Genetic Diversity and the Survival of Populations

Abstract: In this comprehensive review, a range of factors is considered that may influence the significance of genetic diversity for the survival of a population. Genetic variation is essential for the adaptability of a population in which quantitatively inherited, fitness-related traits are crucial. Therefore, the relationship between genetic diversity and fitness should be studied in order to make predictions on the importance of genetic diversity for a specific population. The level of genetic diversity found in a population highly depends on the mating system, the evolutionary history of a species and the population history (the latter is usually unknown), and on the level of environmental heterogeneity. An accurate estimation of fitness remains complex, despite the availability of a range of direct and indirect fitness parameters. There is no general relationship between genetic diversity and various fitness components. However, if a lower level of heterozygosity represents an increased level of inbreeding, a reduction in fitness can be expected. Molecular markers can be used to study adaptability or fitness, provided that they represent a quantitative trait locus (QTL) or are themselves functional genes involved in these processes. Next to a genetic response of a population to environmental change, phenotypic plasticity in a genotype can affect fitness. The relative importance of plasticity to genetic diversity depends on the species and population under study and on the environmental conditions. The possibilities for application of current knowledge on genetic diversity and population survival for the management of natural populations are discussed.     

Genetic Diversity among Ancient Nordic Populations

Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.     

箭叶淫羊藿居群形态及遗传多样性比较研究

箭叶淫羊藿（Epimedium sagittatum）是淫羊藿属中分布最广、形态变异最大、分类学最难处理的一个物种,不同箭叶淫羊藿居群其形态、活性成分等差异较大,质量极其不稳定。本实验选择湖北罗田等12个不同的箭叶淫羊藿地理居群,在武汉植物园进行同园栽培,分析其主要形态数量性状及遗传多样性。结果发现箭叶淫羊藿不同居群在形态上表现出各自明显的差异。基于AFLP数据进行的遗传多样性分析显示,各居群聚类关系与地理分布密切相关,柳州居群（LZ）、西南居群（CL、HH、ZY）、华东华中居群（YT、WN、NF、HS、QZ、SG、LY、LT）依次分出。而形态分层聚类分析显示各居群形态变异复杂,只有部分与遗传多样性有一定的相关性。本研究结果对箭叶淫羊藿分类研究及资源筛选具有重要指导作用。     

水杉栽培居群的遗传多样性研究

利用RAPD技术,对9个水杉(Metasequoiaglyptostroboides)栽培居群的遗传多样性进行了初步研究。用10bp的随机引物16条,共扩增出103个位点,其中37个为多态位点,占35.92%。各居群的多态位点百分率在16.50%~33.01%之间。POPGENEversion1.31软件处理结果如下:居群的Shannon’s信息指数为0.1930。遗传距离在0.0130~0.0650之间,遗传一致度在0.9370~0.9871之间。AMOVA分析结果显示遗传变异主要存在于居群内,占89.05%,居群之间有一定的分化。上述结果表明水杉栽培居群的遗传多样性略低于自然居群,涵盖了自然居群近80%的遗传多样性。由此可以确认栽培水杉的种源是经过混合的,它们在相当程度上代表了自然居群的遗传多样性水平。采自潜江的9株丛枝水杉(Metasequoiaglyptostroboidesvar.caespitosa)没有扩增出特有位点,将其视为一个居群根据遗传一致度作UPGMA聚类分析时,该居群和湖北的3个居群及南京(NJ)、成都(CD)居群聚在一起;单株聚类时丛枝水杉也没有聚成独立的一支,而是比较分散,因此不支持将丛枝水杉作为水杉的一个变种的分类处理。从亲缘关系上看,丛枝水杉应当归属于湖北潜江蚌湖种子园(BH)和湖北潜江广华(GH)居群,这与其分布现状也是吻合的。     

Rh系统单倍型在中国人群中的分布

对中国已发表的125个人群Rh血型系统表型分布频率数据进行了收集和整理。用累积计算法（Counting method)重新计算单倍型频率,通过各单倍型的分布差异分析中国不同地区不同种族、人群的遗传差异,分组比较了不同地区汉族和少数民族人群的基因多样度和基因分化度,结果表明南方少数民族和北方少数民族民族亚群体基因多样度有明显差异,用不同方法计算中小组遗传距离并进行聚类分析。最后,计算了除维吾尔族和哈萨克族外的68个人群间的遗传距离并聚类比较,结果表明Rh基因单倍型的分布与地理分布基本相符。     

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks

The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides , a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.     

缢蛏种群遗传多样性的周年变异分析

利用线粒体COI标记分析了福建省宁德市漳湾镇横屿村滩涂5个月份缢蛏群体(S3,S5,S7,S9,S11)的遗传结构,以期评估不同月份时期种群的遗传多样性差异。基于线粒体COI基因的结果表明,5个缢蛏群体的平均核苷酸差异数位于2.7836-3.6894之间,核苷酸多样性指数位于0.0050-0.0066之间,遗传多样性水平大致表现为S3和S5群体较高于S7和S9群体,明显高于S11群体。AMOVA分析结果显示,群体间遗传变异量占总变异的7.18%,而群体内变异达到了92.82%,说明遗传差异主要来自于群体内部。由此可见,从3月份到11月份,缢蛏群体的遗传多样性水平呈现出下降趋势,尤其是在11月份,差异最为明显。     

吉富罗非鱼群体遗传多样性的AFLP分析

为了分析吉富罗非鱼的遗传多样性,为其育种提供理论依据,本实验利用5对引物组合(E-AGG/M-CTT, E-AGG/M-CTG, E-AAC/M-CAG, E-ACA/M-CTG, E-ACA/M-CAG)对广东省化州光辉养殖场有限公司新选育的吉富罗非鱼第16代群体(F16)进行遗传多样性的AFLP分析.27个个体共检出187个扩增位点,其中多态位点163个,平均每对引物扩增出32.6个位点,多态位点比例87.17%;平均Nei's基因多样性0.2886;平均Shannon's指数0.4339.结果说明实验群体存在较丰富的遗传多样性且保持有较高的遗传杂合度,具有进一步育种和开发的价值.     

大鳞副泥鳅5个野生群体的遗传多样性分析

利用微卫星分子标记分析了天津地区于桥水库、大黄堡湿地、七里海湿地、团泊水库和潮白新河5个野生大鳞副泥鳅群体的遗传多样性。5个群体在12个微卫星位点共检测到98个等位基因,平均等位基因数为8.500;有效等位基因数为2.713;平均观测杂合度为0.526;平均期望杂合度为0.544。5个群体间的遗传分化指数介于0.021~0.106之间,平均遗传分化指数为0.059,属中低水平的遗传分化。AMOVA分析结果显示,在总的变异中,94.1%的遗传变异来自群体内,5.90%的遗传变异来自于群体间。根据Nei’s遗传距离所绘制的系统树显示,于桥水库、团泊水库、七里海湿地和大黄堡湿地4个群体的遗传距离相对较小聚为一支,潮白新河群体单独为一支。遗传瓶颈效应分析表明,该5个群体近期未经受遗传瓶颈效应,处于突变-漂移平衡。总体来看,天津地区5个野生大鳞副泥鳅群体的遗传多样性较高,可作为品种选育的基础群体。     

Genetic Diversity in Introduced Populations with an Allee Effect

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations.     

2个中国藏獒群体遗传多样性及遗传分化的研究

本研究以青海土种犬和藏狮犬为对照,采用RAPD技术对河曲藏獒和青海藏獒群体的遗传多样性及遗传分化进行了分析.研究结果表明,河曲藏獒和青海藏獒群体的多态性位点百分率分别为85.53%和98.16%,平均多态性位点百分率为91.85%.藏獒群体遗传变异分析显示两个藏獒群体的有效等位基因数(Ne)、Nei氏平均预期基因杂合度(H)和Shannon遗传信息指数(I)的平均值分别为1.5354、0.3191和0.4807;且两个藏獒群体93.09%的变异来自群体内,仅6.91%变异来自群体间;两个群体间的基因流为3.3679.研究还发现两个藏獒群体之间的Nei氏标准遗传距离(D)为0.050 5.本研究结果说明藏獒群体内遗传变异丰富,不同地域的藏獒群体之间存在广泛的基因交流,群体之间遗传分化程度很低,这为藏獒品种资源保护与合理开发利用提供了参考.     

Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers

Switchgrass (Panicum virgatum L.) is a warm season, C₄ perennial grass native to most of North America with numerous applications, including use as a bioenergy feedstock species. To date, no studies on genetic diversity in switchgrass have been conducted that use both molecular and morphological markers. The objectives of this study were to assess genetic diversity and determine differences among and between 12 switchgrass populations grown in New Jersey by examining both morphological and molecular characteristics, and to determine whether morphological, molecular, and/or combined data sets can detect ecotype and/or geographical differences at the population level. Twelve plants from each population were characterized with 16 switchgrass expressed sequence tag-simple sequence repeat markers (EST-SSRs) and seven morphological characters. Data was analyzed using GenAlEx and Unweighted Pair-Group Method of Averages (UPGMA) cluster analysis. Most (64%) of the molecular variation in switchgrass populations exists among individuals within populations, with lesser amounts between populations (36%). Upland and lowland populations were distinguished in all three data sets. Some eastern US and midwestern US populations were distinct in all three data sets. Similarities were observed between all three data sets indicating molecular markers may be useful for identifying morphological differences or other adaptive traits. The combined data set was the most useful in differentiating populations based on geography and found separation between midwestern and eastern upland populations. The results indicate that the combination of morphological and molecular markers may be useful in future applications such as genetic diversity studies, plant variety protection, cultivar identification, and/or identifying geographic origin.     

黑颈乌龟两个养殖种群的遗传多样性分析

开展濒危物种养殖群体的遗传多样性研究,对种质资源的保护与利用具有重要意义.选择线粒体COI基因作为本次研究的分子标记,分别从序列组成、单倍型及遗传距离、种群历史动态等方面对黑颈乌龟(Mauremys nigricans)两个养殖种群进行比较分析.结果显示:两个种群的COI序列全长572 bp,A+T含量为55.4％,G...     

Genetic Diversity of Protein Markers in Sheep Populations from Ukraine

Based on polymorphism of genes for antigen factors of six blood-group systems and four blood protein loci, genetic structure and the main variation parameters were studied in three sheep breeds and three sheep breed types constituting the basis of purebred sheep resources in Ukraine. Specific features of the distribution of genotypes and alleles of polymorphic loci were determined in each of the studied sheep groups depending on their origin and production type. The molecular–genetic markers used in the analysis of the genetic relationships between the sheep breeds and breed types were shown to objectively reflect their breeding history and evolution. Integrally, each of the studied gene pools had a specific profile of gene frequencies reflecting breeding specificity, breed history, and genetic differentiation of breeds.     

5种常见珍珠贝的系统发育和遗传多样性分析

利用RAPD标记分析了珠母贝属常见的马氏珠母贝、大珠母贝、珠母贝、解氏珠母贝以及珍珠贝属常见企鹅珍珠贝的系统发育,同时分析了马氏珠母贝和大珠母贝不同地理种群的遗传多样性,并以邻接法(neighbor-joining,NJ)构建了种间及种群间的系统分支图.结果表明:(1)在珍珠贝5种9个种群中,大珠母贝的4个种群最早聚在一起分别成为2个姊妹群,这2个姊妹群聚合为1个单元群后,又与珠母贝聚在一起,然后才与马氏珠母贝姊妹群聚合成的单元群聚合,再与解氏珠母贝聚合,最后才与企鹅珍珠贝聚合;(2)珠母贝属4种珍珠贝进化程度由低到高的等级顺序为解氏珠母贝-马氏珠母贝-珠母贝-大珠母贝;解氏珠母贝是最晚形成的种类;(3)比较5种珍珠贝野生种群的Nei's多样性和Shannon多样性值为:马氏珠母贝(0.411 1和0.593 3)>珠母贝(0.397 1和0.578 4)>企鹅珠母贝(0.383 1和0.549 3)>大珠母贝(0.338 8和0.499 9)>解氏珠母贝(0.301 6和0.445 2);(4)无论是马氏珠母贝,还是大珠母贝,野生种群的遗传多样性值均大于养殖种群.     

Genetic Structure and Diversity of Glycyrrhiza Populations Based on Transcriptome SSR Markers

Plant Molecular Biology Reporter - Glycyrrhiza is a widely used traditional Chinese herb with medicinal value. Recently, however, Glycyrrhiza biodiversity has faced an unprecedented threat due to...     

Genomic Studies of Hereditary Disorders and the Genetic Diversity of Siberian Populations

The review considers the results of genome research on the Russian program Human Genome carried out in the Institute of Medical Genetics (Tomsk) since 1990. The three major fields were molecular cytogenetics and chromosomal disorders, genomics of Mendelian and common diseases, and ethnogenomics of the North Asian population. Several human genes were cytogenetically mapped, and numerical and structural abnormalities associated with human diseases were studied by fluorescence hybridization. Procedures of DNA diagnosis were developed for 15 hereditary diseases. New data were obtained on the genetic heterogeneity of idiopathic hypertrophic cardiomyopathy. The genetic bases of multifactorial (atopic bronchial asthma) and infectious (tuberculosis) diseases were analyzed. The North Eurasian population (41 local populations of 21 ethnic groups) was tested for genetic diversity with numerous genetic markers, including Y-chromosomal haplotypes, autosomal microsatellites, and polymorphic Alu insertions.     

Genetic Diversity of Arginine Catabolic Mobile Element in Staphylococcus epidermidis

Background

The methicillin-resistant Staphylococcus aureus clone USA300 contains a novel mobile genetic element, arginine catabolic mobile element (ACME), that contributes to its enhanced capacity to grow and survive within the host. Although ACME appears to have been transferred into USA300 from S. epidermidis, the genetic diversity of ACME in the latter species remains poorly characterized.

Methodology/Principal Findings

To assess the prevalence and genetic diversity of ACME, 127 geographically diverse S. epidermidis isolates representing 86 different multilocus sequence types (STs) were characterized. ACME was found in 51% (65/127) of S. epidermidis isolates. The vast majority (57/65) of ACME-containing isolates belonged to the predominant S. epidermidis clonal complex CC2. ACME was often found in association with different allotypes of staphylococcal chromosome cassette mec (SCCmec) which also encodes the recombinase function that facilities mobilization ACME from the S. epidermidis chromosome. Restriction fragment length polymorphism, PCR scanning and DNA sequencing allowed for identification of 39 distinct ACME genetic variants that differ from one another in gene content, thereby revealing a hitherto uncharacterized genetic diversity within ACME. All but one ACME variants were represented by a single S. epidermidis isolate; the singular variant, termed ACME-I.02, was found in 27 isolates, all of which belonged to the CC2 lineage. An evolutionary model constructed based on the eBURST algorithm revealed that ACME-I.02 was acquired at least on 15 different occasions by strains belonging to the CC2 lineage.

Conclusions/Significance

ACME-I.02 in diverse S. epidermidis isolates were nearly identical in sequence to the prototypical ACME found in USA300 MRSA clone, providing further evidence for the interspecies transfer of ACME from S. epidermidis into USA300.     

8个山荆子居群遗传多样性的ISSR分析

采用ISSR标记对中国北方地区的8个山荆子居群进行了遗传多样性分析,以探讨山荆子在苹果属植物演化过程中的作用.结果显示:(1)从55个ISSR引物中,筛选出11个多态性引物,共扩增出71个位点,其中多态性位点69个,多态位点达97.47%.(2)在物种水平上,有效等位基因数Ne=1.467 0,Nei's基因多样性(H)为0.284 6,Shannon信息指数(I)为0.439 9,多态位点百分率(PPB)=80.22;基因流(Nm)为1.659 1,居群间基因分化系数(Gst)为0.231 6,Φst值为0.236 0.(3)聚类分析结果显示,在遗传距离为0.155 5、0.136 9、0.125 8处8个山荆子居群分别聚为两大类、三亚类、四小类,但居群聚类位置与地理位置无明显的相关性.(4)山荆子的居群内遗传多样性贡献率占76.40%,而居群间的贡献率占23.60%,说明山荆子的遗传多样性主要分布在居群内,但居群间的遗传分化程度也较高.由此推测,山荆子的起源中心在华北和东北范围内,其中灵空山(山西)和塞罕坝(河北)居群可近似为核心居群;ISSR标记与花部的一些性状可能有连锁关系.