医学应用。与其他民族群体的遗传多样性比较, 对了解各群体的起源、迁徙及相互关系有重要意义。     

Association and differentiation of MHC class I and II polymorphic Alu insertions and HLA-A, -B, -C and -DRB1 alleles in the Chinese Han population

In order to investigate the polymorphism of Alu insertions (POALINs) in the HLA region, we genotyped ten Alu loci (AluMICB, AluTF, AluHJ, AluHG, AluHF in the HLA class I region and AluDPB2, AluDQA2, AluDQA1, AluDRB1, AluORF10 in the HLA class II region) to determine their allele frequencies and associations with the HLA-A, HLA-B, HLA-C and HLA-DRB1 genes in the Chinese Han population. Our results showed the ten-loci POALINs varied in frequency between 0.003 and 0.425. By comparing the data of the ten-loci POALIN in Chinese Han with Japanese and Caucasian data, marked differences were observed between the three ethnic groups at the allelic or haplotypic levels. Each POALIN was in significant linkage disequilibrium with a variety of HLA-A, -B, -C and -DRB1 alleles, and was associated with a variety of HLA-A, -B, -C and -DRB1 allele in Chinese Han. This comparative study of multilocus POALINs in the HLA class I and II regions of the Chinese Han population shows that POALINs alone or as haplotypes together with the HLA class I and II alleles are informative genetic markers for the identification of HLA class I and II allele and variations, such as crossing over events within the same and/or different populations.     

Population Genetics of Euphydryas Butterflies. I. Genetic Variation and the Neutrality Hypothesis

Twenty-one populations of the checkerspot butterfly, Euphydryas editha, and ten populations of Euphydryas chalcedona were sampled for genetic variation at eight polymorphic enzyme loci. Both species possessed loci that were highly variable from population to population and loci that were virtually identical across all populations sampled. Our data indicate that the neutrality hypothesis is untenable for the loci studied, and therefore selection is indicated as the major factor responsible for producing these patterns. Thorough ecological work allowed gene flow to be ruled out (in almost all instances) as a factor maintaining similar gene frequencies across populations. The Lewontin-Krakauer test indicated magnitudes of heterogeneity among standardized variances of gene frequencies inconsistent with the neutrality hypothesis. The question of whether or not to correct this statistic for sample size is discussed. Observed equitability of gene frequencies of multiple allelic loci was found to be greater than that predicted under the neutrality hypothesis. Genetic differentiation persisting through two generations was found between the one pair of populations known to exchange significant numbers of individuals per generation. Two matrices of genetic distance between populations, based on the eight loci sampled, were found to be significantly correlated with a matrix of environmental distance, based on measures of fourteen environmental parameters. Correlations between gene frequencies and environmental parameters, results of multiple regression analysis, and results of principle component analysis showed strong patterns of association and of "explained" variation. The correlation analyses suggest which factors might be further investigated as proximate selective agents.