微卫星标记及其在鸟类中的应用

微卫星DNA作为一种分子标记,以其诸多优点被认为是各类遗传标记中最有价值的一种。目前已被广泛应用于鸟类的研究中。本文介绍了微卫星DNA标记的分布特点、突变机制和作为分子标记的特点,并综述了微卫星DNA标记在鸟类的亲权分析及种类鉴定、遗传图谱构建及基因定位、物种进化历史揭示和遗传多样性研究中应用现状。     

鸟类线粒体DNA研究概述

线粒体DNA作为理想的分子标记已被广泛用于鸟类种群遗传学和进化遗传学的研究,并取得了许多有意义的结果。本文介绍鸟类线粒体DNA的组成、结构特点及多态性的研究,综述近年来有关鸟类分子进化研究的进展情况,对今后的发展进行了初步的探讨。 Abstract:Mitochondrial DNA as a genetic marker has been successfully applied to the study of molecular evolution of birds.The apparently maternal inheritance of mitochondrial DNA and its fast evolution in primary sequence has made it attractive in population and evolutionary genetics.Mitochondrial DNA of birds displays two characteristics not seen in other vertebrates mtDNA,that is,a novel gene order and the absence of an equivalent to the light-strand replication origin.The research on polymorphism of mtDNA can resolve phylogenies of birds both at lower and higher taxonomic levels.Here we review progress on avian molecular evolution in recent years,and make preliminary studies of the development in this field.     

分子标记及其在鸟类分子生态学研究中的应用

分子生态学是一门相当新的分支学科,从前人的研究工作来看,分子标记在这个学科中应用非常广泛,本文描述了RFLP、RAPD、MinisatelliteDNA,MicrosatelliteDNA和AFLP这5个分子标记的优缺点及其在鸟类分子生态学中的应用和研究概况。     

DNA在鸟类分子系统发育研究中的应用

鸟类分子系统发育研究中常用的DNA技术有DNA杂交、RFLP和DNA序列分析等。DNA杂交技术曾在鸟类中有过大规模的应用,并由此诞生了一套新的鸟类分类系统。在鸟类的RFLP分析中,用的最多的靶序列是线粒体DNA。DNA序列分析技术被认为是进行分子系统发育研究最有效、最可靠的方法。在DNA序列分析中,线粒体基因应用最广泛,但由于其自身的一些不足,近年来,不少学者把目光投向了核基因,将线粒体基因和核基因结合起来进行系统发育研究。目前在鸟类分子系统发育中,应用较多的核基因是scnDNA,其内含子可以用于中等阶元水平的系统研究,而外显子主要用于高等阶元的系统研究。除了分子标记自身的问题之外,鸟类分子系统发育研究中还存在着方法上的问题,包括分子标记的选择,样本数量以及数据处理等。今后鸟类分子系统发育研究应该更加注重方法的标准化。     

鸟类分子系统地理学研究进展

分子系统地理学是当代生物地理学的重要分支,是以分子生物学方法重建种内和种上水平的系统发育关系,阐释进化历史,并通过分析近缘生物类群的系统发育关系与其空间和时间分布格局间的相关性构建生物区系历史的研究,是分子生物学与生物地理学结合的产物。中性进化学说和溯祖理论分析的建立,以及线粒体DNA和微卫星标记等分子遗传标记的应用,为分子系统地理学研究的开展提供了理论和实践基础。近年来,分子系统地理方法在鸟类学研究中的应用揭示了许多不同于传统认知的发现,为准确而深入的了解鸟类分子系统地理格局的差异和不同类群的起源中心提供了新颖的证据。目前的研究多从隔离分化说和扩散说的角度对鸟类分子系统地理格局的成因进行分析,而迁徙行为不同对鸟类系统地理格局的影响为成因的解释提供了新的角度。结合区域特点的比较分子系统地理研究,在更广泛的地域和更多类群中开展研究是我国鸟类分子系统地理研究的方向。此外,展望了第二代测序技术对分子生态生物地理研究具有的潜在促进作用。     

CHD基因与非平胸鸟类性别鉴定

自1995年CHD基因被应用于鸟类性别的分子鉴定以来,非平胸类鸟类性别鉴定问题正逐步被解决,CHD基因已经成为非平胸鸟类性别鉴定最重要的分子标记。阐述和分析了CHD基因在扩增目标及引物设计、取样范围及辅助技术和所涉足的科研领域等方面的发展及现状。期望随着CHD基因研究的深入,建立起完善的基于CHD基因的鸟类性别鉴定体系,通过更广泛的应用,促使涉及鸟类性别鉴定的科学研究向着更深、更广的方向发展。     

鸟类微卫星位点的交叉扩增研究进展

微卫星是一种极具应用价值的分子遗传标记,因其具有多态性高、共显性遗传、选择中性、易于操作等特点而广泛应用于遗传学和生态学研究.交叉扩增作为分离微卫星位点的方法之一,具有操作简便、节省时间和费用的优点.本文着重对鸟类,尤其是雉科鸟类中微卫星位点的交叉扩增研究进展及影响微卫星交叉扩增的因素进行综述,旨在为珍稀濒危雉科鸟类的保护遗传学研究提供基础资料.     

分子标记在雀形目鸟类研究中的应用

雀形目鸟类一直以来都是动物学工作者研究的热点。目前,针对雀形目鸟类研究的标记主要有2部分：一部分是线粒体DNA中12SrRNA、细胞色素b序列、ND2基因和ZENK等基因序列;另一部分是基因组DNA中的c-myc、RAG-1、肌球素基因和核β-纤维蛋白厚基因等DNA序列以及微卫星DNA和单核苷酸多态性（SNP）等。本文概述了这些分子遗传标记在雀形目鸟类中的应用和研究状况。     

近代鸟类分类与系统发育研究进展

简要综述了宏观和微观领域的鸟类分类学研究进展.宏观领域介绍了传统形态分类学、数值分类学和支序分类学,结合鸣声分析强调支序分类学的应用.微观领域介绍了Sibley分类系统和近年来出现的主要基于mtDNA的鸟类系统学研究.通过对大量研究工作的分析提出该领域今后应进行综合性研究.     

秧鸡科部分鸟类线粒体基因组的比较及系统发育关系分析

秧鸡科鸟类的系统发育关系尚不明确,本研究通过对秧鸡科11属共17种鸟类的线粒体基因组中各基因进行变异位点和简约信息位点分析。选取变异位点和简约信息位点含量均较高的CR、ND2、ND4、ND5及线粒体基因组分别作为分子标记,采用NJ法、ML法和贝叶斯法分别构建系统发育树。通过对各系统树进行比较分析,结果表明:红胸田鸡、小田鸡、紫水鸡、南秧鸡、黑水鸡、白骨顶鸡、新西兰秧鸡、粟腹秧鸡、红眼斑秧鸡、冲绳秧鸡和奥岛秧鸡的系统发育关系明确;考虑将董鸡属划入苦恶鸟属、粟腹秧鸡划入到纹秧鸡属;支持侏秧鸡科独立成科;完整的线粒体基因组是解决秧鸡科鸟类系统发育关系的最优分子标记。研究结果将为后续增加种属,进一步解决秧鸡科鸟类的系统发育关系提供指导。     

线粒体DNA用作分子标记的可靠性和研究前景

mtDNA作为分子标记的广泛应用,使得系统进化、生物地理、群体遗传、人类学及法医鉴定等领域的研究得到前所未有的发展.但随着对线粒体基因组遗传特性的了解不断加深,以mtDNA作为分子标记的潜在问题便逐渐暴露出来.本文从7个方面对mtDNA应用的可靠性问题进行了讨论,并对今后线粒体基因的应用前景做了初步分析。 Abstract:With some special features,mtDNA is used widely as molecular marker in the fields of systematic evolution,biogeography,population genetics,anthropology,and forensic medicine.However,more and more evidences that challenge the traditional concept on mtDNA features re found increasingly.In this paper,seven facts that could affect the reliability of mtDNA used as molecular marker are reviewed,then the perspective on application of mtDNA is discussed.     

Paternal transmission of mitochondrial DNA as an integral part of mitochondrial inheritance in metapopulations of Drosophila simulans

Maternal inheritance is one of the hallmarks of animal mitochondrial DNA (mtDNA) and central to its success as a molecular marker. This mode of inheritance and subsequent lack of heterologous recombination allows us to retrace evolutionary relationships unambiguously down the matriline and without the confounding effects of recombinant genetic information. Accumulating evidence of biparental inheritance of mtDNA (paternal leakage), however, challenges our current understanding of how this molecule is inherited. Here, using Drosophila simulans collected from an East African metapopulation exhibiting recurring mitochondrial heteroplasmy, we conducted single fly matings and screened F1 offspring for the presence of paternal mtDNA using allele-specific PCR assays (AS–PCR). In all, 27 out of 4092 offspring were identified as harboring paternal mtDNA, suggesting a frequency of 0.66% paternal leakage in this species. Our findings strongly suggest that recurring mtDNA heteroplasmy as observed in natural populations of Drosophila simulans is most likely caused by repeated paternal leakage. Our findings further suggest that this phenomenon to potentially be an integral part of mtDNA inheritance in these populations and consequently of significance for mtDNA as a molecular marker.     

Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.     

GLOBAL MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF HOLARCTIC BREEDING DUNLINS (CALIDRIS ALPINA)

Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.     

动物线粒体基因组研究进展

对动物线粒体分子生物学的最新研究进展进行了较详细的阐述.从线粒体基因组(mtDNA)的研究背景出发,重点介绍了动物线粒体基因组的组成和结构特点,以及目前动物mtDNA与核基因组的关系、线粒体基因的遗传、起源和进化研究中的热点问题.     

蚕类昆虫线粒体DNA研究及其在起源与进化研究中的应用

线粒体DNA(mtDNA)属母系遗传,进化速率较核基因快且基因组结构相对简单,已作为理想的分子标记广泛应用于昆虫群体遗传学及分子系统学等研究。本文对蚕类昆虫线粒体DNA在分子水平上的最新研究进展进行了较详细的阐述,重点介绍了蚕类昆虫线粒体基因组的组成及特征、mtDNA克隆与多态性及在蚕类昆虫分子系统学研究中的应用等。     

Contribution of common deletion to total deletion burden in mitochondrial DNA from inner ear of d-galactose-induced aging rats

Mitochondrial DNA (mtDNA) mutations, especially deletions, have been suggested to play an important role in aging and degenerative diseases. In particular, the common deletion in humans and rats (4977bp and 4834bp deletion, respectively) has been shown to accumulate with age in post-mitotic tissues with high energetic demands. Among numerous deletions, the common deletion has been proposed to serve as a molecular marker for aging and play a critical role in presbyacusis. However, so far no previous publication has quantified the contribution of common deletion to the total burden of mtDNA deletions in tissues during aging process. In the present study, we established a rat model with various degrees of aging in inner ear induced by three different doses of d-galactose (d-gal) administration. Firstly, multiple mtDNA deletions in inner ear were detected by nested PCR and long range PCR. In addition to the common deletion, three novel mtDNA deletions were identified. All four deletions, located in the major arc of mtDNA, are flanked by direct repeats and involve the cytochrome c oxidase (COX) subunit III gene, encoded by mtDNA. Additionally, absolute quantitative real-time PCR assay was used to detect the level of common deletion and total deletion burden of mtDNA. The quantitative data show that the common deletion is the most frequent type of mtDNA deletions, exceeding 67.86% of the total deletion burden. Finally, increased mtDNA copy number, reduced COX activity and mosaic ultrastructural impairments in inner ear were identified in d-gal-induced aging rats. The increase of mtDNA replication may contribute to the accelerated accumulation of mtDNA deletions, which may result in impairment of mitochondrial function in inner ear. Taken together, these findings suggest that the common deletion may serve as an ideal molecular marker to assess the mtDNA damage in inner ear during aging.     

DNA遗传标记在山羊遗传多样性研究上的应用

综述DNA遗传标记在山羊的遗传多样性分析上的应用,并分别叙述了RFLP、线粒体DNA多态性、RAID、微卫星标记、AFLP等几个方面目前在山羊上的研究。