秦巴山区中华蜜蜂种群微卫星DNA遗传分析

【目的】中华蜜蜂Apis cerana cerana是一种兼有生态价值和经济价值的授粉昆虫。本研究拟揭示秦巴山区中华蜜蜂种群遗传多态性现状,探讨中华蜜蜂的种群分化机制及其影响因素。【方法】使用8个微卫星DNA标记评估秦巴山区17个样点共979个蜂群的中华蜜蜂遗传多态性,以长白山中华蜜蜂和阿坝中华蜜蜂作为外群进行种群遗传分化分析。【结果】秦巴山区中华蜜蜂95%的差异来源于样点内,样点间遗传分化系数(Fst)为0.002~0.037,基因流参数Nm为6.51~124.75,与外群的遗传分化分析中均显示秦巴山区中华蜜蜂不存在遗传分化。平均期望杂合度(He)为0.6877±0.1098,平均观察杂合度(Ho)为0.6364±0.1367,平均有效等位基因数(Ne)为3.7488±1.6201个,平均等位基因数(Na)为7.71±2.52个,多态信息含量(PIC)为0.6418±0.1152,香农指数(I)为1.5026±0.3754,这些参数均表明微卫星遗传多态性丰富。中蜂囊状幼虫病流行过的地区,其杂合度、多态信息含量以及等位基因数均显著低于未发病地区。【结论】秦巴山区中华蜜蜂种群数量大,分布均匀,基因流水平高,在650 km距离范围内没有发生种群分化;秦巴山区中华蜜蜂微卫星遗传多态性丰富,仅部分地区中华蜜蜂遗传多态性受中蜂囊状幼虫病的选择压而降低。     

蜜蜂线粒体DNA在遗传分析中的应用

线粒体DNA是动物细胞核外唯一的遗传物质,具有结构简单、进化速度快、母系遗传和基因重组率小等特点。文章在介绍蜜蜂线粒体DNA的结构大小及其多态性的研究的基础上,对其在蜜蜂的种间多态性、亚种间及亚种内多态性、起源进化、群体遗传结构及基因流动、亚种及类型的分类等方面的研究应用进行阐述。     

鱼类线粒体DNA及其在分子群体遗传研究中的应用

鱼类是脊椎动物亚门中种属数量最多的类群,分布广泛,起源复杂,拥有丰富的遗传多样性.多种自然和人为因素对鱼类遗传资源存在不同程度的作用,对鱼类生存和进化有重要影响.采用分子手段探讨鱼类遗传资源现状,可为遗传育种、鱼类进化研究和遗传资源保护等提供一定科学依据.以鱼类线粒体DNA(mtDNA)为代表的分子标记技术已被用于研究鱼类群体遗传结构及其与影响因素间的关系.本文综述了鱼类mtDNA的结构特征及其在鱼类分子群体遗传研究中的应用,对了解和运用mtDNA等分子标记研究鱼类群体遗传具有一定参考价值.     

生态退化的形成原因探讨

生态退化由生态基质、内在的动能因素和外在干扰共同作用的结果, 自然因素和人为活动干扰是生态系统退化的两大驱动力。从自然的角度来讲, 区域地质地貌、气候和水文等的异常变化是生态系统不稳定性和退化的自然成因。人为因素往往叠加在自然因子之上,对生态退化起着加速和主导的作用, 人为因素主要包括人口增长、农业活动、工业与城市化活动、政治与战争、贫困、文化与旅游等, 它们对生态环境的影响是多方面的、深远的、不确定的。     

广西东方蜜蜂遗传多样性分析

[目的]东方蜜蜂Apis cerana是我国重要的经济昆虫,是生态循环中的重要环节,对其进行种群遗传研究能为东方蜜蜂遗传资源的发现、保护和利用提供基础.广西是我国东方蜜蜂重要的产区和分布区之一.[方法]本研究通过33个形态标记、38个微卫星标记和tRNAleu-CO Ⅱ片段的线粒体标记,对广西东方蜜蜂进行遗传分化、特征和遗传多样性分析.[结果]根据形态逐步判别-聚类分析、主成分-聚类分析,微卫星DAPC、Structure分析、聚类树分析、Fst、AMOVA分析,以及线粒体的Fst分析,结果显示广西东方蜜蜂没有发生种群遗传分化.广西东方蜜蜂的微卫星遗传多样性水平在各样点间较为稳定,但线粒体遗传多样性在广西不同样点间的差异较大.线粒体遗传结构易受人为影响,受人为影响小的9个样点线粒体结构中以Acmt01001为主要单倍型;在活框饲养技术发达的北流样点和北海样点,线粒体遗传结构的主要单倍型有2-3种,且Acmt01001比例不是最高的,这意味着人工育王等人为干扰影响较大.[结论]在广西环境基本一致且种群数量较大,基因流通畅的条件下,最远距离约650 km的样点间没有发生遗传分化,意味着东方蜜蜂仅由距离导致遗传分化的距离要大于650 km.根据广西东方蜜蜂遗传多样性现状,对广西东方蜜蜂遗传资源保护和利用提出了建议.     

人类基因组中单核苷酸多态性的检测技术

随着人类基因组测序工作的完成,单核苷酸多态性作为继限制性片段长度多态性和微卫星多态性这2种遗传标记之后的第3代遗传标记,已成为人类后基因组时代的主要研究内容之一。系统地介绍了人类基因组中单核苷酸多态性的传统检测方法、新的方法以及基于生物信息学的方法,并对SNP检测技术的发展进行了展望。     

棉铃虫种群遗传变化的研究(英文)

利用重复序列引物扩增DNA多态性方法研究了几个产棉区的棉铃虫的种群遗传结构变化。结果表明 :实验室种群比自然种群的遗传变化低 ,自然种群间的遗传差异不显著 ,同一地点不同年间种群间存在较大遗传差异 ,表明棉铃虫的迁飞扩散现象比较明显 ;聚类分析结果表明 ,来自辽宁的朝阳种群 (CY)与来自山东高唐 (GT)、江苏大丰 (DF)的种群间的有较强的基因流 ,为我国东北地区棉铃虫主要来自河北、山东等地的假说提供了一定的理论依据。本研究所选用的遗传标记能灵敏地检测种群的遗传结构变化     

鸡的遗传多样性的研究方法及研究进展

遗传多样性是生物学研究中的一个重要领域,研究鸡的遗传多样性,不仅能加强生物多样性的保护。同时对起源进化、分类鉴定及遗传育种等都有重要的意义。本文对目前DNA水平鸡的遗传多样性的研究方法和研究进展进行了详细的阐述。重点介绍了DNA分子标记的特征;概括了在鸡遗传多样性分子标记的方法,包括微卫星分子标记(SSR)、扩增片段长度多态性(AFLP)、随机扩增多态性标记(RAPD)、限制性片段长度多态性标记(RFLP)和单核苷酸多态性标记(SNP)。本文综述了最近有关鸡DNA水平的遗传多样性的研究方法在系统学、遗传结构、生物地理等研究中的应用情况;提出在研究鸡遗传多样性时,可根据研究的目的,选择合适的方法。     

基于微卫星DNA的神农架川金丝猴遗传结构研究

川金丝猴(Rhinopithecus roxellana)是我国特有珍稀濒危物种,了解其种群遗传结构和关键影响因素,对该物种的保护具有重要意义。以我国分布最东端的湖北神农架川金丝猴种群为研究对象,基于非损伤性DNA技术和微卫星DNA遗传标记等分子生物学方法及景观遗传参数,探讨了神农架川金丝猴的遗传多样性和遗传结构,旨在为川金丝猴的研究及川金丝猴种群的可持续发展提供理论基础。利用12个多态性微卫星位点,在455份川金丝猴粪便样品中,共检测到62个微卫星等位基因;共鉴定出316个不同川金丝猴个体;种群的平均期望杂合度、平均观察杂合度和多态性信息含量分别为0.626、0.559和0.650;群体间的Nei's遗传距离为0.046—0.139,分化系数为0.015—0.046。结果表明与其他地区川金丝猴种群相比,神农架川金丝猴种群具有较低的遗传多样性水平,种群内部存在遗传分化趋势;结合景观参数分析表明地理距离不是影响神农架川金丝猴群体间遗传距离的主要因素,而生境中的灌丛和草地以及人类活动干扰可能是影响川金丝猴遗传交流的主要因素。     

单核苷酸多态性检测技术研究进展

单核苷酸多态性(SNP)是个体中最普遍的遗传变异,主要是指在基因组水平上由单个核苷酸的变异所引起的DNA序列多态性。SNP作为第三代遗传标记,具有遗传稳定性强、数量多、分布广等特点,被广泛应用于群体遗传学、疾病相关基因定位研究中,并在疾病的早期诊断、预防、治疗,研究遗传因素对药物代谢的影响,指导药物临床使用等方面发挥重要的作用。鉴于此,建立适合各级平台应用的准确、高效、稳定的SNP分型技术十分必要。目前SNP检测与分析技术众多,在原理上差别很大,适用范围也不尽相同。本文综述了目前临床应用较广的SNP分型方法,简要介绍了各种技术的检测原理和优缺点,并对SNP分型技术前景进行了展望。     

MtDNA COI‐COII marker and drone congregation area: An efficient method to establish and monitor honeybee (Apis mellifera L.) conservation centres

Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of nonlocal subspecies of bees which has had an adverse impact on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. To restore the original diversity of this local honeybee subspecies, different conservation centres were set up in Europe. In this study, we established a black honeybee conservation centre Conservatoire de l'Abeille Noire d'Ile de France (CANIF) in the region of Ile‐de‐France, France. CANIF's honeybee colonies were intensively studied over a 3‐year period. This study included a drone congregation area (DCA) located in the conservation centre. MtDNA COI‐COII marker was used to evaluate the genetic diversity of CANIF's honeybee populations and the drones found and collected from the DCA. The same marker (mtDNA) was used to estimate the interactions and the haplotype frequency between CANIF's honeybee populations and 10 surrounding honeybee apiaries located outside of the CANIF. Our results indicate that the colonies of the conservation centre and the drones of the DCA show similar stable profiles compared to the surrounding populations with lower level of introgression. The mtDNA marker used on both DCA and colonies of the conservation centre seems to be an efficient approach to monitor and maintain the genetic diversity of the protected honeybee populations.     

Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing ‘phyloh’ as a novel phylogenetic diversity analysis tool

The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh ) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh , was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.     

Conserving genetic diversity in the honeybee: Comments on Harpur et al. (2012)

The article by Harpur et al. (2012) ‘Management increases genetic diversity of honey bees via admixture’ concludes that ‘…honey bees do not suffer from reduced genetic diversity caused by management and, consequently, that reduced genetic diversity is probably not contributing to declines of managed Apis mellifera populations’. In the light of current honeybee and beekeeping declines and their consequences for honeybee conservation and the pollination services they provide, we would like to express our concern about the conclusions drawn from the results of Harpur et al. (2012). While many honeybee management practices do not imply admixture, we are convinced that the large-scale genetic homogenization of admixed populations could drive the loss of valuable local adaptations. We also point out that the authors did not account for the extensive gene flow that occurs between managed and wild/feral honeybee populations and raise concerns about the data set used. Finally, we caution against underestimating the importance of genetic diversity for honeybee colonies and highlight the importance of promoting the use of endemic honeybee subspecies in apiculture.     

基因组学技术在生物多样性保护研究中的应用

在分子生物学、细胞生物学、微生物学、遗传学等学科的推动下, 生物多样性研究从仅关注宏观表型的博物学, 迅速演化为涵盖生态系统、物种和遗传多样性等多个维度的综合性生命科学。组学技术, 尤其是DNA测序技术的更新和发展, 使获取DNA序列所需的成本大幅下降, 促进了近年来其在生物多样性研究中取得的一系列令人瞩目成就。本文将从物种水平的遗传多样性和群落水平的物种多样性两个层面总结和介绍与DNA相关的组学技术在生物多样性研究中的一些创新和应用。其中, 物种水平主要是总结单一个体的基因组和单物种多个体在时空多个维度上的群体遗传研究; 而群落水平的物种多样性层面主要总结现有的分子鉴定技术(metabarcoding, eDNA, iDNA等), 以及上述新技术在群落多样性评估、旗舰保护物种监测以及物种间相互作用关系等研究中的应用。     

Ancient DNA perspective on the failed introduction of mongooses in Italy during the XXth century

We used ancient DNA techniques to amplify mitochondrial DNA fragments [cytochrome b (cyt b ) and control region (CR)] from four museum specimens that represent, to our knowledge, the last testimony of the introduction of – now extinct – mongooses in Italy. We assessed the identity, origin and genetic variability of Italian mongooses using a species-level assignation Bayesian approach and haplotype network analysis. The genetic diversity (cyt b and CR) among Italian individuals was null. The cyt b sequences from the four museum specimens clearly established the Indian grey mongoose Herpestes edwardsii as the species having been introduced in Italy in the mid-XXth century. The latter had at least been released twice within a period of 10 years (Circeo NP and Capalbio, c . 200 km northward), probably from the same captive stock of the Giardino Zoologico di Roma. Assessment of genetic variability and haplotype network including native representatives of H. edwardsii suggested that the introduced pool likely originated from Pakistan or India. It appears that a combination of deleterious factors including low genetic diversity, restricted range and nonadaptation to western Palaearctic winter conditions is responsible for the extinction of the species in Italy. However, the lack of knowledge on the life-history traits and population dynamics of H. edwardsii prevents from further discussion of the factors that likely promoted its extinction process.     

中国意大利蜜蜂微卫星遗传多态性

为了分析我国不同生态条件下意大利蜜蜂Apis mellifera ligustica（简称意蜂）的基因特征,对品种间基因交流或基因渗入现象进行监测,完成对我国主要地区意蜂多样性水平的评价。本研究利用10对微卫星（SSR）引物分析了来自我国黑龙江等14个省市自治区31个采集点的意蜂样品的遗传多态性,并与来自德国的喀尼阿兰蜂A. m. carnica（简称喀蜂）和来自美国的意蜂A. m. ligustica进行比对。通过NTSYS-pc2.1和popGene32软件对SSR数据进行多态性分析。结果表明：10对SSR引物中8对表现出较高的遗传稳定性,可作为意蜂遗传多态性标记。遗传一致度在0.61以上时,浙江、四川、甘肃和云南地区的样品出现较严重分化,其他地区的意蜂样品则保持了美国原种意蜂的典型基因特征。东北和新疆地区的样品与德国喀蜂血统亲缘关系较近（遗传距离在0.18149以内）,分析主要原因可能是该地区的意蜂样品杂有黑蜂A. m. mellifera血统。据此提出应在保护各地意蜂原种特性及种群多态性的基础上,科学有效地进行高产品种的繁育。     

Mating in the rain? Climatic variance for polyandry in the honeybee (Apis mellifera jemenitica)

We tested the impact of colony density and climatic conditions on the level of queen polyandry in different wild populations of the honeybee (Apis mellifera jemenitica). We identified the mating frequency of queens by genotyping worker offspring (n = 672) of 28 wild colonies with microsatellite DNA markers. The populations sampled in different climatic regions in Sudan showed a high variance for the queen mating frequency ranging from 9 to 23 estimated matings with an average of 14.00 ± 3.94 (13.16 ± 4.87 effective matings). The degree of polyandry was highly significantly correlated with the rainfall in the various regions. In general, more rainfall resulted in lower mating frequencies. Polyandry did not correlate with colony density or with genetic diversity of the local sample populations. This suggests that variation in polyandry in wild honeybee populations of Sudan is primarily driven by climatic differences among ecosystem variation rather than by the absolute or effective local honeybee population size.     

Multilocus DNA fingerprinting and RAPD reveal similar genetic relationships between strains of Oreochromis niloticus (Pisces: Cichlidae)

Two molecular techniques which reveal highly variable DNA polymorphisms, RAPD and multilocus DNA fingerprinting, were used to evaluate genetic diversity between six aquacultural strains of Oreochromis niloticus (tilapia) from the Philippines. The results using both techniques were in close agreement Within-strain heterozygosity values were similar and were correlated between the two data sets, but statistical errors associated with the RAPD data set were lower. Although genetic distances between strains were greater using DNA fingerprinting, the distances measured using both methods were significantly correlated. Both methods were useful in estimating variation between strains, but they offered different advantages. RAPD was technically easier to perform and produced results with low statistical error, whereas DNA fingerprinting detected greater genetic differentiation between strains. The theoretical basis for using RAPD and multilocus minisatellite markers for population studies is discussed.     

Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories

While genetic diversity of threatened species is a major concern of conservation biologists, historic patterns of genetic variation are often unknown. A powerful approach to assess patterns and processes of genetic erosion is via ancient DNA techniques. Herein, we analyzed mtDNA from historical samples (1800s to present) of Andean Condors (Vultur gryphus) to investigate whether contemporary low genetic variability is the result of recent human expansion and persecution, and compared this genetic history to that of California condors (Gymnogyps californianus).We then explored historic demographies for both species via coalescent simulations. We found that Andean condors have lost at least 17% of their genetic variation in the early 20th century. Unlike California condors, however, low mtDNA diversity in the Andean condor was mostly ancient, before European arrival. However, we found that both condor species shared similar demographies in that population bottlenecks were recent and co‐occurred with the introduction of livestock to the Americas and the global collapse of marine mammals. Given the combined information on genetic and demographic processes, we suggest that the protection of key habitats should be targeted for conserving extant genetic diversity and facilitate the natural recolonization of lost territories, while nuclear genomic data should be used to inform translocation plans.     

分子生物学方法在微生物多样性研究中的应用

微生物多样性是生物多样性的重要组成部分。由于微生物和大生物（动、植物）相比,存在着多种显著差异,因此其多样性,保护及利用也有所不同,尤其是研究方法亟待完善,提高。近年来,分子生物学方法广泛用于微生物多样性的研究并取得了一系列研究成果。本文从四个方面加以介绍：１）微生物总ＤＮＡ制备及其遗传多样性检测方法;２）１６ＳｒＲＮＡ基因序列研究;３）核酸杂交分析技术;４）ＤＮＡ动力学的研究。今后的发展趋势是加